Agonist Binding and G Protein Coupling in Histamine H2 Receptor: A Molecular Dynamics Study

Abstract

The histamine H2 receptor (H2R) plays an important role in the regulation of gastric acid secretion. Therefore, it is a main drug target for the treatment of gastroesophageal reflux or peptic ulcer disease. However, there is as of yet no 3D-structural information available hampering a mechanistic understanding of H2R. Therefore, we created a model of the histamine-H2R-Gs complex based on the structure of the ternary complex of the β2-adrenoceptor and investigated the conformational stability of this active GPCR conformation. Since the physiologically relevant motions with respect to ligand binding and conformational changes of GPCRs can only partly be assessed on the timescale of conventional MD (cMD) simulations, we also applied metadynamics and Gaussian accelerated molecular dynamics (GaMD) simulations. A multiple walker metadynamics simulation in combination with cMD was applied for the determination of the histamine binding mode. The preferential binding pose detected is in good agreement with previous data from site directed mutagenesis and provides a basis for rational ligand design. Inspection of the H2R-Gs interface reveals a network of polar interactions that may contribute to H2R coupling selectivity. The cMD and GaMD simulations demonstrate that the active conformation is retained on a μs-timescale in the ternary histamine-H2R-Gs complex and in a truncated complex that contains only Gs helix α5 instead of the entire G protein. In contrast, histamine alone is unable to stabilize the active conformation, which is in line with previous studies of other GPCRs.

Specific Engineered G Protein Coupling to Histamine Receptors Revealed from Cellular Assay Experiments and Accelerated Molecular Dynamics Simulations

“…In the absence of experimental structures, homology models were built in this study to generate initial complexes of the H 2 R and H 4 R with the mGs, mGsi, and mGsq proteins. A model recently published by Conrad et al [ 76 ] and a model provided by GPCRdb ( , accessed on 10 August 2021 [ 77 ]) were used as simulation starting structures for the H 2 R and the H 4 R, respectively. A computational model of GaMD simulation systems is provided in the Supporting Material (Figure S1) .…”

“…To obtain the H 2 R complexes, the H 2 R–Gs structure that has been published by Conrad et al was used as template comprising H 2 R residues 15–304 [ 76 ]. To obtain the mini-G protein structures mGs, mGsi, and mGsq (according to mGs393, mGsi43, and mGsq71, [ 46 ]), homology modeling was performed on the Gs structure using Modeller 9.16 [ 88 ].…”

The Roles of Cardiovascular H2-Histamine Receptors Under Normal and Pathophysiological Conditions

“…The homology of mouse and human H 2 -histamine receptors at the protein level is about 85% ( Kobayashi et al, 1996 ). The three-dimensional structure of the H 2 R has been studied using virtual crystallisation ( Conrad et al, 2020 ; Hok et al, 2020 ). Histamine has been observed to bind to amino acids in transmembrane domains three and five or six ( Panula et al, 2015 ).…”

Gaussian accelerated molecular dynamics: Principles and applications

“…In this review, we will present the principles and the most recent applications of GaMD. Robust GaMD has been established for advanced simulation studies of a wide range of biomolecular systems, especially the protein-nucleic acid interactions [63][64][65] such as the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene-editing system, 66,67 protein-protein/peptide interactions, [68][69][70][71][72] protein-ligand binding, 55,56,[73][74][75][76] protein folding, 77 protein enzymes, 52,58,[78][79][80][81][82][83][84][85][86][87][88][89][90][91][92] membrane proteins (including GPCRs, 68,69,73,76,[93][94][95] ion channels, 53,96 and γ-secretase 97 ) and carbohydrates, [98][99][100]…”