Intelligent Design, the best explanation of Origins

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Intelligent Design, the best explanation of Origins » Origin of life » Forces Stabilizing Proteins - essential for their correct folding

Forces Stabilizing Proteins - essential for their correct folding

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Forces Stabilizing Proteins - essential for their correct folding

http://reasonandscience.catsboard.com/t2692-forces-stabilizing-proteins-essential-for-their-correct-folding

Proteins are the most complex molecules in life and are involved in basically all biochemical processes. Human cells contain 25000 genes, which can produce upon splicing up to over 100,000 different proteins.

The awe inspiringing spliceosome, the most complex macromolecular machine known, and pre-mRNA processing in eukaryotic cells
http://reasonandscience.catsboard.com/t2180-the-spliceosome-the-splicing-code-and-pre-mrna-processing-in-eukaryotic-cells

Proteins are the end products of the process of transcription and translation that starts with the information stored in the genome.

The function of proteins depends on the right sequence of amino acids, lined up into polypeptide chains of various sizes, ranging from short sequences, like extracellular hemoglobin with 140 amino acids, to monstrously large proteins, like tintin  which is used in sarcomeres, responsible for passive elasticity of striated mu3scles. with lengths that vary from ~27,000 to ~33,000 amino acids (depending on the splice isoform), the largest known protein.

Titin the largest proteins known and titin-telethonin complex - the strongest protein bond found so far in nature
http://reasonandscience.catsboard.com/t2671-titin-the-largest-proteins-known-and-the-titin-telethonin-complex-the-strongest-protein-bond-found-so-far-in-nature

Proteins, in order to become functional, must fold into very specific 3D shapes, which happens right when they come out of the Ribosome, where they are synthesized. Specific protein shape and conformation depends on the interactions between its amino acid side chains. For a protein to function it must fold into a resting state which is a complex three-dimensional structure.  If a protein fails to fold into its functional structure then it is not only without function but it cab become toxic to the cell. As proteins fold, they test a variety of conformations before reaching their final form, which is unique and compact. Folded proteins are stabilized by thousands of noncovalent bonds between amino acids. A relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows. 3

Nobody knows, but since there was no evolution, to produce the first proteome for the first living cells, there are two options : blind, unguided, random lucky events on early earth, or the creative act of a super intelligent agent.

The 3D shape depends on the chemical forces, the chains are folded into a uniquely defined configuration, in which they are held by hydrogen bonds between the peptide nitrogen and oxygen atoms, which make a large contribution to protein stability, but other forces play an essential role as well, like hydrophobic interactions, disulfide bonds,  Charge-charge interactions on the surface of proteins which are electrostatic interactions,  pure ionic interactions, van der Waals forces, but also the surroundings of proteins, and their milieu. Chemical forces between a protein and its immediate environment contribute to protein shape and stability.

A special note deserve Van der Waals forces and interactions, which origins are ultimately a quantum mechanical. (At least the induced dipole portions: how the electrons move with respect to each other and an external electrical field is driven by quantum mechanics.)  2 Remarkably, quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins.  That means, the shape could change by quantum transition, meaning that the protein could ‘jump’ from one shape to another without necessarily forming the shapes in between.    Impressive stuff !! 3

The 20 amino acids used in life are classified in Acidic amino acids, Basic amino acids with net positive charge, polar but uncharged, and nonpolar or hydrophobic amino acids. This variety contributes critically and is important for the processes that drive protein chains to “fold,” that is to form their natural (and functional) structures.

see more:

Amino Acids and peptide bonding
http://reasonandscience.catsboard.com/t2590-origins-what-cause-explains-best-our-existence-and-why#5845

But how could natural processes have foresight, which seems to be absolutely required, to "know" which amino acid sequences would provoke which forces, and how they would fold the protein structure to get functional for specific purposes within the cell ? Let's consider, that in order to have a minimal functional living cell, at least 561 proteins and protein complexes would have to be fully setup, working, and interacting together to confer a functional whole with all life-essential functions :

The last universal common ancestor represents the primordial cellular organism from which diversified life was derived
http://reasonandscience.catsboard.com/t2176-lucathe-last-universal-common-ancestor

A minimal estimate for the gene content of the last universal common ancestor
19 December 2005
A truly minimal estimate of the gene content of the last universal common ancestor, obtained by three different tree construction methods and the inclusion or not of eukaryotes (in total, there are 669 ortholog families distributed in 561 functional annotation descriptions, including 52 which remain uncharacterized)

So there had to be at least 561 proteins of various sizes, set up correctly in order to fold into functional 3D shapes, governed by chemical bond forces interacting between the individual amino acids. So not only is the right amino acid sequence essential but also as a side-effect the right dosage of the bond forces in between the amino acids.  

The problem becomes even more severe when we consider that many, if not most proteins, are governed and build up by primary, secondary, tertiary, and quaternary structures. A quaternary structure refers to two or more polypeptide chains held together by intermolecular interactions to form a multi-subunit complex. And there are proteins, which require co-factors, often made of trace metals, like Iron, molybdenum etc. These cofactors require a pocket of the right size, and binding residues at the right place, and a tunnel where these cofactors can pass through during biosynthesis, to be inserted at the precise location inside the protein.

And there is more:

Molecular Chaperones Help Guide the Folding of Most Proteins
http://reasonandscience.catsboard.com/t1437-chaperones

Most proteins probably do not fold correctly during their synthesis and require a special class of proteins called molecular chaperones to do so. Molecular chaperones are useful for cells because there are many different folding paths available to an unfolded or partially folded protein. Without chaperones, some of these pathways would not lead to the correctly folded (and most stable) form because the protein would become “kinetically trapped” in structures that are off-pathway. Some of these off-pathway configurations would aggregate and be left as irreversible dead ends of nonfunctional (and potentially dangerous) structures. Proteins also require chaperones constantly, after correct folding, to maintain their functional states, which is called proteostasis.

That raises interesting questions: How should and could natural nonintelligent mechanisms forsee the necessity of chaperones in order to get a specific goal and result, that is functional proteins to make living organisms? Nonliving matter has no natural " drive " or purpose or goal to become living. The make of proteins to create life, however, is a multistep process of many parallel acting complex metabolic pathways and production-line like processes to make proteins and other life essential products like lipids, carbohydrates etc. The right folding of proteins is just one of several other essential processes in order to get a functional protein. But a functional protein by its own has no function unless correctly embedded through the right order of assembly at the right place.

Evolution of the correct protein foldings
To explain the origin of correct protein folds is paramount to explain the origin of life, and biodiversity. Its therefore of significant interest to see, how secular science papers explain its origin. Lets have a look at following:

Protein folding as an evolutionary process 1
7 December 2008
To provide a description that is consistent with other natural processes, protein folding is formulated from the principle of increasing entropy. It then becomes evident that protein folding is an evolutionary process among many others. During the course of folding protein structural hierarchy builds up in succession by diminishing energy density gradients in the quest for a stationary state determined by surrounding density-in-energy. Evolution toward more probable states, eventually attaining the stationary state, naturally selects steeply ascending paths on the entropy landscape that correspond to steeply descending paths on the free energy landscape.

The problem with this explanation is massive, and actually, untenable, naive, superficial and demanding. This explanation does not take into consideration that the right energy density at the right place must be precisely fine-tuned. Not any kind of energy density, anywhere within the protein structure will do, but on each place on the polypeptide " ladder ", there must be an emanating force from given amino acid, which will interact with the right strenght with an adjacent or nearby amino acid, which emanating force sums up with other forces to confer the right fold. Trial and error, or natural selection, are too unspecific and random to get a result which is functional 



1. http://www.helsinki.fi/~aannila/arto/folding.pdf
2. https://chemistry.stackexchange.com/questions/53843/does-quantum-mechanics-play-a-role-in-protein-folding
3. https://www.technologyreview.com/s/423087/physicists-discover-quantum-law-of-protein-folding/

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