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Volumn 11, Issue 2, 2007, Pages 182-187

QM/MM studies of enzymes

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; OXIDOREDUCTASE;

EID: 34047191046     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2007.01.684     Document Type: Review
Times cited : (328)

References (52)
  • 1
    • 0017100947 scopus 로고
    • Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
    • Warshel A., and Levitt M. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103 (1976) 227-249
    • (1976) J Mol Biol , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 2
    • 21244497608 scopus 로고    scopus 로고
    • Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
    • Compact overview of QM, MM and QM/MM methodology with detailed discussion of selected QM/MM applications to enzymatic reactions. The authors also discuss the understanding of enzyme catalysis and the performance of QM/MM models in general.
    • Friesner R.A., and Guallar V. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Annu Rev Phys Chem 56 (2005) 389-427. Compact overview of QM, MM and QM/MM methodology with detailed discussion of selected QM/MM applications to enzymatic reactions. The authors also discuss the understanding of enzyme catalysis and the performance of QM/MM models in general.
    • (2005) Annu Rev Phys Chem , vol.56 , pp. 389-427
    • Friesner, R.A.1    Guallar, V.2
  • 3
    • 33748608826 scopus 로고    scopus 로고
    • Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency
    • Bruice T.C. Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency. Chem Rev 106 (2006) 3119-3139
    • (2006) Chem Rev , vol.106 , pp. 3119-3139
    • Bruice, T.C.1
  • 5
    • 33846570818 scopus 로고    scopus 로고
    • Lin H, Truhlar DG: QM/MM: what have we learned, where are we, and where do we go from here? Theor Chem Acc, Epub ahead of print, DOI:10.1007/s00214-006-0143-z. Succinct review of current methodological issues of the QM/MM approach.
  • 6
    • 34047178059 scopus 로고    scopus 로고
    • Senn HM, Thiel W: QM/MM methods for biological systems. In Atomistic Approaches in Modern Biology. (Topics in Current Chemistry, Vol 268). Edited by Reiher M. Berlin: Springer; 2007:173-290. Extensive review of the state of the art of the QM/MM method, including its use in optimization and simulation schemes. Tabular survey of biomolecular applications covering the period 2000 to mid-2006.
  • 7
    • 0346726109 scopus 로고    scopus 로고
    • How enzymes work: analysis by modern rate theory and computer simulations
    • Garcia-Viloca M., Gao J., Karplus M., and Truhlar D.G. How enzymes work: analysis by modern rate theory and computer simulations. Science 303 (2004) 186-195
    • (2004) Science , vol.303 , pp. 186-195
    • Garcia-Viloca, M.1    Gao, J.2    Karplus, M.3    Truhlar, D.G.4
  • 8
    • 33748633480 scopus 로고    scopus 로고
    • Electrostatic basis for enzyme catalysis
    • Systematic presentation of the arguments supporting the concept of electrostatic transition-state stabilization to rationalize enzyme catalysis. Alternative proposals are summarized and held against transition-state stabilization.
    • Warshel A., Sharma P.K., Kato M., Xiang Y., Liu H., and Olsson M.H.M. Electrostatic basis for enzyme catalysis. Chem Rev 106 (2006) 3210-3235. Systematic presentation of the arguments supporting the concept of electrostatic transition-state stabilization to rationalize enzyme catalysis. Alternative proposals are summarized and held against transition-state stabilization.
    • (2006) Chem Rev , vol.106 , pp. 3210-3235
    • Warshel, A.1    Sharma, P.K.2    Kato, M.3    Xiang, Y.4    Liu, H.5    Olsson, M.H.M.6
  • 9
    • 19944408652 scopus 로고    scopus 로고
    • A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method
    • König P.H., Hoffmann M., Frauenheim T., and Cui Q. A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method. J Phys Chem B 109 (2005) 9082-9095
    • (2005) J Phys Chem B , vol.109 , pp. 9082-9095
    • König, P.H.1    Hoffmann, M.2    Frauenheim, T.3    Cui, Q.4
  • 10
    • 18844410543 scopus 로고    scopus 로고
    • Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations
    • Lin H., and Truhlar D.G. Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations. J Phys Chem A 109 (2005) 3991-4004
    • (2005) J Phys Chem A , vol.109 , pp. 3991-4004
    • Lin, H.1    Truhlar, D.G.2
  • 11
    • 19944369519 scopus 로고    scopus 로고
    • An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations
    • Nam K., Gao J., and York D.M. An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations. J Chem Theory Comput 1 (2005) 2-13
    • (2005) J Chem Theory Comput , vol.1 , pp. 2-13
    • Nam, K.1    Gao, J.2    York, D.M.3
  • 12
    • 34548059996 scopus 로고    scopus 로고
    • Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
    • 014905/1-14
    • Schaefer P., Riccardi D., and Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys 123 (2005) 014905/1-14
    • (2005) J Chem Phys , vol.123
    • Schaefer, P.1    Riccardi, D.2    Cui, Q.3
  • 13
    • 25844473576 scopus 로고    scopus 로고
    • a calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols
    • a calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols. J Phys Chem B 109 (2005) 17715-17733
    • (2005) J Phys Chem B , vol.109 , pp. 17715-17733
    • Riccardi, D.1    Schaefer, P.2    Cui, Q.3
  • 14
    • 33646205963 scopus 로고    scopus 로고
    • An efficient real space multigrid QM/MM electrostatic coupling
    • Laino T., Mohamed F., Laio A., and Parrinello M. An efficient real space multigrid QM/MM electrostatic coupling. J Chem Theory Comput 1 (2005) 1176-1184
    • (2005) J Chem Theory Comput , vol.1 , pp. 1176-1184
    • Laino, T.1    Mohamed, F.2    Laio, A.3    Parrinello, M.4
  • 15
    • 33846359282 scopus 로고    scopus 로고
    • An efficient linear-scaling electrostatic coupling for treating periodic boundary conditions in QM/MM simulations
    • Laino T., Mohamed F., Laio A., and Parrinello M. An efficient linear-scaling electrostatic coupling for treating periodic boundary conditions in QM/MM simulations. J Chem Theory Comput 2 (2006) 1370-1378
    • (2006) J Chem Theory Comput , vol.2 , pp. 1370-1378
    • Laino, T.1    Mohamed, F.2    Laio, A.3    Parrinello, M.4
  • 17
    • 15844379169 scopus 로고    scopus 로고
    • Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA
    • Banerjee A., Yang W., Karplus M., and Verdine G.L. Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434 (2005) 612-618
    • (2005) Nature , vol.434 , pp. 612-618
    • Banerjee, A.1    Yang, W.2    Karplus, M.3    Verdine, G.L.4
  • 19
    • 33748283200 scopus 로고    scopus 로고
    • The SCC-DFTB method and its application to biological systems
    • Elstner M. The SCC-DFTB method and its application to biological systems. Theor Chem Acc 116 (2006) 316-325
    • (2006) Theor Chem Acc , vol.116 , pp. 316-325
    • Elstner, M.1
  • 20
    • 33750478314 scopus 로고    scopus 로고
    • High-accuracy computation of reaction barriers in enzymes
    • Demonstration of the use of modern correlated ab initio methods in QM/MM calculations of enzymatic reaction barriers. LCCSD(T0) yields essentially chemical accuracy for the enzymes chorismate mutase and p-hydroxybenzoate hydroxylase.
    • Claeyssens F., Harvey J.N., Manby F.R., Mata R.A., Mulholland A.J., Ranaghan K.E., Schütz M., Thiel S., Thiel W., and Werner H.-J. High-accuracy computation of reaction barriers in enzymes. Angew Chem Int Ed 45 (2006) 6856-6859. Demonstration of the use of modern correlated ab initio methods in QM/MM calculations of enzymatic reaction barriers. LCCSD(T0) yields essentially chemical accuracy for the enzymes chorismate mutase and p-hydroxybenzoate hydroxylase.
    • (2006) Angew Chem Int Ed , vol.45 , pp. 6856-6859
    • Claeyssens, F.1    Harvey, J.N.2    Manby, F.R.3    Mata, R.A.4    Mulholland, A.J.5    Ranaghan, K.E.6    Schütz, M.7    Thiel, S.8    Thiel, W.9    Werner, H.-J.10
  • 21
    • 2442573648 scopus 로고    scopus 로고
    • Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes
    • Xie L., Liu H., and Yang W. Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes. J Chem Phys 120 (2004) 8039-8052
    • (2004) J Chem Phys , vol.120 , pp. 8039-8052
    • Xie, L.1    Liu, H.2    Yang, W.3
  • 22
    • 3242703331 scopus 로고    scopus 로고
    • Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions
    • Liu H., Lu Z., Cisneros G.A., and Yang W. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions. J Chem Phys 121 (2004) 697-706
    • (2004) J Chem Phys , vol.121 , pp. 697-706
    • Liu, H.1    Lu, Z.2    Cisneros, G.A.3    Yang, W.4
  • 23
    • 18644375413 scopus 로고    scopus 로고
    • Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order 'chain-of-replicas' methods
    • 114502/1-7
    • Cisneros G.A., Liu H., Lu Z., and Yang W. Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order 'chain-of-replicas' methods. J Chem Phys (2005) 122 114502/1-7
    • (2005) J Chem Phys , pp. 122
    • Cisneros, G.A.1    Liu, H.2    Lu, Z.3    Yang, W.4
  • 24
    • 3142736515 scopus 로고    scopus 로고
    • Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations
    • Lu Z., and Yang W. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations. J Chem Phys 121 (2004) 89-100
    • (2004) J Chem Phys , vol.121 , pp. 89-100
    • Lu, Z.1    Yang, W.2
  • 25
    • 0000145441 scopus 로고    scopus 로고
    • Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface
    • Zhang Y., Liu H., and Yang W. Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface. J Chem Phys 112 (2000) 3483-3492
    • (2000) J Chem Phys , vol.112 , pp. 3483-3492
    • Zhang, Y.1    Liu, H.2    Yang, W.3
  • 26
    • 85051912728 scopus 로고    scopus 로고
    • Quantum mechanical free energy barrier for an enzymatic reaction
    • 138302/1-4
    • Rod T.H., and Ryde U. Quantum mechanical free energy barrier for an enzymatic reaction. Phys Rev Lett 94 (2005) 138302/1-4
    • (2005) Phys Rev Lett , vol.94
    • Rod, T.H.1    Ryde, U.2
  • 27
    • 33646508010 scopus 로고    scopus 로고
    • Accurate QM/MM free energy calculations of enzyme reactions: methylation by catechol O-methyltransferase
    • Rod T.H., and Ryde U. Accurate QM/MM free energy calculations of enzyme reactions: methylation by catechol O-methyltransferase. J Chem Theory Comput 1 (2005) 1240-1251
    • (2005) J Chem Theory Comput , vol.1 , pp. 1240-1251
    • Rod, T.H.1    Ryde, U.2
  • 28
    • 33745294923 scopus 로고    scopus 로고
    • QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling: application to an enzymatic reaction
    • Kästner J., Senn H.M., Thiel S., Otte N., and Thiel W. QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling: application to an enzymatic reaction. J Chem Theory Comput 2 (2006) 452-461
    • (2006) J Chem Theory Comput , vol.2 , pp. 452-461
    • Kästner, J.1    Senn, H.M.2    Thiel, S.3    Otte, N.4    Thiel, W.5
  • 29
    • 0036667496 scopus 로고    scopus 로고
    • Quantum chemical geometry optimizations in proteins using crystallographic raw data
    • Ryde U., Olsen L., and Nilsson K. Quantum chemical geometry optimizations in proteins using crystallographic raw data. J Comput Chem 23 (2002) 1058-1070
    • (2002) J Comput Chem , vol.23 , pp. 1058-1070
    • Ryde, U.1    Olsen, L.2    Nilsson, K.3
  • 30
    • 33745727307 scopus 로고    scopus 로고
    • Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach
    • Rulíšek L., and Ryde U. Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach. J Phys Chem B 110 (2006) 11511-11518
    • (2006) J Phys Chem B , vol.110 , pp. 11511-11518
    • Rulíšek, L.1    Ryde, U.2
  • 32
    • 32544451640 scopus 로고    scopus 로고
    • Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods
    • Hsiao Y.-W., and Ryde U. Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods. Inorg Chim Acta 359 (2006) 1081-1092
    • (2006) Inorg Chim Acta , vol.359 , pp. 1081-1092
    • Hsiao, Y.-W.1    Ryde, U.2
  • 33
    • 33751504561 scopus 로고    scopus 로고
    • Assigning the protonation states of the key aspartates in β-secretase using QM/MM X-ray structure refinement
    • Yu N., Hayik S.A., Wang B., Liao N., Reynolds C.H., and Merz Jr. K.M. Assigning the protonation states of the key aspartates in β-secretase using QM/MM X-ray structure refinement. J Chem Theory Comput 2 (2006) 1057-1069
    • (2006) J Chem Theory Comput , vol.2 , pp. 1057-1069
    • Yu, N.1    Hayik, S.A.2    Wang, B.3    Liao, N.4    Reynolds, C.H.5    Merz Jr., K.M.6
  • 34
    • 2342565009 scopus 로고    scopus 로고
    • Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction
    • Ranaghan K.E., Ridder L., Szefczyk B., Sokalski W.A., Hermann J.C., and Mulholland A.J. Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction. Org Biomol Chem 2 (2004) 968-980
    • (2004) Org Biomol Chem , vol.2 , pp. 968-980
    • Ranaghan, K.E.1    Ridder, L.2    Szefczyk, B.3    Sokalski, W.A.4    Hermann, J.C.5    Mulholland, A.J.6
  • 35
    • 2942739060 scopus 로고    scopus 로고
    • Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase
    • Ranaghan K.E., and Mulholland A.J. Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase. Chem Commun (2004) 1238-1239
    • (2004) Chem Commun , pp. 1238-1239
    • Ranaghan, K.E.1    Mulholland, A.J.2
  • 36
    • 10344265555 scopus 로고    scopus 로고
    • Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field
    • Szefczyk B., Mulholland A.J., Ranaghan K.E., and Sokalski W.A. Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field. J Am Chem Soc 126 (2004) 16148-16159
    • (2004) J Am Chem Soc , vol.126 , pp. 16148-16159
    • Szefczyk, B.1    Mulholland, A.J.2    Ranaghan, K.E.3    Sokalski, W.A.4
  • 37
    • 27644492410 scopus 로고    scopus 로고
    • Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization
    • Multiple reaction profiles obtained at the B3LYP/CHARMM level support the concept of transition-state stabilization for the Claisen rearrangement in chorismate mutase.
    • Claeyssens F., Ranaghan K.E., Manby F.R., Harvey J.N., and Mulholland A.J. Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization. Chem Commun (2005) 5068-5070. Multiple reaction profiles obtained at the B3LYP/CHARMM level support the concept of transition-state stabilization for the Claisen rearrangement in chorismate mutase.
    • (2005) Chem Commun , pp. 5068-5070
    • Claeyssens, F.1    Ranaghan, K.E.2    Manby, F.R.3    Harvey, J.N.4    Mulholland, A.J.5
  • 38
    • 23244446189 scopus 로고    scopus 로고
    • A definitive mechanism for chorismate mutase
    • Zhang X., Zhang X., and Bruice T.C. A definitive mechanism for chorismate mutase. Biochemistry 44 (2005) 10443-10448
    • (2005) Biochemistry , vol.44 , pp. 10443-10448
    • Zhang, X.1    Zhang, X.2    Bruice, T.C.3
  • 39
    • 33645979392 scopus 로고    scopus 로고
    • The catalytic power of enzymes: conformational selection or transition state stabilization?
    • A kinetic view on enzyme catalysis. Catalytic proposals are connected with kinetic expressions representing the effect of conformational states and the rate constants in the enzyme and in solution. Chorismate mutase serves as illustrative example.
    • Giraldo J., Roche D., Rovira X., and Serra J. The catalytic power of enzymes: conformational selection or transition state stabilization?. FEBS Lett 580 (2006) 2170-2177. A kinetic view on enzyme catalysis. Catalytic proposals are connected with kinetic expressions representing the effect of conformational states and the rate constants in the enzyme and in solution. Chorismate mutase serves as illustrative example.
    • (2006) FEBS Lett , vol.580 , pp. 2170-2177
    • Giraldo, J.1    Roche, D.2    Rovira, X.3    Serra, J.4
  • 40
    • 21944432511 scopus 로고    scopus 로고
    • Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes
    • Comprehensive review.
    • Shaik S., Kumar D., de Visser S.P., Altun A., and Thiel W. Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. Chem Rev 105 (2005) 2279-2328. Comprehensive review.
    • (2005) Chem Rev , vol.105 , pp. 2279-2328
    • Shaik, S.1    Kumar, D.2    de Visser, S.P.3    Altun, A.4    Thiel, W.5
  • 42
    • 3142761726 scopus 로고    scopus 로고
    • Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study
    • Guallar V., and Friesner R.A. Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study. J Am Chem Soc 126 (2004) 8501-8508
    • (2004) J Am Chem Soc , vol.126 , pp. 8501-8508
    • Guallar, V.1    Friesner, R.A.2
  • 44
    • 33747153306 scopus 로고    scopus 로고
    • Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor
    • Technically detailed report highlighting the possible pitfalls in QM/MM studies on enzyme reactivity.
    • Altun A., Shaik S., and Thiel W. Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor. J Comput Chem 27 (2006) 1324-1337. Technically detailed report highlighting the possible pitfalls in QM/MM studies on enzyme reactivity.
    • (2006) J Comput Chem , vol.27 , pp. 1324-1337
    • Altun, A.1    Shaik, S.2    Thiel, W.3
  • 45
    • 33749520822 scopus 로고    scopus 로고
    • QM/MM study of mechanisms for Compound I formation in the catalytic cycle of cytochrome P450cam
    • Zheng J., Wang D., Thiel W., and Shaik S. QM/MM study of mechanisms for Compound I formation in the catalytic cycle of cytochrome P450cam. J Am Chem Soc 128 (2006) 13204-13215
    • (2006) J Am Chem Soc , vol.128 , pp. 13204-13215
    • Zheng, J.1    Wang, D.2    Thiel, W.3    Shaik, S.4
  • 46
    • 25144520939 scopus 로고    scopus 로고
    • Electronic structure of Compound I in human isoforms of cytochrome P450 from QM/MM modeling
    • Bathelt C.M., Zurek J., Mulholland A.J., and Harvey J.N. Electronic structure of Compound I in human isoforms of cytochrome P450 from QM/MM modeling. J Am Chem Soc 127 (2005) 12900-12908
    • (2005) J Am Chem Soc , vol.127 , pp. 12900-12908
    • Bathelt, C.M.1    Zurek, J.2    Mulholland, A.J.3    Harvey, J.N.4
  • 47
    • 33644648714 scopus 로고    scopus 로고
    • In silico design of a mutant of cytochrome P450 containing selenocysteine
    • Cohen S., Kumar D., and Shaik S. In silico design of a mutant of cytochrome P450 containing selenocysteine. J Am Chem Soc 128 (2006) 2649-2653
    • (2006) J Am Chem Soc , vol.128 , pp. 2649-2653
    • Cohen, S.1    Kumar, D.2    Shaik, S.3
  • 48
    • 1842502916 scopus 로고    scopus 로고
    • Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis isomerization of the chromophore in the protein
    • The excited-states dynamics of the photoactivated trans-to-cis isomerization of the PYP chromophore is investigated at the CASSCF/MM level using a surface-hopping algorithm. The reactivity after the photoevent is followed with classical MD and semi-empirical QM/MM. Results include quantum yields, fluorescence lifetimes and mechanistic insights, such as the preferential electrostatic stabilization of the chromophore's excited state in the active site.
    • Groenhof G., Bouxin-Cademartory M., Hess B., de Visser S.P., Berendsen H.J.C., Olivucci M., Mark A.E., and Robb M.A. Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis isomerization of the chromophore in the protein. J Am Chem Soc 126 (2004) 4228-4233. The excited-states dynamics of the photoactivated trans-to-cis isomerization of the PYP chromophore is investigated at the CASSCF/MM level using a surface-hopping algorithm. The reactivity after the photoevent is followed with classical MD and semi-empirical QM/MM. Results include quantum yields, fluorescence lifetimes and mechanistic insights, such as the preferential electrostatic stabilization of the chromophore's excited state in the active site.
    • (2004) J Am Chem Soc , vol.126 , pp. 4228-4233
    • Groenhof, G.1    Bouxin-Cademartory, M.2    Hess, B.3    de Visser, S.P.4    Berendsen, H.J.C.5    Olivucci, M.6    Mark, A.E.7    Robb, M.A.8
  • 49
    • 23944508561 scopus 로고    scopus 로고
    • Properties of the emitting state of the green fluorescent protein resolved at the CASPT2//CASSCF/CHARMM level
    • Sinicropi A., Andruniow T., Ferré N., Basosi R., and Olivucci M. Properties of the emitting state of the green fluorescent protein resolved at the CASPT2//CASSCF/CHARMM level. J Am Chem Soc 127 (2005) 11534-11535
    • (2005) J Am Chem Soc , vol.127 , pp. 11534-11535
    • Sinicropi, A.1    Andruniow, T.2    Ferré, N.3    Basosi, R.4    Olivucci, M.5
  • 51
    • 33747189732 scopus 로고    scopus 로고
    • QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study
    • Sinnecker S., and Neese F. QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study. J Comput Chem 27 (2006) 1463-1475
    • (2006) J Comput Chem , vol.27 , pp. 1463-1475
    • Sinnecker, S.1    Neese, F.2
  • 52
    • 17744364713 scopus 로고    scopus 로고
    • Toward identification of the Compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters
    • Schöneboom J.C., Neese F., and Thiel W. Toward identification of the Compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters. J Am Chem Soc 127 (2005) 5840-5853
    • (2005) J Am Chem Soc , vol.127 , pp. 5840-5853
    • Schöneboom, J.C.1    Neese, F.2    Thiel, W.3


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