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Photo Lynn Kamerlin

Lynn Kamerlin

Professor

Photo Lynn Kamerlin

Force field independent metal parameters using a nonbonded dummy model

Author

  • Fernanda Duarte
  • Paul Bauer
  • Alexandre Barrozo
  • Beat Anton Amrein
  • Miha Purg
  • Johan Åqvist
  • Shina Caroline Lynn Kamerlin

Summary, in English

The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we are able to reproduce both M(2+)-O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase I as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers.

Publishing year

2014-04-24

Language

English

Pages

62-4351

Publication/Series

The Journal of Physical Chemistry Part B

Volume

118

Issue

16

Document type

Journal article

Publisher

The American Chemical Society (ACS)

Keywords

  • Catalytic Domain
  • Cations/chemistry
  • Escherichia coli
  • Escherichia coli Proteins/chemistry
  • Humans
  • Lactoylglutathione Lyase/chemistry
  • Metals/chemistry
  • Models, Chemical
  • Molecular Dynamics Simulation
  • Static Electricity
  • Water/chemistry

Status

Published

ISBN/ISSN/Other

  • ISSN: 1520-5207