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
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 ...
arxiv: Quantitative Biology::Biomolecules
free text keywords: Quantitative Biology - Biomolecules
Funded by
NSF| MRI: Acquisition of a High Performance Computational Cluster for Yale University
  • 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
  • Funder: National Science Foundation (NSF)
  • Project Code: 1307712
  • Funding stream: Directorate for Mathematical & Physical Sciences | Division of Materials Research
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25 references, page 1 of 2

[1] J. Kyte. Structure in Protein Chemistry. Garland Science, New York, 2nd edition, 2007.

[2] G.T. Nolan and P.E. Kavanagh. Random packing of nonspherical particles. Powder Technology, 84:199, 1995.

[3] X. Jia, R. Caulkin, R.A. Williams, Z.Y. Zhou, and A.B. Yu. The role of geometric constraints in random packing of non-spherical particles. Europhys. Lett., 92:68005, 2010.

[4] F.M. Richards. The interpretation of protein structures: Total volume, group volume distributions and packing density. J. Mol. Biol., 82:1, 1974.

[5] J. Liang and K. Dill. Are proteins well-packed? Biophys. J., 81:751, 2001. [OpenAIRE]

[6] P.J. Fleming and F.M. Richards. Protein packing: Dependence on protein size, secondary structure and amino acid composition. J. Mol. Biol., 299:487, 2000.

[7] K. Rother, R. Preissner, A. Goede, and C. Frommel. Inhomogeneous molecular density: Reference packing densities and distribution of cavities within proteins. Bioinformatics, 19, 2003.

[8] J.W. Ponder and F.M. Richards. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for di erent structural classes. J. Mol. Biol., 193:775, 1987.

[9] J.M. Word, S.C. Lovell, J.S. Richardson, and D.C. Richardson. Visualizing and quantifying molecular goodness-of- t: Small-probe contact dots with explicit hydrogen atoms. J. Mol. Biol., 285:1735, 1999.

[10] G. Wang and R.L. Dunbrack Jr. PISCES: A protein sequence culling server. Bioinformatics, 19:1589, 2003.

[11] G. Wang and R.L. Dunbrack Jr. PISCES: Recent improvements to a PDB sequence culling server. Nucleic Acids Res., 33:W94, 2005.

[12] A.Q. Zhou, D. Caballero, C.S. O'Hern, and L. Regan. New insights into the interdependence between amino acid stereochemistry and protein structure. Biophys. J., 105:2403, 2013.

[13] A.Q. Zhou, C.S. O'Hern, and L. Regan. Predicting the side-chain dihedral angle distributions of non-polar, aromatic, and polar amino acids using hard sphere models. Proteins Struct. Funct. Bioinf., 82:2574, 2014.

[14] A.Q. Zhou, C.S. O'Hern, and L. Regan. Revisiting the Ramachandran plot from a new angle. Protein Sci., 20:1166, 2011.

[15] A.Q. Zhou, C.S. O'Hern, and L. Regan. The power of hard-sphere models: Explaining side-chain dihedral angle distributions of Thr and Val. Biophys. J., 102:2345, 2012. [OpenAIRE]

25 references, page 1 of 2
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