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bioRxiv · 10.1101/2022.10.26.513870

Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD)

Deganutti, G.·Pipito, L.·Rujan, R. M.·Weizmann, T.·Griffin, P.·Ciancetta, A.·Moro, S.·Reynolds, C. A.
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Abstract

The structural basis for the pharmacology of G protein-coupled receptors (GPCRs), the most abundant membrane proteins and the target of about 35% of approved drugs, is still a matter of intense study. What makes GPCRs challenging to study is the inherent flexibility and the metastable nature of interaction with extra-and intracellular partners that drive their effects. Here, we present a molecular dynamics (MD) adaptive sampling algorithm, namely multiple walker supervised molecular dynamics (mwSuMD), to address complex structural transitions involving GPCRs without energy input. We first report the binding and unbinding of the vasopressin peptide from its receptor V2. Successively, we present the complete transition of the glucagon-like peptide-1 receptor (GLP-1R) from inactive to active, agonist and Gs-bound state, and the GDP release from Gs. To our knowledge, this is the first time the whole sequence of events leading from an inactive GPCR to the GDP release is simulated without any energy bias. We demonstrate that mwSuMD can address complex binding processes intrinsically linked to protein dynamics out of reach of classic MD.

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Deganutti, G., Pipito, L., Rujan, R. M., Weizmann, T., Griffin, P., Ciancetta, A., Moro, S., Reynolds, C. A.. 2022-10-27. Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD). https://doi.org/10.1101/2022.10.26.513870

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