publication . Preprint . 2015

Random close packing in protein cores

Gaines, Jennifer C.; Smith, W. Wendell; Regan, Lynne; O'Hern, Corey S.;
Open Access English
  • Published: 14 Oct 2015
Abstract
Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions $\phi \approx 0.75$, a value that is similar to close packing 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 using the explicit hydrogen model is proved by its ability to predict the side chain dihedral angle distributions observed in proteins. 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 ...
Subjects
arxiv: Quantitative Biology::Biomolecules
free text keywords: Quantitative Biology - Biomolecules
Funded by
NSF| MRI: Acquisition of a High Performance Computational Cluster for Yale University
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0821132
  • Funding stream: Directorate for Computer & Information Science & Engineering | Division of Computer and Network Systems
,
NSF| Stimuli-responsive nano-materials from designed proteins
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1307712
  • Funding stream: Directorate for Mathematical & Physical Sciences | Division of Materials Research
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