Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics.

ABSTRACT: According to NMR chemical shift data, the ensemble of ubiquitin is a mixture of "open" and "closed" conformations at rapid equilibrium. Pressure perturbations provide the means to study the transition between the two conformers by imposing an additional constraint on the system's partial molar volume. Here we use nanosecond-timescale molecular dynamics simulations to characterize the network of correlated motions accessible to the conformers at low- and high-pressure conditions. Using the isotropic reorientational eigenmode dynamics formalism to analyze our simulation trajectories, we reproduce NMR relaxation data without fitting any parameters of our model. Comparative analysis of our results suggests that the two conformations behave very differently. The dynamics of the "closed" conform

SUBMITTER: Sgourakis NG 

PROVIDER: S-EPMC2553108 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature