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Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.

Published version
Peer-reviewed

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Abstract

Rotamers, namely amino acid side chain conformations common to many different peptides, can be compiled into libraries. These rotamer libraries are used in protein modeling, where the limited conformational space occupied by amino acid side chains is exploited. Here, we construct a sequence-dependent rotamer library from simulations of all possible tripeptides, which provides rotameric states dependent on adjacent amino acids. We observe significant sensitivity of rotamer populations to sequence and find that the library is successful in locating side chain conformations present in crystal structures. The library is designed for applications with basin-hopping global optimization, where we use it to propose moves in conformational space. The addition of rotamer moves significantly increases the efficiency of protein structure prediction within this framework, and we determine parameters to optimize efficiency.

Description

Keywords

Article, B: Biophysical and Biochemical Systems and Processes

Journal Title

J Phys Chem B

Conference Name

Journal ISSN

1520-6106
1520-5207

Volume Title

126

Publisher

American Chemical Society (ACS)
Sponsorship
Engineering and Physical Sciences Research Council (EP/L015552/1)