Campus Units

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

Document Type

Article

Publication Version

Published Version

Publication Date

2007

Journal or Book Title

The Journal of Chemical Physics

Volume

127

Issue

4

First Page

044101

DOI

10.1063/1.2751169

Abstract

We enumerated all compact conformations within simple geometries on the two-dimensional (2D) triangular and three-dimensional (3D) face centered cubic (fcc) lattice. These compact conformations correspond mathematically to Hamiltonian paths and Hamiltonian circuits and are frequently used as simple models of proteins. The shapes that were studied for the 2D triangular lattice included m×n" role="presentation" style="display: inline; line-height: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; position: relative;">m×nm×n parallelograms, regular equilateral triangles, and various hexagons. On the 3D fcc lattice we generated conformations for a limited class of skewed parallelepipeds. Symmetries of the shape were exploited to reduce the number of conformations. We compared surface to volume ratios against protein length for compact conformations on the 3D cubic lattice and for a selected set of real proteins. We also show preliminary work in extending the transfer matrix method, previously developed by us for the 2D square and the 3D cubic lattices, to the 2D triangular lattice. The transfer matrix method offers a superior way of generating all conformations within a given geometry on a lattice by completely avoiding attrition and reducing this highly complicated geometrical problem to a simple algebraic problem of matrix multiplication.

Comments

This article is published as Peto, Myron, Taner Z. Sen, Robert L. Jernigan, and Andrzej Kloczkowski. "Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices." The Journal of chemical physics 127, no. 4 (2007):044101. doi: 10.1063/1.2751169. Posted with permission.

Copyright Owner

American Institute of Physics

Language

en

File Format

application/pdf

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