Quasiharmonic analysis of protein energy landscapes from pressure-temperature molecular dynamics simulations.

ABSTRACT: Positional fluctuations of an atom in a protein can be described as motion in an effective local energy minimum created by the surrounding protein atoms. The dependence of atomic fluctuations on both temperature (T) and pressure (P) has been used to probe the nature of these minima, which are generally described as harmonic in experiments such as x-ray crystallography and neutron scattering. Here, a quasiharmonic analysis method is presented in which the P-T dependence of atomic fluctuations is in terms of an intrinsic isobaric thermal expansivity α_P and an intrinsic isothermal compressibility κ_T. The method is tested on previously reported mean-square displacements from P-T molecular dynamics simulations of lysozyme, which were interpreted to have a pressure-independ

SUBMITTER: Rodgers JM 

PROVIDER: S-EPMC5942443 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature