Long proteins with unique optimal foldings in the H-P model
Author(s)Aichholzer, Oswin; Bremner, David; Demaine, Erik D.; Meijer, Henk; Sacristán, Vera; Soss, Michael; ... Show more Show less
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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.
DepartmentMassachusetts Institute of Technology. Department of Electrical Engineering and Computer Science; Massachusetts Institute of Technology. Laboratory for Computer Science
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.
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