Geometric and physical considerations for realistic protein models

Isaac A. Hubner and Eugene I. Shakhnovich
Phys. Rev. E 72, 022901 – Published 17 August 2005

Abstract

Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well understood and standardized definitions in terms of amino acid backbone geometry and the manner in which hydrogen bonding requirements are satisfied. Recently, “tube” models have been proposed to explain protein secondary structure in terms of the geometrically optimal packing of a featureless cylinder. However, atomically detailed simulations demonstrate that such packing considerations alone are insufficient for defining secondary structure; both excluded volume and hydrogen bonding must be explicitly modeled for helix formation. These results have fundamental implications for the construction and interpretation of realistic and meaningful biomacromolecular models.

  • Figure
  • Received 28 April 2005

DOI:https://doi.org/10.1103/PhysRevE.72.022901

©2005 American Physical Society

Authors & Affiliations

Isaac A. Hubner and Eugene I. Shakhnovich*

  • Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA

  • *Corresponding author. FAX: 617-384-9228. Electronic address: eugene@belok.harvard.edu

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Issue

Vol. 72, Iss. 2 — August 2005

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