Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin.
Combined QM/MM calculations of the active-site of cytochrome P450cam have been performed before and after the binding of P450cam to putidaredoxin. The calculations were carried out for both a 5-coordinated and a 6-coordinated active-site of cytochrome P450cam, with either a water molecule or a carbon monoxide molecule as a 6th distal ligand. An experimentally observed increase in the Fe-S stretching frequency that occurs after cytochrome P450cam binds to putidaredoxin, has been reproduced in our study. Experimentally observed changes in the Fe-C and C-O vibration frequencies that occur after binding of both proteins, have also been reproduced in our study. The computed increase of the Fe-S and Fe-C stretching frequencies is correlated with a corresponding decrease of the Fe-S and Fe-C interatomic distances. According to our calculations, for the active-site with carbon monoxide in the triplet electronic state, the binding process increases the spin densities on the iron and sulfur atoms, which changes the Fe-C and C-O stretching frequencies in opposite directions, in agreement with experimental data.
Freindorf
Marek
M
Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14260, United States. mfrein@buffalo.edu
Shao
Yihan
Y
Kong
Jing
J
Furlani
Thomas R
TR
D001665:Binding Sites; D019475:Camphor 5-Monooxygenase / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D005288:Ferredoxins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D011485:Protein Binding; D017433:Protein Structure, Secondary
D005288:Ferredoxins; C100137:putidaredoxin; D019475:Camphor 5-Monooxygenase