Structural Rearrangements of Rhodopsin Subunits in a Dimer Complex: a Molecular Dynamics Simulation Study

Abstract

The present work reports a 0.1 μs molecular dynamics simulation of a bovine rhodopsin dimer based on a recently reported semi-empirical model obtained by fitting two monomers from the crystal structure to atomic force microscopy maps (Fotiadis et al. Curr Opin Struct Biol 16, 252, 2006). The simulation shows that the quaternary arrangement is stable although subtle rearrangements in its tertiary elements are observed during the first 60 ns of the trajectory. The comparison with a parallel 0.1 μs simulation of a single monomer in the same conditions and using the same protocol allows the study of subunit-subunit interactions on the dimer interface together with the structural effects associated to the dimer formation. The present study describes the interface of a TM4/TM5-TM4/TM5 dimer at an atomistic level including an analysis of the energy contributions to the interaction of each part of the protein involved. We also compare the differences in the structure of the single monomer with those of the dimer subunits with the aim of understanding the changes required for the dimer formation.

Key words:

• Membrane protein
• GPCRs
• Dimerization
• MD simulations
• Lipid bilayers
• GROMACS