Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding.

ABSTRACT: Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force

SUBMITTER: Abriata LA 

PROVIDER: S-EPMC4448524 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature