Protein-Protein Interactions, evidence of design

Protein-Protein Interactions Fine-Tune the Case for Intelligent Design 1

Proteins inside the cell face a similar problem. The cell interior is jam-packed with a large number and variety of proteins. Even the simplest bacterium harbors several thousand different types of proteins with numerous copies of each biomolecule existing in the cell’s interior. In many instances, proteins must interact and bind in a highly specific manner with other proteins to carry out their function. These protein-protein interactions (PPIs) are selective. If the wrong proteins bind to each other, the interaction is of no use to the cell.

The jam-packed environment of the cell complicates things. Just like two friends searching for one another in a crowd, proteins are more likely to encounter a protein “stranger” than the desired “friend.”
Biochemists are currently working to understand the specificity of PPIs and how proteins avoid unintended interactions with “strangers.” Recently, Harvard scientists identified some of the key factors that control PPIs.1 Their research adds to the body of evidence that supports the notion that life’s chemistry is designed, stemming from the work of a Creator.


Factors Controlling PPIs
As I wrote previously, protein surfaces are carefully structured to allow strong interactions between protein pairs while minimizing the strength of the unwanted interactions between protein “strangers.” The most recent work by the Harvard scientists indicates that the concentration of PPI-participating proteins in the cell is also carefully designed.
Proteins that do not engage in PPIs have surfaces that prevent these biomolecules from accidently interacting with other proteins. Because of this structural feature, these proteins can exist at relatively high levels inside the cell. Proteins that interact with only one other protein have specific regions on their surfaces designed to promote the PPI. The remainder of the surfaces are designed to eschew PPIs.
Proteins that interact with at least two other proteins also possess specially designed regions that promote binding with their multiple partners. These multi-partner proteins are much more likely to take part in unintended interactions with the wrong partners because more of their surface is devoted to PPIs. To control unwanted interactions, the concentration of these particular proteins is carefully balanced inside the cell.

1) http://www.reasons.org/articles/protein-protein-interactions-fine-tune-the-case-for-intelligent-design

What explanation do mainstream scientific papers come up with to explain protein-protein interactions ? 

Charting the Interplay between Structure and Dynamics in Complex Networks 1

Their results suggest that just as connections between individual components of a biological network—be they genes, proteins, or cells—influence function, the dynamic properties of a network motif ( All networks, including biological networks, social networks, technological networks (e.g., computer networks and electrical circuits) and more, can be represented as graphs, which include a wide variety of subgraphs. One important local property of networks are so-called network motifs, which are defined as recurrent and statistically significant sub-graphs or patterns. ) relate to the motif's function and could determine its prevalence in biological networks.

Thats a attempt to sound intelligent, and to say nothing relevant..... Happens all the time in scientific papers. No one really understands what they wanted to say.

The origin of protein interactions and allostery in colocalization 2

Two fundamental principles can account for how regulated networks of interacting proteins originated in cells. These are the law of mass action, which holds that the binding of one molecule to another increases with concentration, and the fact that the colocalization of molecules vastly increases their local concentrations. It follows that colocalization can amplify the effect on one protein of random mutations in another protein and can therefore, through natural selection, lead to interactions between proteins and to a startling variety of complex allosteric controls. 

That seems a far fetched explanation, given the fact that there is no guidance to find " correct " protein-protein interactions which yield a positive result of adaptability or survival. 

It also follows that allostery is common and that homologous proteins can have different allosteric mechanisms. Thus, the regulated protein networks of organisms seem to be the inevitable consequence of natural selection operating under physical laws.


1) http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0030369
2) http://www.nature.com/nature/journal/v450/n7172/full/nature06524.html
3) http://www.arn.org/docs/booher/scientific-case-for-ID.html

New Study Classifies and Analyzes Protein-Protein Interfaces 

1

The interfaces we see are features of the protein structure and the protein physics," Skolnick said. "Proteins seem to be primed by their physical characteristics to enable these higher-order molecular interactions to occur with a significant probability. The capacity is a feature of the structure."

1) http://www.news.gatech.edu/2010/12/15/new-study-classifies-and-analyzes-protein-protein-interfaces

The Two Binding Sites Rule 1

Behe's version of the history of life requires a God who intervenes quite frequently to create specific mutations that are almost impossible to account for by random mutation. Behe makes a good case for the problems with random mutation. In fact, his arguments are similar to those put forth by the mutationist camp—a group that I'm in sympathy with. Most biologists would not be able to refute Behe's arguments because they would agree with some of his false premises.


Behe's "Two Binding Sites Rule" is a good example. He argues that in order for two proteins to interact, evolution needs to create a small patch on the surface of each protein where five or six amino acid side chains become compatible with binding. Some of these changes could be neutral so they could arise independently but the analysis of hundreds of known binding sites shows that many of the mutations would be detrimental if they occurred by themselves—a single charged amino acid residue on the surface, for example.

It looks like you need to wait for three or four specific mutations to occur simultaneously in order to get a moderate interaction between two proteins that did not originally bind to each other. And these can't be just any proteins, they have to be proteins where there is a selective advantage to forming a complex. The example I've chosen is a bacterial photosynthesis reaction center where four polypeptides (gold, blue, green, purple) interact with each other and with multiple cofactors (space-filling molecules) to form a very complicated structure. Presumably, there was a time in the past when some of these proteins didn't bind to each other or to the cofactors. Over time, evolution favored variants that could form the complex. How could this happen according to evolutionary theory?

Studies on in vitro mutagenesis show that the probability of forming any de novobinding site is very low. For example, it's quite difficult to engineer specific antibodies that will bind to a particular antigen. The data shows us that you need a library of more than one billion antibody molecules in order to get one that will bind. Those one billion mutations are far from random. They are engineered so that they are confined to a small patch on the surface of the antibody where it is known that other proteins can potentially bind.

Behe argues from this evidence that the probability of creating a new binding site by random mutations is exceedingly small. So small, in fact, that such mutations would only arise in very large populations after several hundred million years of evolution. He bases his argument on some experiments he describes in the first few chapters or his book. 

Behe points out that it is sometimes very difficult for the malaria-causing parasite, Plasmodium falciparum, to develop resistance to some drugs used to treat malaria. That's because the resistance gene has to acquire two specific mutations in order to become resistant. A single mutation does not confer resistance and, in many cases, the single mutation is actually detrimental. P. falciparum can become resistant because the population of these single-cell organisms is huge and they reproduce rapidly. Thus, even though the probability of a double mutation is low it will still happen.

If the probability of a single mutation is about 10-10 per generation then the probability of a double mutation is 10-20. He refers to this kind of double mutation as CCC, for "chloroquine-complexity cluster," named after mutation to chloroquine resistance in P. falciparum.1 Behe's calculation is correct. If two simultaneous are required then the probability will, indeed, be close to 1 in 10^20.

Let's see how this relates to the evolution of protein-protein interactions. Here's how Behe describes it on page 135 of his book.

Now suppose that, in order to acquire some new, useful property, not just one but two new [i]protein-binding sites had to develop. A CCC requires, on average, 10^20, a hundred billion billion, organisms—more than the number of mammals that has ever existed on earth. So if other things were equal, the likelihood of getting two new binding sites would be what we called in Chapter 3 a "double CCC"—the square of a CCC, or one in ten to the fortieth power. Since that's more cells than likely have ever existed on earth, such an event would not be expected to have happened by Darwinian processes in the history of the world. Admittedly, statistics are all about averages, so some freak event like this might happen—it's not ruled out by the force of logic. But it's not biologically reasonable to expect it, or less likely events that occurred in the common descent of life on earth. In short, complexes of just three or more different proteins are beyond the edge of evolution. They are lost in shape space.[/i]

We're all pretty knowledgeable here but how many of you can immediately refute that argument? If you can't then you have no business accusing Behe of being stupid or silly and of dismissing his book as just another example of creationist ignorance. The correct explanation of the problem will undoubtedly appear soon in the comments. Before peeking, why not try and see how you would answer Behe if you were debating him in front of a large audience of creationists?

1) http://sandwalk.blogspot.com.br/2010/10/edge-of-evolution.html