Long Proteins with Unique Optimal Foldings in the H-P Model

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. A preliminary version of this paper appeared at the 17th European Conference on Computational Geometry [2]. 1 Supported by the Austrian Programme for Advanced Research and Technology (APART). 2 Partially supported by NSERC Canada. 3 Supported by DURSI Gen. Cat. 1999SGR00356 and...

• Type: Journal
• Year: 2002
• Where: CORR
• Authors: Oswin Aichholzer, David Bremner, Erik D. Demaine, Henk Meijer, Vera Sacristan, Michael A. Soss
• Keywords: Amino Acid Sequence, Amino Acids, CORR 2002, Education, Proteins