Structure is three to ten times more conserved than sequence—A study of structural response in protein cores

Kristoffer Illergård; David H. Ardell; Arne Elofsson

doi:10.1002/prot.22458

journal article Open Access Jun 08, 2009

Structure is three to ten times more conserved than sequence—A study of structural response in protein cores

Kristoffer Illergård David H. Ardell

Arne Elofsson

Proteins: Structure, Function, and Bioinformatics Vol. 77 No. 3 pp. 499-508 · Wiley

View at Publisher Save 10.1002/prot.22458

Abstract

AbstractProtein structures change during evolution in response to mutations. Here, we analyze the mapping between sequence and structure in a set of structurally aligned protein domains. To avoid artifacts, we restricted our attention only to the core components of these structures. We found that on average, using different measures of structural change, protein cores evolve linearly with evolutionary distance (amino acid substitutions per site). This is true irrespective of which measure of structural change we used, whether RMSD or discrete structural descriptors for secondary structure, accessibility, or contacts. This linear response allows us to quantify the claim that structure is more conserved than sequence. Using structural alphabets of similar cardinality to the sequence alphabet, structural cores evolve three to ten times slower than sequences. Although we observed an average linear response, we found a wide variance. Different domain families varied fivefold in structural response to evolution. An attempt to categorically analyze this variance among subgroups by structural and functional category revealed only one statistically significant trend. This trend can be explained by the fact that beta‐sheets change faster than alpha‐helices, most likely due to that they are shorter and that change occurs at the ends of the secondary structure elements. Proteins 2009. © 2009 Wiley‐Liss, Inc.

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488

Citations

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References

Details

Published: Jun 08, 2009
Vol/Issue: 77(3)
Pages: 499-508
License: View

Authors

Stockholm University

Cite This Article

Kristoffer Illergård, David H. Ardell, Arne Elofsson (2009). Structure is three to ten times more conserved than sequence—A study of structural response in protein cores. Proteins: Structure, Function, and Bioinformatics, 77(3), 499-508. https://doi.org/10.1002/prot.22458

Structure is three to ten times more conserved than sequence—A study of structural response in protein cores

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