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Density functional and electrostatics study of oxidized and reduced ribonucleotide reductase: comparisons with methane monooxygenase

Academic Article
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Overview

authors

  • Lovell, T.
  • Li, J.
  • Noodleman, Louis

publication date

  • September 2002

journal

  • Journal of Biological Inorganic Chemistry  Journal

abstract

  • A combined broken symmetry density functional and electrostatics approach has been used to examine the active sites of the resting (RNR(ox)) and reduced (RNR(red)) forms of class I type ribonucleotide reductase in the protein and solvent environment. Active site cluster geometries and Heisenberg J values are discussed in the context of the available protein data. The total electrostatic interaction energy in the protein comprises a large reaction field component and a much smaller protein field term, the former suggesting strong dielectric polarization between the cluster and protein-solvent dielectrics; the latter is indicative of a very weak link to the protein environment. Decomposition of the protein field term elucidates the major electrostatic interactions between amino acid residues in the RNR R2 local environment and the active site cluster, enabling an energetic comparison of structurally equivalent residues with a related diiron protein, methane monooxygenase.

subject areas

  • Binding Sites
  • Chemistry, Physical
  • Computational Biology
  • Crystallography, X-Ray
  • Escherichia coli
  • Methylococcus capsulatus
  • Models, Molecular
  • Molecular Conformation
  • Oxidation-Reduction
  • Oxygenases
  • Physicochemical Phenomena
  • Protein Structure, Secondary
  • Ribonucleotide Reductases
  • Static Electricity
  • Structure-Activity Relationship
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Research

keywords

  • binuclear non-heme iron
  • density functional theory
  • methane monooxygenase
  • protein electrostatics comparison
  • ribonucleotide reductase
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Identity

International Standard Serial Number (ISSN)

  • 0949-8257

Digital Object Identifier (DOI)

  • 10.1007/s00775-002-358-y

PubMed ID

  • 12203016
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Additional Document Info

start page

  • 799

end page

  • 809

volume

  • 7

issue

  • 7-8

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