Molecular Mechanism Regarding Allosteric Modulation of Ligand Binding and the Impact of Mutations on Dimerization for CCR5 Homodimer.

Abstract

In this work, we combined accelerated molecular dynamics (aMD) and conventional molecular dynamics (cMD) simulations coupled with the potential of mean force (PMF), correlation analysis, principal component analysis (PCA), and protein structure network (PSN) to study the effects of dimerization and the mutations of I52V and V150A on the CCR5 homodimer, in order to elucidate the mechanism regarding cooperativity of the ligand binding between two protomers and to address the controversy about the mutation-induced dimer-separation. The results reveal that the dimer with interface involved in TM1, TM2, TM3, and TM4 is stable for the CCR5 homodimer. The dimerization induces an asymmetric impact on the overall structure and the ligand-binding pocket. As a result, the two protomers exhibit an asymmetric binding to the maraviroc (one anti-HIV drug). The binding of one protomer to the drug is enhanced while the other is weakened. The PSN result further reveals the allosteric pathway of the ligand-binding pocket between the two protomers. Six important residues in the pathway were identified, including two residues unreported. The results from PMF, PCA, and the correlation analysis clearly indicate that the two mutations induce strong anticorrelation motions in the interface, finally leading to its separation. The observations from the work could advance our understanding of the structure of the G protein-coupled receptor dimers and implications for their functions.