Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor

Miao, Yinglong; McCammon, J. Andrew

doi:10.1073/pnas.1800756115

Title: Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor

Journal Article · Mon Mar 05 00:00:00 EST 2018 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1800756115· OSTI ID:1498119

^[1]; McCammon, J. Andrew ^[2]

Univ. of Kansas, Lawrence, KS (United States). Center for Computational Biology and Dept. of Molecular Biosciences
Univ. of California, San Diego, La Jolla, CA (United States). Dept. of Pharmacology and Dept. of Chemistry and Biochemistry

Protein–protein binding is key in cellular signaling processes. Molecular dynamics (MD) simulations of protein–protein binding, however, are challenging due to limited timescales. In particular, binding of the medically important G-protein-coupled receptors (GPCRs) with intracellular signaling proteins has not been simulated with MD to date. Here, we report a successful simulation of the binding of a G-protein mimetic nanobody to the M₂ muscarinic GPCR using the robust Gaussian accelerated MD (GaMD) method. Through long-timescale GaMD simulations over 4,500 ns, the nanobody was observed to bind the receptor intracellular G-protein-coupling site, with a minimum rmsd of 2.48 Å in the nanobody core domain compared with the X-ray structure. Binding of the nanobody allosterically closed the orthosteric ligand-binding pocket, being consistent with the recent experimental finding. In the absence of nanobody binding, the receptor orthosteric pocket sampled open and fully open conformations. The GaMD simulations revealed two low-energy intermediate states during nanobody binding to the M₂ receptor. The flexible receptor intracellular loops contribute remarkable electrostatic, polar, and hydrophobic residue interactions in recognition and binding of the nanobody. As a result, these simulations provided important insights into the mechanism of GPCR–nanobody binding and demonstrated the applicability of GaMD in modeling dynamic protein–protein interactions.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE

OSTI ID:: 1498119

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Vol. 115, Issue 12; ISSN 0027-8424

Publisher:: National Academy of Sciences, Washington, DC (United States)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 71 works

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