Abstract
The inactive conformations of glucagon receptor (GCGR) are widely reported by crystal structures that support the precision structure for drug discovery of type 2 diabetes. The previous study shows that the intracellular part is open in the glucagon-bound GCGR (glu-GCGR) and closed in the apo-GCGR by accelerated molecular dynamics (aMD) simulations. However, the crystal structure of GCGR in complex with partial agonist shows that the intracellular part is closed in the inactive conformation. To understand the differences between the studies of aMD simulations and crystal structure, the 2,500 ns conventional molecular dynamics (cMD) simulations are performed on the simulated model of glu-GCGR. The result shows that the transmembrane helices (TMH) 6 of glu-GCGR is outward ~4 Å to drive the intracellular part of glu-GCGR open until ~390 ns cMD simulations. The (TMH) 6 of glu-GCGR becomes closed after ~490 ns cMD simulations, which are consistent with the crystal structure of GCGR in complex with the partial agonist. To further elucidate the activation mechanism of GCGR deeply, the simulated models of glu-GCGR, apo-GCGR, and antagonist-bound GCGR (ant-GCGR) are constructed to perform 10 of parallel 300 ns aMD simulations, respectively. The results show that both of glu-GCGR and apo-GCGR can generate the open conformations of the intracellular part. But the glu-GCGR has the higher percentage of open conformations than apo-GCGR. The ant-GCGR is restricted to generate the open conformations of the intracellular part by antagonist MK-0893. It indicates that the glu-GCGR, apo-GCGR, and ant-GCGR can be distinguished by the aMD simulated method. Free energy landscape shows that the open conformations of the intracellular part of GCGR are in intermediate state. Our results show that aMD simulations enhance the space samplings of open conformations of GCGR via adding extra boost potential. It indicates that the aMD simulations are an effective way for drug discovery of GCGR.
Highlights
The human glucagon receptor (GCGR), which belongs to one member of class B G-protein-coupled receptors (GPCRs), is a potential drug target of type 2 diabetes (Cho et al, 2012)
The results of accelerated molecular dynamics simulations show that the active conformations are predominant in the intracellular parts of the GCGR in complex with agonist glucagon (Li et al, 2016)
The 2,500 ns of conventional molecular dynamics (cMD) and 9,000 ns of accelerated molecular dynamics (aMD) simulations are performed to elucidate the differences between the crystal structure of the GCGR in complex with a partial agonist and the previous study of aMD simulations (Li et al, 2016)
Summary
The human glucagon receptor (GCGR), which belongs to one member of class B G-protein-coupled receptors (GPCRs), is a potential drug target of type 2 diabetes (Cho et al, 2012). The structure of the GCGR in complex with glucagon analog is determined for elucidating a two-domain binding mechanism in which C-terminal and N-terminal bind to ECD and transmembrane domain (TMD) binding pocket, respectively (Zhang H. et al, 2018). The glucagon-like peptide receptor (GLP-1R) and the GCGR that belonged to members of class B GPCRs have very similar structures, but they have different regulated mechanisms on blood sugar level. The inhibited binding position of GCGR antagonist is at the boundary between transmembrane helices (TMH) and lipid membrane. It can restrict the outward movement of TMH to reduce post-prandial and fasting glucose concentrations (Bagger et al, 2011). The binding pocket of active conformation of GLP-1R is surrounded by seven TMH (Zhang Y. et al, 2017)
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