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Normal mode analysis of the horseradish peroxidase collective motions: Correlation with spectroscopically observed heme distortions
Author(s) -
Laberge Monique,
Kovesi Istvan,
Yonetani Takashi,
Fidy Judit
Publication year - 2006
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20463
Subject(s) - horseradish peroxidase , chemistry , heme , peroxidase , calcium , planarity testing , matrix (chemical analysis) , enzyme , crystallography , biochemistry , organic chemistry , chromatography
Horseradish peroxidase C is a class III peroxidase whose structure is stabilized by the presence of two endogenous calcium atoms. Calcium removal has been shown to decrease the enzymatic activity of the enzyme and significantly affect the spectroscopically detectable properties of the heme, such as the spin state of the iron, heme normal modes, and distortions from planarity. In this work, we report on normal mode analysis (NMA) performed on models subjected to 2 ns of molecular dynamics simulations to describe the effect of calcium removal on protein collective motions and to investigate the correlation between active site (heme) and protein matrix fluctuations. We show that in the native peroxidase model, heme fluctuations are correlated to matrix fluctuations while they are not in the calcium‐depleted model. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 425–429, 2006 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com