Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

C. T. Shih; Z. Y. Su; J. F. Gwan; B. L. Hao; C. H. Hsieh; H. C. Lee

doi:10.1103/PhysRevLett.84.386

Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

C. T. Shih, Z. Y. Su, J. F. Gwan, B. L. Hao, C. H. Hsieh, and H. C. Lee

Phys. Rev. Lett. 84, 386 – Published 10 January 2000

Abstract

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with a large number of switchbacks between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha helices.

Received 9 November 1998

DOI:https://doi.org/10.1103/PhysRevLett.84.386

Authors & Affiliations

C. T. Shih¹, Z. Y. Su¹, J. F. Gwan¹, B. L. Hao^2,3, C. H. Hsieh¹, and H. C. Lee^3,4

¹National Center for High-Performance Computing, Hsinchu, Taiwan, Republic of China
²Institute of Theoretical Physics, Academia Sinica, Beijing, China
³National Center for Theoretical Sciences, Hsinchu, Taiwan, Republic of China
⁴Department of Physics and Center for Complex Systems, National Central University, Chungli, Taiwan, Republic of China