메뉴 건너뛰기




Volumn 4, Issue , 2008, Pages 89-106

Chapter 5 Analyzing Protein NMR pH-Titration Curves

Author keywords

dielectric constant; NMR pH titration curves; pKa values; protein conformational change; protein electrostatics; titration curves

Indexed keywords


EID: 54849407158     PISSN: 15741400     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1574-1400(08)00005-4     Document Type: Chapter
Times cited : (13)

References (93)
  • 3
    • 33947468892 scopus 로고
    • Theory of protein titration curves. I. General equations for impenetrable spheres
    • Tanford C., and Kirkwood J.G. Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 79 (1957) 5333-5339
    • (1957) J. Am. Chem. Soc. , vol.79 , pp. 5333-5339
    • Tanford, C.1    Kirkwood, J.G.2
  • 4
    • 0015520587 scopus 로고
    • Interpretation of protein titration curves. Application to lysozyme
    • Tanford C., and Roxby R. Interpretation of protein titration curves. Application to lysozyme. Biochemistry 11 (1972) 2193-2198
    • (1972) Biochemistry , vol.11 , pp. 2193-2198
    • Tanford, C.1    Roxby, R.2
  • 5
    • 0018945613 scopus 로고
    • Analysis of the acid-base titration curve of hen lysozyme
    • Kuramitsu S., and Hamaguchi K. Analysis of the acid-base titration curve of hen lysozyme. J. Biochem. (Tokyo) 87 (1980) 1215-1219
    • (1980) J. Biochem. (Tokyo) , vol.87 , pp. 1215-1219
    • Kuramitsu, S.1    Hamaguchi, K.2
  • 6
    • 33751499830 scopus 로고
    • Multiple-site titration curves of proteins: An analysis of exact and approximate methods for their calculation
    • Bashford D., and Karplus M. Multiple-site titration curves of proteins: An analysis of exact and approximate methods for their calculation. J. Phys. Chem. 95 (1991) 9556-9561
    • (1991) J. Phys. Chem. , vol.95 , pp. 9556-9561
    • Bashford, D.1    Karplus, M.2
  • 7
    • 0028979982 scopus 로고
    • Abnormally high pKa of an active-site glutamic acid residue in Bacillus circulans xylanase. The role of electrostatic interactions
    • Davoodi J., Wakarchuk W.W., Campbell R.L., Carey P.R., and Surewicz W.K. Abnormally high pKa of an active-site glutamic acid residue in Bacillus circulans xylanase. The role of electrostatic interactions. Eur. J. Biochem. 232 (1995) 839-843
    • (1995) Eur. J. Biochem. , vol.232 , pp. 839-843
    • Davoodi, J.1    Wakarchuk, W.W.2    Campbell, R.L.3    Carey, P.R.4    Surewicz, W.K.5
  • 8
    • 0028983182 scopus 로고
    • pKA values of carboxyl groups in the native and denatured states of Barnase: The pKA values of the denatured state are on average 0.4 units lower than those of model compounds
    • Oliveberg M., Arcus V.L., and Fersht A.R. pKA values of carboxyl groups in the native and denatured states of Barnase: The pKA values of the denatured state are on average 0.4 units lower than those of model compounds. Biochemistry 34 (1995) 9424-9433
    • (1995) Biochemistry , vol.34 , pp. 9424-9433
    • Oliveberg, M.1    Arcus, V.L.2    Fersht, A.R.3
  • 9
    • 0030596490 scopus 로고    scopus 로고
    • Measurement and modelling of sequence-specific pKa values of lysine residues in calbindin D9k
    • Kesvatera T., Jonsson B., Thulin E., and Linse S. Measurement and modelling of sequence-specific pKa values of lysine residues in calbindin D9k. J. Mol. Biol. 259 (1996) 828-839
    • (1996) J. Mol. Biol. , vol.259 , pp. 828-839
    • Kesvatera, T.1    Jonsson, B.2    Thulin, E.3    Linse, S.4
  • 10
    • 0032589144 scopus 로고    scopus 로고
    • His ... Asp catalytic dyad of ribonuclease A: Histidine pKa values in the wild-type, D121N, and D121A enzymes
    • Quirk D.J., and Raines R.T. His ... Asp catalytic dyad of ribonuclease A: Histidine pKa values in the wild-type, D121N, and D121A enzymes. Biophys. J. 76 (1999) 1571-1579
    • (1999) Biophys. J. , vol.76 , pp. 1571-1579
    • Quirk, D.J.1    Raines, R.T.2
  • 11
    • 0015882230 scopus 로고
    • Lysozyme-catalyzed reaction of the N-acetylglucosamine hexasaccharide. Dependence of rate on pH
    • Banerjee S.K., Kregar I., Turk V., and Rupley J.A. Lysozyme-catalyzed reaction of the N-acetylglucosamine hexasaccharide. Dependence of rate on pH. J. Biol. Chem. 248 (1973) 4786-4792
    • (1973) J. Biol. Chem. , vol.248 , pp. 4786-4792
    • Banerjee, S.K.1    Kregar, I.2    Turk, V.3    Rupley, J.A.4
  • 12
    • 0017406875 scopus 로고
    • Effects of ionic strength and temperature on the ionization of the catalytic groups, Asp 52 and Glu 35, in hen lysozyme
    • Kuramitsu S., Ikeda K., and Hamaguchi K. Effects of ionic strength and temperature on the ionization of the catalytic groups, Asp 52 and Glu 35, in hen lysozyme. J. Biochem. (Tokyo) 82 (1977) 585-597
    • (1977) J. Biochem. (Tokyo) , vol.82 , pp. 585-597
    • Kuramitsu, S.1    Ikeda, K.2    Hamaguchi, K.3
  • 13
    • 0015522962 scopus 로고
    • Ionization behavior of the cleft carboxyls in lysozyme-substrate complexes
    • Parsons S.M., and Raftery M.A. Ionization behavior of the cleft carboxyls in lysozyme-substrate complexes. Biochemistry 11 (1972) 1633-1638
    • (1972) Biochemistry , vol.11 , pp. 1633-1638
    • Parsons, S.M.1    Raftery, M.A.2
  • 14
    • 0015522941 scopus 로고
    • Ionization behavior of the catalytic carboxyls of lysozyme. Effects of temperature
    • Parsons S.M., and Raftery M.A. Ionization behavior of the catalytic carboxyls of lysozyme. Effects of temperature. Biochemistry 11 (1972) 1630-1633
    • (1972) Biochemistry , vol.11 , pp. 1630-1633
    • Parsons, S.M.1    Raftery, M.A.2
  • 15
    • 0015522917 scopus 로고
    • Ionization behavior of the catalytic carboxyls of lysozyme. Effects of ionic strength
    • Parsons S.M., and Raftery M.A. Ionization behavior of the catalytic carboxyls of lysozyme. Effects of ionic strength. Biochemistry 11 (1972) 1623-1629
    • (1972) Biochemistry , vol.11 , pp. 1623-1629
    • Parsons, S.M.1    Raftery, M.A.2
  • 16
    • 0033118732 scopus 로고    scopus 로고
    • Structures of orthorhombic lysozyme grown at basic pH and its low-humidity variant
    • Sukumar N., Biswal B.K., and Vijayan M. Structures of orthorhombic lysozyme grown at basic pH and its low-humidity variant. Acta Crystallogr. D Biol. Crystallogr. 55 Pt 4 (1999) 934-937
    • (1999) Acta Crystallogr. D Biol. Crystallogr. , vol.55 , Issue.PART 4 , pp. 934-937
    • Sukumar, N.1    Biswal, B.K.2    Vijayan, M.3
  • 17
    • 0026910551 scopus 로고
    • Electrostatic forces in two lysozymes: Calculations and measurements of histidine pKa values
    • Takahashi T., Nakamura H., and Wada A. Electrostatic forces in two lysozymes: Calculations and measurements of histidine pKa values. Biopolymers 32 (1992) 897-909
    • (1992) Biopolymers , vol.32 , pp. 897-909
    • Takahashi, T.1    Nakamura, H.2    Wada, A.3
  • 18
    • 0019059776 scopus 로고
    • Hydrolysis of 4-methylumbelliferyl N-acetyl-chitotetraoside catalyzed by hen lysozyme
    • Yang Y., and Hamaguchi K. Hydrolysis of 4-methylumbelliferyl N-acetyl-chitotetraoside catalyzed by hen lysozyme. J. Biochem. (Tokyo) 88 (1980) 829-836
    • (1980) J. Biochem. (Tokyo) , vol.88 , pp. 829-836
    • Yang, Y.1    Hamaguchi, K.2
  • 19
    • 0022964504 scopus 로고
    • Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification
    • Klapper I., Hagstrom R., Fine R., Sharp K., and Honig B. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification. Proteins 1 (1986) 47-59
    • (1986) Proteins , vol.1 , pp. 47-59
    • Klapper, I.1    Hagstrom, R.2    Fine, R.3    Sharp, K.4    Honig, B.5
  • 21
    • 0025197061 scopus 로고
    • pKa's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
    • Bashford D., and Karplus M. pKa's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model. Biochemistry 29 (1990) 10219-10225
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 22
    • 0019889036 scopus 로고
    • Calculations of enzymatic reactions: Calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes
    • Warshel A. Calculations of enzymatic reactions: Calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry 20 (1981) 3167-3177
    • (1981) Biochemistry , vol.20 , pp. 3167-3177
    • Warshel, A.1
  • 24
    • 33751560650 scopus 로고    scopus 로고
    • Electrostatic contributions to residue-specific protonation equilibria and proton binding capacitance for a small protein
    • Lindman S., Linse S., Mulder F.A., and Andre I. Electrostatic contributions to residue-specific protonation equilibria and proton binding capacitance for a small protein. Biochemistry 45 (2006) 13993-14002
    • (2006) Biochemistry , vol.45 , pp. 13993-14002
    • Lindman, S.1    Linse, S.2    Mulder, F.A.3    Andre, I.4
  • 25
    • 34250823484 scopus 로고    scopus 로고
    • Probing electrostatic interactions along the reaction pathway of a glycoside hydrolase: Histidine characterization by NMR spectroscopy
    • Schubert M., Poon D.K., Wicki J., Tarling C.A., Kwan E.M., Nielsen J.E., Withers S.G., and McIntosh L.P. Probing electrostatic interactions along the reaction pathway of a glycoside hydrolase: Histidine characterization by NMR spectroscopy. Biochemistry 46 (2007) 7383-7395
    • (2007) Biochemistry , vol.46 , pp. 7383-7395
    • Schubert, M.1    Poon, D.K.2    Wicki, J.3    Tarling, C.A.4    Kwan, E.M.5    Nielsen, J.E.6    Withers, S.G.7    McIntosh, L.P.8
  • 26
    • 0036099192 scopus 로고    scopus 로고
    • Experimental pK(a) values of buried residues: Analysis with continuum methods and role of water penetration
    • Fitch C.A., Karp D.A., Lee K.K., Stites W.E., Lattman E.E., and Garcia-Moreno E.B. Experimental pK(a) values of buried residues: Analysis with continuum methods and role of water penetration. Biophys. J. 82 (2002) 3289-3304
    • (2002) Biophys. J. , vol.82 , pp. 3289-3304
    • Fitch, C.A.1    Karp, D.A.2    Lee, K.K.3    Stites, W.E.4    Lattman, E.E.5    Garcia-Moreno, E.B.6
  • 27
    • 0347298770 scopus 로고    scopus 로고
    • Changes in stability upon charge reversal and neutralization substitution in staphylococcal nuclease are dominated by favorable electrostatic effects
    • Schwehm J.M., Fitch C.A., Dang B.N., Garcia-Moreno E.B., and Stites W.E. Changes in stability upon charge reversal and neutralization substitution in staphylococcal nuclease are dominated by favorable electrostatic effects. Biochemistry 42 (2003) 1118-1128
    • (2003) Biochemistry , vol.42 , pp. 1118-1128
    • Schwehm, J.M.1    Fitch, C.A.2    Dang, B.N.3    Garcia-Moreno, E.B.4    Stites, W.E.5
  • 28
    • 37549044716 scopus 로고    scopus 로고
    • Residue-specific pKa determination of lysine and arginine side chains by indirect 15N and 13C NMR spectroscopy: Application to apo calmodulin
    • Andre I., Linse S., and Mulder F.A. Residue-specific pKa determination of lysine and arginine side chains by indirect 15N and 13C NMR spectroscopy: Application to apo calmodulin. J. Am. Chem. Soc. 129 (2007) 15805-15813
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 15805-15813
    • Andre, I.1    Linse, S.2    Mulder, F.A.3
  • 29
    • 33846011386 scopus 로고    scopus 로고
    • pK(a) values for side-chain carboxyl groups of a PGB1 variant explain salt and pH-dependent stability
    • Lindman S., Linse S., Mulder F.A., and Andre I. pK(a) values for side-chain carboxyl groups of a PGB1 variant explain salt and pH-dependent stability. Biophys. J. 92 (2007) 257-266
    • (2007) Biophys. J. , vol.92 , pp. 257-266
    • Lindman, S.1    Linse, S.2    Mulder, F.A.3    Andre, I.4
  • 31
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules: Theory and applications
    • Sharp K., and Honig B. Electrostatic interactions in macromolecules: Theory and applications. Annu. Rev. Biophys. Chem. 19 (1990) 301-332
    • (1990) Annu. Rev. Biophys. Chem. , vol.19 , pp. 301-332
    • Sharp, K.1    Honig, B.2
  • 32
    • 0018094892 scopus 로고
    • Electrostatic effects in proteins
    • Perutz M.F. Electrostatic effects in proteins. Science 201 (1978) 1187-1191
    • (1978) Science , vol.201 , pp. 1187-1191
    • Perutz, M.F.1
  • 33
    • 28644432877 scopus 로고    scopus 로고
    • Very fast empirical prediction and rationalization of protein pK(a) values
    • Li H., Robertson A.D., and Jensen J.H. Very fast empirical prediction and rationalization of protein pK(a) values. Proteins 61 (2005) 704-721
    • (2005) Proteins , vol.61 , pp. 704-721
    • Li, H.1    Robertson, A.D.2    Jensen, J.H.3
  • 34
    • 0037236095 scopus 로고    scopus 로고
    • Role of the protein side-chain fluctuations on the strength of pairwise electrostatic interactions: Comparing experimental with computed pK(a)s
    • Alexov E. Role of the protein side-chain fluctuations on the strength of pairwise electrostatic interactions: Comparing experimental with computed pK(a)s. Proteins 50 (2003) 94-103
    • (2003) Proteins , vol.50 , pp. 94-103
    • Alexov, E.1
  • 36
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • Antosiewicz J., McCammon J.A., and Gilson M.K. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238 (1994) 415-436
    • (1994) J. Mol. Biol. , vol.238 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.A.2    Gilson, M.K.3
  • 37
    • 37649030225 scopus 로고    scopus 로고
    • Langevin dynamics of proteins at constant pH
    • Walczak A.M., and Antosiewicz J. Langevin dynamics of proteins at constant pH. Physical Rev. E 66 (2002) 1-8
    • (2002) Physical Rev. E , vol.66 , pp. 1-8
    • Walczak, A.M.1    Antosiewicz, J.2
  • 38
    • 9244223045 scopus 로고    scopus 로고
    • Constant pH molecular dynamics in Generalized Born implicit solvent
    • Mongan J., Case D.A., and McCammon J.A. Constant pH molecular dynamics in Generalized Born implicit solvent. J. Comput. Chem. 25 (2004) 2038-2048
    • (2004) J. Comput. Chem. , vol.25 , pp. 2038-2048
    • Mongan, J.1    Case, D.A.2    McCammon, J.A.3
  • 39
    • 38048998514 scopus 로고    scopus 로고
    • Determination of electrostatic interaction energies and protonation state populations in enzyme active sites by global fits of NMR-titration data and pH-activity profiles
    • Søndergaard C.R., McIntosh L.P., Pollastri G., and Nielsen J.E. Determination of electrostatic interaction energies and protonation state populations in enzyme active sites by global fits of NMR-titration data and pH-activity profiles. J. Mol. Biol. 376 (2008) 269-287
    • (2008) J. Mol. Biol. , vol.376 , pp. 269-287
    • Søndergaard, C.R.1    McIntosh, L.P.2    Pollastri, G.3    Nielsen, J.E.4
  • 40
    • 0035957234 scopus 로고    scopus 로고
    • A novel view of pH titration in biomolecules
    • Onufriev A., Case D.A., and Ullmann G.M. A novel view of pH titration in biomolecules. Biochemistry 40 (2001) 3413-3419
    • (2001) Biochemistry , vol.40 , pp. 3413-3419
    • Onufriev, A.1    Case, D.A.2    Ullmann, G.M.3
  • 41
    • 44949260034 scopus 로고    scopus 로고
    • Probing electric fields in proteins in solution by NMR spectroscopy
    • Hass M.A., Jensen M.R., and Led J.J. Probing electric fields in proteins in solution by NMR spectroscopy. Proteins 72 1 (2008) 333-343
    • (2008) Proteins , vol.72 , Issue.1 , pp. 333-343
    • Hass, M.A.1    Jensen, M.R.2    Led, J.J.3
  • 42
    • 34848912277 scopus 로고    scopus 로고
    • Principal component analysis of the pH-dependent conformational transitions of bovine beta-lactoglobulin monitored by heteronuclear NMR
    • Sakurai K., and Goto Y. Principal component analysis of the pH-dependent conformational transitions of bovine beta-lactoglobulin monitored by heteronuclear NMR. Proc. Natl. Acad. Sci. USA 104 (2007) 15346-15351
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 15346-15351
    • Sakurai, K.1    Goto, Y.2
  • 43
    • 0017089701 scopus 로고
    • Potentiometric determination of ionizations at the active site of papain
    • Lewis S.D., Johnson F.A., and Shafer J.A. Potentiometric determination of ionizations at the active site of papain. Biochemistry 15 (1976) 5009-5017
    • (1976) Biochemistry , vol.15 , pp. 5009-5017
    • Lewis, S.D.1    Johnson, F.A.2    Shafer, J.A.3
  • 44
    • 0018344242 scopus 로고
    • Binding of N-acetyl-chitotriose to Asp 52-esterified hen lysozyme
    • Fukae K., Kuramitsu S., and Hamaguchi K. Binding of N-acetyl-chitotriose to Asp 52-esterified hen lysozyme. J. Biochem. 85 (1979) 141-147
    • (1979) J. Biochem. , vol.85 , pp. 141-147
    • Fukae, K.1    Kuramitsu, S.2    Hamaguchi, K.3
  • 45
    • 0022701730 scopus 로고
    • Active-site ionizations of papain. An evaluation of the potentiometric difference titration method
    • Migliorini M., and Creighton D.J. Active-site ionizations of papain. An evaluation of the potentiometric difference titration method. Eur. J. Biochem. 156 (1986) 189-192
    • (1986) Eur. J. Biochem. , vol.156 , pp. 189-192
    • Migliorini, M.1    Creighton, D.J.2
  • 46
    • 29244464347 scopus 로고    scopus 로고
    • The active site cysteine of ubiquitin-conjugating enzymes has a significantly elevated pK(a): Functional implications
    • Tolbert B.S., Tajc S.G., Webb H., Snyder J., Nielsen J.E., Miller B.L., and Basavappa R. The active site cysteine of ubiquitin-conjugating enzymes has a significantly elevated pK(a): Functional implications. Biochemistry 44 (2005) 16385-16391
    • (2005) Biochemistry , vol.44 , pp. 16385-16391
    • Tolbert, B.S.1    Tajc, S.G.2    Webb, H.3    Snyder, J.4    Nielsen, J.E.5    Miller, B.L.6    Basavappa, R.7
  • 47
    • 40649107862 scopus 로고    scopus 로고
    • Isotope-coded, iodoacetamide-based reagent to determine individual cysteine pK(a) values by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
    • Nelson K.J., Day A.E., Zeng B.B., King S.B., and Poole L.B. Isotope-coded, iodoacetamide-based reagent to determine individual cysteine pK(a) values by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal. Biochem. 375 (2008) 187-195
    • (2008) Anal. Biochem. , vol.375 , pp. 187-195
    • Nelson, K.J.1    Day, A.E.2    Zeng, B.B.3    King, S.B.4    Poole, L.B.5
  • 49
    • 0029116114 scopus 로고
    • Aspartic acid 26 in reduced Escherichia coli thioredoxin has a pKa > 9
    • Wilson N.A., Barbar E., Fuchs J.A., and Woodward C. Aspartic acid 26 in reduced Escherichia coli thioredoxin has a pKa > 9. Biochemistry 34 (1995) 8931-8939
    • (1995) Biochemistry , vol.34 , pp. 8931-8939
    • Wilson, N.A.1    Barbar, E.2    Fuchs, J.A.3    Woodward, C.4
  • 50
    • 0029057023 scopus 로고
    • Proton sharing between cysteine thiols in Escherichia coli thioredoxin: Implications for the mechanism of protein disulfide reduction
    • Jeng M.F., Holmgren A., and Dyson H.J. Proton sharing between cysteine thiols in Escherichia coli thioredoxin: Implications for the mechanism of protein disulfide reduction. Biochemistry 34 (1995) 10101-10105
    • (1995) Biochemistry , vol.34 , pp. 10101-10105
    • Jeng, M.F.1    Holmgren, A.2    Dyson, H.J.3
  • 51
    • 0030059821 scopus 로고    scopus 로고
    • Direct measurement of the aspartic acid 26 pKa for reduced Escherichia coli thioredoxin by 13C NMR
    • Jeng M.F., and Dyson H.J. Direct measurement of the aspartic acid 26 pKa for reduced Escherichia coli thioredoxin by 13C NMR. Biochemistry 35 (1996) 1-6
    • (1996) Biochemistry , vol.35 , pp. 1-6
    • Jeng, M.F.1    Dyson, H.J.2
  • 52
    • 54849411390 scopus 로고    scopus 로고
    • Frantz J. G3Data (2007). http://www.frantz.fi/software/g3data.php
    • (2007) G3Data
    • Frantz, J.1
  • 53
    • 33644876024 scopus 로고    scopus 로고
    • PPD v1.0-An integrated, web-accessible database of experimentally determined protein pKa values
    • Toseland C.P., McSparron H., Davies M.N., and Flower D.R. PPD v1.0-An integrated, web-accessible database of experimentally determined protein pKa values. Nucleic Acids Res. 34 (2006) D199-D203
    • (2006) Nucleic Acids Res. , vol.34
    • Toseland, C.P.1    McSparron, H.2    Davies, M.N.3    Flower, D.R.4
  • 54
    • 0036681440 scopus 로고    scopus 로고
    • Empirical relationships between protein structure and carboxyl pKa values in proteins
    • Forsyth W.R., Antosiewicz J.M., and Robertson A.D. Empirical relationships between protein structure and carboxyl pKa values in proteins. Proteins 48 (2002) 388-403
    • (2002) Proteins , vol.48 , pp. 388-403
    • Forsyth, W.R.1    Antosiewicz, J.M.2    Robertson, A.D.3
  • 56
    • 0030945495 scopus 로고    scopus 로고
    • Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
    • Alexov E.G., and Gunner M.R. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Biophys. J. 72 (1997) 2075-2093
    • (1997) Biophys. J. , vol.72 , pp. 2075-2093
    • Alexov, E.G.1    Gunner, M.R.2
  • 57
    • 0033012333 scopus 로고    scopus 로고
    • A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins
    • Mehler E.L., and Guarnieri F. A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins. Biophys. J. 77 (1999) 3-22
    • (1999) Biophys. J. , vol.77 , pp. 3-22
    • Mehler, E.L.1    Guarnieri, F.2
  • 58
    • 0035370422 scopus 로고    scopus 로고
    • Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations
    • Nielsen J.E., and Vriend G. Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations. Proteins 43 (2001) 403-412
    • (2001) Proteins , vol.43 , pp. 403-412
    • Nielsen, J.E.1    Vriend, G.2
  • 60
    • 0026095641 scopus 로고
    • Protonation of interacting residues in a protein by a Monte Carlo method: Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides
    • Beroza P., Fredkin D.R., Okamura M.Y., and Feher G. Protonation of interacting residues in a protein by a Monte Carlo method: Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc. Natl. Acad. Sci. USA 88 (1991) 5804-5808
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 5804-5808
    • Beroza, P.1    Fredkin, D.R.2    Okamura, M.Y.3    Feher, G.4
  • 61
    • 33646794930 scopus 로고    scopus 로고
    • A simple clustering algorithm can be accurate enough for use in calculations of pK's in macromolecules
    • Myers J., Grothaus G., Narayanan S., and Onufriev A. A simple clustering algorithm can be accurate enough for use in calculations of pK's in macromolecules. Proteins 63 (2006) 928-938
    • (2006) Proteins , vol.63 , pp. 928-938
    • Myers, J.1    Grothaus, G.2    Narayanan, S.3    Onufriev, A.4
  • 62
    • 33745099338 scopus 로고    scopus 로고
    • Theoretical investigation of the behavior of titratable groups in proteins
    • Klingen A.R., Bombarda E., and Ullmann G.M. Theoretical investigation of the behavior of titratable groups in proteins. Photochem. Photobiol. Sci. 5 (2006) 588-596
    • (2006) Photochem. Photobiol. Sci. , vol.5 , pp. 588-596
    • Klingen, A.R.1    Bombarda, E.2    Ullmann, G.M.3
  • 63
    • 0035940421 scopus 로고    scopus 로고
    • THEMATICS: A simple computational predictor of enzyme function from structure
    • Ondrechen M.J., Clifton J.G., and Ringe D. THEMATICS: A simple computational predictor of enzyme function from structure. Proc. Natl. Acad. Sci. USA 98 (2001) 12473-12478
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 12473-12478
    • Ondrechen, M.J.1    Clifton, J.G.2    Ringe, D.3
  • 64
    • 0035965145 scopus 로고    scopus 로고
    • Prediction of functionally important residues based solely on the computed energetics of protein structure
    • Elcock A.H. Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol. 312 (2001) 885-896
    • (2001) J. Mol. Biol. , vol.312 , pp. 885-896
    • Elcock, A.H.1
  • 65
    • 0029666454 scopus 로고    scopus 로고
    • The pKa of the general acid/base carboxyl group of a glycosidase cycles during catalysis: A 13C-NMR study of bacillus circulans xylanase
    • McIntosh L.P., Hand G., Johnson P.E., Joshi M.D., Korner M., Plesniak L.A., Ziser L., Wakarchuk W.W., and Withers S.G. The pKa of the general acid/base carboxyl group of a glycosidase cycles during catalysis: A 13C-NMR study of bacillus circulans xylanase. Biochemistry 35 (1996) 9958-9966
    • (1996) Biochemistry , vol.35 , pp. 9958-9966
    • McIntosh, L.P.1    Hand, G.2    Johnson, P.E.3    Joshi, M.D.4    Korner, M.5    Plesniak, L.A.6    Ziser, L.7    Wakarchuk, W.W.8    Withers, S.G.9
  • 66
    • 0031283399 scopus 로고    scopus 로고
    • Complete measurement of the pKa values of the carboxyl and imidazole groups in Bacillus circulans xylanase
    • Joshi M.D., Hedberg A., and McIntosh L.P. Complete measurement of the pKa values of the carboxyl and imidazole groups in Bacillus circulans xylanase. Protein Sci. 6 (1997) 2667-2670
    • (1997) Protein Sci. , vol.6 , pp. 2667-2670
    • Joshi, M.D.1    Hedberg, A.2    McIntosh, L.P.3
  • 67
    • 0034716940 scopus 로고    scopus 로고
    • Hydrogen bonding and catalysis: A novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase
    • Joshi M.D., Sidhu G., Pot I., Brayer G.D., Withers S.G., and McIntosh L.P. Hydrogen bonding and catalysis: A novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase. J. Mol. Biol. 299 (2000) 255-279
    • (2000) J. Mol. Biol. , vol.299 , pp. 255-279
    • Joshi, M.D.1    Sidhu, G.2    Pot, I.3    Brayer, G.D.4    Withers, S.G.5    McIntosh, L.P.6
  • 68
    • 0035964164 scopus 로고    scopus 로고
    • Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase
    • Joshi M.D., Sidhu G., Nielsen J.E., Brayer G.D., Withers S.G., and McIntosh L.P. Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase. Biochemistry 40 (2001) 10115-10139
    • (2001) Biochemistry , vol.40 , pp. 10115-10139
    • Joshi, M.D.1    Sidhu, G.2    Nielsen, J.E.3    Brayer, G.D.4    Withers, S.G.5    McIntosh, L.P.6
  • 71
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • Nicholls A., and Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comp. Chem. 12 (1991) 435-445
    • (1991) J. Comp. Chem. , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 73
    • 0035451052 scopus 로고    scopus 로고
    • What are the dielectric "constants" of proteins and how to validate electrostatic models?
    • Schutz C.N., and Warshel A. What are the dielectric "constants" of proteins and how to validate electrostatic models?. Proteins 44 (2001) 400-417
    • (2001) Proteins , vol.44 , pp. 400-417
    • Schutz, C.N.1    Warshel, A.2
  • 74
    • 0030478456 scopus 로고    scopus 로고
    • Structural determinants of the catalytic reactivity of the buried cysteine of Escherichia coli thioredoxin
    • LeMaster D.M. Structural determinants of the catalytic reactivity of the buried cysteine of Escherichia coli thioredoxin. Biochemistry 35 (1996) 14876-14881
    • (1996) Biochemistry , vol.35 , pp. 14876-14881
    • LeMaster, D.M.1
  • 75
    • 84994973832 scopus 로고
    • Electric field effects on the shielding of protons in C-H bonds
    • Grayson M., and Raynes W. Electric field effects on the shielding of protons in C-H bonds. Magnetic Resonance Chem. 33 (1995) 138-143
    • (1995) Magnetic Resonance Chem. , vol.33 , pp. 138-143
    • Grayson, M.1    Raynes, W.2
  • 76
    • 0034684161 scopus 로고    scopus 로고
    • The core lipocalin, bovine beta-lactoglobulin
    • Sawyer L., and Kontopidis G. The core lipocalin, bovine beta-lactoglobulin. Biochim. Biophys. Acta 1482 (2000) 136-148
    • (2000) Biochim. Biophys. Acta , vol.1482 , pp. 136-148
    • Sawyer, L.1    Kontopidis, G.2
  • 77
    • 0035824880 scopus 로고    scopus 로고
    • Characterization of pH-induced transitions of beta-lactoglobulin: Ultrasonic, densimetric, and spectroscopic studies
    • Taulier N., and Chalikian T.V. Characterization of pH-induced transitions of beta-lactoglobulin: Ultrasonic, densimetric, and spectroscopic studies. J. Mol. Biol. 314 (2001) 873-889
    • (2001) J. Mol. Biol. , vol.314 , pp. 873-889
    • Taulier, N.1    Chalikian, T.V.2
  • 78
    • 0025271463 scopus 로고
    • pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1
    • Pace C.N., Laurents D.V., and Thomson J.A. pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1. Biochemistry 29 (1990) 2564-2572
    • (1990) Biochemistry , vol.29 , pp. 2564-2572
    • Pace, C.N.1    Laurents, D.V.2    Thomson, J.A.3
  • 79
    • 0014718113 scopus 로고
    • Protein denaturation. Part C. Theoretical models for the mechanism of denaturation
    • Tanford C. Protein denaturation. Part C. Theoretical models for the mechanism of denaturation. Adv. Protein Chem. 25 (1970) 1-95
    • (1970) Adv. Protein Chem. , vol.25 , pp. 1-95
    • Tanford, C.1
  • 80
    • 0027231258 scopus 로고
    • On the pH dependence of protein stability
    • Yang A.S., and Honig B. On the pH dependence of protein stability. J. Mol. Biol. 231 (1993) 459-474
    • (1993) J. Mol. Biol. , vol.231 , pp. 459-474
    • Yang, A.S.1    Honig, B.2
  • 81
    • 1642499126 scopus 로고    scopus 로고
    • Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure
    • Alexov E. Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure. Eur. J. Biochem. 271 (2004) 173-185
    • (2004) Eur. J. Biochem. , vol.271 , pp. 173-185
    • Alexov, E.1
  • 82
    • 0034111423 scopus 로고    scopus 로고
    • The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase
    • Lambeir A.M., Backmann J., Ruiz-Sanz J., Filimonov V., Nielsen J.E., Kursula I., Norledge B.V., and Wierenga R.K. The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase. Eur. J. Biochem. 267 (2000) 2516-2524
    • (2000) Eur. J. Biochem. , vol.267 , pp. 2516-2524
    • Lambeir, A.M.1    Backmann, J.2    Ruiz-Sanz, J.3    Filimonov, V.4    Nielsen, J.E.5    Kursula, I.6    Norledge, B.V.7    Wierenga, R.K.8
  • 84
    • 0033852796 scopus 로고    scopus 로고
    • Charge-charge interactions influence the denatured state ensemble and contribute to protein stability
    • Pace C.N., Alston R.W., and Shaw K.L. Charge-charge interactions influence the denatured state ensemble and contribute to protein stability. Protein Sci. 9 (2000) 1395-1398
    • (2000) Protein Sci. , vol.9 , pp. 1395-1398
    • Pace, C.N.1    Alston, R.W.2    Shaw, K.L.3
  • 85
    • 0033544710 scopus 로고    scopus 로고
    • Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability
    • Elcock A.H. Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability. J. Mol. Biol. 294 (1999) 1051-1062
    • (1999) J. Mol. Biol. , vol.294 , pp. 1051-1062
    • Elcock, A.H.1
  • 86
    • 0037114648 scopus 로고    scopus 로고
    • Probing multiple effects on 15N, 13C alpha, 13C beta, and 13C' chemical shifts in peptides using density functional theory
    • Xu X.P., and Case D.A. Probing multiple effects on 15N, 13C alpha, 13C beta, and 13C' chemical shifts in peptides using density functional theory. Biopolymers 65 (2002) 408-423
    • (2002) Biopolymers , vol.65 , pp. 408-423
    • Xu, X.P.1    Case, D.A.2
  • 87
    • 0038407231 scopus 로고    scopus 로고
    • Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts
    • Neal S., Nip A.M., Zhang H., and Wishart D.S. Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J. Biomol. NMR 26 (2003) 215-240
    • (2003) J. Biomol. NMR , vol.26 , pp. 215-240
    • Neal, S.1    Nip, A.M.2    Zhang, H.3    Wishart, D.S.4
  • 88
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    • Dolinsky T.J., Nielsen J.E., McCammon J.A., and Baker N.A. PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32 (2004) W665-W667
    • (2004) Nucleic Acids Res. , vol.32
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4
  • 92
    • 0036787760 scopus 로고    scopus 로고
    • Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins
    • Georgescu R.E., Alexov E.G., and Gunner M.R. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. Biophys. J. 83 (2002) 1731-1748
    • (2002) Biophys. J. , vol.83 , pp. 1731-1748
    • Georgescu, R.E.1    Alexov, E.G.2    Gunner, M.R.3
  • 93
    • 33846614924 scopus 로고    scopus 로고
    • Analysing the pH-dependent properties of proteins using pKa calculations
    • Nielsen J.E. Analysing the pH-dependent properties of proteins using pKa calculations. J. Mol. Graph. 25 (2006) 691-699
    • (2006) J. Mol. Graph. , vol.25 , pp. 691-699
    • Nielsen, J.E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.