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Protocol for Simulations of PEGylated Proteins with Martini 3

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Structural Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2199))

Abstract

Enhancement of proteins by PEGylation is an active area of research. However, the interactions between polymer and protein are far from fully understood. To gain a better insight into these interactions or even make predictions, molecular dynamics (MD) simulations can be applied to study specific protein-polymer systems at molecular level detail. Here we present instructions on how to simulate PEGylated proteins using the latest iteration of the Martini coarse-grained (CG) force-field. CG MD simulations offer near atomistic information and at the same time allow to study complex biological systems over longer time and length scales than fully atomistic-level simulations.

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Author information

Authors and Affiliations

  1. Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands

    Fabian Grünewald, Peter C. Kroon, Paulo C. T. Souza & Siewert J. Marrink

  2. Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands

    Fabian Grünewald, Peter C. Kroon, Paulo C. T. Souza & Siewert J. Marrink

Authors
  1. Fabian Grünewald
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  2. Peter C. Kroon
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  3. Paulo C. T. Souza
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  4. Siewert J. Marrink
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Corresponding author

Correspondence to Siewert J. Marrink .

Editor information

Editors and Affiliations

  1. Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Hong Kong

    Yu Wai Chen

  2. BMI Biotechnology Appraisals & Investments Limited, Wan Chai, Hong Kong

    Chin-Pang Bennu Yiu

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Grünewald, F., Kroon, P.C., Souza, P.C.T., Marrink, S.J. (2021). Protocol for Simulations of PEGylated Proteins with Martini 3. In: Chen, Y.W., Yiu, CP.B. (eds) Structural Genomics. Methods in Molecular Biology, vol 2199. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0892-0_18

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  • DOI: https://doi.org/10.1007/978-1-0716-0892-0_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0891-3

  • Online ISBN: 978-1-0716-0892-0

  • eBook Packages: Springer Protocols

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