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Structure is three to ten times more conserved than sequence-A study of structural response in protein cores
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
2009 (English)In: Proteins: Structure, Function, and Genetics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 77, no 3, 499-508 p.Article in journal (Refereed) Published
Abstract [en]

Protein 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; 77:499-508. (C) 2009 Wiley-Liss, Inc.

Place, publisher, year, edition, pages
2009. Vol. 77, no 3, 499-508 p.
Keyword [en]
protein structure, evolution, secondary structure, accessibility, residue contacts, RMSD
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-127461DOI: 10.1002/prot.22458ISI: 000270849900002OAI: oai:DiVA.org:uu-127461DiVA: diva2:330169
Available from: 2010-07-15 Created: 2010-07-13 Last updated: 2010-07-15Bibliographically approved

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