Long proteins with unique optimal foldings in the H-P model
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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.
Date issued
2003-05Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science; Massachusetts Institute of Technology. Laboratory for Computer ScienceJournal
Computational Geometry
Publisher
Elsevier
Citation
Aichholzer, Oswin, David Bremner, Erik D. Demaine, Henk Meijer, Vera Sacristán, and Michael Soss. “Long Proteins with Unique Optimal Foldings in the H-P Model.” Computational Geometry 25, no. 1–2 (May 2003): 139–159. Copyright © 2002 Elsevier Science B.V.
Version: Final published version
ISSN
09257721