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J Mol Evol. 2010 Jul;71(1):60-9. doi: 10.1007/s00239-010-9364-9. Epub 2010 Jul 7.

Understanding the effect of secondary structures and aggregation on human protein folding class evolution.

Author information

  • 1Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata, 700054, India. tinab@boseinst.ernet.in

Abstract

Using several model organisms it has been shown earlier that protein designability is related to contact density or fraction of buried residues and influence protein evolutionary rates dramatically. Here, using Homo sapiens as a model organism, we have analyzed two main folding classes (all-alpha and all-beta) to examine the factors affecting their evolutionary rates. Since, secondary structures are the most fundamental components of the protein folding classes, we explored the effect of protein secondary structure composition on evolution. Our results show that sheet and helix fractions exhibit positive and negative correlations, respectively, with the rate of protein evolution. On dividing the secondary structure components according to solvent accessibility, linear regression model identified two factors namely buried sheet fraction and relative aggregation propensity. Both these factors together can explain about 13.4% variability in the rate of human protein evolution, while buried sheet residues can alone account to 9.9% variability.

PMID:
20614111
[PubMed - indexed for MEDLINE]
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