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A Discontinuous Potential Model for Protein–Protein Interactions

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Book cover Foundations of Molecular Modeling and Simulation

Part of the book series: Molecular Modeling and Simulation ((MMAS))

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Abstract

Protein–protein interactions play an important role in many biologic and industrial processes. In this work, we develop a two-bead-per-residue model that enables us to account for protein–protein interactions in a multi-protein system using discontinuous molecular dynamics simulations. This model deploys discontinuous potentials to describe the non-bonded interactions and virtual bonds to keep proteins in their native state. The geometric and energetic parameters are derived from the potentials of mean force between sidechain–sidechain, sidechain–backbone, and backbone–backbone pairs. The energetic parameters are scaled with the aim of matching the second virial coefficient of lysozyme reported in experiment. We also investigate the performance of several bond-building strategies.

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Acknowledgments

This work was supported by National Science Foundation (CBET-1236053) and the National Institutes of Health (EB006006). This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1053575.

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Authors and Affiliations

  1. Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, 27695, USA

    Qing Shao & Carol K. Hall

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  1. Qing Shao
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  2. Carol K. Hall
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Correspondence to Carol K. Hall .

Editor information

Editors and Affiliations

  1. Department of Chemical &, Northwestern University, Evanston, Illinois, USA

    Randall Q Snurr

  2. Chemical Engineering, Imperial College London, London, United Kingdom

    Claire S. Adjiman

  3. York Buffalo, The State University of New, Buffalo, New York, USA

    David A. Kofke

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Shao, Q., Hall, C.K. (2016). A Discontinuous Potential Model for Protein–Protein Interactions. In: Snurr, R., Adjiman, C., Kofke, D. (eds) Foundations of Molecular Modeling and Simulation. Molecular Modeling and Simulation. Springer, Singapore. https://doi.org/10.1007/978-981-10-1128-3_1

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