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Large-Scale Molecular Dynamics Simulations of Cellular Compartments

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Structure and Function of Membrane Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2302))

Abstract

Molecular dynamics or MD simulation is gradually maturing into a tool for constructing in vivo models of living cells in atomistic details. The feasibility of such models is bolstered by integrating the simulations with data from microscopic, tomographic and spectroscopic experiments on exascale supercomputers, facilitated by the use of deep learning technologies. Over time, MD simulation has evolved from tens of thousands of atoms to over 100 million atoms comprising an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium. In this chapter, we present a step-by-step outline for preparing, executing and analyzing such large-scale MD simulations of biological systems that are essential to life processes. All scripts are provided via GitHub.

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Acknowledgments

The authors acknowledge start-up funds from the School of Molecular Sciences and Center for Applied Structure Discovery at Arizona State University, and the resources of the OLCF at the Oak Ridge National Laboratory, which is supported by the Office of Science at DOE under Contract No. DEAC05-00OR22725, made available via the INCITE program. We also acknowledge NAMD and VMD developments supported by NIH (P41GM104601) and R01GM098243-02 for supporting our study of membrane proteins.

Author information

Author notes

  1. Eric Wilson and John Vant contributed equally to this work.

Authors and Affiliations

  1. The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA

    Eric Wilson, John Vant, Jacob Layton, Ryan Boyd, Chitrak Gupta, Daipayan Sarkar & Abhishek Singharoy

  2. RADICAL, ECE, Rutgers University, Piscataway, NJ, USA

    Hyungro Lee, Matteo Turilli & Shantenu Jha

  3. Oak Ridge National Laboratory, Oak Ridge, TN, USA

    Benjamín Hernández & Sean Wilkinson

  4. Brookhaven National Laboratory, Upton, NY, USA

    Shantenu Jha

  5. Department of Biological Sciences, Purdue University, West Lafayette, IN, USA

    Daipayan Sarkar

Authors
  1. Eric Wilson
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  2. John Vant
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  3. Jacob Layton
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  4. Ryan Boyd
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  5. Hyungro Lee
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  6. Matteo Turilli
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  7. Benjamín Hernández
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  8. Sean Wilkinson
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  9. Shantenu Jha
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  10. Chitrak Gupta
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  11. Daipayan Sarkar
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  12. Abhishek Singharoy
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Corresponding authors

Correspondence to Chitrak Gupta , Daipayan Sarkar or Abhishek Singharoy .

Editor information

Editors and Affiliations

  1. School of Biological Sciences and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA

    Ingeborg Schmidt-Krey

  2. School of Physics, Georgia Institute of Technology, Atlanta, GA, USA

    James C. Gumbart

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Wilson, E. et al. (2021). Large-Scale Molecular Dynamics Simulations of Cellular Compartments. In: Schmidt-Krey, I., Gumbart, J.C. (eds) Structure and Function of Membrane Proteins. Methods in Molecular Biology, vol 2302. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1394-8_18

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  • DOI: https://doi.org/10.1007/978-1-0716-1394-8_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1393-1

  • Online ISBN: 978-1-0716-1394-8

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