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Structure, Protonation State and Dynamics of Catalase Compound II
Author(s) -
Rovira Carme
Publication year - 2005
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.200400633
Subject(s) - protonation , chemistry , molecular dynamics , residue (chemistry) , catalytic cycle , catalysis , crystallography , heme , crystal structure , computational chemistry , stereochemistry , chemical physics , ion , enzyme , organic chemistry
Density functional calculations are performed to investigate the protonation state of the compound II intermediate (Cpd II) of the catalase reaction cycle. Several scenarios are considered, depending on the protonation state of the active center (heme) and the catalytic His residue. Only the form with a protonated FeO unit (i.e. FeOH) is in agreement with the recent high‐resolution crystal structure, while the traditional description of Cpd II as an oxoferryl species corresponds to a configuration slightly higher in energy. The computed FeO stretch frequency is in agreement with the available experimental data. Molecular dynamics simulations show that the pocket water remains in the region between the His61 and Asn133 catalytic residues, but it occasionally tries to escape towards the main channel in a concerted motion with the Asn133 residue. A possible role for this residue in the process of ligand entry/escape from the binding pocket is proposed.