Journal
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Volume 498, Issue 2, Pages 366-374Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.bbrc.2018.01.160
Keywords
G-protein coupled receptor; Chemosensory receptor; Bitter taste receptor; Homology modeling; Molecular docking; Molecular mechanics/coarse-grained simulations
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Funding
- Ernesto Illy Foundation (Trieste, Italy)
- BioExcel Center of Excellence [H2020-EINFRA-2015-1-675728]
- Human Brain Project (HBP SGA1) within the European Union's Horizon Framework Programme for Research and Innovation [720270]
- Julich-Aachen Research Alliance - High Performance Computing (JARA-HPC) [JARA0023, JARA0082, JARA0165]
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Membrane receptors constitute major targets for pharmaceutical intervention. Drug design efforts rely on the identification of ligand binding poses. However, the limited experimental structural information available may make this extremely challenging, especially when only low-resolution homology models are accessible. In these cases, the predictions may be improved by molecular dynamics simulation approaches. Here we review recent developments of multiscale, hybrid molecular mechanics/coarse-grained (MM/CG) methods applied to membrane proteins. In particular, we focus on our in-house MM/CG approach. It is especially tailored for G-protein coupled receptors, the largest membrane receptor family in humans. We show that our MM/CG approach is able to capture the atomistic details of the receptor/ligand binding interactions, while keeping the computational cost low by representing the protein frame and the membrane environment in a highly simplified manner. We close this review by discussing ongoing improvements and challenges of the current implementation of our MM/CG code. (C) 2018 Elsevier Inc. All rights reserved.
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