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Challenges in Modelling Metalloenzymes

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Transition Metals in Coordination Environments

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 29))

Abstract

Modelling structure and/or reaction mechanism of a metalloenzyme requires constructing reliable computational models. This process usually starts with crystal structure and involves several steps, each potentially influencing the accuracy of the constructed model. In this chapter, we provide an account, from our own works and from the literature, on how one can check the quality of the crystal structure, predict protonation states of titratable residues, including the metal ligands, perform molecular dynamics simulations, chose representative snapshots, and finally, construct a QM cluster model that can be used for mechanistic studies.

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Acknowledgements

This research was supported in part by PL-Grid Infrastructure. Computations were performed in the AGH Cyfronet Supercomputer Centre. Authors acknowledge financial support of the statutory research fund of ICSC PAS. M. Sz. acknowledges the input of Ewelina Biała, the undergraduate student conducting modeling of S25DH under supervision of M. Sz.

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Authors and Affiliations

  1. Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland

    Tomasz Borowski & Maciej Szaleniec

Authors
  1. Tomasz Borowski
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  2. Maciej Szaleniec
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Corresponding authors

Correspondence to Tomasz Borowski or Maciej Szaleniec .

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Editors and Affiliations

  1. Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland

    Ewa Broclawik

  2. Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland

    Tomasz Borowski

  3. Faculty of Chemistry, Jagiellonian University, Kraków, Poland

    Mariusz Radoń

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Borowski, T., Szaleniec, M. (2019). Challenges in Modelling Metalloenzymes. In: Broclawik, E., Borowski, T., Radoń, M. (eds) Transition Metals in Coordination Environments. Challenges and Advances in Computational Chemistry and Physics, vol 29. Springer, Cham. https://doi.org/10.1007/978-3-030-11714-6_17

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