메뉴 건너뛰기




Volumn 107, Issue 42, 2010, Pages 17974-17979

Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase

Author keywords

2D IR spectroscopy; Enzyme dynamics

Indexed keywords

AZIDE; CARBON DIOXIDE; FORMATE DEHYDROGENASE; FORMIC ACID; NICOTINAMIDE ADENINE DINUCLEOTIDE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE;

EID: 78149243959     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0912190107     Document Type: Article
Times cited : (67)

References (55)
  • 1
    • 33748344518 scopus 로고    scopus 로고
    • Linking protein structure and dynamics to catalysis: The role of hydrogen tunnelling
    • Klinman JP (2006) Linking protein structure and dynamics to catalysis: The role of hydrogen tunnelling. Philos Trans R Soc London B 361:1323-1331.
    • (2006) Philos Trans R Soc London B , vol.361 , pp. 1323-1331
    • Klinman, J.P.1
  • 2
    • 70349233664 scopus 로고    scopus 로고
    • Linking protein dynamics to function
    • Klinman JP (2007) Linking protein dynamics to function. Faseb J 21:A645-A645.
    • (2007) Faseb J , vol.21
    • Klinman, J.P.1
  • 3
    • 0141828475 scopus 로고    scopus 로고
    • Kinetic isotope effects as probes for hydrogen tunneling, coupled motion and dynamics contributions to enzyme catalysis
    • Kohen A (2003) Kinetic isotope effects as probes for hydrogen tunneling, coupled motion and dynamics contributions to enzyme catalysis. Prog React Kinet Mec 28:119-156.
    • (2003) Prog React Kinet Mec , vol.28 , pp. 119-156
    • Kohen, A.1
  • 4
    • 85056422813 scopus 로고    scopus 로고
    • Kinetic isotope effects as probes for hydrogen tunneling in enzyme catalysis
    • eds A Kohen and HH Limbach (CRC Press/Taylor & Francis, Boca Raton, FL)
    • Kohen A (2006) Kinetic isotope effects as probes for hydrogen tunneling in enzyme catalysis. Isotope Effects in Chemistry and Biology, eds A Kohen and HH Limbach (CRC Press/Taylor & Francis, Boca Raton, FL), pp 743-764.
    • (2006) Isotope Effects in Chemistry and Biology , pp. 743-764
    • Kohen, A.1
  • 5
    • 33748354485 scopus 로고    scopus 로고
    • The role of enzyme dynamics and tunnelling in catalysing hydride transfer: Studies of distal mutants of dihydrofolate reductase
    • Wang L, Goodey NM, Benkovic SJ, Kohen A (2006) The role of enzyme dynamics and tunnelling in catalysing hydride transfer: Studies of distal mutants of dihydrofolate reductase. Philos Trans R Soc London B 361:1307-1315.
    • (2006) Philos Trans R Soc London B , vol.361 , pp. 1307-1315
    • Wang, L.1    Goodey, N.M.2    Benkovic, S.J.3    Kohen, A.4
  • 6
    • 33748357971 scopus 로고    scopus 로고
    • Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: Flavoprotein and quinoprotein systems
    • Sutcliffe MJ, et al. (2006) Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: Flavoprotein and quinoprotein systems. Philos Trans R Soc London B 361:1375-1386.
    • (2006) Philos Trans R Soc London B , vol.361 , pp. 1375-1386
    • Sutcliffe, M.J.1
  • 7
    • 43649091510 scopus 로고    scopus 로고
    • Tuning of the H-transfer coordinate in primitive versus well-evolved enzymes
    • Yahashiri A, Howell EE, Kohen A (2008) Tuning of the H-transfer coordinate in primitive versus well-evolved enzymes. ChemPhysChem 9:980-982.
    • (2008) ChemPhysChem , vol.9 , pp. 980-982
    • Yahashiri, A.1    Howell, E.E.2    Kohen, A.3
  • 8
    • 37149004947 scopus 로고    scopus 로고
    • Role of Y94 in proton and hydride transfers catalyzed by thymidylate synthase
    • DOI 10.1021/bi701363s
    • Hong BY, Maley F, Kohen A (2007) Role of Y94 in proton and hydride transfers catalyzed by thymidylate synthase. Biochemistry 46:14188-14197. (Pubitemid 350253074)
    • (2007) Biochemistry , vol.46 , Issue.49 , pp. 14188-14197
    • Hong, B.1    Maley, F.2    Kohen, A.3
  • 9
    • 32244432145 scopus 로고    scopus 로고
    • Effects of a distal mutation on active site chemistry
    • DOI 10.1021/bi0518242
    • Wang L, Tharp S, Selzer T, Benkovic SJ, Kohen A (2006) Effects of a distal mutation on active site chemistry. Biochemistry 45:1383-1392. (Pubitemid 43214803)
    • (2006) Biochemistry , vol.45 , Issue.5 , pp. 1383-1392
    • Wang, L.1    Tharp, S.2    Selzer, T.3    Benkovic, S.J.4    Kohen, A.5
  • 10
    • 33750441144 scopus 로고    scopus 로고
    • Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase
    • Wang L, Goodey NM, Benkovic SJ, Kohen A (2006) Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase. Proc Natl Acad Sci USA 103:15753-15758.
    • (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
  • 11
    • 25144458498 scopus 로고    scopus 로고
    • Conformational substates modulate hydride transfer in dihydrofolate reductase
    • Thorpe IF, Brooks CL (2005) Conformational substates modulate hydride transfer in dihydrofolate reductase. J Am Chem Soc 127:12997-13006.
    • (2005) J Am Chem Soc , vol.127 , pp. 12997-13006
    • Thorpe, I.F.1    Brooks, C.L.2
  • 13
    • 33748349036 scopus 로고    scopus 로고
    • Hydride transfer catalysed by Escherichia coli and Bacillus subtilis dihydrofolate reductase: Coupled motions and distal mutations
    • Hammes-Schiffer S, Watney JB (2006) Hydride transfer catalysed by Escherichia coli and Bacillus subtilis dihydrofolate reductase: Coupled motions and distal mutations. Philos Trans R Soc London B 361:1365-1373.
    • (2006) Philos Trans R Soc London B , vol.361 , pp. 1365-1373
    • Hammes-Schiffer, S.1    Watney, J.B.2
  • 15
    • 33748590314 scopus 로고    scopus 로고
    • Vibrationally enhanced tunneling from the temperature dependence of KIE
    • eds A Kohen and HH Limbach (Taylor & Francis/CRC Press, Boca Raton, FL)
    • Schwartz SD (2006) Vibrationally enhanced tunneling from the temperature dependence of KIE. Isotope effects in chemistry and biology, eds A Kohen and HH Limbach (Taylor & Francis/CRC Press, Boca Raton, FL), pp 475-498.
    • (2006) Isotope Effects in Chemistry and Biology , pp. 475-498
    • Schwartz, S.D.1
  • 17
    • 44949134134 scopus 로고    scopus 로고
    • Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach
    • DOI 10.1021/ja801156y
    • Ruiz-Pernia JJ, Tunon I, Moliner V, Hynes JT, Roca M (2008) Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach. J Am Chem Soc 130:7477-7488. (Pubitemid 351813242)
    • (2008) Journal of the American Chemical Society , vol.130 , Issue.23 , pp. 7477-7488
    • Ruiz-Pernia, J.J.1    Tunon, I.2    Moliner, V.3    Hynes, J.T.4    Roca, M.5
  • 18
    • 33745362450 scopus 로고    scopus 로고
    • Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- And intramonomeric correlated motions
    • Pang JY, Pu JZ, Gao JL, Truhlar DG, Allemann RK (2006) Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions. J Am Chem Soc 128:8015-8023.
    • (2006) J Am Chem Soc , vol.128 , pp. 8015-8023
    • Pang, J.Y.1    Pu, J.Z.2    Gao, J.L.3    Truhlar, D.G.4    Allemann, R.K.5
  • 19
    • 85056406805 scopus 로고    scopus 로고
    • Variational transition state theory and multidimensional tunneling for simple and complex reacrions in the gas phase, solids, liquids, and enzymes
    • eds A Kohen and HH Limbach (Taylor & Francis/CRC Press, Boca Raton, FL)
    • Truhlar DG (2006) Variational transition state theory and multidimensional tunneling for simple and complex reacrions in the gas phase, solids, liquids, and enzymes. Isotope Effects in Chemistry and Biology, eds A Kohen and HH Limbach (Taylor & Francis/CRC Press, Boca Raton, FL), pp 579-620.
    • (2006) Isotope Effects in Chemistry and Biology , pp. 579-620
    • Truhlar, D.G.1
  • 20
    • 33646524282 scopus 로고    scopus 로고
    • Coupling between protein and reaction dynamics in enzymatic processes: Application of Grote-Hynes theory to catechol O-methyltransferase
    • Roca M, Moliner V, Tunon I, Hynes JT (2006) Coupling between protein and reaction dynamics in enzymatic processes: Application of Grote-Hynes theory to catechol O-methyltransferase. J Am Chem Soc 128:6186-6193.
    • (2006) J Am Chem Soc , vol.128 , pp. 6186-6193
    • Roca, M.1    Moliner, V.2    Tunon, I.3    Hynes, J.T.4
  • 21
    • 33748633480 scopus 로고    scopus 로고
    • Electrostatic basis for enzyme catalysis
    • Warshel A, et al. (2006) Electrostatic basis for enzyme catalysis. Chem Rev 106:3210-3235.
    • (2006) Chem Rev , vol.106 , pp. 3210-3235
    • Warshel, A.1
  • 22
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman KA, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450:913-916.
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1
  • 23
    • 36849048228 scopus 로고    scopus 로고
    • Intrinsic motions along an enzymatic reaction trajectory
    • Henzler-Wildman KA, et al. (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450:838-844.
    • (2007) Nature , vol.450 , pp. 838-844
    • Henzler-Wildman, K.A.1
  • 24
    • 33748601471 scopus 로고    scopus 로고
    • Tunneling and dynamics in enzymatic hydride transfer
    • Nagel ZD, Klinman JP (2006) Tunneling and dynamics in enzymatic hydride transfer. Chem Rev 106:3095-3118.
    • (2006) Chem Rev , vol.106 , pp. 3095-3118
    • Nagel, Z.D.1    Klinman, J.P.2
  • 25
    • 0000161584 scopus 로고    scopus 로고
    • Ultrafast spectroscopy of protein dynamics
    • Hochstrasser RM (1998) Ultrafast spectroscopy of protein dynamics. J Chem Educ 75:559-564.
    • (1998) J Chem Educ , vol.75 , pp. 559-564
    • Hochstrasser, R.M.1
  • 26
    • 0032418733 scopus 로고    scopus 로고
    • Protein fluctuations are sensed by stimulated infrared echoes of the vibrations of carbon monoxide and azide probes
    • Lim MH, Hamm P, Hochstrasser RM (1998) Protein fluctuations are sensed by stimulated infrared echoes of the vibrations of carbon monoxide and azide probes. Proc Natl Acad Sci USA 95:15315-15320.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 15315-15320
    • Lim, M.H.1    Hamm, P.2    Hochstrasser, R.M.3
  • 27
    • 40349094606 scopus 로고    scopus 로고
    • Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase
    • Fang C, et al. (2008) Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase. Proc Natl Acad Sci USA 105:1472-1477.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 1472-1477
    • Fang, C.1
  • 29
    • 37649012488 scopus 로고    scopus 로고
    • Disulfide bond influence on protein structural dynamics probed with 2D-IR vibrational echo spectroscopy
    • Ishikawa H, Kim S, Kwak K, Wakasugi K, Fayer MD (2007) Disulfide bond influence on protein structural dynamics probed with 2D-IR vibrational echo spectroscopy. Proc Natl Acad Sci USA 104:19309-19314.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 19309-19314
    • Ishikawa, H.1    Kim, S.2    Kwak, K.3    Wakasugi, K.4    Fayer, M.D.5
  • 31
    • 33645455485 scopus 로고    scopus 로고
    • Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy
    • Massari AM, Finkelstein IJ, Fayer MD (2006) Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy. J Am Chem Soc 128:3990-3997.
    • (2006) J Am Chem Soc , vol.128 , pp. 3990-3997
    • Massari, A.M.1    Finkelstein, I.J.2    Fayer, M.D.3
  • 32
    • 26844437371 scopus 로고    scopus 로고
    • The influence of aqueous versus glassy solvents on protein dynamics: Vibrational echo experiments and molecular dynamics simulations
    • Massari AM, et al. (2005) The influence of aqueous versus glassy solvents on protein dynamics: Vibrational echo experiments and molecular dynamics simulations. J Am Chem Soc 127:14279-14289.
    • (2005) J Am Chem Soc , vol.127 , pp. 14279-14289
    • Massari, A.M.1
  • 33
    • 10044251472 scopus 로고    scopus 로고
    • Dynamics of hemoglobin in human erythrocytes and in solution: Influence of viscosity studied by ultrafast vibrational echo experiments
    • McClain BL, Finkelstein IJ, Fayer MD (2004) Dynamics of hemoglobin in human erythrocytes and in solution: Influence of viscosity studied by ultrafast vibrational echo experiments. J Am Chem Soc 126:15702-15710.
    • (2004) J Am Chem Soc , vol.126 , pp. 15702-15710
    • McClain, B.L.1    Finkelstein, I.J.2    Fayer, M.D.3
  • 34
    • 0242407234 scopus 로고    scopus 로고
    • Myoglobin-CO substate structures and dynamics: Multidimensional vibrational echoes and molecular dynamics simulations
    • Merchant KA, et al. (2003) Myoglobin-CO substate structures and dynamics: Multidimensional vibrational echoes and molecular dynamics simulations. J Am Chem Soc 125:13804-13818.
    • (2003) J Am Chem Soc , vol.125 , pp. 13804-13818
    • Merchant, K.A.1
  • 35
    • 0034743152 scopus 로고    scopus 로고
    • Fast protein dynamics probed with infrared vibrational echo experiments
    • Fayer MD (2001) Fast protein dynamics probed with infrared vibrational echo experiments. Annu Rev Phys Chem 52:315-356.
    • (2001) Annu Rev Phys Chem , vol.52 , pp. 315-356
    • Fayer, M.D.1
  • 36
    • 70349241659 scopus 로고    scopus 로고
    • Exploring the molecular origins of protein dynamics in the active site of human carbonic anhydrase II
    • Hill SE, et al. (2009) Exploring the molecular origins of protein dynamics in the active site of human carbonic anhydrase II. J Phys Chem B 113:11505-11510.
    • (2009) J Phys Chem B , vol.113 , pp. 11505-11510
    • Hill, S.E.1
  • 37
    • 0019330801 scopus 로고
    • Kinetic and chemical mechanisms of yeast formate dehydrogenase
    • Blanchard JS, Cleland WW (1980) Kinetic and chemical mechanisms of yeast formate dehydrogenase. Biochemistry 19:3543-3550.
    • (1980) Biochemistry , vol.19 , pp. 3543-3550
    • Blanchard, J.S.1    Cleland, W.W.2
  • 38
    • 0021756501 scopus 로고
    • Variation of transition-state structure as a function of the nucleotide in reactions catalyzed by dehydrogenases. 2. Formate dehydrogenase
    • Hermes JD, Morrical SW, O'Leary MH, Cleland WW (1984) Variation of transition-state structure as a function of the nucleotide in reactions catalyzed by dehydrogenases. 2. Formate dehydrogenase. Biochemistry 23:5479-5488.
    • (1984) Biochemistry , vol.23 , pp. 5479-5488
    • Hermes, J.D.1    Morrical, S.W.2    O'Leary, M.H.3    Cleland, W.W.4
  • 39
    • 33645409623 scopus 로고    scopus 로고
    • Protein engineering of formate dehydrogenase
    • Tishkov VI, Popov VO (2006) Protein engineering of formate dehydrogenase. Biomol Eng 23:89-110.
    • (2006) Biomol Eng , vol.23 , pp. 89-110
    • Tishkov, V.I.1    Popov, V.O.2
  • 40
    • 0027937347 scopus 로고
    • Nad(+)-Dependent Formate Dehydrogenase
    • Popov VO, Lamzin VS (1994) Nad(+)-Dependent Formate Dehydrogenase. Biochem J 301:625-643.
    • (1994) Biochem J , vol.301 , pp. 625-643
    • Popov, V.O.1    Lamzin, V.S.2
  • 42
    • 34249807630 scopus 로고    scopus 로고
    • High-resolution structures of formate dehydrogenase from Candida boidinii
    • Schirwitz K, Schmidt A, Lamzin VS (2007) High-resolution structures of formate dehydrogenase from Candida boidinii. Prot Sci 16:1146-1156.
    • (2007) Prot Sci , vol.16 , pp. 1146-1156
    • Schirwitz, K.1    Schmidt, A.2    Lamzin, V.S.3
  • 43
    • 67651235292 scopus 로고    scopus 로고
    • Examination of enzymatic H-tunneling through kinetics and dynamics
    • Bandaria JN, et al. (2009) Examination of enzymatic H-tunneling through kinetics and dynamics. J Am Chem Soc 131:10151-10155.
    • (2009) J Am Chem Soc , vol.131 , pp. 10151-10155
    • Bandaria, J.N.1
  • 45
    • 34848897271 scopus 로고    scopus 로고
    • Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: A new approach
    • Kwak K, Park S, Finkelstein IJ, Fayer MD (2007) Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: A new approach. J Chem Phys 127:124503.
    • (2007) J Chem Phys , vol.127 , pp. 124503
    • Kwak, K.1    Park, S.2    Finkelstein, I.J.3    Fayer, M.D.4
  • 46
    • 44449086941 scopus 로고    scopus 로고
    • Taking apart the two-dimensional infrared vibrational echo spectra: More information and elimination of distortions
    • Kwak K, Rosenfeld DE, Fayer MD (2008) Taking apart the two-dimensional infrared vibrational echo spectra: More information and elimination of distortions. J Chem Phys 128:204505.
    • (2008) J Chem Phys , vol.128 , pp. 204505
    • Kwak, K.1    Rosenfeld, D.E.2    Fayer, M.D.3
  • 47
    • 0141563472 scopus 로고    scopus 로고
    • Line shapes and photon echoes within a generalized Kubo model
    • Schmidt JR, Sundlass N, Skinner JL (2003) Line shapes and photon echoes within a generalized Kubo model. Chem Phys Lett 378:559-566.
    • (2003) Chem Phys Lett , vol.378 , pp. 559-566
    • Schmidt, J.R.1    Sundlass, N.2    Skinner, J.L.3
  • 49
    • 0032517714 scopus 로고    scopus 로고
    • Non-Markovian dynamics of the vibrations of ions in water from femtosecond infrared three-pulse photon echoes
    • Hamm P, Lim M, Hochstrasser RM (1998) Non-Markovian dynamics of the vibrations of ions in water from femtosecond infrared three-pulse photon echoes. Phys Rev Lett 81:5326-5329. (Pubitemid 128631935)
    • (1998) Physical Review Letters , vol.81 , Issue.24 , pp. 5326-5329
    • Hamm, P.1    Lim, M.2    Hochstrasser, R.M.3
  • 50
    • 33846092981 scopus 로고    scopus 로고
    • Vibrational energy relaxation of azide in water
    • Li SZ, Schmidt JR, Skinner JL (2006) Vibrational energy relaxation of azide in water. J Chem Phys 125:244507.
    • (2006) J Chem Phys , vol.125 , pp. 244507
    • Li, S.Z.1    Schmidt, J.R.2    Skinner, J.L.3
  • 52
    • 33846047459 scopus 로고    scopus 로고
    • Proton-coupled electron transfer in soybean lipoxygenase: Dynamical behavior and temperature dependence of kinetic isotope effects
    • DOI 10.1021/ja0667211
    • Hatcher E, Soudackov AV, Hammes-Schiffer S (2007) Proton-coupled electron transfer in soybean lipoxygenase: Dynamical behavior and temperature dependence of kinetic isotope effects. J Am Chem Soc 129:187-196. (Pubitemid 46068274)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.1 , pp. 187-196
    • Hatcher, E.1    Soudackov, A.V.2    Hammes-Schiffer, S.3
  • 53
    • 34047264783 scopus 로고    scopus 로고
    • Proton tunneling in aromatic amine dehydrogenase is driven by a short-range sub-picosecond promoting vibration: Consistency of simulation and theory with experiment
    • Johannissen LO, Hay S, Scrutton NS, Sutcliffe MJ (2007) Proton tunneling in aromatic amine dehydrogenase is driven by a short-range sub-picosecond promoting vibration: Consistency of simulation and theory with experiment. J Phys Chem B 111:2631-2638.
    • (2007) J Phys Chem B , vol.111 , pp. 2631-2638
    • Johannissen, L.O.1    Hay, S.2    Scrutton, N.S.3    Sutcliffe, M.J.4
  • 54
  • 55
    • 84858106899 scopus 로고    scopus 로고
    • Relaxation and anharmonic couplings of the O-H stretching vibration of asymmetric strongly hydrogen- Bonded complexes
    • Gundogdu K, Bandaria J, Nydegger M, Rock W, Cheatum CM (2007) Relaxation and anharmonic couplings of the O-H stretching vibration of asymmetric strongly hydrogen- bonded complexes. J Chem Phys 127:044501.
    • (2007) J Chem Phys , vol.127 , pp. 044501
    • Gundogdu, K.1    Bandaria, J.2    Nydegger, M.3    Rock, W.4    Cheatum, C.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.