Mei, Zhe - Yale University

Void Study of Protein Cores

There has been continued interest in the arrangements of hydrophobic amino acid residues in protein cores due to their large contribution to the stability of proteins.  Prior study has reported that protein cores possess a packing fraction of φ ≈ 0.56, which is similar to values for random close packing of nonspherical particles. This packing fraction is recovered by packing simulations of mixtures of residues that are isotropically compressed to jamming onset. Here we apply the analysis of void spaces and compare the void distributions in protein crystal structures, hydrophobic residue packing and other random close packing systems. The similarity of void spaces between protein cores and amino acid residue packing shows the potential of simplifying the complicated protein stability and mutation problem into a simple mechanical system.