Random close packing in protein cores

Jennifer C. Gaines, W. Wendell Smith, Lynne Regan, and Corey S. O'Hern
Phys. Rev. E 93, 032415 – Published 28 March 2016

Abstract

Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ0.75, a value that is similar to close packing of equal-sized spheres. A limitation of these analyses was the use of extended atom models, rather than the more physically accurate explicit hydrogen model. The validity of the explicit hydrogen model was proved in our previous studies by its ability to predict the side chain dihedral angle distributions observed in proteins. In contrast, the extended atom model is not able to recapitulate the side chain dihedral angle distributions, and gives rise to large atomic clashes at side chain dihedral angle combinations that are highly probable in protein crystal structures. Here, we employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high-resolution protein structures. We find that these protein cores have ϕ0.56, which is similar to results obtained from simulations of random packings of individual amino acids. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations to protein cores and interfaces of known structure.

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  • Received 14 October 2015
  • Revised 11 February 2016

DOI:https://doi.org/10.1103/PhysRevE.93.032415

©2016 American Physical Society

Physics Subject Headings (PhySH)

  1. Research Areas
  1. Physical Systems
Physics of Living Systems

Authors & Affiliations

Jennifer C. Gaines1,2, W. Wendell Smith3, Lynne Regan1,2,4,5, and Corey S. O'Hern1,2,3,6,7

  • 1Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
  • 2Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut 06520, USA
  • 3Department of Physics, Yale University, New Haven, Connecticut 06520, USA
  • 4Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, USA
  • 5Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
  • 6Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut 06520, USA
  • 7Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA

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Issue

Vol. 93, Iss. 3 — March 2016

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