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Beyond Standard Molecular Dynamics: Investigating the Molecular Mechanisms of G Protein-Coupled Receptors with Enhanced Molecular Dynamics Methods

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G Protein-Coupled Receptors - Modeling and Simulation

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 796))

Abstract

The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field.

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Acknowledgements

The authors’ work on GPCRs is currently supported by NIH grants DA026434 and DA034049. Their computations are run, in part, on resources available through the Scientific Computing Facility at Icahn School of Medicine at Mount Sinai, and in part on advanced computing resources provided by Texas Advanced Computing Center through MCB080077.

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  1. Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA

    Jennifer M. Johnston & Marta Filizola

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  1. Jennifer M. Johnston
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Correspondence to Marta Filizola .

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    Marta Filizola

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Johnston, J.M., Filizola, M. (2014). Beyond Standard Molecular Dynamics: Investigating the Molecular Mechanisms of G Protein-Coupled Receptors with Enhanced Molecular Dynamics Methods. In: Filizola, M. (eds) G Protein-Coupled Receptors - Modeling and Simulation. Advances in Experimental Medicine and Biology, vol 796. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7423-0_6

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