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Studying Functional Disulphide Bonds by Computer Simulations

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Functional Disulphide Bonds

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1967))

Abstract

Biochemical and structural data reveal important aspects of the properties and function of a protein disulphide bond. Molecular dynamics simulations can complement this experimental data and can yield valuable insights into the dynamical behavior of the disulphide bond within the protein environment. Due to the increasing accuracy of the underlying energetic description and the increasing computational power at hand, such simulations have now reached a level, at which they can also make quantitative and experimentally testable predictions. We here give an overview of the computational methods used to predict functional aspects of protein disulphides, including the prestress, protein allosteric effects upon thiol/disulphide exchange, and disulphide redox potentials. We then outline in detail the use of free-energy perturbation methods to calculate the redox potential of a protein disulphide bond of interest. In a step-by-step protocol, we describe the workflow within the MD suite Gromacs, including practical advice on the simulation setup and choice of parameters. For other disulphide-related simulation methods, we refer to resources available online.

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Acknowledgement

We are grateful to the Klaus Tschira Foundation for financial support.

Author information

Authors and Affiliations

  1. Heidelberg Institute for Theoretical Studies, Heidelberg, Germany

    Frauke Gräter

  2. Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany

    Frauke Gräter

  3. Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China

    Wenjin Li

Authors
  1. Frauke Gräter
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  2. Wenjin Li
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Corresponding author

Correspondence to Frauke Gräter .

Editor information

Editors and Affiliations

  1. The Centenary Institute, NHMRC Clinical Trials Centre, Sydney Medical School, University of Sydney, Sydney, NSW, Australia

    Philip Hogg

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Gräter, F., Li, W. (2019). Studying Functional Disulphide Bonds by Computer Simulations. In: Hogg, P. (eds) Functional Disulphide Bonds. Methods in Molecular Biology, vol 1967. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9187-7_6

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  • DOI: https://doi.org/10.1007/978-1-4939-9187-7_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9186-0

  • Online ISBN: 978-1-4939-9187-7

  • eBook Packages: Springer Protocols

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