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Phys Rev E. 2019 Feb;99(2-1):022416. doi: 10.1103/PhysRevE.99.022416.

Void distributions reveal structural link between jammed packings and protein cores.

Treado JD1,2, Mei Z2,3, Regan L2,3,4, O'Hern CS1,2,5,6,7.

Author information

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

Abstract

Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ϕ≈0.56, which is the same as dense, random packing of amino-acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino-acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. We measure the critical exponent τ that characterizes the size distribution of connected void clusters at the onset of percolation. We find that the cluster size statistics are similar for void percolation in packings of amino-acid-shaped particles and randomly placed spheres, but different from that for void percolation in jammed sphere packings. We propose that the connected void regions are a defining structural feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino-acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations.

PMID:
30934238
DOI:
10.1103/PhysRevE.99.022416
[Indexed for MEDLINE]

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