메뉴 건너뛰기




Volumn 54, Issue 4, 2012, Pages 355-376

Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations

Author keywords

Chemical exchange rate; Chemical shift titration; Protein ligand interaction; Protein protein interaction

Indexed keywords

ACCURACY; ARTICLE; BETA SHEET; BIOLOGICAL ACTIVITY; CONCENTRATION (PARAMETERS); CONFORMATIONAL TRANSITION; DISSOCIATION CONSTANT; HETERONUCLEAR SINGLE QUANTUM COHERENCE; MOLECULAR WEIGHT; MONTE CARLO METHOD; NITROGEN NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTUM MECHANICS; SIGNAL NOISE RATIO; SIGNAL TRANSDUCTION; SIMULATION; SYSTEMATIC ERROR; THERMODYNAMICS; TITRIMETRY; VALIDITY;

EID: 84874486080     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-012-9678-6     Document Type: Article
Times cited : (17)

References (50)
  • 2
    • 84857703407 scopus 로고    scopus 로고
    • Quantitative analysis of multisite protein-ligand interactions by NMR: Binding of intrinsically disordered p53 transactivation subdomains with the TAZ2 domain of CBP
    • 10.1021/ja209936u
    • Arai M, Ferreon JC, Wright PE (2012) Quantitative analysis of multisite protein-ligand interactions by NMR: binding of intrinsically disordered p53 transactivation subdomains with the TAZ2 domain of CBP. J Am Chem Soc 134:3792-3803
    • (2012) J Am Chem Soc , vol.134 , pp. 3792-3803
    • Arai, M.1    Ferreon, J.C.2    Wright, P.E.3
  • 3
    • 0242403031 scopus 로고    scopus 로고
    • Chemical exchange in NMR
    • 10.1016/j.pnmrs.2003.08.001
    • Bain AD (2003) Chemical exchange in NMR. Prog Nucl Mag Res Sp 43:63-103
    • (2003) Prog Nucl Mag Res Sp , vol.43 , pp. 63-103
    • Bain, A.D.1
  • 4
    • 0016745184 scopus 로고
    • Stepwise binding of small molecules to proteins. Nuclear magnetic resonance and temperature jump studies of binding of 4-(N-Acetylaminoglucosyl)- N-Acetylglucosamine to lysozyme
    • 10.1021/bi00680a014
    • Baldo JH, Halford SE, Patt SL, Sykes BD (1975) Stepwise binding of small molecules to proteins. Nuclear magnetic resonance and temperature jump studies of binding of 4-(N-Acetylaminoglucosyl)-N-Acetylglucosamine to lysozyme. Biochemistry 14:1893-1899
    • (1975) Biochemistry , vol.14 , pp. 1893-1899
    • Baldo, J.H.1    Halford, S.E.2    Patt, S.L.3    Sykes, B.D.4
  • 5
    • 12044252858 scopus 로고
    • Methodological advances in protein NMR
    • 10.1021/ar00028a001
    • Bax A, Grzesiek S (1993) Methodological advances in protein NMR. Acc Chem Res 26:131-138
    • (1993) Acc Chem Res , vol.26 , pp. 131-138
    • Bax, A.1    Grzesiek, S.2
  • 6
    • 0001303793 scopus 로고
    • A unified theory of exchange effects on nuclear magnetic resonance line shapes
    • 10.1021/ja01034a007
    • Binsch G (1969) A unified theory of exchange effects on nuclear magnetic resonance line shapes. J Am Chem Soc 91:1304-1309
    • (1969) J Am Chem Soc , vol.91 , pp. 1304-1309
    • Binsch, G.1
  • 7
    • 0000195671 scopus 로고
    • Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy
    • 1980CPL.69.185B 10.1016/0009-2614(80)80041-8
    • Bodenhausen G, Ruben DJ (1980) Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy. Chem Phys Lett 69:185-189
    • (1980) Chem Phys Lett , vol.69 , pp. 185-189
    • Bodenhausen, G.1    Ruben, D.J.2
  • 9
    • 24944586285 scopus 로고    scopus 로고
    • Achieving stability of lipopolysaccharide-induced NF-κB activation
    • DOI 10.1126/science.1112304
    • Covert MW, Leung TH, Gaston JE, Baltimore D (2005) Achieving stability of lipopolysaccharide-induced NF-κB activation. Science 309:1854-1857 (Pubitemid 41325095)
    • (2005) Science , vol.309 , Issue.5742 , pp. 1854-1857
    • Covert, M.W.1    Leung, T.H.2    Gaston, J.E.3    Baltimore, D.4
  • 10
    • 0001506476 scopus 로고
    • Nuclear magnetic relaxation study of intermolecular complexes. The mechanism of penicillin binding to serum albumin
    • 10.1021/ja01092a040
    • Fischer JJ, Jardetzky O (1965) Nuclear magnetic relaxation study of intermolecular complexes. The mechanism of penicillin binding to serum albumin. J Am Chem Soc 87:3237-3244
    • (1965) J Am Chem Soc , vol.87 , pp. 3237-3244
    • Fischer, J.J.1    Jardetzky, O.2
  • 12
    • 36049046667 scopus 로고    scopus 로고
    • Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR
    • DOI 10.1016/j.cell.2007.09.039, PII S009286740701269X
    • Gelis I, Bonvin AMJJ, Keramisanou D, Koukaki M, Gouridis G, Karamanou S, Economou A, Kalodimos CG (2007) Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR. Cell 131:756-769 (Pubitemid 350087200)
    • (2007) Cell , vol.131 , Issue.4 , pp. 756-769
    • Gelis, I.1    Bonvin, A.M.J.J.2    Keramisanou, D.3    Koukaki, M.4    Gouridis, G.5    Karamanou, S.6    Economou, A.7    Kalodimos, C.G.8
  • 13
    • 84855269204 scopus 로고    scopus 로고
    • Applications of isothermal titration calorimetry in pure and applied research: Survey of the literature from 2010
    • 10.1002/jmr.1167
    • Ghai R, Falconer RJ, Collins BM (2012) Applications of isothermal titration calorimetry in pure and applied research: survey of the literature from 2010. J Mol Recognit 25:32-52
    • (2012) J Mol Recognit , vol.25 , pp. 32-52
    • Ghai, R.1    Falconer, R.J.2    Collins, B.M.3
  • 14
    • 80755168127 scopus 로고    scopus 로고
    • Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis
    • 10.1007/s10858-011-9538-9
    • Greenwood AI, Rogals MJ, De S, Lu KP, Kovrigin EL, Nicholson LK (2011) Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis. J Biomol NMR 51:21-34
    • (2011) J Biomol NMR , vol.51 , pp. 21-34
    • Greenwood, A.I.1    Rogals, M.J.2    De, S.3    Lu, K.P.4    Kovrigin, E.L.5    Nicholson, L.K.6
  • 16
    • 0036214924 scopus 로고    scopus 로고
    • NMRKIN: Simulating line shapes from two-dimensional spectra of proteins upon ligand binding
    • DOI 10.1023/A:1014985726029
    • Günther UL, Schaffhausen B (2002) NMRKIN: simulating line shapes from two-dimensional spectra of proteins upon ligand binding. J Biomol NMR 22:201-209 (Pubitemid 34296105)
    • (2002) Journal of Biomolecular NMR , vol.22 , Issue.3 , pp. 201-209
    • Gunther, U.L.1    Schaffhausen, B.2
  • 17
    • 36849121702 scopus 로고
    • Dissociation, chemical exchange, and the proton magnetic resonance in some aqueous electrolytes
    • 1953JChPh.21.1688G 10.1063/1.1698644
    • Gutowsky HS, Saika A (1953) Dissociation, chemical exchange, and the proton magnetic resonance in some aqueous electrolytes. J Chem Phys 21:1688-1694
    • (1953) J Chem Phys , vol.21 , pp. 1688-1694
    • Gutowsky, H.S.1    Saika, A.2
  • 18
    • 1542373897 scopus 로고    scopus 로고
    • Distinct monoubiquitin signals in receptor endocytosis
    • DOI 10.1016/j.tibs.2003.09.005, PII S0968000403002299
    • Haglund K, Di Fiore PP, Dikic I (2003) Distinct monoubiquitin signals in receptor endocytosis. Trends Biochem Sci 28:598-603 (Pubitemid 38352806)
    • (2003) Trends in Biochemical Sciences , vol.28 , Issue.11 , pp. 598-604
    • Haglund, K.1    Di Fiore, P.P.2    Dikic, I.3
  • 19
    • 0001743718 scopus 로고
    • 1H NMR spectroscopy by homonuclear semiselective shaped pulse decoupling during acquisition
    • 10.1021/ja00098a070
    • 1H NMR spectroscopy by homonuclear semiselective shaped pulse decoupling during acquisition. J Am Chem Soc 116:8847-8848
    • (1994) J Am Chem Soc , vol.116 , pp. 8847-8848
    • Hammarström, A.1    Otting, G.2
  • 21
    • 0002474486 scopus 로고
    • The NMR receiver: A description and analysis of design
    • 10.1016/0079-6565(78)80002-8
    • Hoult DI (1978) The NMR receiver: a description and analysis of design. Prog Nucl Mag Res Sp 12:41-77
    • (1978) Prog Nucl Mag Res Sp , vol.12 , pp. 41-77
    • Hoult, D.I.1
  • 22
    • 0345267240 scopus 로고    scopus 로고
    • Calcium binding by the N-terminal cellulose-binding domain from Cellulomonas fimi β-1,4-glucanase CenC
    • DOI 10.1021/bi980978x
    • Johnson PE, Creagh AL, Brun E, Joe K, Tomme P, Haynes CA, McIntosh LP (1998) Calcium binding by the N-terminal cellulose-binding domain from Cellulomonas fimi β-1,4-glucanase CenC. Biochemistry 37:12772-12781 (Pubitemid 28433508)
    • (1998) Biochemistry , vol.37 , Issue.37 , pp. 12772-12781
    • Johnson, P.E.1    Louise Creagh, A.2    Brun, E.3    Joe, K.4    Tomme, P.5    Haynes, C.A.6    McIntosh, L.P.7
  • 23
    • 0006925492 scopus 로고
    • Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity
    • 10.1021/ja00052a088
    • Kay LE, Keifer P, Saarinen T (1992) Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J Am Chem Soc 114:10663-10665
    • (1992) J Am Chem Soc , vol.114 , pp. 10663-10665
    • Kay, L.E.1    Keifer, P.2    Saarinen, T.3
  • 24
    • 0028877264 scopus 로고
    • Kinetic analysis of cyclophilin-catalyzed prolyl cis/trans isomerization by dynamic NMR spectroscopy
    • 10.1021/bi00041a039
    • Kern D, Kern G, Scherer G, Fischer G, Drakenberg T (1995) Kinetic analysis of cyclophilin-catalyzed prolyl cis/trans isomerization by dynamic NMR spectroscopy. Biochemistry 34:13594-13602
    • (1995) Biochemistry , vol.34 , pp. 13594-13602
    • Kern, D.1    Kern, G.2    Scherer, G.3    Fischer, G.4    Drakenberg, T.5
  • 26
    • 84865166917 scopus 로고    scopus 로고
    • NMR line shapes and multi-state binding equilibria
    • 10.1007/s10858-012-9636-3
    • Kovrigin EL (2012) NMR line shapes and multi-state binding equilibria. J Biomol NMR 53:257-270
    • (2012) J Biomol NMR , vol.53 , pp. 257-270
    • Kovrigin, E.L.1
  • 27
    • 0001258823 scopus 로고
    • Isotope labeling in solution protein assignment and structural analysis
    • 10.1016/0079-6565(94)80010-3
    • LeMaster DM (1994) Isotope labeling in solution protein assignment and structural analysis. Prog Nucl Mag Res Sp 26:371-419
    • (1994) Prog Nucl Mag Res Sp , vol.26 , pp. 371-419
    • Lemaster, D.M.1
  • 29
    • 38449103508 scopus 로고    scopus 로고
    • NMR methods for studying protein-protein interactions involved in translation initiation
    • 10.1016/S0076-6879(07)30012-8
    • Marintchev A, Frueh D, Wagner G (2007) NMR methods for studying protein-protein interactions involved in translation initiation. Methods Enzymol 430:283-331
    • (2007) Methods Enzymol , vol.430 , pp. 283-331
    • Marintchev, A.1    Frueh, D.2    Wagner, G.3
  • 30
    • 84865185420 scopus 로고    scopus 로고
    • Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations
    • 10.1007/s10858-012-9630-9
    • Markin CJ, Spyracopoulos L (2012) Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations. J Biomol NMR 53:125-138
    • (2012) J Biomol NMR , vol.53 , pp. 125-138
    • Markin, C.J.1    Spyracopoulos, L.2
  • 31
    • 77955562403 scopus 로고    scopus 로고
    • Mechanism for recognition of polyubiquitin chains: Balancing affinity through interplay between multivalent binding and dynamics
    • 10.1021/ja103869x
    • Markin CJ, Xiao W, Spyracopoulos L (2010a) Mechanism for recognition of polyubiquitin chains: balancing affinity through interplay between multivalent binding and dynamics. J Am Chem Soc 132:11247-11258
    • (2010) J Am Chem Soc , vol.132 , pp. 11247-11258
    • Markin, C.J.1    Xiao, W.2    Spyracopoulos, L.3
  • 33
    • 0010957050 scopus 로고
    • Reaction rates by nuclear magnetic resonance
    • 1958JChPh.28.430M 10.1063/1.1744152
    • McConnell HM (1958) Reaction rates by nuclear magnetic resonance. J Chem Phys 28:430-431
    • (1958) J Chem Phys , vol.28 , pp. 430-431
    • McConnell, H.M.1
  • 34
    • 0033609042 scopus 로고    scopus 로고
    • Defining the region of troponin-I that binds to troponin-C
    • DOI 10.1021/bi9829736
    • McKay RT, Tripet BP, Pearlstone JR, Smillie LB, Sykes BD (1999) Defining the region of troponin-I that binds to troponin-C. Biochemistry 38:5478-5489 (Pubitemid 29211233)
    • (1999) Biochemistry , vol.38 , Issue.17 , pp. 5478-5489
    • McKay, R.T.1    Tripet, B.P.2    Pearlstone, J.R.3    Smillie, L.B.4    Sykes, B.D.5
  • 35
    • 0038724478 scopus 로고    scopus 로고
    • Energetics and specificity of interactions within Ub·Uev· Ubc13 human ubiquitin conjugation complexes
    • DOI 10.1021/bi034480t
    • McKenna S, Hu J, Moraes T, Xiao W, Ellison MJ, Spyracopoulos L (2003) Energetics and specificity of interactions within Ub•Uev•Ubc13 human ubiquitin conjugation complexes. Biochemstry 42:7922-7930 (Pubitemid 36807709)
    • (2003) Biochemistry , vol.42 , Issue.26 , pp. 7922-7930
    • McKenna, S.1    Hu, J.2    Moraes, T.3    Xiao, W.4    Ellison, M.J.5    Spyracopoulos, L.6
  • 36
    • 33845560617 scopus 로고
    • Enhancement of nuclear magnetic resonance signals by polarization transfer
    • 10.1021/ja00497a058
    • Morris GA, Freeman R (1979) Enhancement of nuclear magnetic resonance signals by polarization transfer. J Am Chem Soc 101:760-762
    • (1979) J Am Chem Soc , vol.101 , pp. 760-762
    • Morris, G.A.1    Freeman, R.2
  • 37
    • 44949276869 scopus 로고
    • Sensitivity improvement in proton-detected 2-dimensional heteronuclear correlation NMR spectroscopy
    • Palmer AG, Cavanagh J, Wright PE, Rance M (1991) Sensitivity improvement in proton-detected 2-dimensional heteronuclear correlation NMR spectroscopy. J Magn Reson 93:151-170
    • (1991) J Magn Reson , vol.93 , pp. 151-170
    • Palmer, A.G.1    Cavanagh, J.2    Wright, P.E.3    Rance, M.4
  • 38
    • 0034919305 scopus 로고    scopus 로고
    • Nuclear magnetic resonance methods for quantifying microsecond-to- millisecond motions in biological macromolecules
    • DOI 10.1016/S0076-6879(01)39315-1
    • Palmer AG, Kroenke CD, Loria JP (2001) Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Method Enzymol 339:204-238 (Pubitemid 32666562)
    • (2001) Methods in Enzymology , vol.339 , pp. 204-238
    • Palmer III, A.G.1    Kroenke, C.D.2    Loria, J.P.3
  • 39
    • 34249934450 scopus 로고    scopus 로고
    • A touching response to damage
    • DOI 10.1126/science.1143700
    • Petrini JH (2007) Cell signaling. A touching response to damage. Science 316:1138-1139 (Pubitemid 46877466)
    • (2007) Science , vol.316 , Issue.5828 , pp. 1138-1139
    • Petrini, J.H.J.1
  • 40
    • 0024404656 scopus 로고
    • Nuclear magnetic resonance line-shape analysis and determination of exchange rates
    • DOI 10.1016/0076-6879(89)76016-X
    • Rao BDN (1989) Nuclear magnetic resonance line shape analysis and determination of exchange rates. Methods Enzymol 176:279-311 (Pubitemid 20003086)
    • (1989) Methods in Enzymology , vol.176 , pp. 279-311
    • Rao, B.D.N.1
  • 41
    • 33845406931 scopus 로고    scopus 로고
    • Insights into S100 target specificity examined by a new interaction between S100A11 and annexin A2
    • DOI 10.1021/bi061754e
    • Rintala-Dempsey AC, Santamaria-Kisiel L, Liao Y, Lajoie G, Shaw GS (2006) Insights into S100 target specificity examined by a new interaction between S100A11 and annexin A2. Biochemistry 45:14695-14705 (Pubitemid 44906985)
    • (2006) Biochemistry , vol.45 , Issue.49 , pp. 14695-14705
    • Rintala-Dempsey, A.C.1    Santamaria-Kisiel, L.2    Liao, Y.3    Lajoie, G.4    Shaw, G.S.5
  • 42
    • 33947475965 scopus 로고
    • Proton magnetic resonance study of hindered internal rotation in some substituted N, N-dimethylamides
    • 10.1021/j100809a043
    • Rogers MT, Woodbrey JC (1962) Proton magnetic resonance study of hindered internal rotation in some substituted N, N-dimethylamides. J Phys Chem 66:540-546
    • (1962) J Phys Chem , vol.66 , pp. 540-546
    • Rogers, M.T.1    Woodbrey, J.C.2
  • 43
    • 67649670116 scopus 로고    scopus 로고
    • Experimental access to HSQC spectra decoupled in all frequency dimensions
    • 2009JMagR.199.192S 10.1016/j.jmr.2009.04.016
    • Sakhaii P, Haase B, Bermel W (2009) Experimental access to HSQC spectra decoupled in all frequency dimensions. J Magn Reson 199:192-198
    • (2009) J Magn Reson , vol.199 , pp. 192-198
    • Sakhaii, P.1    Haase, B.2    Bermel, W.3
  • 44
    • 0028838568 scopus 로고
    • Dynamics of tryptophan binding to Escherichia coli Trp repressor wild type and AV77 mutant: An NMR study
    • 10.1021/bi00040a033
    • Schmitt TH, Zheng ZW, Jardetzky O (1995) Dynamics of tryptophan binding to Escherichia coli Trp repressor wild type and AV77 mutant: an NMR study. Biochemistry 34:13183-13189
    • (1995) Biochemistry , vol.34 , pp. 13183-13189
    • Schmitt, T.H.1    Zheng, Z.W.2    Jardetzky, O.3
  • 45
    • 0019889796 scopus 로고
    • Energetics and kinetics of interconversion of two myosin subfragment-1•adenosine 5′-diphosphate complexes as viewed by phosphorus-31 nuclear magnetic resonance
    • 10.1021/bi00525a011
    • Shriver JW, Sykes BD (1981) Energetics and kinetics of interconversion of two myosin subfragment-1•adenosine 5′-diphosphate complexes as viewed by phosphorus-31 nuclear magnetic resonance. Biochemistry 20:6357-6362
    • (1981) Biochemistry , vol.20 , pp. 6357-6362
    • Shriver, J.W.1    Sykes, B.D.2
  • 46
    • 0001876029 scopus 로고
    • Computer simulations in magnetic resonance. An object-oriented programming approach
    • 10.1006/jmra.1994.1008
    • Smith SA, Levante TO, Meier BH, Ernst RR (1994) Computer simulations in magnetic resonance. An object-oriented programming approach. J Magn Reson, Ser A 106:75-105
    • (1994) J Magn Reson, ser A , vol.106 , pp. 75-105
    • Smith, S.A.1    Levante, T.O.2    Meier, B.H.3    Ernst, R.R.4
  • 47
    • 77956813169 scopus 로고
    • The investigation of the kinetics of conformational changes by nuclear magnetic resonance spectroscopy
    • 10.1016/S0066-4103(08)60345-2
    • Sutherland IO (1972) The investigation of the kinetics of conformational changes by nuclear magnetic resonance spectroscopy. Annu Rep NMR Spectrosc 4:71-235
    • (1972) Annu Rep NMR Spectrosc , vol.4 , pp. 71-235
    • Sutherland, I.O.1
  • 48
    • 0037432547 scopus 로고    scopus 로고
    • Quantitative NMR studies of high molecular weight proteins: Application to domain orientation and ligand binding in the 723 residue enzyme malate synthase G
    • DOI 10.1016/S0022-2836(03)00238-9
    • Tugarinov V, Kay LE (2003) Quantitative NMR studies of high molecular weight proteins: application to domain orientation and ligand binding in the 723 residue enzyme malate synthase G. J Mol Biol 327:1121-1133 (Pubitemid 36363717)
    • (2003) Journal of Molecular Biology , vol.327 , Issue.5 , pp. 1121-1133
    • Tugarinov, V.1    Kay, L.E.2
  • 49
    • 24744447629 scopus 로고    scopus 로고
    • Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins
    • DOI 10.1002/cbic.200500110
    • Tugarinov V, Kay LE (2005) Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins. ChemBioChem 6:1567-1577 (Pubitemid 41296962)
    • (2005) ChemBioChem , vol.6 , Issue.9 , pp. 1567-1577
    • Tugarinov, V.1    Kay, L.E.2
  • 50
    • 0006117825 scopus 로고
    • 31P NMR spectra of interconverting enzyme bound reactants and products of phosphoryl transfer enzymes
    • 31P NMR spectra of interconverting enzyme bound reactants and products of phosphoryl transfer enzymes. J Magn Reson 41: 467-482
    • (1980) J Magn Reson , vol.41 , pp. 467-482
    • Vasavada, K.V.1    Kaplan, J.I.2    Rao, B.D.N.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.