Water in the polar and nonpolar cavities of the protein interleukin-1β.

ABSTRACT: Water in the protein interior serves important structural and functional roles and is also increasingly recognized as a relevant factor in drug binding. The nonpolar cavity in the protein interleukin-1β has been reported to be filled by water on the basis of some experiments and simulations and to be empty on the basis of others. Here we study the thermodynamics of filling the central nonpolar cavity and the four polar cavities of interleukin-1β by molecular dynamics simulation. We use different water models (TIP3P and SPC/E) and protein force fields (amber94 and amber03) to calculate the semigrand partition functions term by term that quantify the hydration equilibria. We consistently find that water in the central nonpolar cavity is thermodynamically unstable, independent of force field

SUBMITTER: Yin H 

PROVIDER: S-EPMC3005849 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature