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An estimate of the numbers and density of low-energy structures (or decoys) in the conformational landscape of proteins.

Authors :
Vadivel K
Namasivayam G
Source :
PloS one [PLoS One] 2009; Vol. 4 (4), pp. e5148. Date of Electronic Publication: 2009 Apr 09.
Publication Year :
2009

Abstract

Background: The conformational energy landscape of a protein, as calculated by known potential energy functions, has several minima, and one of these corresponds to its native structure. It is however difficult to comprehensively estimate the actual numbers of low energy structures (or decoys), the relationships between them, and how the numbers scale with the size of the protein.<br />Methodology: We have developed an algorithm to rapidly and efficiently identify the low energy conformers of oligo peptides by using mutually orthogonal Latin squares to sample the potential energy hyper surface. Using this algorithm, and the ECEPP/3 potential function, we have made an exhaustive enumeration of the low-energy structures of peptides of different lengths, and have extrapolated these results to larger polypeptides.<br />Conclusions and Significance: We show that the number of native-like structures for a polypeptide is, in general, an exponential function of its sequence length. The density of these structures in conformational space remains more or less constant and all the increase appears to come from an expansion in the volume of the space. These results are consistent with earlier reports that were based on other models and techniques.

Details

Language :
English
ISSN :
1932-6203
Volume :
4
Issue :
4
Database :
MEDLINE
Journal :
PloS one
Publication Type :
Academic Journal
Accession number :
19357778
Full Text :
https://doi.org/10.1371/journal.pone.0005148