Evolution of new protein folds
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(Note: This page is work in progress. I'm cleaning up a page from evowiki and putting it here.)
Some creationists/intelligent design proponents will concede that new genetic information can arise through natural processes (see Evolution of new information). However, they will still claim that "fundamentally new" proteins -- new protein folds and structures -- cannot arise naturally. This page will assess this claim.
The basic misunderstanding which this represents stems from the various problems with applying a naive interpretation of Darwinism to molecular evolution. In essence the argument is that it is not possible for nonfunctional proteins to exist at any stage in the evolutionary history of a particular protein in a particular organism.
As our understanding of the mechanisms of genetic change increases it becomes apparent that gene duplication is an important feature of molecular evolution. Many modern proteins are related by paralogous descent and since duplication can free one copy from functional constraint it is free to mutate ad libitum. This is one possible mechanism by which a protein could adopt a new fold. A function for the protein could arise secondarily. This is still an area where our knowledge is rapidly expanding, however.
One important observation indicates that the differences between proteins adopting different folds may be as small as a single amino-acid: et al., 2000 found that the sequence of the Arc repressor protein adopts a different fold in response to the mutation of a single amino acid. A double mutant was observed to adopt either the native or the induced fold depending on the environmental conditions. The actual change is relatively small on the scale of the entire protein but involves an interchange between different secondary structural states and indicates that fold changes may occur piecewise in response to very small changes in the underlying protein sequence.
Further dubious assumptions which are implied by this argument are:
- Well-defined folding is necessary for function. The importance of "disordered" proteins and disordered regions of proteins is increasingly being recognized:
Despite the fact that intrinsically disordered proteins fail to form fixed 3-D structure under physiological conditions, existing instead as ensembles of conformations, they carry out critically important biological functions (1,2). Several recent reviews (e.g. 3-6) attest to the growing interest in these proteins. [...]Conservative estimates indicate that at least 25% of the sequences in SwissProt contain long disordered regions. Similar analysis on 32 complete genomes resulted in the estimates that the percentage of proteins with long disorder in 22 bacteria, 7 archaea, and 5 eucaryotae ranges from 7-33%, 9-37%, and 36-63%, respectively. (DisProt - Resource for Protein Disorder, references omitted)
- Furthermore, many peptide chains too small to fold can exhibit important functionality.
- Mutating a fold always disrupts function. Sometimes a mutation can seriously alter the shape of a protein's fold, but with little resulting change in function. Often, only a few amino acids form the functionally important active site, and the rest of the folded protein may simply serve as a soluble, non-degrading platform.
- Folds map to function. In reality, the same fold can serve many different functions (see virtually any protein superfamily), and different folds can serve the same function (see the Analogous Enzymes Table (originally published in: Galperin et al. (1998). "Analogous enzymes: Independent inventions in enzyme evolution", Genome Research, 8(8), pp. 779-790).)
- The highly evolved system for degrading misfolded proteins in eukaryotes tells us something meaningful about the viability of mutant folds in pre-LCA prokaryotes. Misfolded proteins can be disadvantageous (as a waste of resources, for example) without being fatal. Modern organisms thus may have mechanisms in place to reduce the occurrence of misfolded proteins. This would inhibit the origin or new folds in modern organisms, but the same mechanisms were not in place early in the evolution of life, when many of the new protein folds evolved.
- The collection of folds observed in extant life represents the universe of viable folds. In actually, we could be stuck with our current collection of a few thousand folds simply because they were what nature hit on first, and most of subsequent history has been operating on the "if it ain't broke, don't fix it" principle.
- This view seems to be confirmed by:
- Hou, J., Sims, G.E., Zhang, C., and Kim, S.H. (2003) "A global representation of the protein fold space." "PNAS" 100(5):2386-90 PNAS Free Full-Text
- These studies found that the protein folds observed in life are non-randomly clustered within the space of possible protein folds:
- However, it also seems to be the case that the universe of possible folds, or at least possible folds that are relatively easily hit on by chance, is fairly small (on the order of 104). The first artificially evolved protein fold, a zinc binding fold, was initially thought to be novel (Keefe, A. D. & Szostak, J. W. (2001) "Functional proteins from a random-sequence library." Nature 410, 715-8.), but was later shown to fit within a known biological fold, and is thus a clear case of analogy (Krishna, S. S. & Grishin, N. V. (2004). "Structurally analogous proteins do exist!" Structure 12, 1125-7.).
- Protein structure has traditionally been studied with techniques such as x-ray crystallography. Proteins that are soluble, and have stable folds, are amenable to crystallization and therefore study through crystallography. Vast amounts of important work on proteins has been done with this method. However, many common, biologically important proteins (such as membrane-embedded proteins and "molten globules") are difficult or impossible to crystallize.
- Thus, making generalizations about proteins in general, based largely on methods that work best on the subset of proteins that are soluble and have regular folds, is a bit like the man who looks for his keys under the street light because that's the only place he can see.
- Michael Y. Galperin, D. Roland Walker and Eugene V. Koonin (1998) "Analogous enzymes: Independent inventions in enzyme evolution", Genome Research, 8(8), pp. 779-790. [http://www.genome.org/cgi/content/abstract/8/8/779 Journal Pubmed
- Keefe, A. D. & Szostak, J. W. (2001) "Functional proteins from a random-sequence library." Nature 410, 715-8.).
- Krishna, S. S. & Grishin, N. V. 2004). "Structurally analogous proteins do exist!" Structure (Camb) 12, 1125-7.
- Sri Krishna S, Grishin NV. (2004). "Structural drift: a possible path to protein fold change." Bioinformatics. Dec. 16, 2004. [Epub ahead of print]
- Newlove T, Konieczka JH, Cordes MH. (2004). "Secondary structure switching in Cro protein evolution." Structure (Camb). 12(4):569-81.
There are about 800 known protein topologies or "folds" (Murzin et al., 1995; Orengo et al., 1997). In principle, all of these folds could have independent evolutionary origins. More likely, some if not many of the known protein folds arose via evolutionary modifications of preexisting structures. In fact, recent reviews (Grishin, 2001; Kinch and Grishin, 2002; Murzin, 1998) have cataloged a variety of structural changes occurring in protein fold evolution, including insertion, deletion, substitution, and rearrangement of secondary structure elements. These examples show that dramatic structural changes in evolution are neither rare nor restricted to a few specific categories.
- Murzin AG. (1998). "How far divergent evolution goes in proteins." Curr Opin Struct Biol. 8(3):380-7.
- Kinch LN, Grishin NV. (2002). "Evolution of protein structures and functions." Curr Opin Struct Biol. 12(3):400-8.
- Lauber T, Schulz A, Schweimer K, Adermann K, Marx UC. (2003). "Homologous proteins with different folds: the three-dimensional structures of domains 1 and 6 of the multiple Kazal-type inhibitor LEKTI." J Mol Biol. 328(1):205-19.
- Grishin NV. (2001). "Fold change in evolution of protein structures." J Struct Biol. 134(2-3):167-85.
- Cordes, M.H., Walsh, N.P., McKnight, C.J., and Sauer, R.T. (1999). "Evolution of a protein fold in vitro." Science 284, 325â€“328. Journal DOI Free online
- Cordes, M.H., Burton, R.E., Walsh, N.P., McKnight, C.J., and Sauer, R.T. (2000). "An evolutionary bridge to a new protein fold." Nat. Struct. Biol. 7, 1129â€“1132. Free online.
- Gough J. (2005). "Convergent evolution of domain architectures (is rare)." Bioinformatics, 21(8):1464-1471. PubMed DOI
- Whitman CP. (2002). "The 4-oxalocrotonate tautomerase family of enzymes: how nature makes new enzymes using a beta-alpha-beta structural motif." Arch Biochem Biophys. 402(1):1-13.PubMed DOI
- Almrud JJ, Kern AD, Wang SC, Czerwinski RM, Johnson WH Jr, Murzin AG, Hackert ML, Whitman CP. (2002). "The crystal structure of YdcE, a 4-oxalocrotonate tautomerase homologue from Escherichia coli, confirms the structural basis for oligomer diversity." Biochemistry. 41(40):12010-24. PubMed.
- Ballicora MA, Dubay JR, Devillers CH, Preiss J. (2005). "Resurrecting the ancestral enzymatic role of a modulatory subunit." J Biol Chem. 280(11):10189-95. PubMed