메뉴 건너뛰기




Volumn 11, Issue 2, 2007, Pages 174-181

Ultrafast catalytic processes in enzymes

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBODIPYRIMIDINE PHOTOLYASE; OXIDOREDUCTASE; PROTOCHLOROPHYLLIDE;

EID: 34047267978     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2007.02.034     Document Type: Review
Times cited : (51)

References (50)
  • 1
    • 33646754084 scopus 로고    scopus 로고
    • 4D ultrafast electron diffraction, crystallography, and microscopy
    • An excellent review of recent breakthroughs in concepts, methodologies and prototypical applications for the development of ultrafast electron techniques. This 4D-resolved method can potentially revolutionize the field of biological dynamics.
    • Zewail A.H. 4D ultrafast electron diffraction, crystallography, and microscopy. Annu Rev Phys Chem 57 (2006) 65-103. An excellent review of recent breakthroughs in concepts, methodologies and prototypical applications for the development of ultrafast electron techniques. This 4D-resolved method can potentially revolutionize the field of biological dynamics.
    • (2006) Annu Rev Phys Chem , vol.57 , pp. 65-103
    • Zewail, A.H.1
  • 2
    • 33748610523 scopus 로고    scopus 로고
    • Advances in time-resolved approaches to characterize the dynamical nature of enzymatic catalysis
    • Callender R., and Dyer R.B. Advances in time-resolved approaches to characterize the dynamical nature of enzymatic catalysis. Chem Rev 106 (2006) 3031-3042
    • (2006) Chem Rev , vol.106 , pp. 3031-3042
    • Callender, R.1    Dyer, R.B.2
  • 3
    • 33748619206 scopus 로고    scopus 로고
    • An NMR perspective on enzyme dynamics
    • Boehr D.D., Dyson H.J., and Wright P.E. An NMR perspective on enzyme dynamics. Chem Rev 106 (2006) 3055-3079
    • (2006) Chem Rev , vol.106 , pp. 3055-3079
    • Boehr, D.D.1    Dyson, H.J.2    Wright, P.E.3
  • 4
    • 12944327750 scopus 로고    scopus 로고
    • Energy landscapes and solved protein-folding problems
    • Wolynes P.G. Energy landscapes and solved protein-folding problems. Philos Transact A Math Phys Eng Sci 363 (2005) 453-464
    • (2005) Philos Transact A Math Phys Eng Sci , vol.363 , pp. 453-464
    • Wolynes, P.G.1
  • 5
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H., Sligar S.G., and Wolynes P.G. The energy landscapes and motions of proteins. Science 254 (1991) 1598-1603
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 6
    • 33746325760 scopus 로고    scopus 로고
    • Relating protein motion to catalysis
    • This nice review examines the linkage between protein conformational motions and enzyme catalysis, with focus on the dynamic effect on enzymatic reactions, using two extensively studied dihydrofolate reductase and liver alcohol dehydrogenase as the testing examples. A network of coupled motions in the proteins was found to facilitate the catalytic hydride transfer reaction.
    • Hammes-Schiffer S., and Benkovic S.J. Relating protein motion to catalysis. Annu Rev Biochem 75 (2006) 519-541. This nice review examines the linkage between protein conformational motions and enzyme catalysis, with focus on the dynamic effect on enzymatic reactions, using two extensively studied dihydrofolate reductase and liver alcohol dehydrogenase as the testing examples. A network of coupled motions in the proteins was found to facilitate the catalytic hydride transfer reaction.
    • (2006) Annu Rev Biochem , vol.75 , pp. 519-541
    • Hammes-Schiffer, S.1    Benkovic, S.J.2
  • 7
    • 33748601471 scopus 로고    scopus 로고
    • Tunneling and dynamics in enzymatic hydride transfer
    • Nagel Z.D., and Klinman J.P. Tunneling and dynamics in enzymatic hydride transfer. Chem Rev 106 (2006) 3095-3118
    • (2006) Chem Rev , vol.106 , pp. 3095-3118
    • Nagel, Z.D.1    Klinman, J.P.2
  • 8
    • 27744493897 scopus 로고    scopus 로고
    • Structural observation of the primary isomerization in vision with femtosecond-stimulated Raman
    • Kukura P., McCamant D.W., Yoon S., Wandschneider D.B., and Mathies R.A. Structural observation of the primary isomerization in vision with femtosecond-stimulated Raman. Science 310 (2005) 1006-1009
    • (2005) Science , vol.310 , pp. 1006-1009
    • Kukura, P.1    McCamant, D.W.2    Yoon, S.3    Wandschneider, D.B.4    Mathies, R.A.5
  • 10
    • 0033723528 scopus 로고    scopus 로고
    • Femtochemistry: atomic-scale dynamics of the chemical bond (Nobel lecture)
    • Zewail A.H. Femtochemistry: atomic-scale dynamics of the chemical bond (Nobel lecture). J Phys Chem A 104 (2000) 5660-5694
    • (2000) J Phys Chem A , vol.104 , pp. 5660-5694
    • Zewail, A.H.1
  • 12
    • 14844361989 scopus 로고    scopus 로고
    • NMR studies of protein structure and dynamics
    • Kay L.E. NMR studies of protein structure and dynamics. J Magn Reson 173 (2005) 193-207
    • (2005) J Magn Reson , vol.173 , pp. 193-207
    • Kay, L.E.1
  • 13
    • 33749052948 scopus 로고    scopus 로고
    • Do we live in a quantum world? Advances in multidimensional coherent spectroscopies refine our understanding of quantum coherences and structural dynamics of biological systems
    • Nagy A., Prokhorenko V., and Miller R.J.D. Do we live in a quantum world? Advances in multidimensional coherent spectroscopies refine our understanding of quantum coherences and structural dynamics of biological systems. Curr Opin Struct Biol 16 (2006) 654-663
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 654-663
    • Nagy, A.1    Prokhorenko, V.2    Miller, R.J.D.3
  • 14
    • 0030823063 scopus 로고    scopus 로고
    • Time-resolved mid-infrared spectroscopy: methods and biological applications
    • Slayton R.M., and Anfinrud P.A. Time-resolved mid-infrared spectroscopy: methods and biological applications. Curr Opin Struct Biol 7 (1997) 717-721
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 717-721
    • Slayton, R.M.1    Anfinrud, P.A.2
  • 15
    • 0345082644 scopus 로고
    • Direct observation of the transition state
    • Polanyi J.C., and Zewail A.H. Direct observation of the transition state. Acc Chem Res 28 (1995) 119-132
    • (1995) Acc Chem Res , vol.28 , pp. 119-132
    • Polanyi, J.C.1    Zewail, A.H.2
  • 16
    • 27944458409 scopus 로고    scopus 로고
    • Enzymatic transition states and transition state analogues
    • This excellent review proposes a requirement for dynamic descriptions of enzymatic transition states and asserts that among dynamic stochastic searches the transition state can be achieved by some local motions at the active site coupled to larger scale dynamic modes of proteins.
    • Schramm V.L. Enzymatic transition states and transition state analogues. Curr Opin Struct Biol 15 (2005) 604-613. This excellent review proposes a requirement for dynamic descriptions of enzymatic transition states and asserts that among dynamic stochastic searches the transition state can be achieved by some local motions at the active site coupled to larger scale dynamic modes of proteins.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 604-613
    • Schramm, V.L.1
  • 17
    • 0141448966 scopus 로고    scopus 로고
    • Thermodynamic and extrathermodymic requirements of enzyme catalysis
    • Wolfenden R. Thermodynamic and extrathermodymic requirements of enzyme catalysis. Biophys Chem 105 (2003) 559-572
    • (2003) Biophys Chem , vol.105 , pp. 559-572
    • Wolfenden, R.1
  • 18
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr D.D., McElheny D., Dyson H.J., and Wright P.E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313 (2006) 1638-1642
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 19
    • 33748799981 scopus 로고    scopus 로고
    • Dynamic visions of enzymatic reactions
    • Vendruscolo M., and Dobson C.M. Dynamic visions of enzymatic reactions. Science 313 (2006) 1586-1587
    • (2006) Science , vol.313 , pp. 1586-1587
    • Vendruscolo, M.1    Dobson, C.M.2
  • 20
    • 33646935697 scopus 로고    scopus 로고
    • Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis
    • This nice review emphasizes the importance of electrostatic preorganization at the active site in the stabilization of transition states, and asserts that the catalytic reaction rate is mainly determined by local electrostatics at the critical configuration and that other effects are relatively small.
    • Olsson M.H.M., Parson W.W., and Warshel A. Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem Rev 106 (2006) 1737-1756. This nice review emphasizes the importance of electrostatic preorganization at the active site in the stabilization of transition states, and asserts that the catalytic reaction rate is mainly determined by local electrostatics at the critical configuration and that other effects are relatively small.
    • (2006) Chem Rev , vol.106 , pp. 1737-1756
    • Olsson, M.H.M.1    Parson, W.W.2    Warshel, A.3
  • 21
    • 33748376521 scopus 로고    scopus 로고
    • Protein dynamics and catalysis: the problems of transition state theory and the subtlety of dynamic control
    • Pineda J.R., and Schwartz S.D. Protein dynamics and catalysis: the problems of transition state theory and the subtlety of dynamic control. Philos Trans R Soc Lond B Biol Sci 361 (2006) 1433-1438
    • (2006) Philos Trans R Soc Lond B Biol Sci , vol.361 , pp. 1433-1438
    • Pineda, J.R.1    Schwartz, S.D.2
  • 23
    • 33748613208 scopus 로고    scopus 로고
    • Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions
    • Pu J., Gao J., and Truhlar D.G. Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. Chem Rev 106 (2006) 3140-3169
    • (2006) Chem Rev , vol.106 , pp. 3140-3169
    • Pu, J.1    Gao, J.2    Truhlar, D.G.3
  • 24
    • 33748614305 scopus 로고    scopus 로고
    • Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis
    • Antoniou D., Basner J., Nunez S., and Schwartz S.D. Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis. Chem Rev 106 (2006) 3170-3187
    • (2006) Chem Rev , vol.106 , pp. 3170-3187
    • Antoniou, D.1    Basner, J.2    Nunez, S.3    Schwartz, S.D.4
  • 25
    • 33644559358 scopus 로고    scopus 로고
    • Enzymes: an integrated view of structure, dynamics and function
    • Agarwal P.K. Enzymes: an integrated view of structure, dynamics and function. Microb Cell Fact 5 (2006) 2
    • (2006) Microb Cell Fact , vol.5 , pp. 2
    • Agarwal, P.K.1
  • 26
    • 20444457978 scopus 로고    scopus 로고
    • Why enzymes are proficient catalysts: beyond the Pauling paradigm
    • Zhang X., and Houk K.N. Why enzymes are proficient catalysts: beyond the Pauling paradigm. Acc Chem Res 38 (2005) 379-385
    • (2005) Acc Chem Res , vol.38 , pp. 379-385
    • Zhang, X.1    Houk, K.N.2
  • 27
    • 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
  • 28
    • 33748584863 scopus 로고    scopus 로고
    • Mechanisms and free energies of enzymatic reactions
    • Gao J., Ma S.H., Major D.T., Nam K., Pu J.Z., and Truhlar D.G. Mechanisms and free energies of enzymatic reactions. Chem Rev 106 (2006) 3188-3209
    • (2006) Chem Rev , vol.106 , pp. 3188-3209
    • Gao, J.1    Ma, S.H.2    Major, D.T.3    Nam, K.4    Pu, J.Z.5    Truhlar, D.G.6
  • 29
    • 33644990365 scopus 로고    scopus 로고
    • Hydrogen tunneling and protein motion in enzyme reactions
    • Hammes-Schiffer S. Hydrogen tunneling and protein motion in enzyme reactions. Acc Chem Res 39 (2006) 93-100
    • (2006) Acc Chem Res , vol.39 , pp. 93-100
    • Hammes-Schiffer, S.1
  • 31
    • 33748593631 scopus 로고    scopus 로고
    • Introduction: principles of enzymatic catalysis
    • An excellent special issue of updated reviews on recent experimental and theoretical studies on enzyme catalysis. The first two sections, including experimental exploration of dynamic contributions to catalysis and computational enzymology, are related to this review here.
    • Schramm V.L. Introduction: principles of enzymatic catalysis. Chem Rev 106 (2006) 3029-3030. An excellent special issue of updated reviews on recent experimental and theoretical studies on enzyme catalysis. The first two sections, including experimental exploration of dynamic contributions to catalysis and computational enzymology, are related to this review here.
    • (2006) Chem Rev , vol.106 , pp. 3029-3030
    • Schramm, V.L.1
  • 32
    • 33748360130 scopus 로고    scopus 로고
    • Introduction. Quantum catalysis in enzymes: beyond the transition state theory paradigm
    • A nice collection of recent insights from experimental and theoretical studies on a potential role of quantum mechanical tunneling in enzymatic-catalyzed hydrogen (proton or hydride) transfer, a process which might need to be described beyond the transition-state theory paradigm.
    • Dutton P.L., Munro A.W., Scrutton N.S., and Sutcliffe M.J. Introduction. Quantum catalysis in enzymes: beyond the transition state theory paradigm. Philos Trans R Soc Lond B Biol Sci 361 (2006) 1293-1294. A nice collection of recent insights from experimental and theoretical studies on a potential role of quantum mechanical tunneling in enzymatic-catalyzed hydrogen (proton or hydride) transfer, a process which might need to be described beyond the transition-state theory paradigm.
    • (2006) Philos Trans R Soc Lond B Biol Sci , vol.361 , pp. 1293-1294
    • Dutton, P.L.1    Munro, A.W.2    Scrutton, N.S.3    Sutcliffe, M.J.4
  • 35
    • 28044469667 scopus 로고    scopus 로고
    • Direct observation of thymine dimer repair in DNA by photolyase
    • Using femtosecond spectroscopy, the functional evolution of DNA repair was mapped out in real time. The electron transfer from the excited reduced flavin to the dimer was shown to occur heterogeneously in 170 ps with a stretched coefficient β = 0.71. The ring splitting and electron return takes 560 ps and the catalytic photocycle is completed within subnanosecond.
    • Kao Y.-T., Saxena C., Wang L., Sancar A., and Zhong D. Direct observation of thymine dimer repair in DNA by photolyase. Proc Natl Acad Sci USA 102 (2005) 16128-16132. Using femtosecond spectroscopy, the functional evolution of DNA repair was mapped out in real time. The electron transfer from the excited reduced flavin to the dimer was shown to occur heterogeneously in 170 ps with a stretched coefficient β = 0.71. The ring splitting and electron return takes 560 ps and the catalytic photocycle is completed within subnanosecond.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 16128-16132
    • Kao, Y.-T.1    Saxena, C.2    Wang, L.3    Sancar, A.4    Zhong, D.5
  • 36
    • 27544442817 scopus 로고    scopus 로고
    • Making light work of enzyme catalysis: protochlorophyllide oxidoreductase
    • Using various spectroscopic methods, the catalytic processes of POR were characterized. The catalytic reaction involves proton and hydride transfer, which is proposed to proceed through two parallel pathways, concerted (3 ps) and sequential (3 ps and 400 ps), from low-temperature and ultrafast studies.
    • Heyes D.J., and Hunter C.N. Making light work of enzyme catalysis: protochlorophyllide oxidoreductase. Trends Biochem Sci 30 (2005) 642-649. Using various spectroscopic methods, the catalytic processes of POR were characterized. The catalytic reaction involves proton and hydride transfer, which is proposed to proceed through two parallel pathways, concerted (3 ps) and sequential (3 ps and 400 ps), from low-temperature and ultrafast studies.
    • (2005) Trends Biochem Sci , vol.30 , pp. 642-649
    • Heyes, D.J.1    Hunter, C.N.2
  • 37
    • 0038305458 scopus 로고    scopus 로고
    • Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors
    • Sancar A. Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem Rev 103 (2003) 2203-2237
    • (2003) Chem Rev , vol.103 , pp. 2203-2237
    • Sancar, A.1
  • 38
    • 3242883632 scopus 로고    scopus 로고
    • Novel insights into the enzymology, regulation and physiological functions of light-dependent protochlorophyllide oxidoreductase in angiosperms
    • Masuda T., and Takamiya K. Novel insights into the enzymology, regulation and physiological functions of light-dependent protochlorophyllide oxidoreductase in angiosperms. Photosynth Res 81 (2004) 1-24
    • (2004) Photosynth Res , vol.81 , pp. 1-24
    • Masuda, T.1    Takamiya, K.2
  • 40
    • 10044280323 scopus 로고    scopus 로고
    • Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair
    • Mees A., Klar T., Hennecke U., Eker A.P.M., Carell T., and Essen L.O. Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Science 306 (2004) 1789-1793
    • (2004) Science , vol.306 , pp. 1789-1793
    • Mees, A.1    Klar, T.2    Hennecke, U.3    Eker, A.P.M.4    Carell, T.5    Essen, L.O.6
  • 41
    • 32344444896 scopus 로고    scopus 로고
    • Photolyases and cryptochromes: common mechanisms of DNA repair and light-driven signaling?
    • Essen L.O. Photolyases and cryptochromes: common mechanisms of DNA repair and light-driven signaling?. Curr Opin Struct Biol 16 (2006) 51-59
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 51-59
    • Essen, L.O.1
  • 42
    • 33745292138 scopus 로고    scopus 로고
    • Light-driven DNA repair by photolyases
    • Essen L.O., and Klar T. Light-driven DNA repair by photolyases. Cell Mol Life Sci 63 (2006) 1266-1277
    • (2006) Cell Mol Life Sci , vol.63 , pp. 1266-1277
    • Essen, L.O.1    Klar, T.2
  • 43
    • 32944466734 scopus 로고    scopus 로고
    • Spectroscopic and kinetic characterization of the light-dependent enzyme protochlorophyllide oxidoreductase (POR) using monovinyl and divinyl substrates
    • Heyes D.J., Kruk J., and Hunter C.N. Spectroscopic and kinetic characterization of the light-dependent enzyme protochlorophyllide oxidoreductase (POR) using monovinyl and divinyl substrates. Biochem J 394 (2006) 243-248
    • (2006) Biochem J , vol.394 , pp. 243-248
    • Heyes, D.J.1    Kruk, J.2    Hunter, C.N.3
  • 44
    • 33748750406 scopus 로고    scopus 로고
    • The first catalytic step of the light-driven enzyme protochlorophyllide oxidoreductase proceeds via a charge transfer complex
    • Heyes D.J., Heathcote P., Rigby S.E.J., Palacios M.A., van Grondelle R., and Hunter C.N. The first catalytic step of the light-driven enzyme protochlorophyllide oxidoreductase proceeds via a charge transfer complex. J Biol Chem 281 (2006) 26847-26853
    • (2006) J Biol Chem , vol.281 , pp. 26847-26853
    • Heyes, D.J.1    Heathcote, P.2    Rigby, S.E.J.3    Palacios, M.A.4    van Grondelle, R.5    Hunter, C.N.6
  • 45
    • 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
  • 46
    • 0041821836 scopus 로고    scopus 로고
    • A perspective on enzyme catalysis
    • Benkovic S.J., and Hammes-Schiffer S. A perspective on enzyme catalysis. Science 301 (2003) 1196-1202
    • (2003) Science , vol.301 , pp. 1196-1202
    • Benkovic, S.J.1    Hammes-Schiffer, S.2
  • 47
    • 33645836711 scopus 로고    scopus 로고
    • Enzyme motions inside and out
    • Benkovic S.J., and Hammes-Schiffer S. Enzyme motions inside and out. Science 312 (2006) 208-209
    • (2006) Science , vol.312 , pp. 208-209
    • Benkovic, S.J.1    Hammes-Schiffer, S.2
  • 49
    • 33750441144 scopus 로고    scopus 로고
    • Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase
    • Wang L., Goodey N.M., Benkovic S.J., and Kohen A. Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase. Proc Natl Acad Sci USA 103 (2006) 15753-15758
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 15753-15758
    • Wang, L.1    Goodey, N.M.2    Benkovic, S.J.3    Kohen, A.4
  • 50
    • 18744380681 scopus 로고    scopus 로고
    • Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase
    • Wong K.F., Selzer T., Benkovic S.J., and Hammes-Schiffer S. Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. Proc Natl Acad Sci USA 102 (2005) 6807-6812
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6807-6812
    • Wong, K.F.1    Selzer, T.2    Benkovic, S.J.3    Hammes-Schiffer, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.