QM/MM molecular dynamics studies of metal binding proteins

Pietro Vidossich, Alessandra Magistrato

Research output: Contribution to journalReview articleResearchpeer-review

49 Citations (Scopus)

Abstract

© 2014 by the authors; licensee MDPI, Basel, Switzerland. Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, a-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metalions.
Original languageEnglish
Pages (from-to)616-645
JournalBiomolecules
Volume4
Issue number3
DOIs
Publication statusPublished - 1 Sep 2014

Keywords

  • Alpha-synuclein
  • Beta-lactamases
  • Car-Parrinello molecular dynamics
  • Enzymatic catalysis
  • Peroxidases
  • QM/MM simulations
  • Ribozymes
  • Transition metals

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