Campus Units

Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Baker Center for Bioinformatics and Biological Statistics

Document Type

Article

Publication Version

Accepted Manuscript

Publication Date

6-25-2007

Journal or Book Title

Journal of Physics: Condensed Matter

Volume

19

Issue

28

First Page

285220

Last Page

285230

DOI

10.1088/0953-8984/19/28/285220

Abstract

One important problem in computational structural biology is protein designability, that is, why protein sequences are not random strings of amino acids but instead show regular patterns that encode protein structures. Many previous studies that have attempted to solve the problem have relied upon reduced models of proteins. In particular, the 2D square and the 3D cubic lattices together with reduced amino acid alphabet models have been examined extensively and have lead to interesting results that shed some light on evolutionary relationship among proteins. Here we perform designability studies on the 2D square lattice and explore the effects of variable overall shapes on protein designability using a binary hydrophobic-polar (HP) amino acid alphabet. Because we rely on a simple energy function that counts the total number of H-H interactions between non-sequential residues, we restrict our studies to protein shapes that have the same number of residues and also a constant number of non-bonded contacts. We have found that there is a marked difference in the designability between various protein shapes, with some of them accounting for a significantly larger share of the total foldable sequences.

Comments

This is a manuscript of an article published as Peto, Myron, Andrzej Kloczkowski, and Robert L. Jernigan. "Shape-dependent designability studies of lattice proteins." Journal of Physics: Condensed Matter 19, no. 28 (2007): 285220. doi: 10.1088/0953-8984/19/28/285220. Posted with permission.

Copyright Owner

IOP Publishing Ltd

Language

en

File Format

application/pdf

Published Version

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