Normal mode analysis of the horseradish peroxidase collective motions: correlation with spectroscopically observed heme distortions.
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.
Laberge
Monique
M
Department of Biophysics and Radiation Biology, Semmelweis University and Biophysics Research Group, MTA-TKI, Puskin u. 9, Budapest 1088, Hungary. labergem@mail.med.upenn.edu
Kovesi
Istvan
I
Yonetani
Takashi
T
Fidy
Judit
J
D000465:Algorithms; D001665:Binding Sites; D002118:Calcium / Q000737:chemistry; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods; D006418:Heme / Q000737:chemistry*; D006735:Horseradish Peroxidase / Q000737:chemistry*; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D013057:Spectrum Analysis / Q000379:methods
D006418:Heme; D006735:Horseradish Peroxidase; D002118:Calcium