Binding and Docking Interactions of NO, CO and O2 in Heme Proteins as Probed by Density Functional Theory

International Journal of Molecular Sciences

Vangelis Daskalakis¹ 

[1] Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, P.O. Box 1527,GR-711 10 Heraklion, Greece; E-Mail:

关键词: density functional theory;    ligand molecules;    protein cavities;    proximal effect;   

DOI  :  10.3390/ijms10094137

来源: mdpi

【 摘 要 】

Dynamics and reactivity in heme proteins include direct and indirect interactions of the ligands/substrates like CO, NO and O₂ with the environment. Direct electrostatic interactions result from amino acid side chains in the inner cavities and/or metal coordination in the active site, whereas indirect interactions result by ligands in the same coordination sphere. Interactions play a crucial role in stabilizing transition states in catalysis or altering ligation chemistry. We have probed, by Density Functional Theory (DFT), the perturbation degree in the stretching vibrational frequencies of CO, NO and O₂ molecules in the presence of electrostatic interactions or hydrogen bonds, under conditions simulating the inner cavities. Moreover, we have studied the vibrational characteristics of the heme bound form of the CO and NO ligands by altering the chemistry of the proximal to the heme ligand. CO, NO and O₂ molecules are highly polarizable exerting vibrational shifts up to 80, 200 and 120 cm⁻¹, respectively, compared to the non-interacting ligand. The importance of Density Functional Theory (DFT) methodology in the investigation of the heme-ligand-protein interactions is also addressed.

【 授权许可】

CC BY   
© 2009 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.