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Enhanced Molecular Dynamics Simulations of Intrinsically Disordered Proteins

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Intrinsically Disordered Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2141))

Abstract

Molecular dynamics simulations represent a powerful tool to gain insights into structural and dynamical features of biomolecular systems. Nevertheless, their recognized limitation in terms of achievable timescales becomes particularly severe when dealing with slow processes. In such cases, the employment of enhanced sampling methods, which allow accelerating the characterization of rare events in a timeframe consistent with conventional computational resources, results as crucial. In particular, such advanced techniques have proven highly valuable in the context of protein folding and, specifically, to explore the conformational ensemble spanned by intrinsically disordered proteins (IDPs). Here, we describe how to set up molecular dynamics simulations with one of these enhanced sampling approaches (namely, Parallel Tempering Metadynamics in the Well-Tempered Ensemble) using the NTAIL peptide as a test case.

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Acknowledgments

The authors wish to thank Fabio Pietrucci and Giovanni Bussi for their invaluable feedback and useful discussion.

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Authors and Affiliations

  1. Department of Pharmacy and Biotechnology, Alma Mater Studiorum—Università di Bologna, Bologna, Italy

    Matteo Masetti & Andrea Cavalli

  2. Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy

    Mattia Bernetti

  3. Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy

    Andrea Cavalli

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  1. Matteo Masetti
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  2. Mattia Bernetti
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  3. Andrea Cavalli
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Correspondence to Andrea Cavalli .

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Editors and Affiliations

  1. Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, København N, Denmark

    Birthe B. Kragelund

  2. Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Karen Skriver

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Masetti, M., Bernetti, M., Cavalli, A. (2020). Enhanced Molecular Dynamics Simulations of Intrinsically Disordered Proteins. In: Kragelund, B.B., Skriver, K. (eds) Intrinsically Disordered Proteins. Methods in Molecular Biology, vol 2141. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0524-0_19

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  • DOI: https://doi.org/10.1007/978-1-0716-0524-0_19

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0523-3

  • Online ISBN: 978-1-0716-0524-0

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