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Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program

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Structural Genomics

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

Abstract

The MCPB.py program greatly facilitates force field parameterization for metal sites in metalloproteins and organometallic compounds. Herein we present an example of MCPB.py to the parameterization of the dioxygen binding metal site of peptidylglycine-alphahydroxylating monooxygenase (PHM), which contains a copper ion. In this example, we also extend the functionality of MCPB.py to support molecular dynamics (MD) simulations in GROMACS through a python script. Illustrative MD simulations were performed using GROMACS and the results were analyzed. Notes about the program were also provided in this chapter, to assist MCPB.py users for metal site parameterizations.

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Acknowledgments

We acknowledge Prof. Justin Lemkul (Virginia Tech) for the GROMACS tutorial for simulating lysozyme in water. We acknowledge the computational support from the High Performance Computing Center (HPCC) at the Institute for Cyber-enabled Research (iCER) at Michigan State University (MSU). Pengfei Li gratefully acknowledges financial support through Prof. Sharon Hammes-Schiffer by the National Institutes of Health (Grant Number GM056207).

Author information

Authors and Affiliations

  1. Department of Chemistry, Yale University, New Haven, CT, USA

    Pengfei Li

  2. Department of Chemistry, Michigan State University, East Lansing, MI, USA

    Kenneth M. Merz Jr.

  3. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA

    Kenneth M. Merz Jr.

  4. Institute of Cyber-Enabled Research, Michigan State University, East Lansing, MI, USA

    Kenneth M. Merz Jr.

Authors
  1. Pengfei Li
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  2. Kenneth M. Merz Jr.
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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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Li, P., Merz, K.M. (2021). Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program. 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_15

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  • DOI: https://doi.org/10.1007/978-1-0716-0892-0_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0891-3

  • Online ISBN: 978-1-0716-0892-0

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