Geometric and statistical properties of the mean-field hydrophobic-polar model, the large-small model, and real protein sequences

C. T. Shih, Z. Y. Su, J. F. Gwan, B. L. Hao, C. H. Hsieh, J. L. Lo, and H. C. Lee
Phys. Rev. E 65, 041923 – Published 11 April 2002
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Abstract

Lattice models, for their coarse-grained nature, are best suited for the study of the “designability problem,” the phenomenon in which most of the about 16 000 proteins of known structure have their native conformations concentrated in a relatively small number of about 500 topological classes of conformations. Here it is shown that on a lattice the most highly designable simulated protein structures are those that have the largest number of surface-core switchbacks. A combination of physical, mathematical, and biological reasons that causes the phenomenon is given. By comparing the most foldable model peptides with protein sequences in the Protein Data Bank, it is shown that whereas different models may yield similar designabilities, predicted foldable peptides will simulate natural proteins only when the model incorporates the correct physics and biology, in this case if the main folding force arises from the differing hydrophobicity of the residues, but does not originate, say, from the steric hindrance effect caused by the differing sizes of the residues.

  • Received 28 March 2001

DOI:https://doi.org/10.1103/PhysRevE.65.041923

©2002 American Physical Society

Authors & Affiliations

C. T. Shih1,6, Z. Y. Su1, J. F. Gwan2, B. L. Hao3, C. H. Hsieh1, J. L. Lo4, and H. C. Lee4,5

  • 1National Center for High-Performance Computing, Hsinchu, Taiwan, Republic of China
  • 2Forum Modellierung, Forschungszentrum Jülich, D-52425 Jülich, Germany
  • 3Institute of Theoretical Physics, Academia Sinica, Beijing, China
  • 4Department of Physics and Department of Life Science, National Central University, Chungli, Taiwan, Republic of China
  • 5Department of Physics, Stanford University, Palo Alto, California 94305
  • 6Department of Physics, Tunghai University, Taichung, Taiwan, Republic of China

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Vol. 65, Iss. 4 — April 2002

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