Reaping the Whirlwind: Protein Function Without Stable Structure

| By on Letters to the Duchess

In the last post in this series, we saw that there is an underlying order to protein folding—that sequences of amino acids that make up proteins have a propensity to form stably-folded structures (alpha helices and beta sheets). As such, we saw that this underlying order greatly increases the probability that proteins can fold up into stable three-dimensional shapes that can perform biological functions. Arguments from the Intelligent Design (ID) movement that evolution is incapable of generating new protein folds and functions, then, are lacking. New, functional protein folds form much more readily that the ID movement claims they do.

As we have seen, the claim that evolution cannot produce new protein folds or functions is an important one for ID. For example, it forms a significant part of Stephen Meyer’s argument that evolution was not capable of producing the diversity of life seen in the so-called “Cambrian explosion”. In his book Darwin’s Doubt, Meyer lays out his argument as follows, once again referencing the work of Douglas Axe (p. 191, emphasis in the original):

… Axe was convinced that explaining the kind of innovation that occurred during the Cambrian explosion and many other events in the history of life required a mechanism that could produce, at least, distinctly new protein folds.

He had another reason for thinking that the ability to produce novel protein folds provided a critical test for the creative power of the mutation and selection mechanism. As an engineer, Axe understood that building a new animal required innovation in form and structure. As a protein scientist, he understood that new protein folds could be viewed as the smallest unit of structural innovation in the history of life. 

It follows that new protein folds represent the smallest unit of structural innovation that natural selection can select.

Briefly restated, Meyer’s argument is as follows: new protein structures are required for evolutionary innovation, and protein folds are the smallest parts that a protein can be divided into. If this is the case, he argues, then new protein folds are the smallest units that natural selection can act on. If evolution is incapable of generating new folds (because they are too rare for evolution to find), then evolution cannot produce anything new.

There are several key claims buried within this argument:

  1. Evolutionary innovation requires new proteins with new functions.
  2. Proteins require new protein folds to acquire new functions.
  3. New protein folds, and thus new functions, are inaccessible to evolution.

In the previous posts in this series we have—for the sake of argument—granted claims #1 and #2 and focused on claim #3. And as we have seen, Meyer is greatly underestimating the fraction of protein sequences that can fold: evolution seems to have no difficulty in finding new proteins with new folds and new functions, such as nylonase. This means his overall argument fails, even on this point alone.

But what about Meyer’s other claims?

Interestingly, the second claim – that new protein folds are required for new functions – is also incorrect, and it further undermines Meyer’s argument. The reason for this is simple: there are many examples known of functional protein regions that are not stably folded. (As an aside, there is a good case to be made that his first claim is also misguided, but that is an argument too long to be explored here in any depth. Suffice it to say that in evolutionary biology we see the “same proteins” being used over and over again to control development in a wide number of distantly related animals. This suggests that even without radical innovation at the protein level, a large amount of biological innovation was and is possible – including that seen in the Cambrian. But I digress.)

Not folded, but functional

When I was a graduate student in the late 1990s and early 2000s, the claim that Meyer makes—that protein functions require stable protein folds—was very much taught as a self-evident truth. The leading molecular and cell biology textbook of the day was Molecular Biology of the Cell by Bruce Alberts and colleagues, and it is no stretch to say that it was viewed as the definitive text in the field. The fourth edition, published in 2002, makes the following claims about protein structure and function (note that conformation in this context is a technical term meaning “shape” or “structure”):

The vast majority of possible protein molecules could adopt many conformations of roughly equal stability, each conformation having different chemical properties. And yet virtually all proteins present in cells adopt unique and stable conformations. How is this possible? The answer lies in natural selection. A protein with an unpredictably variable structure and biochemical activity is unlikely to help the survival of the cell that contains it. Such proteins would therefore have been eliminated by natural selection through the enormously long trial-and-error process that underlies biological evolution. Because of natural selection, not only is the amino acid sequence of a present-day protein such that a single conformation is extremely stable, but this conformation has its chemical properties finely tuned to enable the protein to perform a particular catalytic or structural function in the cell. (pp. 141-142)

This is exactly the view of protein structure and function that I was taught: proteins have stable structures, and that stability is crucial for protein function. It should also be apparent that this is precisely the view that Meyer is working with in his books  Darwin’s Doubt and Signature in the Cell, though of course he takes it further and claims that it renders evolution of new protein structures and functions impossible.

Despite the appeal of this view, and its pervasiveness among biologists of a certain age (myself included), it’s wrong.  As with many things in science, additional evidence has revealed a prior model to be inadequate – and replaced it with a more nuanced model that encompasses both the prior evidence and the new data.

At the time that my textbook was confidently equating protein stability with function, it was already known that many proteins actually function because they do not have a stable structure. Such proteins were first identified in the early 1990s, and numerous examples were known by the time my textbook went to print.  Such proteins came to be known as “intrinsically disordered proteins” or “IDPs”. Proteins were also found to have “intrinsically disordered regions” (IDRs) embedded within stable structures . As you can imagine, the researchers reporting these results faced an uphill battle convincing their reviewers that what they were observing was in fact real. The standard of evidence for challenging what everyone “knew to be true” was high—but eventually, as the evidence accumulated, biologists came to accept the new paradigm. One author summarized the state of the emerging field in 2002 as follows:

In the past few years, a large number of papers on proteins denoted as “natively denatured/unfolded” or “intrinsically unstructured/disordered” have appeared and it has become apparent that this phenomenon is quite general… Moreover, the functional importance of the unstructured state is underlined by the fact that most of these proteins have basic regulatory roles in key cellular processes.

In the years since, further evidence for functional, disordered proteins has continued to pile up. We now know that IDPs and proteins with IDRs contribute to a wide diversity of cellular functions. They do so by rapidly transitioning between different shapes, and interacting with a wide range of other proteins in the process. In some cases, IDPs/IDRs become (transiently) stable when they bind onto another stable protein. In other cases, it seems that they remain in flux and are not stabilized by binding a partner. For both types, their unstable, disordered state is necessary for their function. We also know that IDRs are extremely widespread—most proteins in eukaryotes (i.e. organisms that are not prokaryotes) have at least one IDR in their sequence. The human genome, which has on the order of about 20,000 genes, has an estimated 100,000 IDRs. Disorder is the new order: what was “heresy” in 1990 and “surprising but substantiated” in 2000 is now a well-accepted phenomenon, ready for inclusion in entry-level cell / molecular biology textbooks.

Of course what I learned in my textbooks is still valuable: many proteins do have stable structures, and those structures are important for their functions. Additionally, natural selection is important in maintaining those structures. What we now know is that this picture of protein biology was not so much wrong, but incomplete. Proteins can have stable structures, or not, and be functional. Since natural selection selects for function, it will preserve functional proteins that are stable and functional proteins that are disordered. What was misguided was tying stable protein structure to function in all cases.

IDPs, Axe, and Intelligent Design

The negative implications of finding pervasive, functional, and intrinsically unfolded proteins and protein regions for ID information-based arguments are substantial. Let’s briefly revisit our summary of Meyer’s argument:

  1. Evolutionary innovation requires new proteins with new functions.
  2. Proteins require new protein folds to acquire new functions.
  3. New protein folds, and thus new functions, are inaccessible to evolution.

We can now see that claim #2 is unfounded—proteins can acquire new protein functions without acquiring a new fold. IDPs and IDRs show us that unfolded—but nonetheless functional—sequences are widespread. As such, even if new protein folds were difficult for evolution to produce (and we have seen that they are not) this would not be a barrier to proteins evolving new functions.

Moreover, the observation that IDPs and IDRs are a widespread source of functional protein sequences creates serious problems for Meyer’s claim #3 as well. As we have seen, Meyer claims that protein folds and functions are too rare for evolution to find:

… experiments establishing the extreme rarity of protein folds in sequence space also show why random changes to existing genes inevitably efface or destroy function before they generate fundamentally new folds or functions … If only one out of every 1077 of the alternate sequences are functional, an evolving gene will inevitably wander down an evolutionary dead-end long before it can ever become a gene capable of producing a new protein fold. The extreme rarity of protein folds also entails their functional isolation from each other in sequence space. (Darwin’s Doubt, page 207)

This claim is based on the work of Douglas Axe, who estimated the prevalence of functional protein sequences by estimating the proportion of sequences that could adopt a particular protein fold. Axe’s work took a functional, stably-folded protein (an enzyme) and swapped out groups of amino acids 10 at a time. If those amino acids were capable of folding correctly in the context of the overall enzyme structure, they would allow the enzyme to function. With this method, Axe estimated that only one protein sequence in 1077 would stably fold, and thus only one in 1077 would be functional. Axe’s work has numerous additional caveats which I have discussed at length in my recent co-authored book Adam and the Genome and will not repeat here, but notice this: Axe’s experiment, based as it is on finding stably folded protein sequences, would completely miss IDPs and IDRs since they are not stably folded. Axe’s estimate of the proportion of stably folded proteins as a measure of the proportion of functional proteins is thus far, far too small, since intrinsically disordered proteins would not have been found by his approach. Yet, we know that IDPs and IDRs are everywhere: we have 100,000 in our genome alone.

As such, Meyer is doubly mistaken—new functions can form without new protein folds, and protein functions are far more common than the work he is depending on is capable of detecting. Protein folding can be stable, or it can be a whirlwind of instability—but natural selection can reap function from both.


Notes

Citations

MLA

Venema, Dennis. "Reaping the Whirlwind: Protein Function Without Stable Structure"
http://biologos.org/. N.p., 6 Apr. 2017. Web. 28 May 2017.

APA

Venema, D. (2017, April 6). Reaping the Whirlwind: Protein Function Without Stable Structure
Retrieved May 28, 2017, from http://biologos.org/blogs/dennis-venema-letters-to-the-duchess/reaping-the-whirlwind-protein-function-without-stable-structure

References & Credits

For further reading

Wright PE, and Dyson HJ. (2015). Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol. 16(1):18-29.

Link to the above article (open access)

About the Author

Dennis Venema

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia and Fellow of Biology for BioLogos. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. 

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