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Long proteins with unique optimal foldings in the...
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Long proteins with unique optimal foldings in the H-P model

Abstract

It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a simple combinatorial model designed to answer qualitative questions about the protein folding process. In this paper we consider a problem suggested by Brian Hayes in 1998: what proteins in the two-dimensional H-P model have unique optimal (minimum energy) foldings? In particular, we prove that there are closed chains of monomers (amino acids) with this property for all (even) lengths; and that there are open monomer chains with this property for all lengths divisible by four.

Authors

Aichholzer O; Bremner D; Demaine ED; Meijer H; Sacristán V; Soss M

Volume

25

Pagination

pp. 139-159

Publisher

Elsevier

Publication Date

May 1, 2003

DOI

10.1016/s0925-7721(02)00134-7

Conference proceedings

Computational Geometry

Issue

1-2

ISSN

0925-7721

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