메뉴 건너뛰기




Volumn 48, Issue 2, 2015, Pages 482-489

Perspectives on electrostatics and conformational motions in enzyme catalysis

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; HYDROGEN;

EID: 84923103951     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar500390e     Document Type: Review
Times cited : (130)

References (49)
  • 1
    • 33947547892 scopus 로고
    • Molecular Architecture and Biological Reactions
    • Pauling, L. Molecular Architecture and Biological Reactions Chem. Eng. News 1946, 24, 1375-1377
    • (1946) Chem. Eng. News , vol.24 , pp. 1375-1377
    • Pauling, L.1
  • 2
    • 82455219011 scopus 로고    scopus 로고
    • Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis
    • Hammes, G. G.; Benkovic, S. J.; Hammes-Schiffer, S. Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis Biochemistry 2011, 50, 10422-10430
    • (2011) Biochemistry , vol.50 , pp. 10422-10430
    • Hammes, G.G.1    Benkovic, S.J.2    Hammes-Schiffer, S.3
  • 3
    • 84869761071 scopus 로고    scopus 로고
    • The Protein-Folding Problem, 50 Years on
    • Dill, K. A.; MacCallum, J. L. The Protein-Folding Problem, 50 Years On Science 2012, 338, 1042-1046
    • (2012) Science , vol.338 , pp. 1042-1046
    • Dill, K.A.1    Maccallum, J.L.2
  • 4
    • 84875671597 scopus 로고    scopus 로고
    • Catalytic Efficiency of Enzymes: A Theoretical Analysis
    • Hammes-Schiffer, S. Catalytic Efficiency of Enzymes: A Theoretical Analysis Biochemistry 2013, 52, 2012-2020
    • (2013) Biochemistry , vol.52 , pp. 2012-2020
    • Hammes-Schiffer, S.1
  • 5
    • 84875685397 scopus 로고    scopus 로고
    • Fundamental Challenges in Mechanistic Enzymology: Progress toward Understanding the Rate Enhancements of Enzymes
    • Herschlag, D.; Natarajan, A. Fundamental Challenges in Mechanistic Enzymology: Progress toward Understanding the Rate Enhancements of Enzymes Biochemistry 2013, 52, 2050-2067
    • (2013) Biochemistry , vol.52 , pp. 2050-2067
    • Herschlag, D.1    Natarajan, A.2
  • 7
    • 0016624901 scopus 로고
    • Binding Energy, Specificity, and Enzymic Catalysis: The Circe Effect
    • Jencks, W. P. Binding Energy, Specificity, And Enzymic Catalysis: The Circe Effect Adv. Enzymol. Relat. Areas Mol. Biol. 1975, 43, 219-410
    • (1975) Adv. Enzymol. Relat. Areas Mol. Biol. , vol.43 , pp. 219-410
    • Jencks, W.P.1
  • 8
    • 80053641898 scopus 로고    scopus 로고
    • Direct Measurement of the Protein Response to an Electrostatic Perturbation That Mimics the Catalytic Cycle in Ketosteroid Isomerase
    • Jha, S. K.; Ji, M.; Gaffney, K. J.; Boxer, S. G. Direct Measurement of the Protein Response to an Electrostatic Perturbation That Mimics the Catalytic Cycle in Ketosteroid Isomerase Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 16612-7
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 16612-16617
    • Jha, S.K.1    Ji, M.2    Gaffney, K.J.3    Boxer, S.G.4
  • 9
    • 83755181406 scopus 로고    scopus 로고
    • Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase
    • Schwans, J. P.; Sunden, F.; Gonzalez, A.; Tsai, Y.; Herschlag, D. Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase J. Am. Chem. Soc. 2011, 133, 20052-20055
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 20052-20055
    • Schwans, J.P.1    Sunden, F.2    Gonzalez, A.3    Tsai, Y.4    Herschlag, D.5
  • 10
    • 84904878087 scopus 로고    scopus 로고
    • Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase
    • Liu, C. T.; Layfield, J. P.; Stewart, R. J., III; French, J. B.; Hanoian, P.; Asbury, J. B.; Hammes-Schiffer, S.; Benkovic, S. J. Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase J. Am. Chem. Soc. 2014, 136, 10349-10360
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 10349-10360
    • Liu, C.T.1    Layfield, J.P.2    Stewart, R.J.3    French, J.B.4    Hanoian, P.5    Asbury, J.B.6    Hammes-Schiffer, S.7    Benkovic, S.J.8
  • 11
    • 0037188007 scopus 로고    scopus 로고
    • Nuclear Quantum Effects and Enzyme Dynamics in Dihydrofolate Reductase Catalysis
    • Agarwal, P. K.; Billeter, S. R.; Hammes-Schiffer, S. Nuclear Quantum Effects and Enzyme Dynamics in Dihydrofolate Reductase Catalysis J. Phys. Chem. B 2002, 106, 3283-3293
    • (2002) J. Phys. Chem. B , vol.106 , pp. 3283-3293
    • Agarwal, P.K.1    Billeter, S.R.2    Hammes-Schiffer, S.3
  • 13
    • 68049093016 scopus 로고    scopus 로고
    • Enzymatic Transition States and Dynamic Motion in Barrier Crossing
    • Schwartz, S. D.; Schramm, V. L. Enzymatic Transition States and Dynamic Motion in Barrier Crossing Nat. Chem. Biol. 2009, 5, 551-558
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 551-558
    • Schwartz, S.D.1    Schramm, V.L.2
  • 15
    • 84860338620 scopus 로고    scopus 로고
    • Crucial Role of Protein Flexibility in Formation of a Stable Reaction Transition State in an α-Amylase Catalysis
    • Kosugi, T.; Hayashi, S. Crucial Role of Protein Flexibility in Formation of a Stable Reaction Transition State in an α-Amylase Catalysis J. Am. Chem. Soc. 2012, 134, 7045-7055
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 7045-7055
    • Kosugi, T.1    Hayashi, S.2
  • 16
    • 36849039429 scopus 로고    scopus 로고
    • A Hierarchy of Timescales in Protein Dynamics is Linked to Enzyme Catalysis
    • Henzler-Wildman, K. A.; Lei, M.; Thai, V.; Kerns, S. J.; Karplus, M.; Kern, D. A Hierarchy of Timescales in Protein Dynamics Is Linked to Enzyme Catalysis Nature 2007, 450, 913-916
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1    Lei, M.2    Thai, V.3    Kerns, S.J.4    Karplus, M.5    Kern, D.6
  • 17
    • 0023668190 scopus 로고
    • Construction and Evaluation of the Kinetic Scheme Associated with Dihydrofolate Reductase from Escherichia coli
    • Fierke, C. A.; Johnson, K. A.; Benkovic, S. J. Construction and Evaluation of the Kinetic Scheme Associated with Dihydrofolate Reductase from Escherichia coli Biochemistry 1987, 26, 4085-4092
    • (1987) Biochemistry , vol.26 , pp. 4085-4092
    • Fierke, C.A.1    Johnson, K.A.2    Benkovic, S.J.3
  • 18
    • 0031015737 scopus 로고    scopus 로고
    • Loop and Subdomain Movements in the Mechanism of Escherichia coli Dihydrofolate Reductase: Crystallographic Evidence
    • Sawaya, M. R.; Kraut, J. Loop and Subdomain Movements in the Mechanism of Escherichia coli Dihydrofolate Reductase: Crystallographic Evidence Biochemistry 1997, 36, 586-603
    • (1997) Biochemistry , vol.36 , pp. 586-603
    • Sawaya, M.R.1    Kraut, J.2
  • 19
    • 76549109225 scopus 로고    scopus 로고
    • Millisecond Timescale Fluctuations in Dihydrofolate Reductase Are Exquisitely Sensitive to the Bound Ligands
    • Boehr, D. D.; McElheny, D.; Dyson, H. J.; Wright, P. E. Millisecond Timescale Fluctuations in Dihydrofolate Reductase Are Exquisitely Sensitive to the Bound Ligands Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 1373-1378
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 1373-1378
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 20
    • 79953823548 scopus 로고    scopus 로고
    • A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis
    • Bhabha, G.; Lee, J.; Ekiert, D. C.; Gam, J.; Wilson, I. A.; Dyson, H. J.; Benkovic, S. J.; Wright, P. E. A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis Science 2011, 332, 234-238
    • (2011) Science , vol.332 , pp. 234-238
    • Bhabha, G.1    Lee, J.2    Ekiert, D.C.3    Gam, J.4    Wilson, I.A.5    Dyson, H.J.6    Benkovic, S.J.7    Wright, P.E.8
  • 21
    • 84875675509 scopus 로고    scopus 로고
    • Connecting Protein Conformational Dynamics with Catalytic Function as Illustrated in Dihydrofolate Reductase
    • Fan, Y.; Cembran, A.; Ma, S.; Gao, J. Connecting Protein Conformational Dynamics with Catalytic Function as Illustrated in Dihydrofolate Reductase Biochemistry 2013, 52, 2036-2049
    • (2013) Biochemistry , vol.52 , pp. 2036-2049
    • Fan, Y.1    Cembran, A.2    Ma, S.3    Gao, J.4
  • 22
    • 84875665271 scopus 로고    scopus 로고
    • Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis
    • Klinman, J. P.; Kohen, A. Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis Annu. Rev. Biochem. 2013, 82, 471-496
    • (2013) Annu. Rev. Biochem. , vol.82 , pp. 471-496
    • Klinman, J.P.1    Kohen, A.2
  • 24
    • 1542327706 scopus 로고    scopus 로고
    • Single-Molecule and Transient Kinetics Investigation of the Interaction of Dihydrofolate Reductase with NADPH and Dihydrofolate
    • Zhang, Z. Q.; Rajagopalan, P. T. R.; Selzer, T.; Benkovic, S. J.; Hammes, G. G. Single-Molecule and Transient Kinetics Investigation of the Interaction of Dihydrofolate Reductase with NADPH and Dihydrofolate Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 2764-2769
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 2764-2769
    • Zhang, Z.Q.1    Rajagopalan, P.T.R.2    Selzer, T.3    Benkovic, S.J.4    Hammes, G.G.5
  • 25
    • 29344466944 scopus 로고    scopus 로고
    • Conformation Coupled Enzyme Catalysis: Single-Molecule and Transient Kinetics Investigation of Dihydrofolate Reductase
    • Antikainen, N. M.; Smiley, R. D.; Benkovic, S. J.; Hammes, G. G. Conformation Coupled Enzyme Catalysis: Single-Molecule and Transient Kinetics Investigation of Dihydrofolate Reductase Biochemistry 2005, 44, 16835-16843
    • (2005) Biochemistry , vol.44 , pp. 16835-16843
    • Antikainen, N.M.1    Smiley, R.D.2    Benkovic, S.J.3    Hammes, G.G.4
  • 26
    • 84881658197 scopus 로고    scopus 로고
    • Temporally Overlapped but Uncoupled Motions in Dihydrofolate Reductase Catalysis
    • Liu, C. T.; Wang, L.; Goodey, N. M.; Hanoian, P.; Benkovic, S. J. Temporally Overlapped but Uncoupled Motions in Dihydrofolate Reductase Catalysis Biochemistry 2013, 52, 5332-5334
    • (2013) Biochemistry , vol.52 , pp. 5332-5334
    • Liu, C.T.1    Wang, L.2    Goodey, N.M.3    Hanoian, P.4    Benkovic, S.J.5
  • 28
    • 84890417015 scopus 로고    scopus 로고
    • Preservation of Protein Dynamics in Dihydrofolate Reductase Evolution
    • Francis, K.; Stojkovic, V.; Kohen, A. Preservation of Protein Dynamics in Dihydrofolate Reductase Evolution J. Biol. Chem. 2013, 288, 35961-35968
    • (2013) J. Biol. Chem. , vol.288 , pp. 35961-35968
    • Francis, K.1    Stojkovic, V.2    Kohen, A.3
  • 29
    • 82455175792 scopus 로고    scopus 로고
    • Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis
    • Ramanathan, A.; Agarwal, P. K. Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis PLoS Biol. 2011, 9 e1001193
    • (2011) PLoS Biol. , vol.9 , pp. 1001193
    • Ramanathan, A.1    Agarwal, P.K.2
  • 30
    • 80052149070 scopus 로고    scopus 로고
    • Catalysis by Dihydrofolate Reductase and Other Enzymes Arises from Electrostatic Preorganization, Not Conformational Motions
    • Adamczyk, A. J.; Cao, J.; Kamerlin, S. C. L.; Warshel, A. Catalysis by Dihydrofolate Reductase and Other Enzymes Arises from Electrostatic Preorganization, Not Conformational Motions Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 14115-14120
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 14115-14120
    • Adamczyk, A.J.1    Cao, J.2    Kamerlin, S.C.L.3    Warshel, A.4
  • 31
    • 0031779284 scopus 로고    scopus 로고
    • a Shifts in Small Molecules and HIV Protease: Electrostatics and Conformation
    • a Shifts in Small Molecules and HIV Protease: Electrostatics and Conformation J. Am. Chem. Soc. 1998, 120, 6138-6146
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 6138-6146
    • Luo, R.1    Head, M.S.2    Moult, J.3    Gilson, M.K.4
  • 32
    • 0036001159 scopus 로고    scopus 로고
    • Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites
    • Harris, T. K.; Turner, G. J. Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites IUBMB Life 2002, 53, 85-98
    • (2002) IUBMB Life , vol.53 , pp. 85-98
    • Harris, T.K.1    Turner, G.J.2
  • 33
    • 0025292374 scopus 로고
    • Dissociation Constants for Dihydrofolic Acid and Dihydrobiopterin and Implications for Mechanistic Models for Dihydrofolate Reductase
    • Maharaj, G.; Selinsky, B. S.; Appleman, J. R.; Perlman, M.; London, R. E.; Blakley, R. L. Dissociation Constants for Dihydrofolic Acid and Dihydrobiopterin and Implications for Mechanistic Models for Dihydrofolate Reductase Biochemistry 1990, 29, 4554-4560
    • (1990) Biochemistry , vol.29 , pp. 4554-4560
    • Maharaj, G.1    Selinsky, B.S.2    Appleman, J.R.3    Perlman, M.4    London, R.E.5    Blakley, R.L.6
  • 34
    • 34249823367 scopus 로고    scopus 로고
    • Conformational Change of the Methionine 20 Loop of Escherichia coli Dihydrofolate Reductase Modulates pKa of the Bound Dihydrofolate
    • Khavrutskii, I. V.; Price, D. J.; Lee, J.; Brooks, C. L., 3rd Conformational Change of the Methionine 20 Loop of Escherichia coli Dihydrofolate Reductase Modulates pKa of the Bound Dihydrofolate Protein Sci. 2007, 16, 1087-1100
    • (2007) Protein Sci. , vol.16 , pp. 1087-1100
    • Khavrutskii, I.V.1    Price, D.J.2    Lee, J.3    Brooks, C.L.4
  • 35
    • 84919934356 scopus 로고    scopus 로고
    • Escherichia coli Dihydrofolate Reductase Catalyzed Proton and Hydride Transfers: Temporal Order and the Roles of Asp27 and Tyr100
    • Liu, C. T.; Francis, K.; Layfield, J. P.; Huang, X.; Hammes-Schiffer, S.; Kohen, A.; Benkovic, S. J. Escherichia coli Dihydrofolate Reductase Catalyzed Proton and Hydride Transfers: Temporal Order and the Roles of Asp27 and Tyr100 Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 18231-18236
    • (2014) Proc. Natl. Acad. Sci. U.S.A. , vol.111 , pp. 18231-18236
    • Liu, C.T.1    Francis, K.2    Layfield, J.P.3    Huang, X.4    Hammes-Schiffer, S.5    Kohen, A.6    Benkovic, S.J.7
  • 36
    • 0020492976 scopus 로고
    • Use of Multiple Isotope Effects to Determine Enzyme Mechanisms and Intrinsic Isotope Effects - Malic Enzyme and Glucose-6-Phosphate-Dehydrogenase
    • Hermes, J. D.; Roeske, C. A.; Oleary, M. H.; Cleland, W. W. Use of Multiple Isotope Effects to Determine Enzyme Mechanisms and Intrinsic Isotope Effects-Malic Enzyme and Glucose-6-Phosphate-Dehydrogenase Biochemistry 1982, 21, 5106-5114
    • (1982) Biochemistry , vol.21 , pp. 5106-5114
    • Hermes, J.D.1    Roeske, C.A.2    Oleary, M.H.3    Cleland, W.W.4
  • 37
    • 84904130280 scopus 로고    scopus 로고
    • Practical Aspects of Free-Energy Calculations: A Review
    • Hansen, N.; van Gunsteren, W. F. Practical Aspects of Free-Energy Calculations: A Review J. Chem. Theory Comput. 2014, 10, 2632-2647
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 2632-2647
    • Hansen, N.1    Van Gunsteren, W.F.2
  • 38
    • 84881082892 scopus 로고    scopus 로고
    • Infrared Probes for Studying the Structure and Dynamics of Biomolecules
    • Kim, H.; Cho, M. Infrared Probes for Studying the Structure and Dynamics of Biomolecules Chem. Rev. 2013, 113, 5817-5847
    • (2013) Chem. Rev. , vol.113 , pp. 5817-5847
    • Kim, H.1    Cho, M.2
  • 39
    • 33746017658 scopus 로고    scopus 로고
    • Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory
    • Suydam, I. T.; Snow, C. D.; Pande, V. S.; Boxer, S. G. Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory Science 2006, 313, 200-204
    • (2006) Science , vol.313 , pp. 200-204
    • Suydam, I.T.1    Snow, C.D.2    Pande, V.S.3    Boxer, S.G.4
  • 40
    • 5844252510 scopus 로고
    • Solvatochromic Dyes as Solvent Polarity Indicators
    • Reichardt, C. Solvatochromic Dyes as Solvent Polarity Indicators Chem. Rev. 1994, 94, 2319-2358
    • (1994) Chem. Rev. , vol.94 , pp. 2319-2358
    • Reichardt, C.1
  • 41
    • 84857125236 scopus 로고    scopus 로고
    • Quantitative, Directional Measurement of Electric Field Heterogeneity in the Active Site of Ketosteroid Isomerase
    • Fafarman, A. T.; Sigala, P. A.; Schwans, J. P.; Fenn, T. D.; Herschlag, D.; Boxer, S. G. Quantitative, Directional Measurement of Electric Field Heterogeneity in the Active Site of Ketosteroid Isomerase Proc. Natl. Acad. Sci. U.S.A. 2012, 109, E299-E308
    • (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , pp. 299-E308
    • Fafarman, A.T.1    Sigala, P.A.2    Schwans, J.P.3    Fenn, T.D.4    Herschlag, D.5    Boxer, S.G.6
  • 42
    • 84872576311 scopus 로고    scopus 로고
    • Calculation of Vibrational Shifts of Nitrile Probes in the Active Site of Ketosteroid Isomerase upon Ligand Binding
    • Layfield, J. P.; Hammes-Schiffer, S. Calculation of Vibrational Shifts of Nitrile Probes in the Active Site of Ketosteroid Isomerase upon Ligand Binding J. Am. Chem. Soc. 2013, 135, 717-725
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 717-725
    • Layfield, J.P.1    Hammes-Schiffer, S.2
  • 43
    • 70349303948 scopus 로고    scopus 로고
    • Nitrile Groups As Vibrational Probes of Biomolecular Structure and Dynamics: An Overview
    • Lindquist, B. A.; Furse, K. E.; Corcelli, S. A. Nitrile Groups As Vibrational Probes of Biomolecular Structure and Dynamics: An Overview Phys. Chem. Chem. Phys. 2009, 11, 8119-8132
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 8119-8132
    • Lindquist, B.A.1    Furse, K.E.2    Corcelli, S.A.3
  • 44
    • 84986771087 scopus 로고
    • Linear Solvation Energy Relationships. 8. Solvent Effects on NMR Spectral Shifts and Coupling-Constants
    • Taft, R. W.; Kamlet, M. J. Linear Solvation Energy Relationships. 8. Solvent Effects on NMR Spectral Shifts and Coupling-Constants Org. Magn. Reson. 1980, 14, 485-493
    • (1980) Org. Magn. Reson. , vol.14 , pp. 485-493
    • Taft, R.W.1    Kamlet, M.J.2
  • 45
    • 80054955089 scopus 로고    scopus 로고
    • Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules
    • Waegele, M. M.; Culik, R. M.; Gai, F. Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules J. Phys. Chem. Lett. 2011, 2, 2598-2609
    • (2011) J. Phys. Chem. Lett. , vol.2 , pp. 2598-2609
    • Waegele, M.M.1    Culik, R.M.2    Gai, F.3
  • 47
    • 64849113665 scopus 로고    scopus 로고
    • Trapping Moving Targets with Small Molecules
    • Lee, G. M.; Craik, C. S. Trapping Moving Targets with Small Molecules Science 2009, 324, 213-215
    • (2009) Science , vol.324 , pp. 213-215
    • Lee, G.M.1    Craik, C.S.2
  • 48
    • 61449163022 scopus 로고    scopus 로고
    • Communication Breakdown: Protein Dynamics and Drug Design
    • Peng, J. W. Communication Breakdown: Protein Dynamics and Drug Design Structure 2009, 17, 319-320
    • (2009) Structure , vol.17 , pp. 319-320
    • Peng, J.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.