Putative dynamics of vasopressin in its V1a receptor binding site.

Abstract

The molecular architecture of the GPCRs, including the dynamic set of interactions between the receptor and the ligand, is one of the key structural questions of biophysical approaches. In the present study, molecular dynamics (MD) simulations were performed on the well-validated molecular model of the vasopressin V1a receptor applying different parameters (i.e., force fields, time variation, use of constraints) in order to sample the conformational space of the endogenous ligand arginine vasopressin (AVP), to explore different putative binding modes, and to analyze the simulation results with respect to experimental data. Noteworthy, it is to mention that for the first time a model of the vasopressin receptor remained stable in a 500 ps MD simulation run under vacuo boundary conditions using the Kollman all-atom FF even though no constraints were imposed. Conclusively, we determined an optimized experimental procedure for studying the dynamics and structure-functionship of this highly important family of GPCRs: the use of MD simulations with the Kollman all-atom force-field parameters on a constrained receptor. Our simplified model may be used as a basis for structure based design of new GPCR ligands and for in silico screening of virtual combinatorial chemistry libraries.