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Volumn 454, Issue C, 2009, Pages 233-258

Chapter 9 Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pKa Calculations and Titration Curve Fitting

Author keywords

[No Author keywords available]

Indexed keywords

CURVE FITTING; ELECTRICITY; ENZYME ACTIVITY; ENZYME ANALYSIS; LIGAND BINDING; NUCLEAR MAGNETIC RESONANCE; PH; PRIORITY JOURNAL; PROTEIN STABILITY; PROTEIN STRUCTURE; REVIEW; SENSITIVITY ANALYSIS; ARTICLE; CHEMISTRY; KINETICS; METHODOLOGY; TITRIMETRY;

EID: 59649095261     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(08)03809-3     Document Type: Review
Times cited : (21)

References (39)
  • 1
    • 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
  • 2
    • 0033614791 scopus 로고    scopus 로고
    • Calculated protein and proton motions coupled to electron transfer: Electron transfer from QA- to QB in bacterial photosynthetic reaction centers
    • Alexov E.G., and Gunner M.R. Calculated protein and proton motions coupled to electron transfer: Electron transfer from QA- to QB in bacterial photosynthetic reaction centers. Biochemistry 38 (1999) 8253-8270
    • (1999) Biochemistry , vol.38 , pp. 8253-8270
    • Alexov, E.G.1    Gunner, M.R.2
  • 4
    • 34447297323 scopus 로고    scopus 로고
    • Energetics of protein folding
    • Baldwin R.L. Energetics of protein folding. J. Mol. Biol. 371 (2007) 283-301
    • (2007) J. Mol. Biol. , vol.371 , pp. 283-301
    • Baldwin, R.L.1
  • 5
    • 0036732086 scopus 로고    scopus 로고
    • Constant-pH molecular dynamics using stochastic titration
    • Baptista A.M., Teixeira V.H., and Soares C.M. Constant-pH molecular dynamics using stochastic titration. J. Chem. Phys. 117 (2002) 4184-4200
    • (2002) J. Chem. Phys. , vol.117 , pp. 4184-4200
    • Baptista, A.M.1    Teixeira, V.H.2    Soares, C.M.3
  • 6
    • 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
  • 7
    • 41649119572 scopus 로고    scopus 로고
    • Pore-opening mechanism of the nicotinic acetylcholine receptor evinced by proton transfer
    • Cymes G.D., and Grosman C. Pore-opening mechanism of the nicotinic acetylcholine receptor evinced by proton transfer. Nat. Struct. Mol. Biol. 15 (2008) 389-396
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 389-396
    • Cymes, G.D.1    Grosman, C.2
  • 8
    • 33748593093 scopus 로고    scopus 로고
    • Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins
    • Demchuk E., and Wade R.C. Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins. J. Phys. Chem. 100 (1996) 17373-17387
    • (1996) J. Phys. Chem. , vol.100 , pp. 17373-17387
    • Demchuk, E.1    Wade, R.C.2
  • 10
    • 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
  • 11
    • 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
  • 12
    • 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
  • 14
    • 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
  • 15
    • 23244440384 scopus 로고    scopus 로고
    • Constant pH molecular dynamics with proton tautomerism
    • Khandogin J., and Brooks III C.L. Constant pH molecular dynamics with proton tautomerism. Biophys. J. 89 (2005) 141-157
    • (2005) Biophys. J. , vol.89 , pp. 141-157
    • Khandogin, J.1    Brooks III, C.L.2
  • 16
    • 28644432877 scopus 로고    scopus 로고
    • Very fast empirical prediction and rationalization of protein pKa values
    • Li H., Robertson A.D., and Jensen J.H. Very fast empirical prediction and rationalization of protein pKa values. Proteins 61 (2005) 704-721
    • (2005) Proteins , vol.61 , pp. 704-721
    • Li, H.1    Robertson, A.D.2    Jensen, J.H.3
  • 19
    • 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., Körner 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    Körner, M.5    Plesniak, L.A.6    Ziser, L.7    Wakarchuk, W.W.8    Withers, S.G.9
  • 20
    • 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
  • 21
    • 33646794930 scopus 로고    scopus 로고
    • A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules
    • Myers J., Grothaus G., Narayanan S., and Onufriev A. A simple clustering algorithm can be accurate enough for use in calculations of pKs 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
  • 22
    • 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
  • 23
    • 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
  • 24
    • 59649119370 scopus 로고    scopus 로고
    • University College Dublin, Dublin, Ireland
    • Nielsen J.E. pKaTool (2006), University College Dublin, Dublin, Ireland. http://enzyme.ucd.ie/Science/pKa/pKaTool
    • (2006) pKaTool
    • Nielsen, J.E.1
  • 25
    • 0037305552 scopus 로고    scopus 로고
    • On the evaluation and optimisation of protein X-ray structures for pKa calculations
    • Nielsen J.E., and McCammon J.A. On the evaluation and optimisation of protein X-ray structures for pKa calculations. Protein Sci. 12 (2003) 313-326
    • (2003) Protein Sci. , vol.12 , pp. 313-326
    • Nielsen, J.E.1    McCammon, J.A.2
  • 26
    • 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
  • 27
    • 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
  • 28
    • 45549107077 scopus 로고    scopus 로고
    • Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase
    • Pisliakov A.V., Sharma P.K., Chu Z.T., Haranczyk M., and Warshel A. Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proc. Natl. Acad. Sci. USA 105 (2008) 7726-7731
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 7726-7731
    • Pisliakov, A.V.1    Sharma, P.K.2    Chu, Z.T.3    Haranczyk, M.4    Warshel, A.5
  • 29
    • 0010624785 scopus 로고    scopus 로고
    • The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins
    • Sham Y.Y., Muegge I., and Warshel A. The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. Biophys. J. 74 (1998) 1744-1753
    • (1998) Biophys. J. , vol.74 , pp. 1744-1753
    • Sham, Y.Y.1    Muegge, I.2    Warshel, A.3
  • 30
    • 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
  • 32
    • 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
  • 33
    • 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
  • 34
    • 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
  • 37
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • 29
    • Vriend G. WHAT IF: A molecular modeling and drug design program. J. Mol. Graph 8 (1990) 52-56 29
    • (1990) J. Mol. Graph , vol.8 , pp. 52-56
    • Vriend, G.1


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