메뉴 건너뛰기




Volumn 33, Issue 3, 2008, Pages 104-112

Enzymatic reaction sequences as coupled multiple traces on a multidimensional landscape

Author keywords

[No Author keywords available]

Indexed keywords

GLUTAMATE DEHYDROGENASE;

EID: 39949083747     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2007.12.001     Document Type: Article
Times cited : (17)

References (53)
  • 1
    • 0028023724 scopus 로고
    • Statistical mechanics of kinetic proofreading in protein folding in vivo
    • Gulukota K., and Wolynes P.G. Statistical mechanics of kinetic proofreading in protein folding in vivo. Proc. Natl. Acad. Sci. U. S. A. 91 (1994) 9292-9296
    • (1994) Proc. Natl. Acad. Sci. U. S. A. , vol.91 , pp. 9292-9296
    • Gulukota, K.1    Wolynes, P.G.2
  • 2
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: a synthesis
    • Bryngelson J.D., et al. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21 (1995) 167-195
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1
  • 3
    • 0037133221 scopus 로고    scopus 로고
    • Proteins: paradigms of complexity
    • Frauenfelder H. Proteins: paradigms of complexity. Proc. Natl. Acad. Sci. U. S. A. 99 Suppl. 1 (2002) 2479-2480
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , Issue.SUPPL. 1 , pp. 2479-2480
    • Frauenfelder, H.1
  • 4
    • 0037058950 scopus 로고    scopus 로고
    • Sequential vs. parallel protein-folding mechanisms: experimental tests for complex folding reactions
    • Wallace L.A., and Matthews C.R. Sequential vs. parallel protein-folding mechanisms: experimental tests for complex folding reactions. Biophys. Chem. 101-102 (2002) 113-131
    • (2002) Biophys. Chem. , vol.101-102 , pp. 113-131
    • Wallace, L.A.1    Matthews, C.R.2
  • 5
    • 33646922285 scopus 로고    scopus 로고
    • A statistical thermodynamic model of the protein ensemble
    • Hilser V.J., et al. A statistical thermodynamic model of the protein ensemble. Chem. Rev. 106 (2006) 1545-1558
    • (2006) Chem. Rev. , vol.106 , pp. 1545-1558
    • Hilser, V.J.1
  • 8
    • 0032558971 scopus 로고    scopus 로고
    • How fumarase recycles after the malate → fumarate reaction. Insights into the reaction mechanism
    • Rose I.A. How fumarase recycles after the malate → fumarate reaction. Insights into the reaction mechanism. Biochemistry 37 (1998) 17651-17658
    • (1998) Biochemistry , vol.37 , pp. 17651-17658
    • Rose, I.A.1
  • 9
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: a plausible model
    • Monod J., et al. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12 (1965) 88-118
    • (1965) J. Mol. Biol. , vol.12 , pp. 88-118
    • Monod, J.1
  • 10
    • 33645801770 scopus 로고    scopus 로고
    • Atomic description of an enzyme reaction dominated by proton tunneling
    • Masgrau L., et al. Atomic description of an enzyme reaction dominated by proton tunneling. Science 312 (2006) 237-241
    • (2006) Science , vol.312 , pp. 237-241
    • Masgrau, L.1
  • 11
    • 0019333892 scopus 로고
    • Determination of the chemical mechanism of glutamate dehydrogenase from pH studies
    • Rife J.E., and Cleland W.W. Determination of the chemical mechanism of glutamate dehydrogenase from pH studies. Biochemistry 19 (1980) 2328-2333
    • (1980) Biochemistry , vol.19 , pp. 2328-2333
    • Rife, J.E.1    Cleland, W.W.2
  • 12
    • 0035852994 scopus 로고    scopus 로고
    • Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering
    • Nakasako M., et al. Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering. Biochemistry 40 (2001) 3069-3079
    • (2001) Biochemistry , vol.40 , pp. 3069-3079
    • Nakasako, M.1
  • 13
    • 0021433269 scopus 로고
    • Carbonyl oxygen exchange evidence of imine formation in the glutamate dehydrogenase reaction and identification of the "occult role" of NADPH
    • Fisher H.F., and Viswanathan T.S. Carbonyl oxygen exchange evidence of imine formation in the glutamate dehydrogenase reaction and identification of the "occult role" of NADPH. Proc. Natl. Acad. Sci. U. S. A. 81 (1984) 2747-2751
    • (1984) Proc. Natl. Acad. Sci. U. S. A. , vol.81 , pp. 2747-2751
    • Fisher, H.F.1    Viswanathan, T.S.2
  • 14
    • 0019887944 scopus 로고
    • Cryoenzymological studies of the oxidative deamination of L-glutamate by glutamate dehydrogenase. Spectral resolution of transient and product complexes
    • Johnson R.E., et al. Cryoenzymological studies of the oxidative deamination of L-glutamate by glutamate dehydrogenase. Spectral resolution of transient and product complexes. J. Biol. Chem. 256 (1981) 3817-3821
    • (1981) J. Biol. Chem. , vol.256 , pp. 3817-3821
    • Johnson, R.E.1
  • 15
    • 0016254135 scopus 로고
    • Equilibrium kinetic study of the catalytic mechanism of oxidative deamination of alanine by bovine liver glutamate dehydrogenase
    • Silverstein E., and Sulebele G. Equilibrium kinetic study of the catalytic mechanism of oxidative deamination of alanine by bovine liver glutamate dehydrogenase. Biochemistry 13 (1974) 1815-1818
    • (1974) Biochemistry , vol.13 , pp. 1815-1818
    • Silverstein, E.1    Sulebele, G.2
  • 16
    • 0020014461 scopus 로고
    • The role of protein fluctuations in enzyme action: a review
    • Welch G.R., et al. The role of protein fluctuations in enzyme action: a review. Prog. Biophys. Mol. Biol. 39 (1982) 109-146
    • (1982) Prog. Biophys. Mol. Biol. , vol.39 , pp. 109-146
    • Welch, G.R.1
  • 17
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H., et al. The energy landscapes and motions of proteins. Science 254 (1991) 1598-1603
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1
  • 18
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: dynamic landscapes and population shifts
    • Kumar S., et al. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9 (2000) 10-19
    • (2000) Protein Sci. , vol.9 , pp. 10-19
    • Kumar, S.1
  • 19
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr D.D., et al. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313 (2006) 1638-1642
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1
  • 20
    • 33748619206 scopus 로고    scopus 로고
    • An NMR perspective on enzyme dynamics
    • Boehr D.D., et al. An NMR perspective on enzyme dynamics. Chem. Rev. 106 (2006) 3055-3079
    • (2006) Chem. Rev. , vol.106 , pp. 3055-3079
    • Boehr, D.D.1
  • 21
    • 67650040559 scopus 로고
    • Linked functions and reciprocal effects in hemoglobin: a second look
    • Wyman Jr. J. Linked functions and reciprocal effects in hemoglobin: a second look. Adv. Protein Chem. 19 (1964) 223-286
    • (1964) Adv. Protein Chem. , vol.19 , pp. 223-286
    • Wyman Jr., J.1
  • 22
    • 0016412390 scopus 로고
    • Energetics of ligand binding to proteins
    • Weber G. Energetics of ligand binding to proteins. Adv. Protein Chem. 29 (1975) 1-83
    • (1975) Adv. Protein Chem. , vol.29 , pp. 1-83
    • Weber, G.1
  • 23
    • 33947547892 scopus 로고
    • Molecular architecture and biological reactions
    • Pauling L. Molecular architecture and biological reactions. Chem. Eng. News 24 (1946) 1375
    • (1946) Chem. Eng. News , vol.24 , pp. 1375
    • Pauling, L.1
  • 24
    • 0002062389 scopus 로고
    • Free-energy management in protein reactions: concepts, complications, and compensation
    • Welch G.R. (Ed), Wiley-Interscience
    • Lumry R., and Gregory R.B. Free-energy management in protein reactions: concepts, complications, and compensation. In: Welch G.R. (Ed). The Fluctuating Enzyme (1986), Wiley-Interscience pp. 1
    • (1986) The Fluctuating Enzyme
    • Lumry, R.1    Gregory, R.B.2
  • 25
    • 0025937741 scopus 로고
    • Transduction of enzyme-ligand binding energy into catalytic driving force
    • Fisher H.F., and Singh N. Transduction of enzyme-ligand binding energy into catalytic driving force. FEBS Lett. 294 (1991) 1-5
    • (1991) FEBS Lett. , vol.294 , pp. 1-5
    • Fisher, H.F.1    Singh, N.2
  • 26
    • 0023702575 scopus 로고
    • A unifying model of the thermodynamics of formation of dehydrogenase-ligand complexes
    • Fisher H.F. A unifying model of the thermodynamics of formation of dehydrogenase-ligand complexes. Adv. Enzymol. Relat. Areas Mol. Biol. 61 (1988) 1-46
    • (1988) Adv. Enzymol. Relat. Areas Mol. Biol. , vol.61 , pp. 1-46
    • Fisher, H.F.1
  • 27
    • 0032932960 scopus 로고    scopus 로고
    • The location of active site opening and closing events in the prehydride transfer phase of the oxidative deamination reaction catalyzed by bovine liver glutamate dehydrogenase using a novel pH jump approach
    • Saha S.K., and Fisher H.F. The location of active site opening and closing events in the prehydride transfer phase of the oxidative deamination reaction catalyzed by bovine liver glutamate dehydrogenase using a novel pH jump approach. Biochim. Biophys. Acta 1431 (1999) 261-265
    • (1999) Biochim. Biophys. Acta , vol.1431 , pp. 261-265
    • Saha, S.K.1    Fisher, H.F.2
  • 28
    • 0027402679 scopus 로고
    • The real-time resolution of proton-related transient-state steps in an enzymatic reaction. The early steps in the oxidative deamination reaction of bovine liver glutamate dehydrogenase
    • Singh N., et al. The real-time resolution of proton-related transient-state steps in an enzymatic reaction. The early steps in the oxidative deamination reaction of bovine liver glutamate dehydrogenase. J. Biol. Chem. 268 (1993) 21-28
    • (1993) J. Biol. Chem. , vol.268 , pp. 21-28
    • Singh, N.1
  • 29
    • 0022485788 scopus 로고
    • NADPH binding induced proton ionization as a cause of nonlinear heat capacity changes in glutamate dehydrogenase
    • Fisher H.F., et al. NADPH binding induced proton ionization as a cause of nonlinear heat capacity changes in glutamate dehydrogenase. Biochemistry 25 (1986) 2910-2915
    • (1986) Biochemistry , vol.25 , pp. 2910-2915
    • Fisher, H.F.1
  • 30
    • 0030824129 scopus 로고    scopus 로고
    • Isoergonic cooperativity in glutamate dehydrogenase complexes: a new form of allostery
    • Fisher H.F., and Tally J. Isoergonic cooperativity in glutamate dehydrogenase complexes: a new form of allostery. Biochemistry 36 (1997) 10807-10810
    • (1997) Biochemistry , vol.36 , pp. 10807-10810
    • Fisher, H.F.1    Tally, J.2
  • 31
    • 0015500319 scopus 로고
    • Ultraviolet spectrophotometric characterization of a glutamate dehydrogenase-reduced coenzyme-ketoglutarate complex
    • Cross D.G. Ultraviolet spectrophotometric characterization of a glutamate dehydrogenase-reduced coenzyme-ketoglutarate complex. J. Biol. Chem. 247 (1972) 784-789
    • (1972) J. Biol. Chem. , vol.247 , pp. 784-789
    • Cross, D.G.1
  • 32
    • 0027996050 scopus 로고
    • The demonstration of a glutamate dehydrogenase-NADP-L-glutamate charge-transfer complex and its location on the reaction pathway
    • Saha S.K., et al. The demonstration of a glutamate dehydrogenase-NADP-L-glutamate charge-transfer complex and its location on the reaction pathway. J. Biol. Chem. 269 (1994) 29592-29597
    • (1994) J. Biol. Chem. , vol.269 , pp. 29592-29597
    • Saha, S.K.1
  • 33
    • 0030049324 scopus 로고    scopus 로고
    • Interpretation of transient-state kinetic isotope effects
    • Fisher H.F., and Saha S.K. Interpretation of transient-state kinetic isotope effects. Biochemistry 35 (1996) 83-88
    • (1996) Biochemistry , vol.35 , pp. 83-88
    • Fisher, H.F.1    Saha, S.K.2
  • 34
    • 0030047372 scopus 로고    scopus 로고
    • A difference in the sequence of steps in the reactions catalyzed by two closely homologous forms of glutamate dehydrogenase
    • Maniscalco S.J., et al. A difference in the sequence of steps in the reactions catalyzed by two closely homologous forms of glutamate dehydrogenase. Biochemistry 35 (1996) 89-94
    • (1996) Biochemistry , vol.35 , pp. 89-94
    • Maniscalco, S.J.1
  • 35
    • 0031939584 scopus 로고    scopus 로고
    • The use of multiwavelength kinetic analysis approach to identify and characterize intermediate complexes in the reductive amination reaction catalyzed by bovine liver glutamate dehydrogenase
    • Saha S.K., et al. The use of multiwavelength kinetic analysis approach to identify and characterize intermediate complexes in the reductive amination reaction catalyzed by bovine liver glutamate dehydrogenase. Biochim. Biophys. Acta 1382 (1998) 8-12
    • (1998) Biochim. Biophys. Acta , vol.1382 , pp. 8-12
    • Saha, S.K.1
  • 36
    • 0032514650 scopus 로고    scopus 로고
    • Identification and characterization of kinetically competent carbinolamine and α-iminoglutarate complexes in the glutamate dehydrogenase-catalyzed oxidation of L-glutamate using a multiwavelength transient state approach
    • Maniscalco S.J., et al. Identification and characterization of kinetically competent carbinolamine and α-iminoglutarate complexes in the glutamate dehydrogenase-catalyzed oxidation of L-glutamate using a multiwavelength transient state approach. Biochemistry 37 (1998) 14585-14590
    • (1998) Biochemistry , vol.37 , pp. 14585-14590
    • Maniscalco, S.J.1
  • 37
    • 0036619762 scopus 로고    scopus 로고
    • A close-packed planar 4-atom motif serves as a variable-pathway mechanistic switching device in enzymatic catalysis
    • Fisher H.F., and Maniscalco S.J. A close-packed planar 4-atom motif serves as a variable-pathway mechanistic switching device in enzymatic catalysis. Bioorg. Chem. 30 (2002) 199-210
    • (2002) Bioorg. Chem. , vol.30 , pp. 199-210
    • Fisher, H.F.1    Maniscalco, S.J.2
  • 38
    • 0037507289 scopus 로고    scopus 로고
    • The direct measurement of thermodynamic parameters of reactive transient intermediates of the L-glutamate dehydrogenase reaction
    • Maniscalco S.J., et al. The direct measurement of thermodynamic parameters of reactive transient intermediates of the L-glutamate dehydrogenase reaction. J. Biol. Chem. 278 (2003) 16129-16134
    • (2003) J. Biol. Chem. , vol.278 , pp. 16129-16134
    • Maniscalco, S.J.1
  • 39
    • 0015501882 scopus 로고
    • + by L-glutamate dehydrogenase
    • + by L-glutamate dehydrogenase. Biochim. Biophys. Acta 289 (1972) 28-36
    • (1972) Biochim. Biophys. Acta , vol.289 , pp. 28-36
    • Cross, D.G.1
  • 40
    • 0020491340 scopus 로고
    • Glutamate dehydrogenase catalyzes the reduction of a Schiff base (delta 1-pyrroline-2-carboxylic acid) by NADPH
    • Fisher H.F., et al. Glutamate dehydrogenase catalyzes the reduction of a Schiff base (delta 1-pyrroline-2-carboxylic acid) by NADPH. J. Biol. Chem. 257 (1982) 13208-13210
    • (1982) J. Biol. Chem. , vol.257 , pp. 13208-13210
    • Fisher, H.F.1
  • 41
    • 0022434002 scopus 로고
    • Reversible reduction of an α-imino acid to an α-amino acid catalyzed by glutamate dehydrogenase: effect of ionizable functional groups
    • Srinivasan R., and Fisher H.F. Reversible reduction of an α-imino acid to an α-amino acid catalyzed by glutamate dehydrogenase: effect of ionizable functional groups. Biochemistry 24 (1985) 618-622
    • (1985) Biochemistry , vol.24 , pp. 618-622
    • Srinivasan, R.1    Fisher, H.F.2
  • 42
    • 0024297109 scopus 로고
    • Proton/product time course ratios: a new approach to transient-state kinetic analysis
    • Fisher H.F., et al. Proton/product time course ratios: a new approach to transient-state kinetic analysis. J. Biol. Chem. 263 (1988) 11704-11710
    • (1988) J. Biol. Chem. , vol.263 , pp. 11704-11710
    • Fisher, H.F.1
  • 43
    • 0026518623 scopus 로고
    • A slow obligatory proton release step precedes hydride transfer in the liver glutamate dehydrogenase catalytic mechanism
    • Fisher H.F., et al. A slow obligatory proton release step precedes hydride transfer in the liver glutamate dehydrogenase catalytic mechanism. Biochim. Biophys. Acta 1119 (1992) 52-56
    • (1992) Biochim. Biophys. Acta , vol.1119 , pp. 52-56
    • Fisher, H.F.1
  • 44
    • 0018265645 scopus 로고
    • Thermodynamics of heterotropic interactions. The glutamate dehydrogenase-NADPH-glutamate complex
    • Subramanian S., et al. Thermodynamics of heterotropic interactions. The glutamate dehydrogenase-NADPH-glutamate complex. J. Biol. Chem. 253 (1978) 8369-8374
    • (1978) J. Biol. Chem. , vol.253 , pp. 8369-8374
    • Subramanian, S.1
  • 45
    • 0019330199 scopus 로고
    • Thermodynamic interaction parameters of a reactive enzyme ternary complex: glutamate dehydrogenase-NADPH-alpha-ketoglutarate
    • Fisher H.F., and Stickel D.C. Thermodynamic interaction parameters of a reactive enzyme ternary complex: glutamate dehydrogenase-NADPH-alpha-ketoglutarate. FEBS Lett. 113 (1980) 11-14
    • (1980) FEBS Lett. , vol.113 , pp. 11-14
    • Fisher, H.F.1    Stickel, D.C.2
  • 46
    • 0019320330 scopus 로고
    • pH-dependent thermodynamic parameters of the glutamate dehydrogenase-alpha-ketoglutarate-NADPH complex
    • Fisher H.F., et al. pH-dependent thermodynamic parameters of the glutamate dehydrogenase-alpha-ketoglutarate-NADPH complex. Biochim. Biophys. Acta 615 (1980) 27-33
    • (1980) Biochim. Biophys. Acta , vol.615 , pp. 27-33
    • Fisher, H.F.1
  • 47
    • 0015524230 scopus 로고
    • The mechanism of glutamate dehydrogenase reaction. IV. Evidence for random and rapid binding of substrate and coenzyme in the burst phase
    • Colen A.H., et al. The mechanism of glutamate dehydrogenase reaction. IV. Evidence for random and rapid binding of substrate and coenzyme in the burst phase. J. Biol. Chem. 247 (1972) 7905-7909
    • (1972) J. Biol. Chem. , vol.247 , pp. 7905-7909
    • Colen, A.H.1
  • 48
    • 0018270637 scopus 로고
    • Effect of ammonia on the glutamate dehydrogenase catalyzed oxidative deamination of L-glutamate: production of an ammonia-containing intermediate in the "burst" phase
    • Brown A., et al. Effect of ammonia on the glutamate dehydrogenase catalyzed oxidative deamination of L-glutamate: production of an ammonia-containing intermediate in the "burst" phase. Biochemistry 17 (1978) 2031-2034
    • (1978) Biochemistry , vol.17 , pp. 2031-2034
    • Brown, A.1
  • 49
    • 0018801606 scopus 로고
    • Effect of ammonia on the glutamate dehydrogenase catalyzed oxidative deamination of L-glutamate. The steady state
    • Brown A., et al. Effect of ammonia on the glutamate dehydrogenase catalyzed oxidative deamination of L-glutamate. The steady state. Biochemistry 18 (1979) 5924-5928
    • (1979) Biochemistry , vol.18 , pp. 5924-5928
    • Brown, A.1
  • 50
    • 0033565447 scopus 로고    scopus 로고
    • The structure of bovine glutamate dehydrogenase provides insights into the mechanism of allostery
    • Peterson P.E., and Smith T.J. The structure of bovine glutamate dehydrogenase provides insights into the mechanism of allostery. Structure 7 (1999) 769-782
    • (1999) Structure , vol.7 , pp. 769-782
    • Peterson, P.E.1    Smith, T.J.2
  • 51
    • 0017887398 scopus 로고
    • Transient-state kinetics of L-glutamate dehydrogenase: mechanism of alpha-ketoglutarate inhibition in the burst phase
    • Colen A.H. Transient-state kinetics of L-glutamate dehydrogenase: mechanism of alpha-ketoglutarate inhibition in the burst phase. Biochemistry 17 (1978) 528-533
    • (1978) Biochemistry , vol.17 , pp. 528-533
    • Colen, A.H.1
  • 52
    • 0033556161 scopus 로고    scopus 로고
    • Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum
    • Stillman T.J., et al. Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum. J. Mol. Biol. 285 (1999) 875-885
    • (1999) J. Mol. Biol. , vol.285 , pp. 875-885
    • Stillman, T.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.