Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs

Matthew G. Quesne, Tomasz Borowski, Sam P. de Visser

Research output: Contribution to journalArticlepeer-review

Abstract

Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.
Original languageEnglish
Pages (from-to)2562-2581
Number of pages20
JournalChemistry - A European Journal
Volume22
Issue number8
Early online date23 Dec 2015
DOIs
Publication statusPublished - 18 Feb 2016

Keywords

  • computational modeling
  • density functional theory
  • enzyme catalysis
  • enzyme mechanisms
  • QM/MM

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