Density functional and electrostatics study of oxidized and reduced ribonucleotide reductase; comparisons with methane monooxygenase.
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.
Lovell
Timothy
T
Department of Molecular Biology TPC-15, The Scripps Research Institute, La Jolla, CA 92037, USA. tlovell@scripps.edu
Li
Jian
J
Noodleman
Louis
L
D001665:Binding Sites; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D019295:Computational Biology; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology; D020619:Methylococcus capsulatus / Q000201:enzymology; D008958:Models, Molecular; D008968:Molecular Conformation; D010084:Oxidation-Reduction; D010105:Oxygenases / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012264:Ribonucleotide Reductases / Q000737:chemistry*; D055672:Static Electricity; D013329:Structure-Activity Relationship
D010105:Oxygenases; C021555:methane monooxygenase; D012264:Ribonucleotide Reductases