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Setting Up All-Atom Molecular Dynamics Simulations to Study the Interactions of Peripheral Membrane Proteins with Model Lipid Bilayers

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Intracellular Lipid Transport

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1949))

Abstract

All-atom molecular dynamics (MD) simulations enable the study of biological systems at atomic detail, complement the understanding gained from experiment, and can also motivate experimental techniques to further examine a given biological process. This method is based on statistical mechanics; it predicts the trajectory of atoms over time by solving Newton’s Laws of motion taking into account all forces. Here, we describe the use of this methodology to study the interaction between peripheral membrane proteins and a lipid bilayer. Specifically, we provide step-by-step instructions to set up MD simulations to study the binding and interaction of the amphipathic helix of Osh4, a lipid transport protein, and Thanatin, an antimicrobial peptide (AMP), with model lipid bilayers using both fully detailed lipid tails and the highly mobile membrane-mimetic (HMMM) method to enhance conformational sampling.

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Acknowledgments

The AAMD and HMMM method discussed here were used to study the binding mechanism of ALPS to model membranes, results are presented in [11, 40], respectively; the Thanatin system is currently under study. These simulation trajectories were partially supported by NSF grant DBI-1145652 and MCB-1149187 and the High Performance Deepthought & Deepthought 2 Computing Clusters at the University of Maryland, College Park administered by the Division of Information Technology. The AAMD runs were possible thanks to time on the Anton Computer provided by the Pittsburgh Supercomputing Center (PSC) through Grant R01GM116961 from the National Institutes of Health and our specific time associated with the grant PSCA14030P. The Anton machine at PSC was generously made available by D.E. Shaw Research.

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Authors and Affiliations

  1. Department of Chemistry, The University of Chicago, Chicago, IL, USA

    Viviana Monje-Galvan

  2. Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA

    Viviana Monje-Galvan, Linnea Warburton & Jeffery B. Klauda

  3. Biophysics Program, University of Maryland, College Park, MD, USA

    Jeffery B. Klauda

Authors
  1. Viviana Monje-Galvan
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  2. Linnea Warburton
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  3. Jeffery B. Klauda
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Corresponding author

Correspondence to Viviana Monje-Galvan .

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Editors and Affiliations

  1. Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and CNRS, Valbonne, France

    Guillaume Drin

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Monje-Galvan, V., Warburton, L., Klauda, J.B. (2019). Setting Up All-Atom Molecular Dynamics Simulations to Study the Interactions of Peripheral Membrane Proteins with Model Lipid Bilayers. In: Drin, G. (eds) Intracellular Lipid Transport. Methods in Molecular Biology, vol 1949. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9136-5_22

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  • DOI: https://doi.org/10.1007/978-1-4939-9136-5_22

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9135-8

  • Online ISBN: 978-1-4939-9136-5

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