2013
DOI: 10.1073/pnas.1300011110
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Interplay of physics and evolution in the likely origin of protein biochemical function

Abstract: The intrinsic ability of protein structures to exhibit the geometric and sequence properties required for ligand binding without evolutionary selection is shown by the coincidence of the properties of pockets in native, single domain proteins with those in computationally generated, compact homopolypeptide, artificial (ART) structures. The library of native pockets is covered by a remarkably small number of representative pockets (∼400), with virtually every native pocket having a statistically significant mat… Show more

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Cited by 55 publications
(80 citation statements)
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References 42 publications
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“…9 They are just a consequence of the packing of secondary structural elements that give rise to the library of small molecule ligand binding sites as well. 64 Thus, once again, HIs are also seen to be nothing special, rather they are an intrinsic coarse-grained feature of the majority of a protein's surface that nature has taken advantage of.…”
Section: Discussionmentioning
confidence: 99%
“…9 They are just a consequence of the packing of secondary structural elements that give rise to the library of small molecule ligand binding sites as well. 64 Thus, once again, HIs are also seen to be nothing special, rather they are an intrinsic coarse-grained feature of the majority of a protein's surface that nature has taken advantage of.…”
Section: Discussionmentioning
confidence: 99%
“…It seems that the promiscuous behaviour is an integral part of evolutionary designs of proteins (Soskine and Tawfik, 2010;Goldsmith and Tawfik, 2012;Skolnick and Gao, 2013). This area is providing a great insight into how enzyme activities evolved.…”
Section: Catalytic Promiscuity Offers Under-exploited Opportunity Andmentioning
confidence: 99%
“…So, promiscuity is one facet of the evolutionary design of enzymes. As Skolnick et al [84] state, promiscuous behaviour is the biochemical noise (low level, ligand-protein interactions) which was nearly impossible to eliminate as enzyme molecules evolved to assume specialised catalytic roles.…”
Section: Catalytic Promiscuity: Beyond Lipasesmentioning
confidence: 99%
“…Furthermore, local molten globule behaviour optimizes the catalytic function of the GST in detoxification [87]. So, catalytic promiscuity may not be just accidental "noise" [84] but part of an intentional biocatalytic design.…”
Section: Catalytic Promiscuity: Beyond Lipasesmentioning
confidence: 99%