Normal mode analysis of the horseradish peroxidase collective motions: Correlation with spectroscopically observed heme distortions

Monique Laberge, Istvan Kovesi, Takashi Yonetani, Judit Fidy

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Abstract

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.

Original languageEnglish
Pages (from-to)425-429
Number of pages5
JournalBiopolymers
Volume82
Issue number4
DOIs
Publication statusPublished - Jul 1 2006

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Keywords

  • Collective motions
  • Horseradish peroxidase
  • Normal mode analysis
  • Protein fluctuations

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

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