The irreducibly complex ATP Synthase nanomachine, amazing evidence of design

The irreducibly complex ATP Synthase nanomachine, amazing evidence of design

https://reasonandscience.catsboard.com/t1439-the-irreducibly-complex-atp-synthase-nanomachine-amazing-evidence-of-design

1. ATP synthase is a molecular energy-generating nano-turbine ( It produces energy in the form of Adenine triphosphate ATP. Once charged, ATP can be “plugged into” a wide variety of molecular machines to perform a wide variety of functions). It consists of two very different subunits that have to be externally and stably tethered together, just the right distance apart. The two major subunits (F0 & F1) are connected together by an external tether, and just the right distance apart. This tether doesn’t have anything to do with the functionality of either subunit but without it ATP synthase would not be able to perform its function. One of the subunits has to be embedded in the cell membrane so that an energy gradient can be formed ( The proton energy gradient is like the water in a dam, feeding a water turbine to generate energy). The second subunit has to be stably tethered to the membrane the proper distance away.
2. This is an irreducibly complex system, where a minimal number of at least five functional parts of ATP synthase must work together in an interlocked way, in a joint venture to bear function. The challenge is particularly onerous because these components are highly complex in all of life and are interdependent to provide energy for life. Individually, the subunits have no function whatsoever ( Not even in different setups). Besides ATP synthase, the membrane is essential to pump protons across the membrane. This setup cannot be the product of evolution, because it had to be fully operational and functional to start life ( The origin of life has nothing to do with evolution). No life form without ATP synthase is known.
3. We know by experience that complex machines made of various interlocked subparts with specific functions are always created by intelligent minds.  Therefore, ATP synthase is definitely evidence of a powerful intelligent creator, who knew how to create power-generating turbines.

Rob Stadler (2022): ATP synthase is made of at least eight distinct proteins and more than twenty protein units.
Lane N, The Vital Question. (2016)…the most impressive nanomachine of them all…This is precision nanoengineering of the highest order, a magical device, and the more we learn about it the more marvelous it becomes.

Tan, Change; Stadler, Rob. The Stairway To Life:
The cell uses the proton gradient to charge “batteries” such as adenosine triphosphate (ATP), hence the “coupling” part of chemiosmotic coupling. ATP is a nearly universal battery in life. Once charged, it can be “plugged into” a wide variety of molecular machines to perform a wide variety of functions: activating amino acids for protein synthesis, copying DNA, untangling DNA, breaking bonds, transporting molecules, or contracting muscles. Like rechargeable batteries, ATP cycles frequently between powering gadgets and recharging. Although a human body contains only about sixty grams of ATP at any given moment, it is estimated that humans regenerate approximately their own weight in molecules of ATP every day. Because chemiosmotic coupling is essential for life and is highly conserved across all of life, abiogenesis must include a purely natural means to arrive at chemiosmotic coupling. This requires a membrane, a mechanism for pumping protons across the membrane, and a mechanism for producing or “recharging” ATP. The challenge is particularly onerous because these three components are highly complex in all of life and are interdependent to provide energy for life. In other words, the pumping of protons is of no use unless the membrane is there to maintain a gradient of protons. The membrane has no function for energy generation unless there is a mechanism for pumping protons across it. Similarly, the method of ATP production is of no use without a proton gradient across a membrane.

Oxidative phosphorylation is an apparently more complex process where a proton-motive force across a membrane powers an ATP synthase enzyme complex (a molecular machine) to make ATP from ADP and inorganic phosphate.  Oxidative phosphorylation is coupled to oxidative pathways that release large amounts of free energy, and makes the vast majority of the ATP in respiring cells.  Surprisingly, oxidative phosphorylation appears to be at least as ancient as glycolysis and fermentation, and operates in both anaerobic and aerobic environments. Oxidative phosphorylation may have played a key role in the origin of life 13

Proton gradients across membranes are the primary energy source coupled to ATP synthesis, and this system, now referred to as chemiosmosis, must have accompanied the evolution of primitive protocells into the first forms of cellular life. 13

Behe (2022): During the Q&A period, a questioner asked him directly: How could a mindless Darwinian process produce such a stunning piece of work? (ATP synthase)
Walker’s entire reply (paraphrasing): “Slowly, through some sort of intermediate or other.” Far out of earshot I muttered two simple words: “Game over.” If a Nobel laureate who has worked on one of life’s most fundamental systems for four decades can’t give an account of how it supposedly arose through a series of lucky mutations and natural selection—despite knowing its innermost workings in spectacular detail—then it’s reasonable to conclude no such account exists, and the effort to find one is a snipe hunt.
https://wng.org/articles/fearfully-and-wonderfully-made-1663727703

Structural Biochemistry/The Evolution of Membranes
F- and A/V- type ATPases are membrane-embedded proteins and were feasibly present in the LUCA (last universal common ancestor) due to their omnipresence in modern cellular life. 11
https://en.wikibooks.org/wiki/Structural_Biochemistry/The_Evolution_of_Membranes

Evolution of the F0F1 ATP Synthase Complex in Light of the Patchy Distribution of Different Bioenergetic Pathways across Prokaryotes
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154653/ 2014 Sep 4
This highlights the patchy distribution of many pathways across different lineages, and suggests either up to 26 independent origins or 17 horizontal gene transfer events.
Comment: If one origing by unguided random events is extremely unlikely, imagine 26 independent origins !! The clearly better explanation is that an intelligent designer created these molecular turbines from the get go, fully developed, and working, and distributed them in the various life forms.

A critically important macromolecule—arguably “second in importance only to DNA”—is ATP. ATP is an abbreviation for adenosine triphosphate, a complex molecule that contains the nucleoside adenosine and a tail consisting of three phosphates. As far as known, all organisms from the simplest bacteria to humans use ATP as their primary energy currency. In each of the approximately one hundred trillion human cells is about one billion ATP molecules.
Without ATP, life as we understand it could not exist. All the books in the largest library in the world may not be able to contain the information needed to understand and construct the estimated 100,000 complex macromolecule machines used in humans.  Anything less than an entire ATP molecule will not function and a manufacturing plant which is less then complete cannot produce a functioning ATP. Dr. Jerry Bergman
New X-ray crystallographic studies have revealed the working of adenosine triphosphate synthase, the basis of energy transport in all living organisms.
ATP captures the chemical energy released by the combustion of nutrients and transfers it to reactions that require energy, e.g. the building up of cell components, muscle contraction, transmission of nerve messages and many other functions. ATP synthase molecules located within mitochondria stick out on the mitochondria, attached to their inner surfaces in mushroom-like clusters. When food is broken down or metabolized for energy, the last stages of the process occur within the mitochondria.

ATP synthase is an irreducibly complex motor—a proton-driven motor divided into rotor and stator portions. Protons can flow freely through the CF0 complex without the CF1 complex, so that if it would have emerged first, a pH gradient could not have been established within the thylakoids. The δ and critical χ protein subunits of the CF1 complex are synthesized in the cytosol and imported into the chloroplast in everything from Chlorella to Eugenia in the plant kingdom.  All of the parts must be shipped to the right location, and all must be the right size and shape, down to the very tiniest detail. Using a factory assembly line as an analogy, after all the otherwise useless and meaningless parts have been manufactured in different locations and shipped in to a central location, they are then assembled, and, if all goes as intended, they fit together perfectly to produce something useful. But the whole process has been carefully designed to function in that way. The whole complex must be manufactured and assembled in just one certain way, or nothing works at all. Since nothing works until everything works, there is no series of intermediates that natural selection could have followed gently up the back slope of mount impossible. The little proton-driven motor known as ATP synthase consists of eight different subunits, totalling more than 20 polypeptide* chains, and is an order of magnitude smaller than the bacterial flagellar motor, which is equally impossible for proponents of evolution to explain.  10


ATP synthase is an irreducible complex molecular motor par excellence. Disconnect one of its components, disturb one of its forms, replace some of your AA positions,  and the system loses function altogether. Try to build it slowly, step by step, by mindless unguided processes, where would the energy come from to build it, if it is the energy provider for life? Remember though that the energy that produces ATP synthase is essential to life, virtually for all forms of life. And unless the proton gradient is in place, ATP synthase would be useless. 

The physiology and habitat of the last universal common ancestor
Cells conserve energy via chemiosmotic coupling14 with rotor–stator-type ATP synthases or via substrate-level phosphorylation (SLP)15. LUCA’s genes encompass components of two enzymes of energy metabolism: phosphotransacetylase (PTA) and an ATP synthase subunit 13

Since evolution by natural selection requires reproduction, and since reproduction requires life, which requires ATPase, the enzyme is, therefore, a prerequisite for evolution. But with evolution out of order until ATPase ‘appears’, evolution is not even in the running as a model to explain the origin of the molecular motor.

At least five of the below-mentioned parts are ESSENTIAL and IRREDUCIBLE. Take away one, and ATP synthase ceases to function. Neither could any of the sub-parts simply be co-opted from anywhere else. That would be the same as to say, in order to make a motor function, and a cylinder is missing, go search and find any cylinder nearby, co-opt it, and solved is the problem. The thing is that cylinders come in all size, specification, materials etc. And there is no goal-oriented search of parts that fit through evolution Evolution has no foresight. Furthermore, there must be the information on how and when and where to mount the parts, at the exact place, in the right sequence.  That's a far fetch for a mindless tinkerer to be able to achieve. 

1.The nucleotide binding stator subunits (“cylinders”) :  The electrostatic interaction of these rotor and stator charges is essential for torque generation
2.The central stalk (“crankshaft”) : The torsional elasticity of the central stalk and the bending and stretching elasticity of the peripheral stalk create an elastic coupling between Fo and F1. It is essential.
3, The A/V rotor subunit (“adapter”) ; It is not used in all ATP synthase motors, and can, therefore, be reduced.
4. The Rotor ring (“turbine”) ;  A ring of 8–15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous FOF1-ATPase.
5. The Jon channel-forming subunit ; Subunit a harbours the ion channel that provides access to the binding site on the c11 ring in the middle of the membrane from the periplasmic surface. The channel is essential for the operation of the enzyme because mutants in which the channel is blocked are completely inactive in both the ATP synthesis and/or coupled ATP hydrolysis mode
6. The peripheral stalk (“pushrod”) ; The peripheral stalk of F-ATPases is an essential component of these enzymes. It extends from the membrane distal point of the F1 catalytic domain along the surface of the F1 domain with subunit a in the membrane domain.
7 - 11 do not exist in all atp synthase motors. 

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC27776/
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846802/
4. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043045
5. http://onlinelibrary.wiley.com/doi/10.1046/j.1432-1033.2002.03264.x/pdf
6. https://www.ncbi.nlm.nih.gov/pubmed/16697972

There are at least 5 subunit parts essential to maintain the basic function of the ATP synthase motor.

If the substrates like crude oil required to make gasoline are not provided at the correct refinery place at the Oil industrial plant, the refinery process cannot happen. Same happens inside the cell.  In order for mitochondria to function, shuttling of ADP, ATP, phosphates and other substrates is essential. That process does not catch much attention but is actually life essential for eukaryotic cells to function. We need the right charge of ADP and ATP, the electrochemical gradient inside the inner membrane,  the ADP/ATP carrier proteins that drive the substrates around, and carrier proteins that shuttle the phosphate that is required along with ADP for ATP synthesis to the right place at ATP synthase motors, ready to be used , to be added to ADP to make ATP. That seems an ingeniously precise orchestrated process requiring several indispensable parts. ATP synthase is a prime example of intelligent design and should be able to convince even the most skeptic that intelligent design is the best explanation for its origin.
 



12


Rotary ATPases1





5. Composite models of rotary ATPase subtypes and their “machine elements.” F-, A- and V-type composite models are shown in similar color schemes in transparent light gray  Below are “exploded” views depicting individual “machine elements” at higher resolution derived from crystal structures. (A) bovine mitochondrial F-type ATP synthase, (B) T. thermophilus A-type ATPase/synthase, (C) yeast V-type ATPase.

1, nucleotide binding stator subunits (“cylinders”) in the picture below A, and B; The electrostatic interaction of these rotor and stator charges is essential for torque generation 4




2, central stalk (“crankshaft”) ; 

5



The torsional elasticity of the central stalk and the bending and stretching elasticity of the peripheral stalk create an elastic coupling between Fo and F1. Is is essential.


3, A/V rotor subunit (“adapter”) ;

It is not used in all ATP synthase motors, and can therefore be reduced.

4, rotor ring (“turbine”);  A ring of 8–15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous FOF1-
ATPase.  6





5, ion channel forming subunit; Subunit a harbors the ion channel that provides access to the binding site on the c11 ring in the middle of the membrane from the periplasmic surface. The channel is essential for the operation of the enzyme  because mutants in which the channel is blocked are completely inactive in both the ATP synthesis and/or coupled ATP hydrolysis mode



Model for the interaction of organotin compounds with F-ATP synthases. ATP synthesis from ADP and Pi is coupled to the downhill flux of ions across the membrane-bound F0 portion. The lower part shows a section through the subunit a channel along the membrane normal. During ATP synthesis hydrated ions enter the mouth of the channel and strip off part of their hydration shell at the selectivity filter (only Na+ ions can pass the filter). If hydrophobic organotin compounds are present, they accumulate within the membrane and easily penetrate into the entrance of the channel. Here, they interact with a site near the selectivity filter, which disables incoming ions to shed their hydration shell. As a consequence, the ions do not proceed through the channel and ATP synthesis is blocked. 8



6, peripheral stalk (“pushrod”); The peripheral stalk of F-ATPases is an essential component of these enzymes. It extends from the membrane distal point of the F1 catalytic domain along the surface of the F1 domain with subunit an in the membrane domain. 7



7a and b, A/V peripheral stalk connector subunits (“rockers”)

The stator is also referred to as the peripheral or extrinsic stalk. The stator functions to hold F1 fixed to allow rotation of the rotor within the core of F1. It provides a structural support and is not involved directly in the catalytic reaction. Breaking the stator uncouples ATP hydrolysis from proton translocation because the F1 core can spin instead of the rotor. 9

It does not exist in bovine ATP synthase, and can, therefore, be reduced. 

8, small central stalk subunit (“ratchet” in prokaryotes) ; 
9, eukaryotic additional central stalk subunit (“lock”) (2WPD); 
10, IF1  (“brake”) (1OHH);
11, eukaryotic V-type additional peripheral stalk subunit (“brake”)

8 - 11 are not used in all ATP synthase proteins.

Side view of the A-ATPase. The stator subunits (A, B, E, G and I) are labeled in white and the rotor subunits (D, F, C and L) are labeled in black. (b) View from above. The black arrow indicates the rotational direction of the central stalk during ATP synthesis and the white arrows indicate the torque in the A3B3 nucleotide-binding domain that subunit E counteracts. 2

Side view of the A-ATPase. The stator subunits (A, B, E, G and I) are labeled in white and the rotor subunits (D, F, C and L) are labeled in black. (b) View from above. The black arrow indicates the rotational direction of the central stalk during ATP synthesis and the white arrows indicate the torque in the A3B3 nucleotide-binding domain that subunit E counteracts.





Molecular machines, like the rotary ATPases, described here, seem to have much in common with man-made machines. However, the analogies hold only to a certain point and are in large parts not fully understood. What is evident is that several billion years of evolution  why not rather the intelligent designer's geniality have resulted in biological motors that are unsurpassed in efficiency, fine-tuning to their environment and sustainability. Understanding their detailed function at the molecular level is not only important to satisfy our curiosity, but will certainly have implications for understanding human physiology, including mitochondrial disorders, bioenergetics and the processes of aging, as well as impacting nano-engineering and many other fields afar.



Bacterial rotary ATPases have regulatory functions within their small central stalk subunit that can modulate rotary ATPase function; a low-affinity ATP binding site in this subunit allows a switch to proton pumping mode if ATP concentrations are high, but prevents ATP hydrolysis when ATP levels are low. This allows replenishment of proton gradients that also drive the bacterial flagellar motor if there is no shortage of ATP. If ATP levels are low, a conformational change occurs and the subunit intercalates in between the nucleotide binding subunits thus preventing ATP hydrolysis, but still allowing synthesis, just like a ratchet. Eukaryotic F-type ATP synthases are never supposed to run in reverse and have evolved a third central stalk subunit that prevents conformational changes in this regulatory subunit and an additional inhibitor protein termed IF1 that intercalates
with F1 to prevent ATP hydrolysis under ischemic conditions. In contrast to the bacterial regulatory mechanism, which is ATP-dependent, the mitochondrial IF1 protein is regulated by pH.5








The protein adenosine triphosphate synthase, better known as ATPase, is nature’s smallest rotary motor. “You can take a spoonful of that protein,” says biophysicist Klaus Schulten of the University of Illinois Urbana-Champaign, “and it generates as much torque as a Mercedes engine.” 3

A remarkable molecular motor that in the laboratory produces torque from chemical fuel, ATPase works the other direction in humans — converting torque into ATP, the basic fuel of life, the chemical energy that fuels muscle contraction, transmission of nerve messages and many other functions. Probably the most abundant protein in all living organisms, ATPase is the power plant of metabolism. In an active day, an adult human can produce and consume its body weight or more of ATP, nearly all of it produced by ATPase.


The ATP synthase is a finely tuned nanomachine composed of 23 or more separate protein subunits. The ATP synthase can work both in the forward direction, producing ATP from ADP and phosphate in response to an electrochemical gradient, or in reverse, generating an electrochemical gradient by ATP hydrolysis. To distinguish it from other enzymes that hydrolyze ATP, it is also called an F1Fo ATP synthase or F-type ATPase.

Resembling a turbine, ATP synthase is composed of both a rotor and a stator. To prevent the catalytic head from rotating, a stalk at the periphery of the complex (the stator stalk) connects the head to stator subunits embedded in the membrane. A second stalk in the center of the assembly (the rotor stalk) is connected to the rotor ring in the membrane that turns as protons flow through it, driven by the electrochemical gradient across the membrane. As a result, proton flow makes the rotor stalk rotate inside the stationary head, where the catalytic sites that assemble ATP from ADP and Pi are located. Three α and three β subunits of similar structure alternate to form the head. Each of the three β subunits has a catalytic nucleotide-binding site at the α/β interface. These catalytic sites are all in different conformations, depending on their interaction with the rotor stalk. This stalk acts like a camshaft, the device that opens and closes the valves in a combustion engine. As it rotates within the head, the stalk changes the conformations of the β subunits sequentially. One of the possible conformations of the catalytic sites has high affinity for ADP and Pi, and as the rotor stalk pushes the binding site into a different conformation, these two substrates are driven to form ATP. In this way, the mechanical force exerted by the central rotor stalk is directly converted into the chemical energy of the ATP phosphate bond. Serving as a proton-driven turbine, the ATP synthase is driven by H+ flow into the matrix to spin at about 8000 revolutions per minute, generating three molecules of ATP per turn. In this way, each ATP synthase can produce roughly 400 molecules of ATP per second.



ATP synthase. The three-dimensional structure of the F1Fo ATP synthase, determined by x-ray crystallography. Also known as an F-type ATP ase, it consists of an Fo part (from “oligomycin-sensitive factor”) in the membrane and the large, catalytic F1 head in the matrix. Under mild dissociation conditions, this complex separates into its F1 and Fo components, which can be isolated and studied individually. (A) Diagram of the enzyme complex showing how its globular head portion (green) is kept stationary as proton-flow across the membrane drives a rotor (blue) that turns inside it. (B) In bovine heart mitochondria, the Fo rotor ring in the membrane (light blue) has eight c subunits. It is attached to the γ subunit of the central stalk (dark blue) by the ε subunit (purple). The catalytic F1 head consists of a ring of three α and three β subunits (light and dark green), and it directly converts mechanical energy into chemical-bond energy in ATP , as described in the text. The elongated peripheral stalk of the stator (orange) is connected to the F1 head by the small δ subunit (red) at one end, and to the a subunit in the membrane (pink oval) at the other. Together with the c subunits of the ring rotating past it, the a subunit creates a path for protons through the membrane. (C) The symbol for ATP synthase used throughout this book. The closely related ATP synthases of mitochondria, chloroplasts, and bacteria synthesize ATP by harnessing the protonmotive force across a membrane. This powers the rotation of the rotor against the stator in a counterclockwise direction, as seen from the F1 head. The same enzyme complex can also pump protons against their electrochemical gradient by hydrolyzing ATP , which then drives the clockwise rotation of the rotor. The direction of operation depends on the net free-energy change (ΔG) for the coupled processes of H+ translocation across the membrane and the synthesis of ATP from ADP and Pi. Measurement of the torque that the ATP synthase can produce by ATP hydrolysis reveals that the ATP synthase is 60 times more powerful than a diesel engine of equal dimensions.



Fo ATP synthase rotor rings. (A) Atomic force microscopy image of ATP synthase rotors from the cyanobacterium Synechococcus elongatus in a lipid bilayer.  (B) The x-ray structure of the Fo ring of the ATP synthase from Spirulina platensis, another cyanobacterium, shows that this rotor has 15 c subunits. In all ATP synthases, the c subunits are hairpins of two membrane-spanning α helices (one subunit is highlighted in gray). The helices are highly hydrophobic, except for two glutamine and glutamate side chains (yellow) that create proton-binding sites in the membrane.

The membrane-embedded rotors of ATP synthases consist of a ring of identical c subunits. Each c subunit is a hairpin of two membrane-spanning α helices that contain a proton-binding site defined by a glutamate or aspartate in the middle of the lipid bilayer. The a subunit, which is part of the stator , makes two narrow channels at the interface between the rotor and stator, each spanning half of the membrane and converging on the proton-binding site at the middle of the rotor subunit. Protons flow through the two half-channels down their electrochemical gradient from the crista space back into the matrix. A negatively charged side chain in the binding site accepts a proton arriving from the crista space through the first half-channel, as it rotates past the a subunit. The bound proton then rides round in the ring for a full cycle, whereupon it is thought to be displaced by a positively charged arginine in the a subunit, and escapes through the second half-channel into the matrix. Thus proton flow causes the rotor ring to spin against the stator like a proton-driven turbine. The mitochondrial ATP synthase is of ancient origin: essentially the same enzyme occurs in plant chloroplasts and in the plasma membrane of bacteria or archaea. The main difference between them is the number of c subunits in the rotor ring. In mammalian mitochondria, the ring has 8 subunits. In yeast mitochondria, the number is 10; in bacteria and archaea, it ranges from 11 to 13; in plant chloroplasts, there are 14; and the rings of some cyanobacteria contain 15 c subunits. The c subunits in the rotor ring can be thought of as cogs in the gears of a bicycle. A high gear, with a small number of cogs, is advantageous when the supply of protons is limited, as in mitochondria, but a low gear, with a large number of cogs in the wheel, is preferable when the proton gradient is high. This is the case in chloroplasts and cyanobacteria, where protons produced through the action of sunlight are plentiful. Because each rotation produces three molecules of ATP in the head, the synthesis of one ATP requires around three protons in mitochondria but up to five in photosynthetic organisms. It is the number of c subunits in the ring that defines how many protons need to pass through this marvelous device to make each molecule of ATP, and thereby how high a ratio of ATP to ADP can be maintained by the ATP synthase. In principle, ATP synthase can also run in reverse as an ATP-powered proton pump that converts the energy of ATP back into a proton gradient across the membrane. In many bacteria, the rotor of the ATP synthase in the plasma membrane changes direction routinely, from ATP synthesis mode in aerobic respiration, to ATP hydrolysis mode in anaerobic metabolism. In this latter case, ATP hydrolysis serves to maintain the proton gradient across the plasma membrane, which is used to power many other essential cell functions including nutrient transport and the rotation of bacterial flagella. The V-type ATPases that acidify certain cellular organelles are architecturally similar to the F-type ATP synthases, but they normally function in reverse.

Mitochondrial Cristae Help to Make ATP Synthesis Efficient

In the electron microscope, the mitochondrial ATP synthase complexes can be seen to project like lollipops on the matrix side of cristae membranes. Recent studies by cryoelectron microscopy and tomography have shown that this large complex is not distributed randomly in the membrane, but forms long rows of dimers along the cristae ridges



The dimer rows induce or stabilize these regions of high membrane curvature, which are otherwise energetically unfavorable. Indeed, the formation of ATP synthase dimers and their assembly into rows are required for cristae formation and have far-reaching consequences for cellular fitness. By contrast with bacterial or chloroplast ATP synthases, which do not form dimers, the mitochondrial complex contains additional subunits, located mostly near the membrane end of the stator stalk. Several of these subunits are found to be dimer-specific. If these subunits are mutated in yeast, the ATP synthase in the membrane remains monomeric, the mitochondria have no cristae, cellular respiration drops by half, and the cells grow more slowly. Electron tomography suggests that the proton pumps of the respiratory chain are located in the membrane regions at either side of the dimer rows. Protons pumped into the crista space by these respiratory-chain complexes are thought to diffuse very rapidly along the membrane surface, with the ATP synthase rows
creating a proton “sink” at the cristae tips



ATP synthase dimers at cristae ridges and ATP production. At the crista ridges, the ATP synthases (yellow) form a sink for protons (red). The proton pumps of the electron-transport chain (green) are located in the membrane regions on either side of the crista. As illustrated, protons tend to diffuse along the membrane from their source to the proton sink created by the ATP synthase. This allows efficient ATP production despite the small H+ gradient between the cytosol and matrix. Red arrows show the direction of the proton flow.

The ATP synthase needs a proton gradient of about 2 pH units to produce ATP at the rate required by the cell, irrespective of the membrane potential. The H+ gradient across the inner mitochondrial membrane is only 0.5 to 0.6 pH units. The cristae thus seem to work as proton traps that enable the ATP synthase to make efficient use of the protons pumped out of the mitochondrial matrix. That seems one more evidence of the ingenious design of the creator. The right placement and the cristae had to be there right from the start

Special Transport Proteins Exchange ATP and ADP Through the Inner Membrane

Like all biological membranes, the inner mitochondrial membrane contains numerous specific transport proteins that allow particular substances to pass through. One of the most abundant of these is the ADP/ATP carrier protein



The ADP/ATP carrier protein. (A) The ADP/ATP carrier protein is a small membrane protein that carries the ATP produced on the matrix side of the inner membrane to the intermembrane space, and the ADP that is needed for ATP synthesis into the matrix. (B) In the ADP/ATP carrier, six transmembrane α helices define a cavity that binds either ADP or ATP . In this x-ray structure, the substrate is replaced by a tightly bound inhibitor instead (colored). When ADP binds from outside the inner membrane, it triggers a conformational change and is released into the matrix. In exchange, a molecule of ATP quickly binds to the matrix side of the carrier and is transported to the intermembrane space. From there the ATP diffuses through the outer mitochondrial membrane to the cytoplasm, where it powers the energy-requiring processes in the cell.

This carrier shuttles the ATP produced in the matrix through the inner membrane to the intermembrane space, from where it diffuses through the outer mitochondrial membrane to the cytosol. In exchange, ADP passes from the cytosol into the matrix for recycling into ATP. ATP4– has one more negative charge than ADP3–, and the exchange of ATP and ADP is driven by the electrochemical gradient across the inner membrane so that the more negatively charged ATP is pushed out of the matrix, and the less negatively charged ADP is pulled in. The ADP/ATP carrier is but one member of a mitochondrial carrier family: the inner mitochondrial membrane contains about 20 related carrier proteins exchanging various other metabolites, including the phosphate that is required along with ADP for ATP synthesis. In some specialized fat cells, mitochondrial respiration is uncoupled from ATP synthesis by the uncoupling protein, another member of the mitochondrial carrier family. In these cells, known as brown fat cells, most of the energy of oxidation is dissipated as heat rather than being converted into ATP. In the inner membranes of the large mitochondria in these cells, the uncoupling protein allows protons to move down their electrochemical gradient without passing through ATP synthase. This process is switched on when heat generation is required, causing the cells to oxidize their fat stores at a rapid rate and produce heat rather than ATP. Tissues containing brown fat serve as “heating pads,” helping to revive hibernating animals and to protect newborn human babies from the cold.

If the substrates like crude oil required to make gasoline are not provided at the correct refinery place at the Oil industrial plant, the refinery process cannot happen. Same happens inside the cell.  In order for mitochondria to function, shuttling of ADP, ATP, phosphates and other substrates is essential. That process does not catch much attention but  is actually life essential for eukaryotic cells to function. We need the right charge of ADP and ATP, the electrochemical gradient inside the inner membrane,  the ADP/ATP carrier proteins that drive the substrates around, and carrier proteins that shuttle the phosphate that is required along with ADP for ATP synthesis to the right place at ATP synthase motors, ready to be used , to be added to ADP to make ATP. That seems an ingeniously precise orchestrated process requiring several indispensable parts.    


ATP Synthase, an irreducible complex Energy-Generating Rotary Motor Engine




http://reasonandscience.heavenforum.org/t1439-atp-synthase#2089

https://physiology.knoji.com/why-do-we-breathe-oxygen/

The air we breathe is comprised of a variety of molecules of which only 20.9% is oxygen. The average person breathes in approximately 432 liters of oxygen per day (this is equivalent to 1216 cans of soda). The tissues of the body need a minimum of 352.8 liters of oxygen per day, and this is assuming the person is at rest. The brain, which is only 2% of the body mass, needs almost 20% of the oxygen that is brought in. If the brain doesn’t receive oxygen for more than 3 minutes, the cells will begin to die. Once brain cells cease to function, permanent damage sets in.

It is a common understanding that without oxygen (O2) we will die. Hold your breath for too long and you will feel light headed.
many don’t understand why we need oxygen. Why can’t we just use carbon dioxide or some sort of other gas to survive? In order to get to the bottom of this, we have to take a look at how our body makes energy.

The body needs energy and the energy that the body requires is known as ATP (adenosine triphosphate). It is a chemical energy that the enzymes of the body recognize. Give cells another form of chemical energy like gasoline, and the cells won’t know what to do with it. It’s like hooking up an iPod to a car battery. Sure, the battery has energy, but not the type of energy the iPod can use.

Our cells work very hard to make ATP.  Cells without ATP simply stop functioning and die. It’s the same thing as taking the batteries out of your television remote. It just won’t work anymore.  At any given time, a cell contains about 1 billion ATP. An active cell will use approximately 2 million ATP per second.  In terms of weight, all of the ATP in our bodies weighs around 50g. Interestingly enough of the 2500 calories we bring in per day, that will make up to 180 kg of ATP. But, the nice thing about ATP is that it is like a rechargeable battery. Once it is used, it can be reassembled to be used again.

If ATP is so important, how do we make it? One of the reasons we eat is to recharge the ATP. The major source of energy for the body comes from sugar. We eat the sugar, digest it into smaller sugar molecules then send these molecules to our cells. At the cellular level, the sugar molecule (more commonly referred as glucose) is sent through a series of chemical reactions to strip it free of electrons. These electrons, which have a negative charge, are shuttled to a series of proteins (electron transport chain) embedded in a specialized organelle called the mitochondria. The electrons are dropped off then travel from one protein to the next.  This flow of electrons forces some of these proteins to do the job they were designed to do: serve as a chemical pump. Essentially, this is electricity within a cell. These proteins pump hydrogen ions (H+) from one compartment of the mitochondria to another.

After awhile, a high number of hydrogen ions are crammed into one area of the mitochondria and want to flow to the other area that is now low in hydrogen ions. But the only way they can get back to the other area is through a specialized protein called ATP synthase. When the H+ pass through it, they cause the ATP synthase to turn much like water through a sprinkler head. This spinning action in essence reassembles the ATP molecule, recharging it, if you will. This protein is so effective that it can make approximately 600 ATP per second. Amazing.

http://www.lifesorigin.com/chap14/ATP-synthase-synthetase.php

ATP synthase is an incredible enzyme. It is the smallest rotary motor in the world. The protons moved across the cell membrane by the electron donor/acceptor/dehydrogenase complex  serve as the energy source for ATP synthase.

ATP synthase lets these proteins flow back to the other side of the cell membrane, and this powers a small rotary motor imbedded inside the membrane and causes it to spin. The spinning portion called the rotor has a stalk attached to it. The stalk is not straight but rather curved. Because other peptide chains surround the stalk, as the stalk spins, it forces these surrounding proteins to move. This allows these surrounding proteins to create ATP from ADP.

ATP synthase was one of the first enzymes because it is absolutely necessary for many of the organisms that are thought to have existed on the primitive earth. All of the bacteria that oxidize non-organic chemicals to obtain energy use ATP synthase to make ATP.

The enzyme is composed of 8 distinct peptide chains. If any one of the chains is missing, the enzyme does not function. So ATP synthase is an irreducibly complex system. If a system involving ATP synthase is required for the origin of life, then it will never get off the ground. The protein is too complex and contains too much knowledge.

https://releasingthetruth.wordpress.com/tag/irreducible-complexity/

Evolutionary scientists have suggested that the head portion of ATP synthase evolved from a class of proteins used to unwind DNA during DNA replication, i.e, the hexameric helicase enzyme.

How could ATP synthase “evolve” from something that needs ATP, manufactured by ATP synthase, to function? Absurd “chicken-egg” paradox! Also, consider that ATP synthase is made by processes that all need ATP—such as the unwinding of the DNA helix with helicase to allow transcription and then translation of the coded information into the proteins that make up ATP synthase. And manufacture of the 100 enzymes/machines needed to achieve this needs ATP! And making the membranes in which ATP synthase sits needs ATP, but without the membranes it would not work. This is a really vicious circle for evolutionists to explain.

http://www.answersingenesis.org/articles/tj/v17/n3/photosynthesis

ATP synthase is an irreducibly complex motor—a proton-driven motor divided into rotor and stator portions. Protons can flow freely through the CF0 complex without the CF1 complex so that if it evolved first, a pH gradient could not have been established within the thylakoids. The δ and critical χ protein subunits of the CF1 complex are synthesized in the cytosol and imported into the chloroplast in everything from Chlorella to Eugenia in the plant kingdom. All of the parts must be shipped to the right location, and all must be the right size and shape, down to the very tiniest detail. Using a factory assembly line as an analogy, after all the otherwise useless and meaningless parts have been manufactured in different locations and shipped into a central location, they are then assembled, and, if all goes as intended, they fit together perfectly to produce something useful. But the whole process has been carefully designed to function in that way. The whole complex must be manufactured and assembled in just one certain way, or nothing works at all. Since nothing works until everything works, there is no series of intermediates that natural selection could have followed gently up the back slope of mount impossible. The little proton-driven motor known as ATP synthase consists of eight different subunits, totaling more than 20 polypeptides* chains, and is an order of magnitude smaller than the bacterial flagellar motor, which is equally impossible for evolutionists to explain.

The recognition that many protein complexes function as molecular-level machines is one of the most remarkable advances in biochemistry during the last part of the twentieth century.

The F1-F0 ATPase turbine interacts with the part of the complex that looks like a “mushroom stalk.” This stalklike component functions as a rotor.8 The flow of positively charged hydrogen ions (or in some instances sodium ions) through the F0 component embedded in the cell membrane drives the rotation of the rotor.9 A rod-shaped protein structure that also extends above the membrane surface performs as a stator. This protei

Ribbon representation with c subunits in the three asymmetric units shown in different colors. (a) Side view. (b) View from the cytoplasmic side. (c) Electrostatic surface potential with assigned solvent regions and membrane borders. Red, negative; blue, positive; gray, neutral. Detergents are shown in ball-and-stick representation. Red spheres are water molecules. Difference map densities (Fo - Fc) at the hydrophobic surface of the protein are shown at 3sigma in gray mesh. Dashed lines represent hydrophobic protein regions in contact with the alkyl chains of the lipid bilayer. (d) Longitudinal section showing the interior surface of the ring.

http://www.rcsb.org/pdb/101/motm.do?momID=72

n rod interacts with the turbine holding it stationary as the rotor rotates. The electrical current that flows through the channels of the F0 complex is transformed into mechanical energy that drives the rotor’s movement. A cam that extends at a right angle from the rotor’s surface causes displacements of the turbine. These back-and-forth motions are used to produce ATP (adenosine triphosphate). The cell uses this compound as a source of chemical energy to drive the operation of cellular processes

MOLECULAR MECHANICS OF ATP SYNTHASE
ATP: The Perfect Energy Currency for the Cell
The structure of the c15 ring of the S. platensis ATP synthase.
ATP SYNTHASE — A MARVELLOUS ROTARY ENGINE OF THE CELL
ATP synthase FAQ
Complex Molecules found in all living species

http://5e.plantphys.net/article.php?ch=7&id=74
http://defendingchrist.org/atp-synthase-an-energy-generating-rotary-motor-engine/
http://www.reasons.org/articles/atp-synthase-ratchets-up-the-case-for-intelligent-design
http://www.life.illinois.edu/crofts/bioph354/lect10.html
http://creation.com/atp-synthase#txtRef3
http://www.nature.com/nature/journal/v521/n7551/abs/nature14365.html?message-global=remove

http://creation.com/design-in-living-organisms-motors-atp-synthase



Evolution of proton pumping ATPases: Rooting the tree of life
https://pubmed.ncbi.nlm.nih.gov/24408574/

1) http://www.tandfonline.com/doi/full/10.4161/bioa.23301#abstract
2) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912985/
3) http://www.psc.edu/science/2004/schulten/protein_motors_incorporated.html/
4) http://what-when-how.com/molecular-biology/atp-synthase-molecular-biology/
5) http://nature.berkeley.edu/~goster/pdfs/BBA.pdf
6) http://www.home.uni-osnabrueck.de/wjunge/public/270.pdf
7) http://www.ncbi.nlm.nih.gov/pubmed/16697972
8 ) http://www.pnas.org/content/101/31/11239.full
9 ) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415626/
10 ) https://answersingenesis.org/evidence-against-evolution/shining-light-on-the-evolution-of-photosynthesis/
11) https://en.wikibooks.org/wiki/Structural_Biochemistry/The_Evolution_of_Membranes
12. https://sci-hub.tw/http://www.nature.com/nrm/journal/v1/n2/full/nrm1100_149a.html?foxtrotcallback=true
13) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/

ATP Synthase
 

The ATPase Family

 
 

F-ATPases

 
 

V-ATPases

 
 

A-ATPases

 
 

P-ATPases

 
 

E-ATPases

 


 

F-ATPases – How They Work

 
 
 
 

Diagram showing the rotary motor of ATP synthase. Courtesy of Yoshida & Hisabori Lab

 
 

http://www.evolutionnews.org/2013/01/spectacular_new_1068501.html

To see is to believe. There is something very powerful, cutting through endless words and arguments, about seeing a clearly designed molecular mechanism at work.

http://www.biblicalcreation.org.uk/scientific_issues/bcs092.html

Recent papers on ATP synthase 1

Here is a list of references to ~50 most recent (as they appear in PubMed) publications that might be of interest to researchers working with ATP synthase. This list is monthly updated; freshly added references are marked as . If you know about a recent paper you do not see here, I will really appreciate if you let me know. 

You may also want to download my full reference database in MEDLINE format (it surely does not have all ATP synthase articles published, but ~4000 refs I have selected in the last ten years should cover about 80%). This database is monthly updated with references I publish here.

---

Reference list

•  Ectopic ATP synthase facilitates transfer of HIV-1 from antigen presenting cells to CD4+ target cells. (Yavlovich, A et al. 2012) 
  
  
  
•  Single-molecule analysis of inhibitory pausing states of V1-ATPase. (Uner, NE et al. 2012) 
  
  
  
•  Structural evidence of a new catalytic intermediate in the pathway of ATP hydrolysis by F1-ATPase from bovine heart mitochondria. (Rees, DM et al. 2012) 
  
  
  
•  Shrimp ATP synthase genes complement yeast null mutants for ATP hydrolysis but not synthesis activity. (Wuthisathid, K et al. 2012) 
  
  
  
•  Relationship of proton motive force and the F(0)F (1)-ATPase with bio-hydrogen production activity of Rhodobacter sphaeroides: effects of diphenylene iodonium, hydrogenase inhibitor, and its solvent dimethylsulphoxide. (Hakobyan, L et al. 2012) 
  
  
  
•  Cellular and tissue expression of DAPIT, a phylogenetically conserved peptide. (Kontro, H et al. 2012) 
  
  
  
•  Specific evolution of f(1)-like ATPases in mycoplasmas. (Beven, L et al. 2012) 
  
  
  
•  Accumulation of newly synthesised F1 in vivo in Arabidopsis mitochondria provides evidence for modular assembly of the plant F1Fo ATP synthase. (Li, L et al. 2012) 
  
  
  
•  ATP synthase oligomerization: from the enzyme models to the mitochondrial morphology. (Habersetzer, J et al. 2012) 
  
  
  
•  A novel biosensor regulated by the rotator of F(0)F(1)-ATPase to detect deoxynivalenol rapidly. (Zhao, Y et al. 2012) 
  
  
  
•  Engineering rotor ring stoichiometries in the ATP synthase. (Pogoryelov, D et al. 2012) 
  
  
  
•  A novel acyclic oligomycin A derivative formed via retro-aldol rearrangement of oligomycin A. (Lysenkova, LN et al. 2012) 
  
  
  
•  Novel Antibiotics Targeting Respiratory ATP Synthesis in Gram-positive Pathogenic Bacteria. (Balemans, W et al. 2012) 
  
  
  
•  Absence of anionic phospholipids in Kluyveromyces lactis cells is fatal without F1-catalysed ATP hydrolysis. (Palovicova, V et al. 2012) 
  
  
  
•  Binding of the phytopolyphenol piceatannol disrupts beta/gamma subunit interactions and the rate limiting step of steady state rotational catalysis in the Escherichia coli F1-ATPase. (Sekiya, M et al. 2012) 
  
  
  
• Reconstitution of Vacuolar type rotary H+-ATPase/synthase from Thermus thermophilus. (Kishikawa, JI and Yokoyama, K 2012) 
  
  
  
• Multiple proteins with essential mitochondrial functions have glycosylated isoforms. (Burnham-Marusich, AR and Berninsone, PM 2012) 
  
  
  
• Molecular Mechanism of ATP Hydrolysis in F(1)-ATPase Revealed by Molecular Simulations and Single-Molecule Observations. (Hayashi, S et al. 2012) 
  
  
  
• A rotary nano ion pump: a molecular dynamics study. (Lohrasebi, A and Feshanjerdi, M 2012) 
  
  
  
• Transcriptional organization of the large and the small ATP synthase operons, atpI/H/F/A and atpB/E, in Arabidopsis thaliana chloroplasts. (Malik, Ghulam M et al. 2012) 
  
  
  
• The Structure of Subunit E of the Pyrococcus horikoshii OT3 A-ATP Synthase Gives Insight into the Elasticity of the Peripheral Stalk. (Balakrishna, AM et al. 2012) 
  
  
  
• The function of mitochondrial F(O)F(1) ATP-synthase from the whiteleg shrimp Litopenaeus vannamei muscle during hypoxia. (Martinez-Cruz, O et al. 2012) 
  
  
  
• Structure of the c(10) ring of the yeast mitochondrial ATP synthase in the open conformation. (Symersky, J et al. 2012) 
  
  
  
• Elastic deformations of the rotary double motor of single F(o)F(1)-ATP synthases detected in real time by Forster resonance energy transfer. (Ernst, S et al. 2012) 
  
  
  
• HcRed, a Genetically Encoded Fluorescent Binary Cross-Linking Agent for Cross-Linking of Mitochondrial ATP Synthase in Saccharomyces cerevisiae. (Gong, L et al. 2012) 
  
  
  
• Assessing the actual contribution of IF1, an inhibitor of mitochondrial FoF1, to ATP homeostasis, cell growth, mitochondrial morphology and cell viability. (Fujikawa, M et al. 2012) 
  
  
  
• Rotary catalysis of the stator ring of F(1)-ATPase. (Iino, R and Noji, H 2012) 
  
  
  
• Rotational catalysis in proton pumping ATPases: From E. coli F-ATPase to mammalian V-ATPase. (Futai, M et al. 2012) 
  
  
  
• Compensatory upregulation of respiratory chain complexes III and IV in isolated deficiency of ATP synthase due to TMEM70 mutation. (Havlickova-Karbanova, V et al. 2012) 
  
  
  
• Thermodynamic and kinetic stabilization of divanadate in the monovanadate/divanadate equilibrium using a Zn-cyclene derivative: Towards a simple ATP synthase model. (Sell, H et al. 2012) 
  
  
  
• Glucose-modulated mitochondria adaptation in tumor cells: a focus on ATP synthase and inhibitor factor 1. (Domenis, R et al. 2012) 
  
  
  
• Principal role of the arginine finger in rotary catalysis of F1-ATPase. (Komoriya, Y et al. 2012) 
  
  
  
• F1Fo-ATPase, F-type proton-translocating ATPase, at the plasma membrane is critical for efficient influenza virus budding. (Gorai, T et al. 2012) 
  
  
  
• Mitochondrial gene therapy improves respiration, biogenesis and transcription in G11778A Leber's hereditary optic neuropathy and T8993G Leigh's syndrome cells. (Iyer, S et al. 2012) 
  
  
  
• Purification, characterization and reconstitution into membranes of the oligomeric c-subunit ring of thermophilic F(o)F(1)-ATP synthase expressed in Escherichia coli. (Yumen, I et al. 2012) 
  
  
  
• Thiol modulation of the chloroplast ATP synthase is dependent on the energization of thylakoid membranes. (Konno, H et al. 2012) 
  
  
  
• Characterization of new mutations in the mycobacterial ATP synthase: New insights in the binding of the diarylquinoline TMC207 to the ATP synthase c-ring structure. (Segala, E et al. 2012) 
  
  
  
• The dynamic stator stalk of rotary ATPases. (Stewart, AG et al. 2012) 
  
  
  
• Three-color Forster resonance energy transfer within single F(O)F(1)-ATP synthases: monitoring elastic deformations of the rotary double motor in real time. (Ernst, S et al. 2012) 
  
  
  
• Subunit F modulates ATP binding and migration in the nucleotide-binding subunit B of the A(1)A (O) ATP synthase of Methanosarcina mazei Go1. (Raghunathan, D et al. 2012) 
  
  
  
• PK11195 Inhibits Mitophagy Targeting the F1Fo-ATPsynthase in Bcl-2 Knock-Down Cells. (Seneviratne, MS et al. 2012) 
  
  
  
• The chemo-mechanical coupled model for F(1)F(0)-motor. (Xu, L and Liu, F 2012) 
  
  
  
• The Mitochondrial ATPase Inhibitory Factor 1 Triggers a ROS-Mediated Retrograde Prosurvival and Proliferative Response. (Formentini, L et al. 2012) 
  
  
  
• Thioredoxin-insensitive plastid ATP synthase that performs moonlighting functions. (Kohzuma, K et al. 2012) 
  
  
  
• Role of Charged Residues in the Catalytic Sites of Escherichia coli ATP Synthase. (Ahmad, Z et al. 2011) 
  
  
  
• Overexpression of coupling factor 6 attenuates exercise-induced physiological cardiac hypertrophy by inhibiting PI3K/Akt signaling in mice. (Sagara, S et al. 2012) 
  
  
  
• Dephosphorylation of the core clock protein KaiC in the cyanobacterial KaiABC circadian oscillator proceeds via an ATP synthase mechanism. (Egli, M et al. 2012) 
  
  
  
• F(1)-ATPase: a prototypical rotary molecular motor. (Kinosita, K Jr 2012) 
  
  
  
• Effect of structural modulation of polyphenolic compounds on the inhibition of Escherichia coli ATP synthase. (Ahmad, Z et al. 2012) 
  
  
  
• Kinetic Equivalence of Transmembrane pH and Electrical Potential Differences in ATP Synthesis. (Soga, N et al. 2012) 
  
  
  
• Promiscuous archaeal ATP synthase concurrently coupled to Na+ and H+ translocation. (Schlegel, K et al. 2012) 
  
  
  
• Local translation of ATP synthase subunit 9 mRNA alters ATP levels and the production of ROS in the axon. (Natera-Naranjo, O et al. 2012) 
  
  
  
• Human ABCC1 interacts and colocalizes with ATP synthase alpha, revealed by interactive proteomics analysis. (Yang, Y et al. 2012) 
  
  
  
• beta-amyloid Peptide Binds and Regulates Ectopic ATP Synthase alpha-Chain on Neural Surface. (Xing, SL et al. 2012) 
  
  
  
• Subnanometre-resolution structure of the intact Thermus thermophilus H(+)-driven ATP synthase. (Lau, WC and Rubinstein, JL 2011
  

http://www.atpsynthase.info/News.html

https://releasingthetruth.wordpress.com/tag/irreducible-complexity/

Proposals of evolution of ATP Synthase

Comparative Genomics and Evolution of Energy Conversion

http://www.macromol.uni-osnabrueck.de/Comparative_genomics.php

Origin of the ATP Synthase

The F-type ATP synthases show homology to another family of rotating machines, namely the V-type ATPases which are found in archaea and in eukaryotic membranes. By analyzing the homology pattern for different subunits of these related enzymes we have put forward a scenario of their origin from primordial protein translocases.


Physico-Chemical and Evolutionary Constraints for the Formation and Selection of First Biopolymers: Towards the Consensus Paradigm of the Abiogenic Origin of Life

http://www.macromol.uni-osnabrueck.de/paperMulk/mulkid_Chem_biodiv.pdf


) New functions (as well as new enzymes, organs, or mechanisms) seem to develop by co-option/modification of pre-existing entities. As
Darwin has noted ; throughout nature almost every part of each living being has probably served, in a slightly modified condition, for diverse purposes, and has acted in the living machinery of many ancient and distinct specific forms. In particular, new enzymes emerge routinely either after duplication of genes, followed by their separate evolution, and/or due to the rearrangement and re-shuffling of genes.

Inventing ( i didn't know that evolution can invent something ) the dynamo machine: the evolution of the F-type and V-type ATPases

http://www.nature.com/nrmicro/journal/v5/n11/abs/nrmicro1767.html

The rotary proton- and sodium-translocating ATPases are reversible molecular machines present in all cellular life forms that couple ion movement across membranes with ATP hydrolysis or synthesis. Sequence and structural comparisons of F- and V-type ATPases have revealed homology between their catalytic and membrane subunits, but not between the subunits of the central stalk that connects the catalytic and membrane components. Based on this pattern of homology, we propose that these ATPases originated from membrane protein translocases, which, themselves, evolved from RNA translocases. We suggest that in these ancestral translocases, the position of the central stalk was occupied by the translocated polymer.


RNA translocases

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0039632#term=ancchart

5.6 Synthesis of ATP by the ATP Synthase Enzyme

The conversion of proton electrochemical energy into chemical free energy is accomplished by a single protein complex known as ATP synthase. This enzyme catalyzes a phosphorylation reaction, which is the formation of ATP by the addition of inorganic phosphate (Pi) to ADP

ADP-3 + Pi-2 + H+ _____> ATP-4 + H2O. (5)

The reaction is energetically uphill (DG = +32 kJ/mol) and is driven by proton transfer through the ATP synthase protein. The ATP Synthase complex is composed of two major subunits, CF0 and CF1 . The CF0 subunit spans the photosynthetic membrane and forms a proton channel through the membrane. The CF1 subunit is attached to the top of the CF0 on the outside of the membrane and is located in the aqueous space. CF1 is composed of several different protein subunits, referred to as a, b, g, d and e. The top portion of the CF1 subunit is composed of three ab-dimers that contain the catalytic sites for ATP synthesis. A recent major breakthrough has been the elucidation of the structure of ATPase of beef heart mitochondria by Abrahams et al. (1994). The molecular processes that couple proton transfer through the protein to the chemical addition of phosphate to ADP are poorly understood. It is known that phosphorylation can be driven by a pH gradient, a transmembrane electric field, or a combination of the two. Experiments indicate that three protons must pass through the ATP synthase complex for the synthesis of one molecule of ATP. However, the protons are not involved in the chemistry of adding phosphate to ADP. Paul Boyer and coworkers have proposed an alternating binding site mechanism for ATP synthesis (Boyer, 1993). One model based on their proposal is that there are three catalytic sites on each CF1 that cycle among three different states (Fig. 15). The states differ in their affinity for ADP, Pi and ATP. At any one time, each site is in a different state. This model is supported by the structure of ATPase elucidated by Abrahams et al. (1994). Initially, one catalytic site on CF1 binds one ADP and one inorganic phosphate molecule relatively loosely. Due to a conformational change of the protein, the site becomes a tight binding site, that stabilizes ATP. Next, proton transfer induces an alteration in protein conformation that causes the site to release the ATP molecule into the aqueous phase. In this model, the energy from the proton electrochemical gradient is used to lower the affinity of the site for ATP, allowing its release to the water phase. The three sites on CF1 act cooperatively, i.e., the conformational states of the sites are linked. It has been proposed that protons affect the conformational change by driving the rotation of the top part (the three ab-dimers) of CF1. Such a rotating model has recently been supported by recording of a rotation of the gamma subunit relative to the alpha-beta subunits by Sabbert et al. (1996). This revolving site mechanism would require rates as high as 100 revolutions per second. It is worth noting that flagella that propel some bacteria are driven by a proton pump and can rotate at 60 revolutions per second.

The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio

Abstract

http://www.lifesorigin.com/chap14/ATP-synthase-synthetase.php

ATP synthase is an incredible enzyme. It is the smallest rotary motor in the world. The protons moved across the cell membrane by the electron donor/acceptor/dehydrogenase complex (figure 14.6) serve as the energy source for ATP synthase.

  ATP synthase lets these proteins flow back to the other side of the cell membrane, and this powers a small rotary motor imbedded inside the membrane and causes it to spin. The spinning portion called the rotor has a stalk attached to it. The stalk is not straight but rather curved. Because other peptide chains surround the stalk, as the stalk spins, it forces these surrounding proteins to move. This allows these surrounding proteins to create ATP from ADP.

  ATP synthase was one of the first enzymes because it is absolutely necessary for many of the organisms that are thought to have existed on the primitive earth. All of the bacteria that oxidize non-organic chemicals to obtain energy use ATP synthase to make ATP.

  The enzyme is composed of 8 distinct peptide chains. If any one of the chains is missing, the enzyme does not function. So ATP synthase is an irreducibly complex system. The subunits, their amino acid number, information and knowledge are shown in table 14.2. The operation of ATP synthase is illustrated in figure 14.9. The table and the figure together explain why this was not the first protein to synthesize ATP. If a system involving ATP synthase is required for the origin of life, then it will never get off the ground. The protein is too complex and contains too much knowledge.

How did LUCA make a living? Chemiosmosis in the origin of life 1

One   of   the   biggest   stumbling   blocks   to   the   idea   of ‘chemiosmosis early’ is the daunting complexity of the ATP synthase   –   a   nanomachine   comprising   a   rotary   motor powered by a flow of protons through the membrane stalk, coupled to the rotating head that forms ATP from ADP and phosphate. The two main domains, the stalk and the rotating head,  have  no  obvious  homologues  among  other  proteins. ATP synthase is certainly the product of Darwinian evolution at the level of genes and proteins.

The fact that both archaea and bacteria possess similar ATP synthase  enzymes  (A-  and  F-type  ATPases,  respectively) implies  that an ATPase  ancestral  to both types  did  indeed evolve in the vents.

The  amino  acid  substitutions common to the membrane rotor subunits predict that Naþ-dependent ATPases arose in parallel in independent lineages.

the first ATPases harnessed a  natural  proton  gradient  in  alkaline  vents,  the  magnitude (roughly 1000-fold concentration difference) and polarity of that gradient (alkaline inside) being virtually identical to that in modern cells.

It seems to me Nick Lane is making himself a fool by making such baseless assertions not providing a shred of evidence, but basing his inference on wishful thinking. If the evolution of one ATP synthase motor is extremely unlikely, imagine two, independently, in convergent manner...... Furthermore, Lane ignores that atp synthase is not the only machine required , there are several others.

Sodium ATPases  are then derived in several lineages independently, involving a few parallel amino acid substitutions to proton ATPases under the guiding hand of selection.

More funny is imho that in order to make ATP synhtase, alll the advanced machinery depending on DNA to RNA Polymerase, Ribosome etc. is required..... LOL. How is it possible that no peers are questioning this obvious fact ?  

It is worth noting here that we do not envisage the ancestral ATPase as embedded in the inorganic walls, but rather in organic lipids lining  the  walls.

More science fiction......

At present,   there   is   nothing   to   suggest   that   any   simpler intermediates did actually precede the ATPase, and no need for them to do so.

Well, how in fact atp synthase arose is what has to be explained first hand....  suggesting " guiding hands of selection " is putting almost supernatural powers to the capabilities of natural selection, its becoming almost the universal answer for anything that has no more serious explanation, i'd say such explanations belong to marvel comics, but not to serious origin of life scenarios and scientific papers.

There is no reason why a rotor-stator type ATPase could not be ‘invented’de novo; in terms of complexity it requires no more evolutionary innovation than the  origin  of  a  primordial  ribosome,  which  everyone  would agree didevolve.

So because supposedly the Ribosome did evolve, ATP synthase likely evolved as well. Amazing. What our author forgets, is, that both, ATP synthase, and the ribosome, both would have NO USE unless fully functioning and embedded in the respective production lines..... so why should they evolve in the first place ??

1) http://www.researchgate.net/publication/41167227_How_did_LUCA_make_a_living_Chemiosmosis_in_the_origin_of_life

Structural study on the architecture of the bacterial ATP synthase Fo motor 1



View at the rotor-stator region of the bacterial Fo ATP synthase. (A) Model of the ATP synthase, viewed from the periplasmic side of a bacterial cell. The F1 complex (green) harbors the catalytic sites, which convert ADP and Pi into ATP (arrow). The Fo complex consists of the rotor ring (blue) and the stator region (red/orange). Ions (yellow spheres) enter a pathway through the stator region, bind to the rotor, and are released to the other side of the membrane after an almost complete revolution. (Figure created by Paolo Lastrico, Max Planck Institute of Biophysics.) (B) I. tartaricus Fo ATP synthase was purified, and 2D crystals were grown. Cryo-EM yielded a projection map (gray) showing electron densities of the c-ring and its neighboring regions: The c-ring (yellow model) from the periplasmic side and up to seven adjacent helices (red, brown, and blue) belonging to the stator a- and b-subunits became visible. A bundle of four helices (red) is in contact with the c-ring. A fifth helix (brown) adjacent to the four-helix bundle interacts very closely with one of the c-subunit helices.



1) http://www.pnas.org/content/109/30/E2050/1/F5.expansion.html

further readings :

http://advances.sciencemag.org/content/advances/1/4/e1500106.full.pdf
http://www.pnas.org/content/109/30/E2050.full.pdf+html

Macromolecular organization of ATP synthase and complex I in whole mitochondria 1

Long rows of ATP synthase dimers were observed in intact mitochondria and cristae membrane fragments of all species that were examined. The dimer rows were found exclusively on tightly curved cristae edges. The distance between dimers along the rows varied, but within the dimer the distance between F1 heads was constant. The angle between monomers in the dimer was 70° or above.



Molecular organization of cristae membranes. ATP synthase and complex I occupy different regions of the mitochondrial cristae. The ATP synthase forms dimer rows (yellow) at the cristae tips, whereas the proton pumps of the electron transfer chain (green), in particular complex I, reside predominantly in the adjacent membrane regions. Protons (red) pumped into the cristae space by the electron transport complexes flow back into the matrix through the ATP synthase rotor, driving ATP production. We propose that this conserved arrangement generates a local proton gradient in the cristae space, which would explain how the dimer rows help to optimize mitochondrial ATP synthesis, and provide a functional role for the mitochondrial cristae.

The proton-pumping machines (green) are arranged along folds of the cristae (blue) so that the protons don’t wander away from the ATP synthase machines (yellow).  Since Complexes I, III, and IV act as proton “sources” and ATP synthase as proton “sinks”, a flow is set up toward the tight folds where the ATP synthase (yellow) are located.
In addition, the ATP synthase engines are so arranged in pairs (dimers), their F0 parts almost touching, their F1 parts separated, by angles ranging from 40° to 70° depending on the species.  These dimers are then arranged in long rows like one might see in a hydroelectric plant.  In this way, the flow of protons is channeled exactly where it is needed for optimal performance of the turbines.  Concerning this “striking arrangement,” the authors said, “We propose that the supramolecular organization of respiratory chain complexes as proton sources and ATP synthase rows as proton sinks in the mitochondrial cristae ensures[b] optimal conditions for efficient ATP synthesis. 2






1) http://www.pnas.org/content/108/34/14121.full
2) http://crev.info/2011/08/110817-your_rotary_engines_are_arranged_in_factories/#sthash.sKepfAzn.dpuf

ATP Synthase-- Movie Narrative 1

Concentration gradients are a key component of the biological world. The potential energy from these gradients is often used to perform biological work.

Here we will focus on hydrogen ion concentration gradients. Hydrogen ions, are also known as protons.

A gradient exists when there is a higher concentration of a molecule in one compartment compared to a neighboring compartment.

This animation will demonstrate how the potential energy that results from a hydrogen ion gradient uses ADP and inorganic phosphate, also known as Pi, to synthesize ATP.

This process involves an enzyme complex called ATP synthase.

Gradients and the potential energy they create are key aspects of the biological world. A good example of the use of a gradient occurs in the mitochondria when ATP is synthesized. ATP is synthesized by ATP synthase, a large complex of membrane-bound protein.

Here we see ATP synthase, along with other membrane-bound proteins.

Notice the large difference in the number of hydrogen ions on the two sides of the membrane. This difference is a hydrogen ion, or proton, concentration gradient.

The energy associated with this gradient is used to synthesize ATP from ADP and Pi. This occurs at the ATP synthase complex.

One hydrogen ion enters the ATP synthase complex from the intermembrane space and a second hydrogen ion leaves it on the matrix space. The upper part of the ATP synthase complex rotates when a new hydrogen ion enters.

Once three protons have entered the matrix space, there is enough energy in the ATP synthase complex to synthesize one ATP. In this way, the energy in the hydrogen ion gradient is used to make ATP.

Now let's watch the process again...

Notice how the proton enters the ATP synthase and exits into the matrix space. Once three more hydrogen ions have crossed the membrane, another molecule of ATP will be made. In this example, the hydrogen ion gradient is large enough to produce six ATP molecules.

Please watch as the remaining ATP molecules are synthesized...

The process has now completed, and the result is an equal number of protons on each side of the inner membrane. Without a gradient, there is no more energy available to make ATP.

In biological systems, however, a gradient is always maintained. The mitochondrial hydrogen ion gradient is generated as electrons pass through three membrane complexes. That process can be seen in the mitochondrial electron transport chain animation.



The mitochondria, a key site of ATP synthesis. Its structure is an important aspect of ATP production.



ATP synthase and the complexes that form the electron transport chain (ETC) are located throughout the cisternae.



Here we see how ATP is oriented in the inner membrane of the mitochondria.



In this example, a large proton, or hydrogen, gradient is already in place.



ADP and Pi (inorganic phosphate) have now been added. They are the substrates used to synthesize ATP.



First, a proton from the intermembrane space enters the ATP synthase complex.



Next, another proton leaves the ATP synthase complex and exits into the matrix space.



Finally, the upper portion of the ATP synthase complex rotates slightly to prepare for the next set of protons to enter and exit the complex.



The lower portion of the ATP synthase complex combines ADP and Pi to synthesize ATP.



In biolgical systems a proton gradient is maintained by the electron transport chain. In our example, however, the ETC is not functional. The proton gradient has equalized, and there is no energy left to synthesize more ATP.

1) http://vcell.ndsu.nodak.edu/animations/atpgradient/movie-flash.htm

http://www.nature.com/nature/journal/v459/n7245/abs/nature08145.html

Adenosine triphosphate (ATP), the universal fuel of the cell, is synthesized from adenosine diphosphate (ADP) and inorganic phosphate (Pi) by 'ATP synthase' (FOF1-ATPase). During respiration or photosynthesis, an electrochemical potential difference of protons is set up across the respective membranes. This powers the enzyme's electrical rotary nanomotor (FO), which drives the chemical nanomotor (F1) by elastic mechanical-power transmission, producing ATP with high kinetic efficiency.

Attempts to understand in detail the mechanisms of torque generation in this simple and robust system have been both aided and complicated by a wealth of sometimes conflicting data.

A rotary molecular motor that can work at near 100% efficiency.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1692765/

A single molecule of F1-ATPase is by itself a rotary motor in which a central gamma-subunit rotates against a surrounding cylinder made of alpha3beta3-subunits. Driven by the three betas that sequentially hydrolyse ATP, the motor rotates in discrete 120 degree steps, as demonstrated in video images of the movement of an actin filament bound, as a marker, to the central gamma-subunit. Over a broad range of load (hydrodynamic friction against the rotating actin filament) and speed, the F1 motor produces a constant torque of ca. 40 pN nm. The work done in a 120 degree step, or the work per ATP molecule, is thus ca. 80 pN nm. In cells, the free energy of ATP hydrolysis is ca. 90 pN nm per ATP molecule,
We confirmed in vitro that F1 indeed does ca. 80 pN nm of work under the condition where the free energy per ATP is 90 pN nm. The high efficiency may be related to the fully reversible nature of the F1 motor: the ATP synthase, of which F1 is a part, is considered to synthesize ATP from ADP and phosphate by reverse rotation of the F1 motor. Possible mechanisms of F1 rotation are discussed.

http://www.pnas.org/content/early/2011/10/12/1106787108.full.pdf

We found that the maximum work performed by F1-ATPase per 120° step is nearly equal to the thermodynamical maximum work that can be extracted from a single ATP hydrolysis under a broad range of conditions. Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F1-ATPase.

Visualization of ATP Synthase Dimers in Mitochondria by Electron Cryo-tomography

Great video:

http://www.jove.com/video/51228/visualization-atp-synthase-dimers-mitochondria-electron-cryo

Scientist Harnesses ATP Synthase   
     
How would you like shorter waits at airports?  fast screening for disease?  the ability to detect biological warfare agents quickly?  That may be possible soon – thanks to an amazing man-and-nature cooperative technology reported by Science Daily.  A team led by Wayne Frasch at Arizona State is on the verge of an invention that can do these things, because he was fascinated by the world’s tiniest molecular motor, ATP synthase, and found a way to harness it’s rotational energy.
    You can read all about it in the article.  What’s most interesting, though, is what the press release said about ATP synthase (also called F0-F1 ATPase, with two functional domains, F0 and F1), – and what it did not say about evolution:

Even more incredible than the device itself, is that it is based on the world’s tiniest rotary motor: a biological engine measured on the order of molecules.
    Frasch works with the enzyme F1-adenosine triphosphatase, better known as F1-ATPase.  This enzyme, only 10 to 12 nanometers in diameter, has an axle that spins and produces torque.  This tiny wonder is part of a complex of proteins key to creating energy in all living things, including photosynthesis in plants.  F1-ATPase breaks down adenosine triphosphate (ATP) to adenosine diphospahte [sic] (ADP), releasing energy.  Previous studies of its structure and characteristics have been the source of two Nobel Prizes awarded in 1979 and 1997.
    It was through his own detailed study of the rotational mechanism of the F1-ATPase, which operates like a three-cylinder Mazda rotary motor, that Frasch conceived of a way to take this tiny biological powerhouse and couple it with science applications outside of the human body.

The device is sure to find additional applications.  This article said nothing about how the “three-cylinder Mazda rotary motor” analogue, essential for energy control in all living things, might have evolved.
    ATP synthase has become a favorite molecular machine for the Intelligent Design movement as evidence of irreducibly complex structures.  

The line between natural technology and human technology is seamless.  Where does blind nature end and intelligent design begin?  How would an independent observer happening upon the nanostructure know where thenatural ended and the artificial began?  If he were rightly to infer design for the nanoprobe and its blinking light, on what basis would he infer chance and mindless natural forces had built the Mazda-like rotary engine?  The design inference is appropriate in both cases.
    Was evolutionary theory helpful at all for this wondrous invention that may revolutionize biomedical testing and enhance national security?  The scientist was intrigued by a natural nanotech motor and found a way to use it for human good.  Would it have added anything to spin an imaginary story set in some mythical prehistory about how ATP synthase evolved?
    Come now.  Early scientists were motivated by the design and orderliness of nature that they viewed as the handiwork of an all-wise, omnipotent Creator.  Today’s story is a classic case of intelligent-design-guided science and technology, just like the old days.  Darwinism is a parasite on the process of discovering and advancing the knowledge that really matters to us. 

ATP synthase: majestic molecular machine made by a mastermind

http://creation.com/atp-synthase




Figure 1. The whole ATP synthase machine with individually manufactured protein subunits each labelled with Greek letters. H^[size=9]+ ions (protons) flow through a special tunnel in ATP synthase, as the arrow indicates. This induces mechanical motion, forcing the axle and base to spin together like a turbine. Nearly 100% of the spinning momentum is converted to chemical energy in the formation of ATP molecules! Three ATPs are produced for every 10 protons.
(Adapted from Kanehisa Laboratories, <www.genome.jp/kegg>)[/size]


Life depends on an incredible enzyme called ATP synthase, the world’s tiniest rotary motor.¹ This tiny protein complex makes an energy-rich compound, ATP (adenosine triphosphate). Each of the human body’s 14 trillion cells performs this reaction about a million times per minute. Over half a body weight of ATP is made and consumed every day!
All living things need to make ATP, often called the “energy currency of life”. ATP is a small molecule with a big job: to provide immediately usable energy for cellular machines. ATP-driven protein machines power almost everything that goes on inside living cells, including manufacturing DNA, RNA, and proteins, clean-up of debris, and transporting chemicals into, out of, and within cells. Other fuel sources will not power these cellular protein machines for the same reasons that oil, wind, or sunlight will not power a gasoline engine.
Logical thinking about an automobile engine leads us to think that only a clever person (with mind and will) could make a machine that converts energy from one form to another for the purpose of moving a car.²The machine shows orderly, non-random proportions and clever use of interdependent parts that are the right size, shape and strength to work together for an overall purpose. The same inference from machine back to maker is validly inferred from machines found in “nature” back to their Creator.³ Everyone knows that a painting comes from a painter, because the painting shows specified complexity, or a complex and recognizable pattern that is not a property of the paint. That is, the paint molecules do not spontaneously organize themselves into a portrait of Mona Lisa, for example.⁴

[size=10]Figure 2: Ribbon diagram of a top view of the head portion of ATP synthase, called “F₁-ATPase”. It has six protein subunits, and consists of three active sites, where three ATP molecules are formed for each full rotation of the axle. The very top end of the axle is just visible, leaning against the upper right inside wall of F₁. Cellular machinery constructs the head, after which it self-assembles onto the base.
(www.rcsb.org/pdb/explore/images.do?structureId=2F43)[/size]


ATP synthase occurs on the inner membranes of bacterial cells, and the innermost membranes of both mitochondria and chloroplasts, which are membrane-bound structures inside animal and plant cells (see figure 1).
ATP synthase manufactures ATP from two smaller chemicals, ADP and phosphate. ATP synthase is so small that it is able to manipulate these tiny molecules, one at a time. ATP synthase must convert some other form of energy into new ATPs. This energy is in the form of a hydrogen ion (H⁺) gradient, which is generated by a different whole protein system to ATP synthase.⁵ Hydrogen ions pour through ATP synthase like wind through a windmill. This comprises a positively charged electric current, in contrast to our electric motors, which use a negative current of electrons.
ATP synthase is a complex engine and pictures are necessary to describe it. Scientists use clever techniques to resolve the exact locations of each of many thousands of atoms that comprise large molecules like ATP synthase.⁶ This protein complex contains at least 29 separately manufactured subunits that fit together into two main portions: the head (figure 2) and the base (figure 3).⁷ The base is anchored to a flat membrane (figure 1) like a button on a shirt (except that buttons are fixed in one place, whereas ATP synthase can migrate anywhere on the plane of its membrane). The head of ATP synthase forms a tube (figure 2). It comprises six units, in three pairs. These form three sets of docking stations, each one of which will hold an ADP and a phosphate. ATP synthase includes a stator (stationary part), which arcs around the outside of the structure to help anchor the head to the base (figure 1).

[size=10]Figure 3: A ribbon diagram (side-view) of the base of ATP synthase, called the ‘F₀’ portion. It is made of twelve helical protein subunits arranged in a circle, forming the wall of a tube. This tube provides a tunnel across the membrane (not shown) in which it is anchored .
(www.rcsb.org/pdb/explore/images.do?structureId=2CYD)[/size]


Now we can look at the amazing, efficient way that this marvelous micro-machine works. Notice in figure 1 a helical axle labeled “γ” in the middle of the ATP synthase. This axle runs through the center of both the head and base of ATP synthase like a pencil inside a cardboard toilet paper tube.
Here is the “magic”: When a stream of tiny hydrogen ions (protons) flows through the base and out the side of ATP synthase, passing across the membrane, they force the axle and base to spin.⁸ The stiff central axle pushes against the inside walls of the six head proteins, which become slightly deformed and reformed alternately.⁹ Each of your trillions of cells has many thousands of these machines spinning at over 9,000 rpm.¹⁰
The spinning axle causes squeezing motions of the head so as to align an ADP next to a phosphate, forming ATP … in bucket loads. Many other cellular protein machines use ATP, breaking it down to ADP and phosphate again. This is then recycled back into ATP by ATP synthase. Lubert Stryer, author of Biochemistry adds,

“… the enzyme appears to operate near 100% efficiency …”.¹¹

[size=10]Figure 4: Overall 3-D molecular structure of ATP synthase rotor by Stock et al ⁷, minus the stator.[/size]
This motor is incredibly high-tech design in nano-size.
Evolutionary scientists have suggested that the head portion of ATP synthase evolved from a class of proteins used to unwind DNA during DNA replication.¹²
However, how could ATP synthase “evolve” from something that needs ATP, manufactured by ATP synthase, to function? This bizarre suggestion underlines the role of our beliefs in how we interpret origins. Evolutionists are often driven by a bias which they do not admit: methodological naturalism. This is the assumption that the processes which explain theoperation of phenomena are all we can use to describe the origin of those phenomena. This philosophy excludes God, by decree (not because of science or reason).¹³
Creation scientists, looking at the same ATP synthase “phenomenon” also have a bias: supernatural origins are possible in a theistic universe. The big question is: whose bias is correct? I submit that a creation bias is clearly true because it makes sense according to the principles of causality as well as the revealed Word of the Creator Himself.
We might also consider that ATP synthase is made by processes that all need ATP—such as the unwinding of the DNA helix with helicase to allow transcription and then translation of the coded information into the proteins that make up ATP synthase. And manufacture of the 100 enzymes/machines needed to achieve this needs ATP! And making the membranes in which ATP synthase sits needs ATP, but without the membranes it would not work. This is a really vicious circle for evolutionists to explain.
What about the characteristics of the One who designed the amazing abilities of the ATP synthase nano-motor? Keep in mind that the smaller a machine is, the more ingenious the effort needed to build it.
ATP synthase speaks of wisdom, intelligence, capability, or rationality in its creator, some of the exact attributes of God as revealed in the Bible! When we investigate His handiwork, we are both obeying His command in [url=http://biblia.com/bible/esv/Genesis 1.28]Genesis 1:28[/url] to do the work necessary to “subdue the earth”, and we have even more reason to praise and enjoy Him for His providence and genius.

Double Ratchet Found in ATP Synthase

http://crev.info/2011/03/double_ratchet_found_in_atp_synthase/

Posted on March 16, 2011 in Amazing Facts, Cell Biology, Intelligent Design
ATP synthase, the rotary engine in all living things, has another trick in its design specs: a ratcheting mechanism that improves the efficiency of ATP synthesis.  ATP is the “energy currency” of cellular life, so the efficiency of production of ATP is of vital importance.  (For background and animation, see CMI article.)
    Three European scientists, reporting in PNAS,1 used quantum mechanical approaches to study the energy flow during production of ATP in the beta subunits (the active sites of the motor-driven enzyme).  The alpha subunit rotates like a waterwheel (12/22/2003), engaging a camshaft called the gamma subunit.  Three ATP are formed in the beta portion for each 360° cycle.  That results in one ATP for each 120 degrees of rotation: “There are three active sites at which the reaction may take place and these are subject to conformational changes during the revolving cycle,” they explained (a conformational change indicates moving parts).  Hints that more was going on each 1/3 turn were brought to light when other researchers noticed slight pauses at 90° and 30°.
    The authors found two transition states within the 120° motion that favor the reaction one way, like a ratchet.  The first of these transition states occurs via a double proton transfer.  The second occurs via a conformational change as the third phosphate ion bonds with oxygen on ADP (adenosine diphosphate), forming ATP (adenosine triphosphate).  “These two TSs [transition states] are concluded crucial for ATP synthesis,” they said.  They found that as the enzyme progresses into these states, energy barriers are set up that block the reverse direction, just like a ratchet on a tool.  “This change could indicate a ‘ratchet’ mechanism for the enzyme to ensure efficacy of ATP synthesis by shifting residue conformation and thus locking access to the crucial TSs.”2
    It’s “demanding” to study these machines.  “The complex function of ATP synthase makes this enzyme special compared to many other enzymes and makes computational investigation challenging,” they said.  Many other teams study these amazing molecular machines, and a full understanding of the reaction mechanism awaits elucidation, but the authors felt “we have shown how the positions of alpha-S344 and alpha-R373 [two amino acid residues in the active site] may drastically influence the rate and, in this way, attenuate the reversal of these reaction steps.”
    Since ATP synthase is known to permit both synthesis and hydrolysis of ATP, (i.e., the motor is reversible), it will be interesting to see if the ratchets have some kind of clutch mechanism to favor hydrolysis under certain conditions.  For more on ATP synthase, see 09/22/2010, 08/04/2010, 01/07/2010, 05/25/2009, 03/27/2008, and 08/10/2004, or search on “ATP synthase” in the search bar above.

---

1.  Tamás Beke-Somfai, Per Lincoln, and Bengt Nordén, “Double-lock ratchet mechanism revealing the role of [alpha]SER-344 in F0F1 ATP synthase,” Proceedings of the National Academy of Sciences, published online before print March 7, 2011, doi: 10.1073/pnas.1010453108.
2.  The authors measured energy barriers of 43 kJ/mol and 40 kJ/mol in the two transition state ratchets.

Over the last eight years of reports on ATP synthase in these pages, the trend has been to find more and more detail supporting efficient design, and less and less credibility these molecular rotary engines could have evolved by chance.  Remember that they are vital to every living cell – even primitive bacteria.  Now we see that individual amino acid positions in the active site are critical.  Even “point mutations of alpha-S347Q and alpha-S347A have dramatic effects on ATP synthase function both for synthesis and hydrolysis,” they said, pointing out that one known mutation reduces function and another disables it altogether.  No wonder these amazing machines are “highly conserved” (unevolved) in all domains of life.
    The authors did not mention evolution except for one quick stink bomb, “Performing this reaction efficiently is likely a key biochemical reason for the early evolutionary development of the enzyme complex, so understanding the detailed catalytic steps is most desirable.”  What?  The need for efficiency somehow caused accidents to occur that “developed,” in some blind, unguided way, this finely-tuned, multi-part, 100% efficient engine beyond human capability to manufacture?  “Evolutionary development” is an oxymoron, like blind guide.  Let’s repair the sentence: “Performing this reaction efficiently is likely a key biochemical reason for the original design of the enzyme complex, so understanding the detailed catalytic steps is most praiseworthy.”  Ah, much better.

ATP synthase regulation:  The nanoscopic rotary engines (08/10/2004) that keep your cells humming (08/25/2004) have a problem during cell division.  How do they maintain their lickety-split whirring activity (01/30/2005) while reproducing all their parts?  Rak and Tzagaloff at Columbia University tried to figure that out and published their results in PNAS.³  They began by pointing out another challenge: some of the genes are in the mitochondria, not just in the nucleus.  What controls which genes get expressed?  How does the nucleus signal the organelle when to produce more protein products? 

The authors won a SEQOTW prize for that last sentence, unfortunately, but that was their only mention of evolution in the whole paper.  They went on to talk about the complex assembly of ATP synthase with parts from both nuclear and mitochondrial genes.  One finding is that the two parts of the rotary motor are constructed separately and then assembled.  Three enzyme chaperones that are encoded by the mitochondrial genome, Atp6p, Atp8p and Atp9p, appear to be critical to the assembly, but timing is everything: “Interaction of Atp6p with the Atp9p ring is probably a late assembly event as the resultant complex can cause an unregulated proton leak leading to dissipation of the mitochondrial membrane potential.  The incorporation of Atp6p into the complex has, therefore, been inferred to occur at a stage when the structural elements necessary for coupling proton transfer to ATP synthesis or hydrolysis are already in place.”  They went on to show how these three factors go into action only after the motor is assembled – and that the motor itself regulates the translation of the enzymes needed to bring it into action.
[/list]

Evolution, as in Mutation and Selection, Has Been Demonstrated in ATP Synthase

1




Mutations have been shown to confer a survival advantage to ATP synthase motors in an extremophile. Yet this rotary motor has been a popular illustration for intelligent design. What are we to conclude from the new evidence?
An open-access paper in PNAS shows that part of the rotary motor of ATP synthase -- a vital molecular machine for almost all living things -- has experienced mutation and selection. We recently featured a dramatic animation of how this motor works. As an exquisite, irreducibly complex device, it looks like evidence par excellence for design. Yet it mutated, and it still works. In the case of alkaliphilic bacterium Bacillus pseudofirmus OF4, it works better with the mutation.

The data indicate a direct connection between the precisely adapted ATP synthase c-ring stoichiometry and its ion-to-ATP ratio on cell physiology, and also demonstrate the bioenergetic challenges and evolutionary adaptation strategies of extremophiles.(Emphasis added.)

Let's begin with several unquestioned facts:


It's still ATP synthase.
The structure and mechanism work the same.
The mutated version fits well within known variations of the motor.
This bacterium lives in a highly stressed, high-alkaline environment.
The unmutated version of the motor works in the bacterium, albeit not as efficiently.
The mutation amounts to a substitution of one amino acid for another.
ATP synthase is otherwise "highly conserved" from bacteria to humans.
The mutation has no bearing on the origin of the machine.

Here's some background: In the c-ring (the portion of the machine that rotates like a merry-go-round around a central pore), protons attach to c-subunits and drive the rotation so that the other primary domain can synthesize ATP. The number of c-ring subunits varies between species from 5 to 17. This kind of bacterium normally has 12, but the extremophile version has 13.
C-ring subunits contain a conserved motif of glycine repeats (G) in the form GxGxGxG. In Bacillus pseudofirmus OF4, however, the researchers found alanine had replaced the glycine, producing AxAxAxA. This had the effect of creating a 13-subunit ring, with a tighter fit. The modification improved proton pumping, but only in highly alkaline environments (pH > 10). Protons are hard to come by in alkaline environments. Anything that improves the efficiency of utilizing the weakened proton motive force (pmf) would be adaptive.
Glycine and alanine are two of the simplest amino acids. Glycine has a hydrogen (H) for its side group, whereas alanine has a methyl group (CH₃). The codons for the two are also similar. Any of these triplets can code for glycine: GGU, GGC, GGA, and GGG. Any of these triplets can code for alanine: GCU, GCC, GCA, and GCG. It's clear that a single point mutation, like from GGU to GCU, could switch from one to the other. Such variations within an enzyme are common if they do not destroy function of the enzyme.
Consider the extreme environment of this bacterium. It lives in highly alkaline soils. Any individual with a mutation that improves its ability to extract proton fuel for its motors is likely to proliferate. The mutant is not creating a new function; it's merely conserving an existing function. The structure and operation of the motor remain the same; the authors said, "several high-resolution structures of isolated rotor rings have demonstrated an overall conserved structural appearance and functionality." The mutation has the effect of creating a tighter and stabler fit that improves pumping efficiency in the extreme alkaline environment. If it were as effective in more neutral or acidic environments, why would the GxGxGxG motif be so highly conserved?
In other words, because the environment of this bacterium is stressful, extreme conditions call for desperate measures. More importantly, the mutational pathway for its adaptation is simple, well within the "edge of evolution" accessible to natural variation and selection as described by Michael Behe in his book, The Edge of Evolution (2008). Behe described mutational pathways, consisting of one or two mutations, that allow malaria to escape when stressed by chemical agents trying to kill it. He demonstrated that the probability of those lifesaving mutations do not exceed the probabilistic resources available; adding more required mutations, though, quickly exceeds them.
The authors indicated that the mutations they found are within the range of functional variation:

Our data indicate that B. pseudofirmus OF4 can assemble and operate ATP synthases with different stoichiometries of c-rings in the range of c11 to c15, but robust growth at high pH is restricted to strains with a majority of c-rings with at least the c13 stoichiometry.

When protons are in short supply, having more c-ring subunits helps. That's why this extremophile benefits with the alanine motif, because it adds a subunit and tightens the fit of the c-ring in the membrane. It's only when the pH gets above 10 that the mutation is beneficial. Otherwise, if it were a generally beneficial change, all species would use it. Instead, the GxGxGxG motif is the conserved form, even in similar bacteria that live in neutral environments.
The authors say that the location of the particular mutation is a mutational hotspot. Other extremophiles are known to have particular variations there. But one cannot mutate these delicate motors willy-nilly:

The changes in the tertiary structure of these mutants have no influence on complex stability with respect to pH, temperature, or detergent, but further mutations finally destabilize the c-ring.

The authors end by stating that this mutation could have spread quickly in the population. With i indicating the number of c-ring subunits, the rate of ATP production is i x pmf (proton motive force). The mutant proliferates because it has a slightly improved production rate of ATP:

The alanine motif is a necessary, but insufficient, adaptation of alkaliphilic Bacillus bacteria. It has a direct influence on the c-ring stoichiometry and its indigenous property to determine the ATP synthase i value, and thus directly modulates the cell's physiology and bioenergetics, facilitating growth at pH >10. Remarkably, and in agreement with previous work, this observation also suggests thati can be adapted by just one or two selected mutations. This property enables adaptation to new environmental challenges, a process that can occur within a rather short evolutionary time frame.

It's an interesting paper that demonstrates adaptive selection on a small scale. But since the changes are well within the edge of evolution, since they only affect bacteria in a stressed environment, and since they do not alter the irreducible complexity of functional parts, the findings do not alter the inference to design. If anything, they show the weakness of evolutionary theory. It can only permit small-scale adaptations under special conditions, provided the changes do not destabilize the complex machinery.
And who knows; it could be argued that the "mutational hotspot" that permits this adaptability to environmental challenges was itself designed.

1) http://www.evolutionnews.org/2013/05/evolution_found071671.html

ATP synthases: molecular nano power plants

http://reasonandscience.heavenforum.org/t1439p15-atp-synthase#4550

From Marcos Eberlin's excellent book : Fomos planejados (we were planned )

https://pt-br.widbook.com/ebook/read/fomos-planejados



Figure 1. A "rudimentary" design of one of the largest nanomolecular wonders of life: the ATP synthase motor. The smallest and most efficient power plant on this planet powering the production of energy of Life. One of the essential requirements for Life is energy. Living organisms require large amounts of energy, and the molecule that stores and releases energy of life is adenosine triphosphate represented by the acronym ATP (Figure 2). And then there is a need for a huge amount of this molecule. And to synthesize it with efficiency and optimization, Life requires adenosine - a heterocyclic nitrogenous base, a ribose sugar molecule (one sugar) and three phosphates. Note the difficulty here for any unguided process  you "want to imagine" to form such a molecule. Sugars are formed by formaldehyde - essentially - a highly reactive molecule. Sugars are reactive and unstable, and reaction media that allow synthesis of sugars are incompatible with the means of synthesis of nitrogenous bases. Anions phosphate precipitate in the presence of metal ions such as Ca2 +, for example. And links between phosphate anions involve slow reactions, and need to be catalyzed by enzymes. Therefore, this molecule synthesis routes give a hell lot of work that only the machinery of life can perform. And to make matters worse for the task, the ATP molecule is unstable and hydrolyzes easily in water, and is exothermical (gives off heat). And then to establish the third phosphate connection, which requires most energy,  life must go against the kinetics and enthalpy and so uses the only way to overcome such cumber thermodynamic: a machine, and an incredible nanomachine: ATP synthase (Figure 1 ).




Figure 2. The ATP molecule - a chemical masterpiece- to generate the energy of Life.
The ATP synthase is the name given to a true nanomolecular "power plant"  made by turbines and protein reactors, that in a spectacular and artfully crafted way, synthesizes - and reverse the synthesis - the molecule of ATP (adenosine triphosphate) from ADP (adenosine bifosfate) and anions of inorganic phosphate in the cells (Figure 1). A nanomolecular marvel of technology, chemistry and mechanical engineering mega intelligent.

 Carved like a work of chemical art , beautiful and awe-inspiring - it appears to challenge failed theories - ATP synthase has the smallest engine known in this universe. And this engine, professional thing, it performs like  a perfect and finely tuned ballet,  a synchronized set of thousands and thousands of inter- and intramolecular interactions. This plant also has input channels and output protons also artfully constructed with extreme skill and sophistication and astonishing precision, and nanometrical distances and forces set and finely calculated for the purpose of building a nanomolecular plant maximized to produce  chemical energy.

With a nanomolecular turbine powered by protons and which transmits its movement through a molecular rotor, and channels that direct the movement of these protons - kind of molecular slides to the water parks, the ATP synthase has fascinated many electrical and  chemical engineers primarily - for its perfection in performing reactions and producing energy. In it, we also have "molecular pins" that attach the rotor to the chemical reactor (F1 unit) catalyst, which accommodates within itself the reagents and literally confines them and "Squeezes", so as to accelerate the desired chemical reaction. And that tightens and loosens are all promoted by a synchronized spin - one opens and closes nanometrically set - governed by a molecular piece of oval shape crankshaft type in camshafts, those that man added to their combustion engines (Figure 3).
A fantastic chemical reaction then occurs in the ATP synthase: ADP + ATP → PO4-. And the whole machinery of ATP synthase is there fitted perfectly in the cell wall of the inner mitochondrial membrane , that hyper mega high tech " cell ship" . And all with homochiral molecules, AA type lefthanded only.

 The ATP synthase is therefore a show of sophistication, specification and aperiodicity, and hyper mega irreducible complexity . Disconnect one of its components, disturb one of its forms, replace some of your AA position, and there are thousands and thousands of them, and the system loses function altogether. Try to build it slowly, step by step, by mindless unguided processes, will it be possible? Viable at the molecular level? Where would the energy come from to build it, if it is the energy provider of life? Remember though that the energy that produces ATP synthase is essential to life, virtually for all forms of life. And it is power required  at the right time at the right flow! The structure of ATP synthase is so ingenious that its elucidation earned a Nobel Prize in 1997, as the enormity and significance of the feat. Our cells contain thousands of these nanomotors embedded in their mitochondria, and installed in their membranes. And these nanomotors - nano power plants - are about 200,000 times smaller than a pinhead. And that nanomotor is there for the sole purpose of forcing the occurrence of a single reaction: the third phosphate bond in ADP "crushing it" along with phosphate to form ATP (Figure 5).
The ATP molecules are used in key processes in the cell which require energy, which is released , then regenerating ADP and a free phosphate. The energy produced is directed, for example in humans, for contraction of muscles, beating of the heart and processes in the brain, whereas the reaction products are economically and wisely recycled . In the center of the ATP synthase is a small rotor which rotates around 100 revolutions per second, synthesizing 3 ATP molecules per revolution, or 300 molecules of ATP per second! Only for our thinking and walking, we recycle proportional to our body weight (80 kg) of ATP every day. Each enzyme in the ATP synthase is composed of 31 other proteins that, in turn, are made of thousands of amino acids precisely arranged. Remove any of the 31 proteins and the motor becomes simply useless.
The ATP synthase, along with the Scourge, is one of the most "striking" examples of mega irreducible complexity we see around the corner in life. And there's more: all the immense set of genetic information and RNA, plus dozens of proteins needed to build the ATP synthase, are in total even more irreducibly complex than the ATP synthase itself. The car factory is -by principle - more irreducibly complex than the car it manufactures.





* Figure 4. A crankshaft running. Principle "copied" from the ATP synthase? May be plagiarism?

Described in more details chemical and biochemical (insane task), the ATP synthase is a protein complex consisting of several proteins that fit perfectly synchronously, and - in a synchronized chemical ballet - in the form of a "mushroom". This nano mill is in thousands "installed" on the inner membrane of the mitochondria (Figure 6). There are two main components: (1) head - a spherical area comprised by the catalytic portion of the enzyme known as Factor connection 1, or simply F1, which measures about 90 Å in diameter; and (2) basic - called F0 - fixing the whole to the inner membrane of mitochondria. High resolution SEM micrographs revealed that the head (1) and the bottom part (2) are joined by a central rod - formed by subunits F1 and F0 - relatively narrow (45) which is connected to a peripheral button 90-100 Å in diameter. A mitochondria located in human liver cells has about 15,000 copies of ATP synthase


Figure 5. The most efficient way to conduct a chemical reaction known in this universe, "the hard way"! In the ATP synthase, a protein complex jointly embraces a ADP difosfate  molecule and one anion phosphate (Pi) providing energy and forcing them "mechanically" by reacting (Figure 2). Reaction occurred "by force", the engine spins at 8,500 RPM and the protein complex "opens" then its arms, by the action of the crankshaft driven by an engine and rotor, and releases the product, the tri-phosphate ATP molecule. The ATP synthase is the smallest rotary engine known today. To give you an idea of ​​its tiny size, in a millimeter, can be grouped, side by side, approximately about 100 000 ATP synthases. This engine is driven not by power, but by "proton energy"; that is, by a countercurrent flow of protons.
The ATP synthase would then be the headless product of evolution, not guided or inexcusable evidence of intelligent design? Remember that without energy there is no life, and in life there is no power without ATP, and in life there is no ATP without ATP synthase. The ATP synthase is thus more one of the great "chicken-egg" dilemmas  of Life! For all biochemical processes that coordinate the functioning and structure need to be supplied ATP synthase molecule itself produces: ATP. About 14 trillion body cells at this point are conducting this biochemical reaction via ATP synthase, in about a million times per minute through mitochondria.
To give you even more ingenius details of this fabulous machine, note that the F1 region of ATP synthase (F1-ATPase) is made up of six protein units, and divided into three pairs of active sites. These units form regions which provide "chemical hugs" through a docking site for ADP and phosphate. An anchoring (or stator) is curved on the outside of the structure in order to fix the base (F0) to the head (F1). Three molecules of ATP are formed for each complete shaft rotation. Chemical engineering of ATP synthase is  shown - there's no denying - intelligent and mega efficient . The complex has a spiral shaft, called "Y", which is the circumference between F0 and F1 and allows the connection of one region to the other, like a pen within a cardboard tube. The intelligent design of this nanomolecular machine causes the flow of protons, across the membrane, turn the shaft and the base. So it's not turning the base and the axis "attracts" the protons, as originally thought, but it is the flow of protons turning the engine. The turning occurs when the central axis (y) puts pressure on the inner walls of the six proteins in the F1 region thus result in a smooth structural deformation with consequent reformation alternately. My vote here for the "pinnacle" of chemical engineering in the nanomolecular this universe. Heck, what a  genius mind that knew Chemistry as anyone else, to come up with something like that!

Note further that the F0 subunit, which is fixed on the membrane of mitochondria, rotates clockwise. Laterally annexed the F0, is another input channel subunit which serves as the channel where the protons will be directed to the engine. The rotation is synchronized around its own axis and provides that individually protons enter and exit, respectively. Since the protons are attracted to the input channel, they connect to F0, and follow  nearly a complete rotation, they then are  conveyed to an output channel present on the same side frame attached to where F0 enters. The subunit F1 (F1 ATPase) is that attracts molecules adenosine diphosphate (ADP) and phosphate (Pi), which are released together with ATP.


Figure 6. 3D view at the molecular level of ATP synthase: nano power plant vital to life on this planet.

But there is even more wonder in the ATP synthase: the rotational mechanism used for F0 is performed routinely when there is a high concentration of protons in the cytosol and a low concentration of ATP inside the mitochondria. But when these concentrations are reversed, the enzyme " understands biochemically" that its function was successful, and if it continues, will promote serious imbalance in the cell. Control is everything! In this situation, the ATP synthase "thinks and reacts," and and makes its F0 turn now in the opposite direction, and the mechanism is reversed, and the proton exit channel now becomes the input channel, and the  protons inside the organelle return to the cytosol. ATP molecules are now converted to ADP and phosphate free, in a chemical "retro-reaction" . A chemical balance nano-mechanically directed and controlled! Since you know this fantastic nanomachine a little better  at the molecular level, , what do you think: chance or design?
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Referências e notas
1. "ATP synthase — a marvellous rotary engine of the cell" M. Yoshida, E. Muneyuki, T. Hisabori, Nature Reviews Molecular Cell Biology 2001, 2, 669.
2. Paul D. Boyer. The ATP Synthase - a splendid molecular machine. Annual Review of Biochemistry, Vol. 66: 717-749 (July 1997)

Origin of ATP synthase

Because of its fundamental importance in sustaining life, organisms evolved ATP synthase (ATPase) early during evolution, making it one of the oldest of enzymes - even predating photosynthetic and respiratory enzyme machinery.As a result, ATPase has remained a highly conserved enzyme throughout all kingdoms of life:the ATPases found in the thylakoid membranes of chloroplasts and in the inner membranes of mitochondria in eukaryotes retain essentially the same structure and function as their enzymatic counterparts in the plasma membranes of bacteria.In particular, the subunits that are essential for catalysis show striking homology between species. 1


Evolution of the F 0 F 1 ATP Synthase Complex in Light of the Patchy Distribution of Different Bioenergetic Pathways across Prokaryotes 2

Bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. Apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. Most bioenergetic pathways have a similar general structure, with an electron transport chain composed of protein complexes acting as electron donors and acceptors, as well as a central cytochrome complex, mobile electron carriers, and an ATP synthase. While each pathway has been studied in considerable detail in isolation, not much is known about their relative evolutionary relationships. Wanting to address how this metabolic diversity evolved, we mapped the distribution of nine bioenergetic modes on a phylogenetic tree based on 16S rRNA sequences from 272 species representing the full diversity of prokaryotic lineages. This highlights the patchy distribution of many pathways across different lineages, and suggests either up to 26 independent origins or 17 horizontal gene transfer events. Next, we used comparative genomics and phylogenetic analysis of all subunits of the F0F1 ATP synthase, common to most bacterial lineages regardless of their bioenergetic mode. Our results indicate an ancient origin of this protein complex, and no clustering based on bioenergetic mode, which suggests that no special modifications are needed for the ATP synthase to work with different electron transport chains. Moreover, examination of the ATP synthase genetic locus indicates various gene rearrangements in the different bacterial lineages, ancient duplications of atpIand of the beta subunit of the F0 subcomplex, as well as more recent stochastic lineage-specific and species-specific duplications of all subunits. We discuss the implications of the overall pattern of conservation and flexibility of the F0F1ATP synthase genetic locus.

Author Summary
Bacteria and archaea are the most primitive forms of life on Earth, invisible to the naked eye and not extremely varied or impressive in their appearance. Nevertheless, they are characterized by an amazing metabolic diversity, especially in the different processes they use to generate energy in the form of ATP. This allows them to persist in diverse and often extreme habitats. Wanting to address how this metabolic diversity evolved, we mapped the distribution of nine bioenergetic modes across all the major lineages of bacteria and archaea. We find a patchy distribution of the different pathways, which suggests either frequent innovations, or gene transfer between unrelated species. We also examined the F-type ATP synthase, a protein complex which is central to all bioenergetic processes, and common to most types of bacteria regardless of how they harness energy from their environment. Our results indicate an ancient origin for this protein complex, and suggest that different species, without necessitating major innovation, used their pre-existing ATP synthase and adapted it to work with different bioenergetic pathways. We also describe gene duplications and rearrangements of the ATP synthase subunits in different lineages, which suggest further flexibility and robustness in the control of ATP synthesis.


1) https://www.ebi.ac.uk/interpro/potm/2005_12/Page1.htm
2) http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003821

Proton Gradient, Cell Origin, ATP Synthase

Why do virtually all cells "breathe" by pumping protons (hydrogen ions) across a membrane? According to molecular biologist Leslie Orgel, this is the single most counterintuitive idea in biology after Darwin's, and the only one to bear comparison with the concepts of Heisenberg, Schrödinger, and Einstein (Orgel 1999).
Pioneered by the eccentric British biochemist Peter Mitchell , largely in his own research laboratories in a renovated country house in rural Cornwall, the concept was controversial for more than twenty years. This period of controversy was known as the "ox-phos wars" (after "oxidative phosphorylation," the mechanism of synthesis in respiration). The wars drew to an end only after Mitchell received the Nobel Prize in 1978.

There's an irony here. Mitchell's Nobel was for work in chemistry, yet his ideas are actually about the elimination of chemistry. In the same way that the genetic code enables information to transcend chemistry, so Mitchell's proton gradients enable cellular metabolism to transcend chemistry.

The use of proton gradients gives an insight not only into how life got going in the first place, but also, perhaps, its deepest stalling point: the evolution of complex eukaryotic (nucleated) cells, which arose just once in 4 billion years of evolution.


How Cells Breathe
Our own cells burn food with oxygen and contrive to conserve the energy released in the form of ATP (the universal energy currency of life) — a process called aerobic respiration. How do cells do it? More to the point, how don't they?

Back in the 1940s, Efraim Racker had just figured out the mechanism by which cells glean a little energy from the breakdown of glucose in the absence of oxygen, a pathway known as glycolysis. In glycolysis, phosphate groups are transferred directly from sugar molecules onto ADP to form ATP. The whole pathway is pure chemistry, involving the reaction of one molecule with another, and therefore obeys the laws of stoichiometry; that is, you can balance the equations. Not surprisingly, Racker and others immediately tried to transfer their insights to the quantitatively far more important process of aerobic respiration, which supplies more than 80 percent of our ATP.

But one glaring problem with aerobic respiration is that it doesn't balance. Exactly how much ATP is produced per oxygen molecule consumed? The amount varies, but it's somewhere around 2.5 ATP molecules. That works out to 28–38 ATPs per glucose — again, a variable number, and never an integer (Silverstein 2005). Aerobic respiration is not stoichiometric, so it's really not chemistry. And that's why the long search for a high-energy chemical intermediate (a molecule able to transfer the energy from the oxidation of glucose to form ATP) was doomed to failure.

In place of such an intermediate, Mitchell proposed a proton gradient across a membrane: the proton motive force (Mitchell 1961). It works much like a hydroelectric dam. The energy released by the oxidation of food (via a series of steps) is used to pump protons across a membrane — the dam — creating, in effect, a proton reservoir on one side of the membrane. The flow of protons through amazing protein turbines embedded in this membrane powers the synthesis of ATP in much the same way that the flow of water through mechanized turbines generates electricity. This explains why respiration is not stoichiometric: a gradient, by its very nature, is composed of gradations.


Fine Details

Mitchell was completely wrong about some of the details, but his overall conception was right, even revolutionary — literally revolutionary, as in, the ATP synthase enzyme revolves. The flow of protons through the membrane turbines rotates the stalk of the ATP synthase, and the conformational changes induced by this rotation catalyze ATP synthesis. This mechanism was first proposed by Paul Boyer, who long disagreed with Mitchell over the mechanics and was later proved right in this particular by John Walker, using X-ray crystallography. Boyer and Walker shared the Nobel Prize in 1997.
The molecular biological achievements of the last two decades culminated in 2010 with the deciphering of the crystal structure of another respiratory complex, the enormous (for a protein) complex I, by Walker's Cambridge colleague Leonid Sazanov (Efremov et al. 2010). Again, the structure betrays the mechanism — in this case not a rotary motor but, even more surprisingly, a lever mechanism not unlike the piston of a steam engine .

Yet without in any way decrying these virtuosic accomplishments, the questions that drove Mitchell in the first place remain surprisingly unanswered. We know in nearly atomic detail how respiration works. We know far less about why it works that way.


Proton Motivation
Mitchell worked on mitochondria because he could; they are a tractable experimental model. But he came at the question from the standpoint of bacterial physiology — how do bacteria keep their insides different from the outside? Throughout his life, Mitchell saw the detailed mechanism of respiration in this far broader sense: Membrane proteins can create gradients across a membrane, and these gradients can in turn power work. Proton gradients powering ATP synthesis were just a special case to Mitchell.

What he can hardly have envisaged so clearly was the pervasive role of protons. Although cells can generate sodium, potassium, or calcium gradients, proton gradients rule supreme. Protons power respiration not only in mitochondria, but also in bacteria and archaea (members of another domain of prokaryotes, which look much like bacteria but have very different biochemistry). Proton gradients are equally central to all forms of photosynthesis, as well as to bacterial motility (via the famous flagellar motor, a rotary motor similar to the ATP synthase) and homeostasis (the import and export of many molecules in and out of the is coupled directly to the proton gradient). Even fermenters, which don't need proton gradients to generate ATP, maintain the proton motive force, using ATP derived from fermentation to power proton pumping.

In short, Mitchell knew protons were important, but he could hardly have guessed at just how important. But why protons? Because they were there from the very beginning, says Michael Russell, a geochemist at NASA's Jet Propulsion Laboratory in Pasadena.

Proton Gradients at the Origin of Life
For the last two decades, Russell has been the dynamic force behind the emerging paradigm shift in our understanding of the origin of life. Drawing on a background in ore geochemistry (many ores are precipitated by hydrothermal vent systems), Russell postulates that alkaline vents, akin to the modern Lost City vent system in the mid-Atlantic  were the ideal incubators for life, providing a steady supply of hydrogen gas, carbon dioxide, mineral catalysts, and a labyrinth of interconnected micropores (natural compartments similar to cells, with filmlike membranes; Lane et al. 2010). Alkaline vents are, in essence, electrochemical reactors that operate in a state far from equilibrium.
But the centerpiece of Russell's conception lies in natural proton gradients. Four billion years ago, alkaline fluids bubbled into what would then have been mildly acidic oceans (CO2 levels were about a thousand times higher than they are today, and CO2 forms carbonic acid in solution, rendering the oceans mildly acidic). Acidity is just a measure of proton concentration, which was about four orders of magnitude (four pH units) higher in the oceans than in vent fluids. That difference gave rise to a natural proton gradient across the vent membranes that had the same polarity (outside positive) and a similar electrochemical potential (about 200 millivolts [mV] across the membrane) as modern cells have.

Russell has long maintained that natural proton gradients played a central role in powering the origin of life. There are, of course, big open questions — not least, how the gradients might have been tapped by the earliest cells, which certainly lacked such sophisticated protein machinery as the ATP synthase. There are a few possible abiotic mechanisms, presently under scrutiny in Russell's lab and elsewhere. But thermodynamic arguments, remarkably, suggest that the only way life could have started at all is if it found a way to tap the proton gradients (Lane et al. 2010).

Why Proton Gradients Are Necessary
The reason proton gradients are required boils back down to chemistry. Life hydrogenates carbon dioxide. In other words, to convert carbon dioxide into organic molecules, life attaches hydrogen atoms to CO2. There are only so many ways of doing this, and all life uses just five primary pathways. All but one of these costs energy (for example, the energy of the sun in photosynthesis). The exception is an ancient pathway called the acetyl-CoA pathway, in which hydrogen gas is reacted, via a few steps, with CO2. This pathway is exothermic (releasing energy that can be captured as ATP) right through to pyruvate, one of the central molecules in cell metabolism. It's "a free lunch that you're paid to eat," in the words of Everett Shock.
But there's a problem, pointed out by William Martin in collaboration with Russell (Martin & Russell 2007). All cells that use the acetyl-CoA pathway today depend on proton gradients. None of them can grow by fermentation — that is, by the chemistry of glycolysis. Why not? Because CO2 is a stable molecule and does not react easily, even with hydrogen — even when thermodynamics says it should react. CO2 is a bit like oxygen in this respect: Once it starts to react, it's not easily stopped. But a fire needs a spark to get it going, and so, too, does CO2. Cells need the equivalent of a spark to get CO2 to react, and for cells, that spark is ATP. The problem is that the reaction of CO2 with H2 releases energy, but not a lot — only enough to make 1 ATP. That means cells have to spend 1 ATP to gain 1 ATP, so there's no net gain. If there's no gain, there's no growth; no growth, no life.

Gradients break that cycle. It's not quite true to say that the reaction of CO2 with H2 releases enough energy to make 1 ATP: it's actually enough to make 1.5 ATPs. But of course there's no such thing as 1.5 ATPs, at least not by stoichiometric chemistry; so the spare energy from the reaction, as chemistry, is lost . But that doesn't happen with a gradient . In principle, a reaction can be repeated over and over again, just to pump a proton over a membrane. When enough protons have accumulated, the proton motive force powers the formation of ATP. So a gradient allows cells to save up protons as "loose 
change", and that makes all the difference in the world — the difference between growth and no growth, life and no life.

The Origin of Complex Life
Two greyscale transmission electron micrographs, which are labeled D and E, show mitochondria in different organisms. The photomicrograph in panel D shows a cross-section through a large dinoflagellate mitochondrion. Because the mitochondrion is folded, different parts of it look like stacked layers in the cross-section. The inner membrane is folded into hundreds of cristae, which look like inward-facing, finger-shaped projections. Panel E shows a cross-section of twelve mitochondria in a Paramecium cell. Each mitochondrion has either a circular or oval shape. The mitochondria are filled with inner membranes, which look like finger-shaped projections or small circles.
Despite their power, protons have their share of problems, and these problems might explain why life got stuck in a rut for 2 billion years. All complex life on Earth today is composed of a certain type of complex cell, known as a eukaryotic cell. Generally much larger than bacteria or archaea, the eukaryotic cell contains a nucleus, and a much larger genome, and all kinds of specialized organelles (little organs), such as mitochondria. The strange thing is that eukaryotes have repeatedly given rise to large, complex, multicellular organisms like plants, animals, fungi, and algae — but prokaryotes show little or no tendency to evolve greater morphological complexity, despite their biochemical virtuosity. Why not?

One possible answer relates to the control of proton gradients. All eukaryotic cells turn out to have mitochondria, or once had them and later lost them by reductive evolution back toward a prokaryotic state. No mitochondria, no eukaryotes . All mitochondria capable of oxidative phosphorylation have retained a tiny genome of their own, which appears to be necessary to maintain control over membrane potential (Allen 2003). A membrane potential of 150 mV across the 5-nanometer membrane gives a field strength of 30 million volts per meter — equivalent to a bolt of lightning. This huge electrochemical potential makes the mitochondrial membranes totally different from any other membrane system in the cell (such as the endoplasmic reticulum) which, according to Allen, is why mitochondrial genes are needed locally in cellular subregions. In effect, by responding to local changes in electrochemical potential, they prevent the cell from electrocuting itself. No mitochondrial genome, no oxidative phosphorylation. It could be, then, that bacteria can't expand in cell and genome size because they can't physically associate the right set of genes with their energetic membranes. Lacking mitochondria, bacteria cannot grow large and complex, because they can't control respiration over a wide area of energetic membranes (Lane & Martin, in press). If that's the case, the acquisition of mitochondria and the origin of complexity could be one and the same event.

The question is, what kind of a cell acquired mitochondria in the first place? Most large-scale genomic studies suggest that the answer is an archaeon — that is, a prokaryotic cell that is in most respects like a bacterium. That begs the question, how did mitochondria get inside an archaeon? The answer is a mystery but might go some way toward explaining why complex life derives from a single common ancestor, which arose just once in the 4 billion years of life on Earth.


Summary
Peter Mitchell's demonstration that ATP synthesis is powered by proton gradients was one of the most counterintuitive discoveries in biology, and it took a long time to be accepted. The precise mechanisms by which a proton gradient is formed and coupled to ATP synthesis (chemiosmotic coupling) is now known in atomic detail, but the broader question that drove Mitchell — why are proton gradients so central to life? — is still little explored. Recent research suggests that proton gradients are strictly necessary to the origin of life and highlights the geological setting in which natural gradients form across membranes, in much the same way as they do in cells. But the dependence of life on proton gradients might also have prevented the evolution of life beyond the prokaryotic level of complexity, until the unique chimeric origin of the eukaryotic cell overcame this obstacle.

References and Recommended Reading

Allen, J. F. The function of genomes in bioenergetic organelles. Philosophical Transactions of the Royal Society of London B: Biological Sciences 358, 19–37 (2003)

Efremov, R. G., Baradaran, R. & Sazanov, L. The architecture of respiratory complex I. Nature 465, 441–445 (2010) doi:10.1038/nature09066

Lane, N., Allen, J. F. & Martin, W. How did LUCA make a living? Chemiosmosis in the origin of life. Bioessays 32, 271–280 (2010) doi:10.1002/bies.200900131

Lane, N. & Martin, W. The energetics of genome complexity. Nature 467, 929-934 (2010)

Martin, W. & Russell, M. On the origin of biochemistry at an alkaline hydrothermal vent. Philosophical Transactions of the Royal Society of London B: Biological Sciences 362, 1887–1925 (2007)

Mitchell, P. Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature 191, 144–148 (1961) doi:10.1038/191144a0

Orgel, L. Are you serious, Dr Mitchell? Nature 402, 17 (1999) doi:10.1038/46903

Russell, M. J. First life. American Scientist 94, 32–39 (2006)

Silverstein, T. The mitochondrial phosphate-to-oxygen ratio is not an integer. Biochemistry and Molecular Biology Education 33, 416–417 (2005)

1) http://www.nature.com/scitable/topicpage/why-are-cells-powered-by-proton-gradients-14373960

http://web2.uconn.edu/gogarten/articles/GogartenTaizPhotoSynthesisRes1992.pdf

We can conclude that this last common ancestor already uses its ATPases to synthesize ATP

Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states

https://elifesciences.org/content/5/e21598

A molecular model that provides a framework for interpreting the wealth of functional information obtained on the E. coli F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk’s ε subunit in an extended autoinhibitory conformation in all three states. The Fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30° to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F1 attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit a from two sides.