Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method

DOI Web Site 12 References Open Access
  • Kato Koichiro
    Department of applied chemistry, Graduate School of Engineering, Kyushu University Center for Molecular System, Kyushu University
  • Yamamoto Ami
    Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University
  • Watanabe Chiduru
    Center for Biosystems Dynamics Research, RIKEN JST PRESTO
  • Fukuzawa Kaori
    Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University Graduate School of Pharmaceutical Sciences, Osaka University

Description

<p>The fragment molecular orbital (FMO) method enables quantum mechanical calculations for macromolecules by dividing the target into fragments. However, most calculations, even for metalloproteins, have been performed by removing metal ions from the structures registered in the Protein Data Bank (PDB). For more realistic and useful calculations, FMO calculations must be performed without removing the metal ions. In this study, we discuss the results obtained from FMO calculations performed using 6-31G* and model core potentials (MCPs) for metal proteins containing Zn and Mg ions. Subsequently, we analyze the differences in atomic charges and interactions.</p>

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