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Int. J. Mol. Sci. 2009, 10(9), 4137-4156; doi:10.3390/ijms10094137

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

1 Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, P.O. Box 1527,GR-711 10 Heraklion, Greece 2 Department of Chemistry, University of Crete, P.O. Box 2208, 71003, Voutes – Heraklion, Greece
* Author to whom correspondence should be addressed.
Received: 10 August 2009 / Revised: 30 August 2009 / Accepted: 15 September 2009 / Published: 22 September 2009
(This article belongs to the Special Issue Application of Density Functional Theory)
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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.
Keywords: density functional theory; ligand molecules; protein cavities; proximal effect density functional theory; ligand molecules; protein cavities; proximal effect
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Daskalakis, V.; Varotsis, C. Binding and Docking Interactions of NO, CO and O2 in Heme Proteins as Probed by Density Functional Theory. Int. J. Mol. Sci. 2009, 10, 4137-4156.

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