Understanding the Mechanism of Activation/Deactivation of GLP-1R via Accelerated Molecular Dynamics Simulation
Xiuchan Xiao
A B E , Miao Qin A B , Fuhui Zhang C , Yan Su C , Bo Zhou B D E and Zheng Zhou A B
+ Author Affiliations
- Author Affiliations
A School of Material Science and Environmental Engineering, Chengdu Technological University, Chengdu 611730, China.
B Center of Big Data for Smart Environmental Protection, Chengdu Technological University, Chengdu 611730, China.
C School of Chemistry, Sichuan University, Chengdu 610064, China.
D School of Electronic Engineering, Chengdu Technological University, Chengdu 611730, China.
E Corresponding authors. Email: xxchan@edtu.edu.cn; bozhou@zju.edu.cn
Australian Journal of Chemistry 74(3) 211-218 https://doi.org/10.1071/CH20127
Submitted: 22 April 2020 Accepted: 18 August 2020 Published: 17 September 2020
Journal Compilation © CSIRO 2021 Open Access CC BY-NC-ND
Abstract
Glucagon-like peptide-1 receptor (GLP-1R), as a member of the class B G protein-coupled receptors (GPCRs), plays a crucial role in regulating blood glucose level signal recognition through its activation. The conformation changes during the activation pathway are of particular importance for its function. To investigate the activation mechanism of GLP-1R, the crystal structures of active and inactive forms are chosen to perform a total of 2 μs of accelerated molecular dynamics (aMD) simulations and 400 ns of conventional molecular dynamics (cMD) simulations. With the aid of structural analysis and potential of mean force (PMF) calculations, we reveal the role of different helices in the activation and deactivation process and obtain the intermediate states during activation and deactivation that are difficult to capture in experiments. Protein structure network (PSN) was utilised to clarify the allosteric communication pathways of activation and deactivation and reveal the mechanisms of its activation and deactivation. The results could advance our understanding of the activation mechanism of GLP-1R and the related drug design.
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