Abstract
The (Fe-O) moiety of Cytochrome c oxidase ferryl intermediate of the dioxygen activation reaction and the oxy-myoglobin (Mb-O2) structure have been probed by QM/MM (hybrid quantum mechanical/ molecular mechanical) calculations using Density Functional Theory (DFT)/MM to elucidate the effect of the heme propionates and the protein matrix on the chemistry of heme Fe-O moieties. On this line, we have probed the role of His97 in various protonation states of the heme propionate-6 in Mb and compared the results to that of the Cytochrome c oxidase chemistry.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Ozaki, S.-I., Roach, M.P., Matsui, T., Watanabe, Y.: Investigations of the Roles of the Distal Heme Environment and the Proximal Heme Iron Ligand in Peroxide Activation by Heme Enzymes via Molecular Engineering of Myoglobin. Acc. Chem. Res. 34, 818–825 (2001)
Daskalakis, V., Farantos, S.C., Varotsis, C.: Assigning Vibrational Spectra of Ferryl-Oxo Intermediates of Cytochrome c Oxidase by Periodic Orbits and Molecular Dynamics. J. Am. Chem. Soc. 130, 12385–12393 (2008)
Daskalakis, V., Farantos, S.C., Guallar, V., Varotsis, C.: Vibrational Resonances and CuB Displacement Controlled by Proton Motion in Cytochrome c Oxidase. J. Phys. Chem. B 114, 1136–1143 (2010)
Daskalakis, V., Farantos, S.C., Guallar, V., Varotsis, C.: Regulation of Electron and Proton Transfer by the Protein Matrix of Cytochrome c Oxidase. J. Phys. Chem. B 115, 3648–3655 (2011)
Chu, K., Vojtchovsky, J., McMahon, B.H., Sweet, R.M., Berendzen, J., Schlichting, I.: Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin. Nature 403, 921–923 (2000)
Schotte, F., Lim, M., Jackson, T.A., Smirnov, A.V., Soman, J., Olson, J.S., Phillips Jr., G.N., Wulff, M., Anfinrud, P.A.: Watching a Protein as it Functions with 150-ps Time-Resolved X-ray Crystallography. Science 300, 1944–1947 (2003)
Unno, M., Chen, H., Kusama, S., Shaik, S., Ikeda-Saito, M.: Structural Characterization of the Fleeting Ferric Peroxo Species in Myoglobin: Experiment and Theory. J. Am. Chem. Sci. 129, 13394–13395 (2007)
Chen, H., Ikeda-Saito, M., Shaik, S.: Nature of the Fe-O2 Bonding in Oxy-Myoglobin: Effect of the Protein. J. Am. Chem. Soc. 130, 14778–14790 (2008)
Berenshtein, E., Mayer, B., Goldberg, C., Kitrossky, N., Chevion, M.: Patterns of Mobilization of Copper and Iron Following Myocardial Ischemia: Possible Predictive Criteria for Tissue Injury. J. Mol. Cell. Cardiol. 29, 3025–3034 (1997)
Gunter, M.R., Sampath, V., Caughey, W.S.: Potential roles of myoglobin autoxidation in myocardial ischemia-reperfusion injury. Free Radic. Biol. Med. 26, 1388–1395 (1999)
Postnikova, G.B., Moiseeva, S.A., Shekhovtsova, E.A.: The Main Role of Inner Histidines in the Molecular Mechanism of Myoglobin Oxidation Catalyzed by Copper Compounds. Inorg. Chem. 49, 1347–1354 (2010)
Rifkind, J.M., Lauer, L.D., Chiang, S.C., Li, N.C.: Copper and oxidation of hemoglobin: a comparison of horse and human hemoglobins. Biochemistry 15, 5337–5343 (1976)
Christova, P.K., Devedzhiev, Y.D., Atanasov, B.P., Volkenshtein, M.V.: [Study of electron transfer in hemoproteins. IV. Oxidation of sperm whale oxymoglobin catalyzed by copper ions]. Mol. Biol. (Mosk.) 14, 1088–1097 (1980)
Pople, J., Scott, A., Wong, M.: Scaling Factors for Obtaining Fundamental Vibrational Frequencies and Zero-Point Energies from HF/6-31G* and MP2/6-31G* Harmonic Frequencies. Isr. J. Chem. 33, 345–350 (1993)
Hirota, S., Li, T., Philips Jr., G.N., Olson, J.S., Mukai, M., Kitagawa, T.: Perturbation of the Fe−O2 Bond by Nearby Residues in Heme Pocket: Observation of ν(Fe-O2) Raman Bands for Oxymyoglobin Mutants. J. Am. Chem. Soc. 118, 7845–7846 (1996)
Noodleman, L.J.: Valence bond description of antiferromagnetic coupling in transition metal dimers. Chem. Phys. 74, 5737–5743 (1981); Noodleman, L., Peng, C.Y., Case, D.A., Mouesca Coord, J.M.: Orbital interactions, electron delocalization and spin coupling in iron-sulfur clusters. Chem. Rev. 144, 199–244 (1995)
Reed, A.E., Weinstock, R.B., Weinhold, F.: Natural Population Analysis. J. Chem. Phys. 83, 735–746 (1985)
Shibata, T., Nagao, S., Fukaya, M., Tai, H., Nagatomo, S., Morihashi, K., Matsuo, T., Hirota, S., Suzuki, A., Imai, K., Yamamoto, Y.: Effect of Heme Modification on Oxygen Affinity of Myoglobin and Equilibrium of the Acid−Alkaline Transition in Metmyoglobin. J. Am. Chem. Soc. 132, 6091–6098 (2010); Shikama K.: The Molecular Mechanism of Autoxidation for Myoglobin and Hemoglobin: A Venerable Puzzle. Chem. Rev. 98, 1357–1374 (1998); Allen, K.E., Cornforth, D.P.: Myoglobin Oxidation in a Model System as Affected by Nonheme Iron and Iron Chelating Agents. J. Agric. Food Chem. 54, 10134–10140 (2006); Murakami, T., Morishima, I., Matsui, T., Ozaki, S.-I., Hara, I., Yang, H.-J., Watanabe, Y.: Effects of the Arrangement of a Distal Catalytic Residue on Regioselectivity and Reactivity in the Coupled Oxidation of Sperm Whale Myoglobin Mutants. J. Am. Chem. Soc. 121, 2007–2011 (1999); Grunwald, E.W., Richards, M.P.: Mechanisms of Heme Protein-Mediated Lipid Oxidation Using Hemoglobin and Myoglobin Variants in Raw and Heated Washed Muscle. J. Agric. Food Chem. 54, 8271–8280 (2006)
Harada, K., Makino, M., Sugimoto, H., Hirota, S., Matsuo, T., Shiro, Y., Hisaeda, Y., Hayashi, T.: Structure and Ligand Binding Properties of Myoglobins Reconstituted with Monodepropionated Heme: Functional Role of Each Heme Propionate Side Chain. Biochemistry 46, 9406–9416 (2007)
Bashford, D., Case, D.A., Dalvit, C., Tennant, L., Wright, P.E.: Electrostatic calculations of side-chain pKa values in myoglobin and comparison with NMR data for histidines. Biochemistry 32, 8045–8056 (1993)
Carver, J.A., Bradbury, J.H.: Assignment of proton NMR resonances of histidine and other aromatic residues in met-, cyano-, oxy-, and (carbon monoxy) myoglobins. Biochemistry 23, 4890–4905 (1984)
Daskalakis, V., Giatromanolakis, M., Porrini, M., Farantos, S.C., Gervasi, O.: Grid Computing Multiple Shooting Algorithms for Extended Phase Space Sampling and Long Time Propagation in Molecular Dynamics. Computer Physics 4, 1–18 (2011)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Daskalakis, V., Farantos, S.C., Varotsis, C. (2012). Tuning Heme Functionality: The Cases of Cytochrome c Oxidase and Myoglobin Oxidation. In: Murgante, B., et al. Computational Science and Its Applications – ICCSA 2012. ICCSA 2012. Lecture Notes in Computer Science, vol 7333. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31125-3_24
Download citation
DOI: https://doi.org/10.1007/978-3-642-31125-3_24
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-31124-6
Online ISBN: 978-3-642-31125-3
eBook Packages: Computer ScienceComputer Science (R0)