Analyses of protein cores reveal fundamental differences between solution and crystal structures.

ABSTRACT: There have been several studies suggesting that protein structures solved by NMR spectroscopy and X-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures solved by both methods. We also find significant differences between NMR and crystal structures-in the root-mean-square deviations of the C _α atomic positions, identities of core amino acids, backbone, and side-chain dihedral angles, and packing fraction of core residues. In contrast to prior studies, we identify the physical basis for these differences by modeling protein cores as jammed packings of amino acid-shaped particles. We find that we can tune the jammed packing fraction by varying the degree of thermalization used to

SUBMITTER: Mei Z 

PROVIDER: S-EPMC7415476 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature