Shape-dependent designability studies of lattice proteins

Thumbnail Image
Date
2007-06-25
Authors
Peto, Myron
Kloczkowski, Andrzej
Jernigan, Robert
Major Professor
Advisor
Committee Member
Journal Title
Journal ISSN
Volume Title
Publisher
Authors
Research Projects
Organizational Units
Journal Issue
Is Version Of
Versions
Series
Department
Biochemistry, Biophysics and Molecular BiologyBaker Center for Bioinformatics and Biological Statistics
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.

Description
Keywords
Citation
DOI
Copyright
Mon Jan 01 00:00:00 UTC 2007
Collections