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Volumn 1804, Issue 2, 2010, Pages 352-361

Role of protein motions on proton transfer pathways in human carbonic anhydrase II

Author keywords

Carbonic anhydrase; Conformational dynamics; Pathway; Proton transfer

Indexed keywords

ALANINE; AMINO ACID; CARBONATE DEHYDRATASE II; HISTIDINE; WATER;

EID: 74449086022     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2009.09.004     Document Type: Article
Times cited : (12)

References (63)
  • 1
    • 36949083936 scopus 로고
    • Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism
    • Mitchell P. Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature 191 (1961) 144-148
    • (1961) Nature , vol.191 , pp. 144-148
    • Mitchell, P.1
  • 3
    • 0032143387 scopus 로고    scopus 로고
    • Proton translocation by bacteriorhodopsin and heme-copper oxidases
    • Wikström M. Proton translocation by bacteriorhodopsin and heme-copper oxidases. Curr. Opin. Struct. Biol. 8 (1998) 480-488
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 480-488
    • Wikström, M.1
  • 5
    • 33749052047 scopus 로고    scopus 로고
    • Chance and design-proton transfer in water, channels and bioenergetic proteins
    • Wraight C.A. Chance and design-proton transfer in water, channels and bioenergetic proteins. Biochim. Biophys. Acta 1757 (2006) 886-912
    • (2006) Biochim. Biophys. Acta , vol.1757 , pp. 886-912
    • Wraight, C.A.1
  • 6
    • 0242527943 scopus 로고
    • Quarton G., Melnechuk T., and Schmitt F.O. (Eds), Rockefeller University Press, New York
    • Onsager L. In: Quarton G., Melnechuk T., and Schmitt F.O. (Eds). The Neurosciences (1967), Rockefeller University Press, New York 75-79
    • (1967) The Neurosciences , pp. 75-79
    • Onsager, L.1
  • 7
    • 0342959328 scopus 로고
    • The motion of ions: principles and concepts
    • Onsager L. The motion of ions: principles and concepts. Science 166 (1969) 1359-1364
    • (1969) Science , vol.166 , pp. 1359-1364
    • Onsager, L.1
  • 8
    • 0020967882 scopus 로고
    • Hydrogen bonded chain mechanisms for proton conduction and proton pumping
    • Nagle J.F., and Nagle T.N. Hydrogen bonded chain mechanisms for proton conduction and proton pumping. J. Mem. Biol. 74 (1983) 1-14
    • (1983) J. Mem. Biol. , vol.74 , pp. 1-14
    • Nagle, J.F.1    Nagle, T.N.2
  • 9
    • 0002036605 scopus 로고
    • Sur la decomposition de l'eau et des corps qu'elle tient en dissolution a l'aide de l'electricite galvanique
    • Grotthuss C.J.T.V. Sur la decomposition de l'eau et des corps qu'elle tient en dissolution a l'aide de l'electricite galvanique (Theory of decomposition of liquids by electric currents). Ann. Chim. 58 (1806) 54-74
    • (1806) Ann. Chim. , vol.58 , pp. 54-74
    • Grotthuss, C.J.T.V.1
  • 10
    • 33748969865 scopus 로고    scopus 로고
    • Proton transfer 200 years after von Grotthuss: insights from ab initio simulations
    • Marx D. Proton transfer 200 years after von Grotthuss: insights from ab initio simulations. ChemPhysChem 7 (2006) 1848-1870
    • (2006) ChemPhysChem , vol.7 , pp. 1848-1870
    • Marx, D.1
  • 11
    • 0032711930 scopus 로고    scopus 로고
    • Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems
    • Monard G., and Merz Jr. K.M. Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Acc. Chem. Res. 32 (1999) 904-911
    • (1999) Acc. Chem. Res. , vol.32 , pp. 904-911
    • Monard, G.1    Merz Jr., K.M.2
  • 12
    • 0034321020 scopus 로고    scopus 로고
    • Proton transfer in bacteriorhodopsin: structure, excitation, IR spectra, and potential energy surface analyses by an ab initio QM/MM method
    • Hyashi S., and Ohmine I. Proton transfer in bacteriorhodopsin: structure, excitation, IR spectra, and potential energy surface analyses by an ab initio QM/MM method. J. Phys. Chem. B 104 (2000) 10678-10691
    • (2000) J. Phys. Chem. B , vol.104 , pp. 10678-10691
    • Hyashi, S.1    Ohmine, I.2
  • 13
    • 34548059996 scopus 로고    scopus 로고
    • Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
    • Schaefer P., Riccardi D., and Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J. Chem. Phys. 123 (2005) 14905-14919
    • (2005) J. Chem. Phys. , vol.123 , pp. 14905-14919
    • Schaefer, P.1    Riccardi, D.2    Cui, Q.3
  • 14
    • 0141642135 scopus 로고    scopus 로고
    • On the mechanism of ATP hydrolysis in F1-ATPase
    • Dittrich M., Hayashi S., and Schulten C. On the mechanism of ATP hydrolysis in F1-ATPase. Biophysical J. 85 (2003) 2253-2266
    • (2003) Biophysical J. , vol.85 , pp. 2253-2266
    • Dittrich, M.1    Hayashi, S.2    Schulten, C.3
  • 15
    • 33644989063 scopus 로고    scopus 로고
    • Computer simulation of proton solvation and transport in aqueous and biomolecular system
    • Voth G.A. Computer simulation of proton solvation and transport in aqueous and biomolecular system. Acc. Chem. Res. 39 (2006) 143-150
    • (2006) Acc. Chem. Res. , vol.39 , pp. 143-150
    • Voth, G.A.1
  • 16
    • 12344266417 scopus 로고    scopus 로고
    • Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models
    • Braun-Sand S., Stajbl M., and Warshel A. Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models. Biophysical J. 87 (2004) 2221-2239
    • (2004) Biophysical J. , vol.87 , pp. 2221-2239
    • Braun-Sand, S.1    Stajbl, M.2    Warshel, A.3
  • 17
    • 1342281185 scopus 로고    scopus 로고
    • Analyzing free energy relationships for proton translocations in enzymes: carbonic anhydrase revisited
    • Schutz C.N., and Warshel A. Analyzing free energy relationships for proton translocations in enzymes: carbonic anhydrase revisited. J. Phys Chem. B. 108 (2004) 2066-2075
    • (2004) J. Phys Chem. B. , vol.108 , pp. 2066-2075
    • Schutz, C.N.1    Warshel, A.2
  • 19
    • 0026504259 scopus 로고
    • Computer simulation of the initial proton transfer step in human carbonic anhydrase I
    • Åqvist J., and Warshel A. Computer simulation of the initial proton transfer step in human carbonic anhydrase I. J. Mol. Biol. 224 (1992) 7-14
    • (1992) J. Mol. Biol. , vol.224 , pp. 7-14
    • Åqvist, J.1    Warshel, A.2
  • 20
    • 0027012925 scopus 로고
    • Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase
    • Warshel A., and Hwang J.K. Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase. Faraday Discuss 93 (1992) 225-238
    • (1992) Faraday Discuss , vol.93 , pp. 225-238
    • Warshel, A.1    Hwang, J.K.2
  • 21
    • 0035850352 scopus 로고    scopus 로고
    • Proton conduction by a chain of water molecules in carbonic anhydrase
    • Isaev A., and Scheiner S. Proton conduction by a chain of water molecules in carbonic anhydrase. J. Phys. Chem. B 105 (2001) 6420-6426
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6420-6426
    • Isaev, A.1    Scheiner, S.2
  • 22
    • 0037473097 scopus 로고    scopus 로고
    • Is a "proton wire" concerted or stepwise? A model study of proton transfer in carbonic anhydrase
    • Cui Q., and Kaplus M. Is a "proton wire" concerted or stepwise? A model study of proton transfer in carbonic anhydrase. J. Phys. Chem. B 107 (2003) 1071-1078
    • (2003) J. Phys. Chem. B , vol.107 , pp. 1071-1078
    • Cui, Q.1    Kaplus, M.2
  • 23
    • 33749043747 scopus 로고    scopus 로고
    • Et tu, Grotthuss! and other unfinished stories
    • Cukierman S. Et tu, Grotthuss! and other unfinished stories. Biochim. Biophys. Acta 1757 (2006) 876-885
    • (2006) Biochim. Biophys. Acta , vol.1757 , pp. 876-885
    • Cukierman, S.1
  • 27
    • 0016722749 scopus 로고
    • The catalytic mechanism of carbonic anhydrase
    • Steiner H., Jonsson B.H., and Lindskog S. The catalytic mechanism of carbonic anhydrase. Eur. J. Biochem. 59 (1975) 253-259
    • (1975) Eur. J. Biochem. , vol.59 , pp. 253-259
    • Steiner, H.1    Jonsson, B.H.2    Lindskog, S.3
  • 28
    • 33845278732 scopus 로고
    • The catalytic mechanism of carbonic-anhydrase - implication of a rate limiting protolysis of water
    • Silverman D.N., and Lindskog S. The catalytic mechanism of carbonic-anhydrase - implication of a rate limiting protolysis of water. Acc. Chem. Res. 21 (1988) 30-36
    • (1988) Acc. Chem. Res. , vol.21 , pp. 30-36
    • Silverman, D.N.1    Lindskog, S.2
  • 29
    • 0009593678 scopus 로고
    • Unexpected pH-dependent conformation of His-64, the proton shuttle of carbonic anhydrase-II
    • Nair S.K., and Christianson D.W. Unexpected pH-dependent conformation of His-64, the proton shuttle of carbonic anhydrase-II. J. Am. Chem. Soc. 113 (1991) 9455
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 9455
    • Nair, S.K.1    Christianson, D.W.2
  • 31
    • 0024421430 scopus 로고
    • Role of histidine-64 in the catalytic mechanism of human carbonic anhydrase-II studied with a site-specific mutant
    • Tu C., Silverman D.N., Forsman C., Jonsson B.H., and Lindskog S. Role of histidine-64 in the catalytic mechanism of human carbonic anhydrase-II studied with a site-specific mutant. Biochemistry 28 (1989) 7913-7918
    • (1989) Biochemistry , vol.28 , pp. 7913-7918
    • Tu, C.1    Silverman, D.N.2    Forsman, C.3    Jonsson, B.H.4    Lindskog, S.5
  • 33
    • 34548724094 scopus 로고    scopus 로고
    • Solvent-mediated proton transfer in catalysis by carbonic anhydrase
    • Silverman D.N., and McKenna R. Solvent-mediated proton transfer in catalysis by carbonic anhydrase. Acc. Chem. Res. 40 (2007) 669-675
    • (2007) Acc. Chem. Res. , vol.40 , pp. 669-675
    • Silverman, D.N.1    McKenna, R.2
  • 34
    • 33947367836 scopus 로고    scopus 로고
    • Preferred orientations of His64 in human carbonic anhydrase II
    • Maupin C.M., and Voth G.A. Preferred orientations of His64 in human carbonic anhydrase II. Biochemistry 46 (2007) 2938-2947
    • (2007) Biochemistry , vol.46 , pp. 2938-2947
    • Maupin, C.M.1    Voth, G.A.2
  • 37
    • 0035852857 scopus 로고    scopus 로고
    • Structural and kinetic analysis of the chemical rescue of the proton transfer function of carbonic anhydrase II
    • Duda D., Tu C., Qian M., Laipis P., Agbandje-McKenna M., Silverman D.N., and McKenna R. Structural and kinetic analysis of the chemical rescue of the proton transfer function of carbonic anhydrase II. Biochemistry 40 (2001) 1741-1748
    • (2001) Biochemistry , vol.40 , pp. 1741-1748
    • Duda, D.1    Tu, C.2    Qian, M.3    Laipis, P.4    Agbandje-McKenna, M.5    Silverman, D.N.6    McKenna, R.7
  • 38
    • 0242669318 scopus 로고    scopus 로고
    • Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome P450cam
    • Taraphder S., and Hummer G. Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome P450cam. J. Am. Chem. Soc. 125 (2003) 3931-3940
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 3931-3940
    • Taraphder, S.1    Hummer, G.2
  • 39
    • 34548823782 scopus 로고    scopus 로고
    • Identification of proton-transfer pathways in human carbonic anhydrase II
    • Roy A., and Taraphder S. Identification of proton-transfer pathways in human carbonic anhydrase II. J. Phys. Chem. B 111 (2007) 10563-10576
    • (2007) J. Phys. Chem. B , vol.111 , pp. 10563-10576
    • Roy, A.1    Taraphder, S.2
  • 40
    • 67649534573 scopus 로고    scopus 로고
    • Mapping proton-wires in proteins: carbonic anhydrase and GFP chromophore biosynthesis
    • Shinobu A., and Agmon N. Mapping proton-wires in proteins: carbonic anhydrase and GFP chromophore biosynthesis. J. Phys. Chem. A 113 (2009) 7253-7266
    • (2009) J. Phys. Chem. A , vol.113 , pp. 7253-7266
    • Shinobu, A.1    Agmon, N.2
  • 41
    • 0030906757 scopus 로고    scopus 로고
    • Hydration of an alpha-helical peptide: comparison of theory and molecular dynamics simulation
    • Hummer G., Garcia A.E., and Soumpasis D.M. Hydration of an alpha-helical peptide: comparison of theory and molecular dynamics simulation. Proteins: Struct. Func. Gen. 27 (1997) 471-480
    • (1997) Proteins: Struct. Func. Gen. , vol.27 , pp. 471-480
    • Hummer, G.1    Garcia, A.E.2    Soumpasis, D.M.3
  • 42
    • 16444385400 scopus 로고
    • Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid
    • Torrie G.M., and Valleau J.P. Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid. Chem. Phys. Lett. 28 (1974) 578-581
    • (1974) Chem. Phys. Lett. , vol.28 , pp. 578-581
    • Torrie, G.M.1    Valleau, J.P.2
  • 43
    • 0035277126 scopus 로고    scopus 로고
    • Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations
    • Souaille M., and Roux B. Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations. Comput. Phys. Comm. 135 (2001) 40-57
    • (2001) Comput. Phys. Comm. , vol.135 , pp. 40-57
    • Souaille, M.1    Roux, B.2
  • 45
    • 0344270866 scopus 로고    scopus 로고
    • Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA
    • Hagan M.F., Dinner A.R., Chendler D., and Chakraborty A.K. Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA. Proc. Nat. Acad. Sci. 100 (2003) 13922-13927
    • (2003) Proc. Nat. Acad. Sci. , vol.100 , pp. 13922-13927
    • Hagan, M.F.1    Dinner, A.R.2    Chendler, D.3    Chakraborty, A.K.4
  • 46
    • 34547628903 scopus 로고    scopus 로고
    • Reaction coordinate of an enzymatic reaction revealed by transition path sampling
    • Quaytman S.L., and Schwartz S.D. Reaction coordinate of an enzymatic reaction revealed by transition path sampling. Proc. Nat. Acad. Sci. 104 (2007) 12253-12258
    • (2007) Proc. Nat. Acad. Sci. , vol.104 , pp. 12253-12258
    • Quaytman, S.L.1    Schwartz, S.D.2
  • 47
    • 1942437505 scopus 로고    scopus 로고
    • Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase β closing
    • Radhakrishnan R., and Schlick T. Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase β closing. Proc. Nat. Acad. Sci. 101 (2004) 5970-5975
    • (2004) Proc. Nat. Acad. Sci. , vol.101 , pp. 5970-5975
    • Radhakrishnan, R.1    Schlick, T.2
  • 48
    • 34250327509 scopus 로고    scopus 로고
    • A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase
    • Crehuet R., and Field M.J. A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase. J. Phys. Chem. B 111 (2007) 5708-5718
    • (2007) J. Phys. Chem. B , vol.111 , pp. 5708-5718
    • Crehuet, R.1    Field, M.J.2
  • 49
    • 34548494273 scopus 로고    scopus 로고
    • Transition path sampling simulations of biological systems
    • Dellago C., and Bolhuis P.G. Transition path sampling simulations of biological systems. Top. Curr. Chem. 268 (2007) 291-317
    • (2007) Top. Curr. Chem. , vol.268 , pp. 291-317
    • Dellago, C.1    Bolhuis, P.G.2
  • 50
    • 0026463503 scopus 로고
    • Structure of native and apo carbonic anhydrase-II and structure of some of its anion ligand complexes
    • Häkansson K., Carlsson M., Svensson A., and Liljas A. Structure of native and apo carbonic anhydrase-II and structure of some of its anion ligand complexes. J. Mol. Biol. 227 (1992) 1192-1204
    • (1992) J. Mol. Biol. , vol.227 , pp. 1192-1204
    • Häkansson, K.1    Carlsson, M.2    Svensson, A.3    Liljas, A.4
  • 52
    • 0015222647 scopus 로고
    • The interpretation of protein structures: estimation of static accessibility
    • Lee B., and Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55 (1971) 379-400
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 53
    • 0003742069 scopus 로고
    • Department of Biochemistry and Molecular Biology, University College London
    • Hubbard S.J., and Thornton J.M. 'NACCESS', Computer Program (1993), Department of Biochemistry and Molecular Biology, University College London
    • (1993) 'NACCESS', Computer Program
    • Hubbard, S.J.1    Thornton, J.M.2
  • 54
    • 36849068466 scopus 로고    scopus 로고
    • Effect of electrostatic interactions on the formation of proton transfer pathways in human carbonic anhydrase II
    • Roy A., and Taraphder S. Effect of electrostatic interactions on the formation of proton transfer pathways in human carbonic anhydrase II. J. Chem. Sci. 119 (2007) 545-552
    • (2007) J. Chem. Sci. , vol.119 , pp. 545-552
    • Roy, A.1    Taraphder, S.2
  • 55
    • 33746972783 scopus 로고    scopus 로고
    • Proton transfer pathways in the mutant His-64-Ala of human carbonic anhydrase II
    • Roy A., and Taraphder S. Proton transfer pathways in the mutant His-64-Ala of human carbonic anhydrase II. Biopolymer 82 (2006) 623-630
    • (2006) Biopolymer , vol.82 , pp. 623-630
    • Roy, A.1    Taraphder, S.2
  • 56
    • 0037237571 scopus 로고    scopus 로고
    • The refined atomic structure of carbonic anhydrase II at 1.05 angstrom resolution: implications of chemical rescue of proton transfer
    • Duda D., Govindasamy L., Agbandje-McKenna M., Tu C., Silverman D.N., and McKenna R. The refined atomic structure of carbonic anhydrase II at 1.05 angstrom resolution: implications of chemical rescue of proton transfer. Acta Cryst. D59 (2003) 93-104
    • (2003) Acta Cryst. , vol.D59 , pp. 93-104
    • Duda, D.1    Govindasamy, L.2    Agbandje-McKenna, M.3    Tu, C.4    Silverman, D.N.5    McKenna, R.6
  • 57
    • 13444269025 scopus 로고    scopus 로고
    • Structural and kinetic characterization of active-site histidine as a proton shuttle in catalysis by human carbonic anhydrase II
    • Fisher Z., Prada J.A.H., Tu C., Duda D., Yoshioka C., An H., Govindsamy L., Silverman D.N., and McKenna R. Structural and kinetic characterization of active-site histidine as a proton shuttle in catalysis by human carbonic anhydrase II. Biochemistry 44 (2005) 1097-1105
    • (2005) Biochemistry , vol.44 , pp. 1097-1105
    • Fisher, Z.1    Prada, J.A.H.2    Tu, C.3    Duda, D.4    Yoshioka, C.5    An, H.6    Govindsamy, L.7    Silverman, D.N.8    McKenna, R.9
  • 58
    • 55949084842 scopus 로고    scopus 로고
    • A theoretical study on the detection of proton transfer pathways in some mutants of human carbonic anhydrase II
    • Roy A., and Taraphder S. A theoretical study on the detection of proton transfer pathways in some mutants of human carbonic anhydrase II. J. Phys. Chem. B 112 (2008) 13597-13607
    • (2008) J. Phys. Chem. B , vol.112 , pp. 13597-13607
    • Roy, A.1    Taraphder, S.2
  • 59
    • 0000728542 scopus 로고
    • Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
    • Lee F.S., Chu Z.T., and Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J. Comput. Chem. 14 (1993) 161-185
    • (1993) J. Comput. Chem. , vol.14 , pp. 161-185
    • Lee, F.S.1    Chu, Z.T.2    Warshel, A.3
  • 61
    • 70349153122 scopus 로고    scopus 로고
    • Transition path sampling study of the conformational fluctuation of His-64 in human carbonic anhydrase II
    • Roy A., and Taraphder S. Transition path sampling study of the conformational fluctuation of His-64 in human carbonic anhydrase II. J. Phys. Chem. B 113 (2009) 12555-12564
    • (2009) J. Phys. Chem. B , vol.113 , pp. 12555-12564
    • Roy, A.1    Taraphder, S.2
  • 62
    • 67650513577 scopus 로고    scopus 로고
    • Elucidation of the proton transport mechanism in human carbonic anhydrase II
    • Maupin C.M., McKenna R., Silverman D.N., and Voth G.A. Elucidation of the proton transport mechanism in human carbonic anhydrase II. J. Am. Chem. Soc. 131 (2009) 7598-7608
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 7598-7608
    • Maupin, C.M.1    McKenna, R.2    Silverman, D.N.3    Voth, G.A.4
  • 63
    • 56249123954 scopus 로고    scopus 로고
    • Role of hydrophilic residues in proton transfer during catalysis by human carbonic anhydrase II
    • Zheng J., Avvaru B.S., Tu C., McKenna R., and Silverman D. Role of hydrophilic residues in proton transfer during catalysis by human carbonic anhydrase II. Biochemistry 47 (2008) 12028-12036
    • (2008) Biochemistry , vol.47 , pp. 12028-12036
    • Zheng, J.1    Avvaru, B.S.2    Tu, C.3    McKenna, R.4    Silverman, D.5


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