全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...
Biomolecules  2013 

Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions

DOI: 10.3390/biom3030662

Keywords: enzyme, reaction, mechanism, model, quantum mechanics, QM/MM

Full-Text   Cite this paper   Add to My Lib

Abstract:

Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods.

References

[1]  Claeyssens, F.; Harvey, J.N.; Manby, F.R.; Mata, R.A.; Mulholland, A.J.; Ranaghan, K.E.; Schütz, M.; Thiel, S.; Thiel, W.; Werner, H.J. High-accuracy computation of reaction barriers in enzymes. Angew. Chem. 2006, 118, 7010–7013, doi:10.1002/ange.200602711.
[2]  Matthews, B.W.; Sigler, P.B.; Henderson, R.; Blow, D.M. Three-Dimensional structure of tosyl α-chymotrypsin. Nature 1967, 214, 652–656, doi:10.1038/214652a0.
[3]  Hedstr?m, L. Serine protease mechanism and specificity. Chem. Rev. 2002, 102, 4501–4523, doi:10.1021/cr000033x.
[4]  Lassila, J.K.; Zalatan, J.G.; Herschlag, D. Biological phosphoryl-transfer reactions: Understanding mechanism and catalysis. Annu. Rev. Biochem. 2011, 80, 669–702, doi:10.1146/annurev-biochem-060409-092741.
[5]  Asbóth, B.; Náray-Szabó, G. Mechanism of action of d-xylose isomerase. Curr. Protein Pept. Sci. 2000, 1, 237–254, doi:10.2174/1389203003381333.
[6]  Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The protein data bank. Nucleic Acids Res. 2000, 28, 235–242, doi:10.1093/nar/28.1.235.
[7]  Wade, R.C.; Luty, B.A.; Demchuk, E.; Madura, J.D.; Davis, M.E.; Briggs, J.M.; McCammon, J.A. Simulation of enzyme-substrate encounter with gated active sites. Nat. Struct. Biol. 1994, 1, 65–69, doi:10.1038/nsb0194-65.
[8]  Hammes-Schiffer, S.; Benkovic, S.J. Relating protein motion to catalysis. Annu. Rev. Biochem. 2006, 75, 519–541, doi:10.1146/annurev.biochem.75.103004.142800.
[9]  McGeagh, J.D.; Ranaghan, K.E.; Mulholland, A.J. Protein dynamics and enzyme catalysis: Insights from simulations. Biochim. Biophys. Acta 2011, 1814, 1077–1092, doi:10.1016/j.bbapap.2010.12.002.
[10]  Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; Wiley: New York, NY, USA, 1991.
[11]  Ranaghan, K.E.; Mulholland, A.J. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. Int. Rev. Phys. Chem. 2010, 29, 65–133, doi:10.1080/01442350903495417.
[12]  Senn, H.M.; Thiel, W. QM/MM methods for biomolecular systems. Angew. Chem. Int. Ed. 2009, 48, 1198–1229, doi:10.1002/anie.200802019.
[13]  Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G.A.; et al. Gaussian 09. Revision B.01; Gaussian, Inc.: Wallingford, CT, USA, 2010.
[14]  Szabo, A.; Ostlund, N.S. Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory; Dover Publications: Mineola, NY, USA, 1996.
[15]  Jacobsen, H.; Cavallo, L. Directions for Use of Density Functional Theory: A Short Introduction Manual for Chemists. In Handbook of Computational Chemistry; Leszczynski, J., Ed.; Springer: Berlin, Germany, 2011; pp. 97–133.
[16]  Vreven, T.; Morokuma, K. Hybrid methods: ONIOM(QM:MM) and QM/MM. Annu. Repts Comput. Chem. 2006, 2, 35–51, doi:10.1016/S1574-1400(06)02003-2.
[17]  Poltev, V. Molecular Mechanics: Method and Applications. In Handbook of Computational Chemisry; Leszczynski, J., Ed.; Springer: Berlin, Germany, 2011; pp. 260–291.
[18]  Case, D.A.; Darden, T.A.; Cheatham, T.E., III; Simmerling, C.L.; Wang, J.; Duke, R.E.; Luo, R.; Walker, R.C.; Zhang, W.; Merz, K.M.; et al. AMBER 11. University of California, San Francisco, 2010.
[19]  Christen, M.; Hunenberger, P.H.; Bakowies, D.; Baron, R.; Bürgi, R.; Geerke, D.P.; Heinz, T.N.; Kastenholz, M.A.; Krautler, V.; Oostenbrink, C.; et al. The gromos software for biomolecular simulation: Gromos05. J. Comp. Chem. 2005, 26, 1719–1751, doi:10.1002/jcc.20303.
[20]  Available online: http://www.gromacs.org/ (accessed on 6 August 2013).
[21]  Brooks, B.R.; Brooks, C.L., III; Mackerell, A.D.; Nilsson, L.; Petrella, R.J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; et al. CHARMM: The biomolecular simulation program. J. Comp. Chem. 2009, 30, 1545–1615, doi:10.1002/jcc.21287.
[22]  Jorgensen, W.L.; Tirado-Rives, J. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc. Natl. Acad. Sci. USA 2005, 102, 6665–6670, doi:10.1073/pnas.0408037102.
[23]  Nowak, W. Applications of Computational Methods to Simulations of Proteins Dynamics. In Handbook of Computational Chemistry; Leszczynski, J., Ed.; Springer: Berlin, Germany, 2011; pp. 1129–1155.
[24]  Marx, D.; Hutter, J. Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods; Cambridge University Press: Cambridge, UK, 2009.
[25]  R?thlisberger, D.; Khersonsky, O.; Wollacott, A.M.; Jiang, J.; DeChancie, J.; Betker, J.; Gallaher, J.L.; Althoff, E.A.; Zanghellini, A.; Dym, O.; et al. Kemp elimination catalysts by computational enzyme design. Nature 2008, 453, 190–195, doi:10.1038/nature06879.
[26]  Náray-Szabó, G.; Surján, P.R. Bond orbital framework for rapid calculation of environmental effects on molecular potential energy surfaces. Chem. Phys. Lett. 1983, 96, 499–501, doi:10.1016/0009-2614(83)80739-8.
[27]  Hu, H.; Yang, W. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu. Rev. Phys. Chem. 2008, 59, 573–560, doi:10.1146/annurev.physchem.59.032607.093618.
[28]  Warshel, A.; Florian, J. Empirical Valence Bond and Related Approaches; Wiley: New York, NY, USA, 2004.
[29]  Kamerlin, S.C.L.; Cao, J.; Rosta, E.; Warshel, A. On unjustifiably misrepresenting the EVB approach while simultaneously adopting it. J. Phys. Chem. B 2009, 113, 10905–10915, doi:10.1021/jp901709f.
[30]  Bentzien, J.; Muller, R.P.; Florián, J.; Warshel, A. Hybrid ab initio quantum mechanics/molecular mechanics calculations of free energy surfaces for enzymatic reactions: The nucleophilic attack in subtilisin. J. Phys. Chem B 1998, 102, 2293–2301, doi:10.1021/jp973480y.
[31]  Rocchia, W.; Alexov, E.; Honig, B. Extending the applicability of the nonlinear poisson-boltzmann equation: Multiple dielectric constants and multivalent ions. J. Phys. Chem. B 2001, 105, 6507–6514, doi:10.1021/jp010454y.
[32]  Sarkar, S.; Witham, S.; Zhang, J.; Zhenirovskyy, M.; Rocchia, W.; Alexov, E. DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes. Comm. Comp. Phys. 2013, 13, 269–284.
[33]  Tomasi, J.; Mennucci, B.; Cammi, R. Quantum mechanical continuum solvation models. Chem. Rev. 2005, 105, 2999–3094, doi:10.1021/cr9904009.
[34]  Polgár, L. Mechanisms of Protease Action; CRC Press: Boca Raton, FL, USA, 1989.
[35]  Brenner, S. The molecular evolution of genes and proteins: A tale of two serines. Nature 1988, 334, 528–530, doi:10.1038/334528a0.
[36]  Asbóth, B.; Polgár, L. Transition-state stabilization at the oxyanion binding sites of serine and thiol proteinases: Hydrolyses of thiono and oxygen esters. Biochemistry 1983, 22, 117–122, doi:10.1021/bi00270a017.
[37]  Carter, P.; Wells, J.A. Functional interaction among catalytic residues in subtilisin BPN’. Proteins Struct. Funct. Genet. 1990, 7, 335–342, doi:10.1002/prot.340070405.
[38]  Blow, D.M.; Birktoft, J.J.; Hartley, B.S. Role of a buried acid group in the mechanism of action of chymotrypsin. Nature 1969, 221, 337–340, doi:10.1038/221337a0.
[39]  Polgár, L.; Bender, M.L. The nature of general base-general acid catalysis in serine proteases. Proc. Natl. Acad. Sci. USA 1969, 64, 1335–1342, doi:10.1073/pnas.64.4.1335.
[40]  Bachovchin, W.W. Confirmation of the assignment of the low-field proton resonance of serine proteases by using specifically nitrogen-15 labeled enzyme. Proc. Natl. Acad. Sci. USA 1985, 82, 7948–7951, doi:10.1073/pnas.82.23.7948.
[41]  Kossiakoff, A.A.; Spencer, S.A. Direct determination of the protonation states of aspartic acid-102 and histidine-57 in the tetrahedral intermediate of the serine proteases: Neutron structure of trypsin. Biochemistry 1981, 20, 6462–6474, doi:10.1021/bi00525a027.
[42]  Sprang, S.; Standing, T.; Fletterick, R.J.; Stroud, R.M.; Finer-Moore, J.; Xuong, N.H.; Hamlin, R.; Rutter, W.J.; Craik, C.S. The Three-dimensional structure of Asn102 mutant of trypsin: Role of Asp102 in serine protease catalysis. Science 1987, 237, 905–909.
[43]  Szeltner, Z.; Rea, D.; Renner, V.; Fül?p, V.; Polgár, L. Electrostatic effects and binding determinants in the catalysis of prolyl oligopeptidase. Site specific mutagenesis at the oxyanion binding site. J. Biol. Chem. 2002, 277, 42613–42622.
[44]  Warshel, A.; Náray-Szabó, G.; Sussman, F.; Hwang, J.K. How do serine proteases really work? Biochemistry 1989, 28, 3629–3637, doi:10.1021/bi00435a001.
[45]  Warshel, A. Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites. J. Biol. Chem. 1998, 273, 27035–27038, doi:10.1074/jbc.273.42.27035.
[46]  Kamerlin, S.C.L.; Sharma, P.K.; Chu, Z.T.; Warshel, A. Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization. Proc. Natl. Acad. Sci. USA 2010, 107, 4075–4080, doi:10.1073/pnas.0914579107.
[47]  Gérczei, T.; Asbóth, B.; Náray-Szabó, G. Conservative electrostatic potential patterns at enzyme active sites. The anion-cation-anion triad. J. Chem. Inf. Comput. Sci. 1999, 39, 310–315, doi:10.1021/ci980128o.
[48]  Náray-Szabó, G.; Fuxreiter, M.; Warshel, A. Electrostatic Basis of Enzyme Catalysis. In Computational Approaches to Biochemical Reactivity; Warshel, A., Náray-Szabó, G., Eds.; Kluwer: Dordrecht, The Netherlands, 1997; pp. 237–293.
[49]  Umeyama, H.; Nakagawa, S.; Kudo, T. Role of Asp102 in the enzymatic reaction of bovine beta-trypsin. A molecular orbital study. J. Mol. Biol. 1981, 150, 409–421, doi:10.1016/0022-2836(81)90556-8.
[50]  Náray-Szabó, G. Electrostatic effect on catalytic rate enhancement in serine proteinases. Int. J. Quant. Chem. 1982, 22, 575–582, doi:10.1002/qua.560220309.
[51]  Ishida, T.; Kato, S. Theoretical perspectives on the reaction mechanism of serine proteases: The reaction free energy profiles of the acylation process. J. Am. Chem. Soc. 2003, 125, 12035–12048, doi:10.1021/ja021369m.
[52]  Topf, M.; Richards, W.G. Theoretical studies on the deacylation step of serine protease catalysis in the gas phase, in solution, and in elastase. J. Am. Chem. Soc. 2004, 126, 14631–14641, doi:10.1021/ja047010a.
[53]  Hudáky, P.; Perczel, A. A self-stabilized model of the chymotrypsin catalytic pocket. The energy profile of the overall catalytic cycle. Proteins Struct. Funct. Bioinf. 2006, 62, 749–759, doi:10.1002/prot.20827.
[54]  Zhou, Y.; Zhang, Y. Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate. Chem. Commun. 2011, 47, 1577–1579, doi:10.1039/c0cc04112b.
[55]  Florián, J.; Warshel, A. Phosphate ester hydrolysis in aqueous solution: Associative versus dissociative mechanisms. J. Phys. Chem. B 1998, 102, 719–734, doi:10.1021/jp972182y.
[56]  Bernardi, F.; Bottoni, A.; de Vivo, M.; Garavelli, M.; Keser?, G.; Náray-Szabó, G. A hypothetical mechanism for HIV-1 integrase catalytic action: DFT modelling of a bio-mimetic environment. Chem. Phys. Lett. 2002, 362, 1–7, doi:10.1016/S0009-2614(02)01027-8.
[57]  Franzini, E.; Fantucci, P.; de Gioia, L. Density functional theory investigation of guanosine triphosphate models. Catalytic role of Mg2+ ions in phosphate ester hydrolysis. J. Mol. Catal. A 2003, 204, 409–417.
[58]  Lahiri, S.D.; Zhang, G.; Dunaway-Mariano, D.; Allen, K.N. The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction. Science 2003, 299, 2067–2071, doi:10.1126/science.1082710.
[59]  Blackburn, G.M.; Williams, N.H.; Gamblin, S.J.; Smerdon, S.J. The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction. Science 2003, 301, 1184c, doi:10.1126/science.1085796.
[60]  Baxter, N.J.; Bowler, M.W.; Alizadeh, T.; Cliff, M.J.; Hounslow, A.M.; Wu, B.; Berkowitz, D.B.; Williams, N.H.; Blackburn, G.M.; Waltho, J.P. Atomic details of near-transition state conformers for enzyme phosphoryl transfer revealed by MgF3- rather than by phosphoranes. Proc. Natl. Acad. Sci. USA 2010, 107, 4555–4560, doi:10.1073/pnas.0910333106.
[61]  Webster, C.E. High-energy intermediate or stable transition state analogue: Theoretical perspective of the active site and mechanism of β-phosphoglucomutase. J. Am. Chem. Soc. 2004, 126, 6840–6841, doi:10.1021/ja049232e.
[62]  Berente, I.; Beke, T.; Náray-Szabó, G. Quantum mechanical studies on the existence of a trigonal bipyramidal phosphorane intermediate in enzymatic phosphate ester hydrolysis. Theor. Chem. Acc. 2007, 118, 129–134, doi:10.1007/s00214-007-0255-0.
[63]  Barabás, O.; Pongrácz, V.; Kovári, J.; Wilmanns, M.; Vértessy, B.G. Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase. J. Biol. Chem. 2004, 279, 42907–42915.
[64]  Ivanov, I.; Tainer, J.A.; McCammon, J.A. Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc. Natl. Acad. Sci. USA 2007, 104, 1465–1470, doi:10.1073/pnas.0603468104.
[65]  Cavalli, A.; de Vivo, M.; Recanatini, M. Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase. Chem. Eur. J. 2007, 13, 8437–8444, doi:10.1002/chem.200700044.
[66]  Smith, G.K.; Ke, Z.; Guo, H. Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies. J. Phys. Chem. B 2011, 115, 13713–13722, doi:10.1021/jp207532s.
[67]  Kamerlin, S.C.L.; McKenna, C.E.; Goodman, M.F.; Warshel, A. A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: Implications for the mechanism of DNA polymerases. Biochemistry 2009, 48, 5963–5971, doi:10.1021/bi900140c.
[68]  Wong, K.-Y.; Gao, J. Insight into the phosphodiesterase mechanism from combined QM/MM free energy simulations. FEBS J. 2011, 278, 2579–2595, doi:10.1111/j.1742-4658.2011.08187.x.
[69]  Lior-Hoffmann, L.; Wang, L.; Wang, S.; Geacintov, N.E.; Broyde, S.; Zhang, Y. Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion. Nucleic Acids Res. 2012, 40, 9193–9205, doi:10.1093/nar/gks653.
[70]  Xu, D.; Guo, H. Ab initio QM/MM studies of the phosphoryl transfer reaction catalyzed by PEP Mutase suggest a dissociative metaphosphate transition state. J. Phys. Chem. B 2008, 112, 4102–4108, doi:10.1021/jp0776816.
[71]  Xu, D.; Guo, H.; Liu, Y.; York, D.M. Theoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: Solvent effects, thio effects, and implications for enzymatic reactions. J. Phys. Chem. B 2005, 109, 13827–13834, doi:10.1021/jp051042i.
[72]  De Vivo, M.; Dal Peraro, M.; Klein, M.L. Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism. J. Am. Chem. Soc. 2008, 130, 10955–10962, doi:10.1021/ja8005786.
[73]  Rosta, E.; Woodcock, H.L.; Brooks, B.R.; Hummer, G. Artificial reaction coordinate “Tunneling” in free-energy calculations: The catalytic reaction of RNase H. J. Comput. Chem. 2009, 30, 1634–1641, doi:10.1002/jcc.21312.
[74]  Schlichting, I.; Reinstein, J. pH influences fluoride coordination number of the AIFx phosphoryl transfer transition state analog. Nat. Struct. Biol. 1999, 6, 721–723, doi:10.1038/11485.
[75]  De Vivo, M.; Ensing, B.; Dal Peraro, M.; Gomez, G.A.; Christianson, D.W.; Klein, M.L. Proton shuttles and phosphatase activity in soluble epoxide hydrolase. J. Am. Chem. Soc. 2007, 129, 387–394, doi:10.1021/ja066150c.
[76]  Ram Prasad, B.; Plotnikov, N.V.; Warshel, A. Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping. J. Phys. Chem. B 2013, 117, 153–163.
[77]  Kamerlin, S.C.L.; Florián, J.; Warshel, A. Associative versus dissociative mechanisms of phosphate monoester hydrolysis: On the interpretation of activation entropies. ChemPhysChem 2008, 9, 1767–1773, doi:10.1002/cphc.200800356.
[78]  Finzel, B.C.; Poulos, T.L.; Kraut, J. Crystal structure of yeast cytochrome c peroxidase refined at 1.7 ? resolution. J. Biol. Chem. 1984, 269, 32759–32767.
[79]  Poulos, T.L.; Edwards, S.L.; Wariishi, H.; Gold, M.H. Crystallographic Refinement of lignin peroxidase at 2 ?. J. Biol. Chem. 1993, 268, 4429–4440.
[80]  Patterson, W.R.; Poulos, T.L.; Goodin, D.B. Identification of a porphyrin Pi cation radical in ascorbate peroxidase compound I. Biochemistry 1995, 34, 4342–4345, doi:10.1021/bi00013a024.
[81]  Gajhede, M.; Schuller, D.J.; Henriksen, A.; Smith, A.T.; Poulos, T.L. Crystal structure of horseradish peroxidase C at 2.15 ? resolution. Nat. Struct. Biol. 1997, 4, 1032–1038, doi:10.1038/nsb1297-1032.
[82]  Patterson, W.R.; Poulos, T.L. Crystal structure of recombinant pea cytosolic ascorbate peroxidase. Biochemistry 1995, 34, 4331–4341, doi:10.1021/bi00013a023.
[83]  Menyhárd, D.K.; Náray-Szabó, G. Electrostatic effect on electron transfer at the active site of heme peroxidases: A comparative molecular orbital study on Cytochrome C peroxidase and ascorbate peroxidase. J. Phys. Chem. B 1999, 103, 227–233, doi:10.1021/jp981765k.
[84]  Jensen, G.M.; Bunte, S.W.; Warshel, A.; Goodin, D.B. Energetics of cation radical formation at the proximal active site tryptophan of cytochrome c peroxidase and ascorbate peroxidase. J. Phys. Chem. 1998, 102, 8221–8228.
[85]  Wirstam, M.; Blomberg, M.R.A.; Siegbahn, P.E.M. Reaction mechanism of compound i formation in heme peroxidases: A density functional theory study. J. Am. Chem. Soc. 1999, 121, 10178–10185, doi:10.1021/ja991997c.
[86]  Hiner, A.N.; Martínez, J.I.; Arnao, M.B.; Acosta, M.; Turner, D.D.; Lloyd Raven, E.; Rodríguez-López, J.N. Detection of a tryptophan radical in the reaction of ascorbate peroxidase with hydrogen peroxide. Eur. J. Biochem. 2001, 268, 3091–3098, doi:10.1046/j.1432-1327.2001.02208.x.
[87]  Heimdal, J.; Rydberg, P.; Ryde, U. Protonation of the proximal histidine ligand in heme peroxidases. J. Phys. Chem. B 2008, 112, 2501–2510, doi:10.1021/jp710038s.
[88]  De Visser, S.P. What affects the quartet-doublet energy splitting in peroxidase enzymes? J. Phys. Chem. A 2005, 109, 11050–11057, doi:10.1021/jp053873u.
[89]  Bathelt, C.M.; Mulholland, A.J.; Harvey, J.N. QM/MM studies of the electronic structure of the compound I intermediate in cytochrome c peroxidase and ascorbate peroxidase. J. Chem. Soc. Dalton Trans. 2005, 3470–3476.
[90]  Derat, E.; Cohen, S.; Shaik, S.; Altun, A.; Thiel, W. Principal active species of horseradish peroxidase compound I: A hybrid quantum mechanical/molecular mechanical study. J. Am. Chem. Soc. 2005, 127, 13611–13621, doi:10.1021/ja0534046.
[91]  Jensen, K.P.; Ryde, U. Importance of proximal hydrogen bonds in haem proteins. Mol. Phys. 2003, 101, 2003–2018, doi:10.1080/0026897031000109383.
[92]  Guallar, V.; Wallrapp, F.H. QM/MM methods: Looking inside heme proteins biochemisty. Biophys. Chem. 2010, 149, 1–11, doi:10.1016/j.bpc.2010.03.010.
[93]  Vlasitsa, J.; Jakopitscha, C.; Bernroitnera, M.; Zamockya, M.; Furtmüllera, P.G.; Obingera, C. Mechanisms of catalase activity of heme peroxidases. Arch. Biochem. Biophys. 2010, 500, 74–81, doi:10.1016/j.abb.2010.04.018.
[94]  Harris, D.L.; Loew, G.H. Proximal ligand effects on electronic structure and spectra of compound I of peroxidases. J. Porphyr. Phthalocyanins 2001, 5, 334–344, doi:10.1002/jpp.316.
[95]  Nelson, D.R.; Goldstone, J.V.; Stegeman, J.J. The cytochrome P450 genesis locus: The origin and evolution of animal cytochrome P450s. Phil. Trans. R. Soc. B 2013, 368, 20120474, doi:10.1098/rstb.2012.0474.
[96]  Guengerich, F.P. Chapter 10 (6.45). In Cytochrome P450: Structure, Mechanism, and Biochemistry, 2nd ed.; Ortiz de Montellano, P.R., Ed.; Plenum Press: New York, NY, USA, 1995; pp. 450–452.
[97]  Shaik, S.; Kumar, D.; de Visser, S.P.; Altun, A.; Thiel, W. Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. Chem. Rev. 2005, 105, 2279–2328, doi:10.1021/cr030722j.
[98]  Rittle, J.; Green, M.T. Cytochrome P450 Compound I: Capture, characterization, and C-H Bond activation kinetics. Science 2010, 330, 933–937, doi:10.1126/science.1193478.
[99]  De Visser, S.P.; Ogliaro, F.; Sharma, P.K.; Shaik, S. Hydrogen bonding modulates the selectivity of enzymatic oxidation by P450: A chameleon oxidant behavior by compound I. Angew. Chem. Int. Ed. 2002, 41, 1947–1951, doi:10.1002/1521-3773(20020603)41:11<1947::AID-ANIE1947>3.0.CO;2-W.
[100]  De Visser, S.P.; Ogliaro, F.; Sharma, P.K.; Shaik, S. What factors affect the regioselectivity of oxidation by cytochrome p450? A DFT study of allylic hydroxylation and double bond epoxidation in a model reaction. J. Am. Chem. Soc. 2002, 124, 11809–11826, doi:10.1021/ja026872d.
[101]  Ogliaro, F.; Cohen, S.; de Visser, S.P.; Shaik, S. Medium polarization and hydrogen bonding effects on compound I of cytochrome P450: What kind of a radical it really is? J. Am. Chem. Soc. 2000, 122, 12892–12893, doi:10.1021/ja005619f.
[102]  Lonsdale, R.; Oláh, J.; Mulholland, A.J.; Harvey, J.N. Does compound I vary significantly between isoforms of cytochrome P450? J. Am. Chem. Soc. 2011, 133, 15464–15474, doi:10.1021/ja203157u.
[103]  Schmider, J.; Greenblatt, D.J.; Fogelman, S.M.; von Moltke, L.L.; Shader, R.I. Metabolism of dextromethorphan in vitro: Involvement of cytochromes P450 2D6 and 3A3/4, with a possible role of 2E1. Biopharm. Drug. Dispos. 1997, 18, 227–240, doi:10.1002/(SICI)1099-081X(199704)18:3<227::AID-BDD18>3.0.CO;2-L.
[104]  Daly, J. Metabolism of acetanilides and anisoles with rat liver microsomes. Biochem. Pharmacol. 1970, 19, 2979–2993, doi:10.1016/0006-2952(70)90084-5.
[105]  Bray, H.G.; James, S.P.; Thorpe, W.V.; Wasdell, M.R. The metabolism of ethers in the rabbit. 1. anisole and diphenyl ether. Biochem. J. 1953, 54, 547–551.
[106]  Olsen, L.; Rydberg, P.; Rod, T.H.; Ryde, U. Prediction of activation energies for hydrogen abstraction by cytochrome P450. J. Med. Chem. 2006, 49, 6489–6499, doi:10.1021/jm060551l.
[107]  Oláh, J.; Mulholland, A.J.; Harvey, J.N. Determinants of selectivity in drug metabolism by cytochrome P450: QM/MM modeling of dextromethorphan oxidation by CYP2D6. Proc. Natl. Acad. Sci. USA 2011, 108, 6050–6055.
[108]  Ingelman-Sundberg, M. Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): Clinical consequences, evolutionary aspects and functional diversity. Pharmacogenomics J. 2005, 5, 6–13, doi:10.1038/sj.tpj.6500285.
[109]  Rowland, P.; Blaney, F.E.; Smyth, M.G.; Jones, J.J.; Leydon, V.R.; Oxbrow, A.K.; Lewis, C.J.; Tennant, M.G.; Modi, S.; Eggleston, D.S.; et al. Crystal structure of human cytochrome P450 2D6. J. Biol. Chem. 2006, 281, 7614–7622, doi:10.1074/jbc.M511232200.
[110]  McLaughlin, L.A.; Paine, M.J.I.; Kemp, C.A.; Maréchal, J.D.; Flanagan, J.U.; Ward, R.; Sutcliffe, M.J.; Roberts, G.C.K.; Wolf, C.R. Why is quinidine an inhibitor of cytochrome P450 2D6? The role of key active-site residues in quinidine binding. J. Biol. Chem. 2005, 280, 38617–38624, doi:10.1074/jbc.M505974200.
[111]  Flanagan, J.U.; Maréchal, J.D.; Ward, R.; Kemp, C.A.; McLaughlin, L.A.; Sutcliffe, M.J.; Roberts, G.C.K.; Paine, M.J.I.; Wolf, C.R. Phe120 contributes to the regiospecificity of cytochrome P450 2D6: Mutation leads to the formation of a novel dextromethorphan. Biochem. J. 2004, 380, 353–360, doi:10.1042/BJ20040062.
[112]  Lonsdale, R.; Houghton, K.T.; ?urek, J.; Bathelt, C.M.; Foloppe, N.; de Groot, M.J.; Harvey, J.N.; Mulholland, A.J. Quantum mechanics/molecular mechanics modeling of regioselectivity of drug metabolism in cytochrome P450 2C9. J. Am. Chem. Soc. 2013, 135, 8001–8015, doi:10.1021/ja402016p.
[113]  Zhang, L.; Kudo, T.; Takaya, N.; Shoun, H. The B′ helix determines cytochrome P450nor specificity for the electron donors NADH and NADPH. J. Biol. Chem. 2002, 277, 33842–33847.
[114]  De Vries, S.; Schr?der, I. Comparison between the nitric oxide reductase family and its aerobic relatives, the cytochrome oxidases. Biochem. Soc. Trans. 2002, 30, 662–667.
[115]  Richardson, D.; Felgate, H.; Watmough, N.; Thomson, A.; Baggs, E. Mitigating release of the potent greenhouse gas N(2)O from the nitrogen cycle - could enzymic regulation hold the key? Trends Biotechnol. 2009, 27, 388–397, doi:10.1016/j.tibtech.2009.03.009.
[116]  Wink, D.A.; Hines, H.B.; Cheng, R.Y.S.; Switzer, C.H.; Flores-Santana, W.; Vitek, M.P.; Ridnour, L.A.; Colton, C.A.J. Nitric oxide and redox mechanisms in the immune response. Leukocyte Biol. 2011, 89, 873–891, doi:10.1189/jlb.1010550.
[117]  Chao, L.Y.; Rine, J.; Marletta, M.A. Spectroscopic and kinetic studies of nor1, a cytochrome p450 nitric oxide reductase from the fungal pathogen Histoplasma capsulatum. Arch. Biochem. Biophys. 2008, 480, 132–137, doi:10.1016/j.abb.2008.09.001.
[118]  Shiro, Y.; Fujii, M.; Iizuka, T.; Adachi, S.; Tsukamoto, K.; Nakahara, K.; Shoun, H. Spectroscopic and kinetic studies on reaction of cytochrome P450nor with nitric oxide. Implication for its nitric oxide reduction mechanism. J. Biol. Chem. 1995, 270, 1617–1623.
[119]  Harris, D.L. Cytochrome P450nor: A nitric oxide reductase - structure, spectra, and mechanism. Int. J. Quantum Chem. 2002, 288, 183–200, doi:10.1002/qua.10111.
[120]  Tsukamoto, K.; Nakamura, S.; Shimizu, K. SAM1 semiempirical calculations on the catalytic cycle of nitric oxide reductase from Fusarium oxysporum. J. Mol. Struct. (THEOCHEM) 2003, 624, 309–322, doi:10.1016/S0166-1280(03)00003-4.
[121]  Averill, B.A. Dissimilatory nitrite and nitric oxide reductases. Chem. Rev. 1996, 96, 2951–2964, doi:10.1021/cr950056p.
[122]  Daiber, A.; Nauser, T.; Takaya, N.; Kudo, T.; Weber, P.; Hultschig, C.; Shoun, H.; Ullrich, V. Isotope effects and intermediates in the reduction of NO by P450NOR. J. Inorg. Biochem. 2002, 88, 343–352, doi:10.1016/S0162-0134(01)00386-5.
[123]  Lehnert, N.; Praneeth, V.K.K.; Paulat, F. Electronic structure of Fe(II)-porphyrin nitroxyl complexes: Molecular mechanism of fungal nitric oxide reductase (P450nor). J. Comput. Chem. 2006, 27, 1338–1351, doi:10.1002/jcc.20400.
[124]  Krámos, B.; Menyhárd, D.K.; Oláh, J. Direct hydride shift mechanism and stereoselectivity of P450nor confirmed by QM/MM calculations. J. Phys. Chem. B 2012, 116, 872–885, doi:10.1021/jp2080918.
[125]  Suzuki, N.; Higuchi, T.; Urano, Y.; Kikuchi, K.; Uchida, T.; Mukai, M.; Kitagawa, T.; Nagano, T. First synthetic no-heme-thiolate complex relevant to nitric oxide synthase and cytochrome P450nor. J. Am. Chem. Soc. 2000, 122, 12059–12060, doi:10.1021/ja005670j.
[126]  Shimizu, H.; Obayashi, E.; Gomi, Y.; Arakawa, H.; Park, S.Y.; Nakamura, H.; Adachi, S.; Shoun, H.; Shiro, Y. Proton delivery in no reduction by fungal nitric-oxide reductase. cryogenic crystallography, spectroscopy, and kinetics of ferric-no complexes of wild-type and mutant enzymes. J. Biol. Chem. 2000, 275, 4816–4826, doi:10.1074/jbc.275.7.4816.
[127]  Menyhárd, D.K.; Keser?, G.M. Binding mode analysis of the NADH cofactor in nitric oxide reductase: A theoretical study. J. Mol. Graphics Model. 2006, 25, 363–372, doi:10.1016/j.jmgm.2006.02.003.
[128]  Oshima, R.; Fushinobu, S.; Su, F.; Zhang, L.; Takaya, N.; Shoun, H. Structural evidence for direct hydride transfer from NADH to cytochrome P450nor. J. Mol. Biol. 2004, 342, 207–217, doi:10.1016/j.jmb.2004.07.009.
[129]  Riplinger, C.; Neese, F. The reaction mechanism of cytochrome P450 NO reductase: A detailed quantum mechanics/molecular mechanics study. ChemPhysChem 2011, 12, 3192–3203, doi:10.1002/cphc.201100523.
[130]  Callens, M.; Tomme, P.; Kerstens-Hilderson, H.; Cornelis, W.; Vangrysperre, W.; de Bruyne, C.K. Metal ion binding to d-xylose isomerase from streptomyces violaceoruber. Biochem. J. 1988, 250, 285–291.
[131]  Farber, G.K.; Machin, P.; Almo, S.C.; Petsko, G.A.; Hajdu, J. X-ray laue diffraction from crystals of xylose isomerase. Proc. Natl. Acad. Sci. USA 1988, 85, 112–118, doi:10.1073/pnas.85.1.112.
[132]  Collyer, C.A.; Henrick, K.; Blow, D.M. Mechanism for aldose-ketose interconversion by D-Xylose isomerase involving ring opening followed by a 1,2-hydride shift. J. Mol. Biol. 1990, 212, 211–235, doi:10.1016/0022-2836(90)90316-E.
[133]  Jenkins, J.; Janin, J.; Rey, F.; Chidmi, M.; Tilbeurgh, H.; Lasters, I.; Maeyer, M.; Belle, D.; Wodak, S.; Lauwereys, M.; et al. Protein engineering of xylose (Glucose) isomerase from actinoplanes missouriensis. 1. Crystallography and site-directed mutagenesis of metal binding sites. Biochemistry 1992, 31, 5449–5458, doi:10.1021/bi00139a005.
[134]  Hu, H.; Liu, H.; Shi, Y. The reaction pathway of the isomerization of d-xylose catalyzed by the enzyme d-xylose isomerase: A theoretical study. Proteins Struct. Funct. Genet. 1997, 27, 545–555, doi:10.1002/(SICI)1097-0134(199704)27:4<545::AID-PROT7>3.0.CO;2-9.
[135]  Fuxreiter, M.; Farkas, ?.; Náray-Szabó, G. Molecular modeling of xylose isomerase catalysis: The role of electrostatics and charge transfer to metals. Protein Eng. 1995, 8, 925–933, doi:10.1093/protein/8.9.925.
[136]  Fábián, P.; Asbóth, B.; Náray-Szabó, G. The role of electrostatics in the ring-opening step of xylose isomerase catalysis. J. Mol. Struct. Theochem. 1994, 307, 171–178, doi:10.1016/0166-1280(94)80126-6.
[137]  Lambeir, A.M.; Lauwereys, M.; Stanssens, P.; Mrabet, N.T.; Snauwaert, J.; van Tilbeurgh, H.; Matthyssens, G.; Lasters, I.; de Maeyer, M.; Wodak, S.J.; et al. Protein engineering of xylose (glucose) isomerase from actinoplanes missouriensis. 3. Changing metal specificity and the PH profile by site-directed mutagenesis. Biochemistry 1992, 31, 5459–5466, doi:10.1021/bi00139a006.
[138]  Garcia-Viloca, M.; Alhambra, C.; Truhlar, D.G.; Gao, J. Quantum dynamics of hydride transfer catalyzed by bimetallic electrophilic catalysis: Synchronous motion of Mg2+ and H- in xylose isomerase. J. Am. Chem. Soc. 2002, 124, 7268–7269, doi:10.1021/ja026383d.
[139]  Garcia-Viloca, M.; Alhambra, C.; Truhlar, D.G.; Gao, J. Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects. J. Comput. Chem. 2003, 24, 177–190, doi:10.1002/jcc.10154.
[140]  Masgrau, L.; Roujeinikova, A.; Johannissen, L.O.; Hothi, P.; Basran, J.; Ranaghan, K.E.; Mulholland, A.J.; Sutcliffe, M.J.; Scrutton, N.S.; Leys, D. Atomic description of an enzyme reaction dominated by proton tunneling. Science 2006, 312, 237–241, doi:10.1126/science.1126002.
[141]  Iyengar, S.S.; Sumner, I.; Jakowski, J. Hydrogen tunneling in an enzyme active site: A quantum wavepacket dynamical perspective. J. Phys. Chem. B 2008, 112, 7601–7613, doi:10.1021/jp7103215.

Full-Text

Contact Us

[email protected]

QQ:3279437679

WhatsApp +8615387084133