메뉴 건너뛰기




Volumn 53, Issue 3, 2012, Pages 257-270

NMR line shapes and multi-state binding equilibria

Author keywords

Exchange; Kinetics; Ligand binding; Line shape analysis; NMR; Proteins

Indexed keywords

ARTICLE; BINDING AFFINITY; DIMERIZATION; ISOMERIZATION; LIGAND BINDING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN FUNCTION; SIMULATION; THERMODYNAMICS; TITRIMETRY;

EID: 84865166917     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-012-9636-3     Document Type: Article
Times cited : (69)

References (45)
  • 2
    • 0030166213 scopus 로고    scopus 로고
    • A unified approach to dynamic NMR based on a physical interpretation of the transition probability
    • Bain AD, Duns GJ (1996) A unified approach to dynamic NMR based on a physical interpretation of the transition probability. Can J Chem 74:819-824 (Pubitemid 126423891)
    • (1996) Canadian Journal of Chemistry , vol.74 , Issue.6 , pp. 819-824
    • Bain, A.D.1    Duns, G.J.2
  • 3
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr DD, Nussinov R, Wright PE (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 5(11):789-796
    • (2009) Nat Chem Biol , vol.5 , Issue.11 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 5
    • 77957188861 scopus 로고    scopus 로고
    • Site-specific investigation of the steady-state kinetics and dynamics of the multistep binding of bile acid molecules to a lipid carrier protein
    • doi:10.1002/chem.20100.0498
    • Cogliati C, Ragona L, D'Onofrio M, Gunther U, Whittaker S, Ludwig C, Tomaselli S, Assfalg M, Molinari H (2010) Site-specific investigation of the steady-state kinetics and dynamics of the multistep binding of bile acid molecules to a lipid carrier protein. Chemistry Eur J 16(37):11300-11310. doi:10.1002/chem.20100 0498
    • (2010) Chemistry Eur J , vol.16 , Issue.37 , pp. 11300-11310
    • Cogliati, C.1    Ragona, L.2    D'onofrio, M.3    Gunther, U.4    Whittaker, S.5    Ludwig, C.6    Tomaselli, S.7    Assfalg, M.8    Molinari, H.9
  • 6
    • 77957231785 scopus 로고    scopus 로고
    • Induced fit, conformational selection and independent dynamic segments: An extended view of binding events
    • Csermely P, Palotai R, Nussinov R (2010) Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci 35(10):539-546
    • (2010) Trends Biochem Sci , vol.35 , Issue.10 , pp. 539-546
    • Csermely, P.1    Palotai, R.2    Nussinov, R.3
  • 7
    • 67849119942 scopus 로고    scopus 로고
    • Binding mechanism of an SH3 domain studied by NMR and ITC
    • doi:10.1021/ja808255d
    • Demers JP, Mittermaier A (2009) Binding mechanism of an SH3 domain studied by NMR and ITC. J Am Chem Soc 131(12): 4355-4367. doi:10.1021/ja808255d
    • (2009) J Am Chem Soc , vol.131 , Issue.12 , pp. 4355-4367
    • Demers, J.P.1    Mittermaier, A.2
  • 8
    • 77951680126 scopus 로고    scopus 로고
    • Analyzing protein folding cooperativity by differential scanning calorimetry and NMR spectroscopy
    • doi:10.1021/ja100815a
    • Farber P, Darmawan H, Sprules T, Mittermaier A (2010) Analyzing protein folding cooperativity by differential scanning calorimetry and NMR spectroscopy. J Am Chem Soc 132(17): 6214-6222. doi:10.1021/ja100815a
    • (2010) J Am Chem Soc , vol.132 , Issue.17 , pp. 6214-6222
    • Farber, P.1    Darmawan, H.2    Sprules, T.3    Mittermaier, A.4
  • 9
    • 0028503463 scopus 로고
    • A heteronuclear correlation experiment for simultaneous determination of 15N longitudinal decay and chemical exchange rates of systems in slow equilibrium
    • Farrow NA, Zhang O, Forman-Kay JD, Kay LE (1994) A heteronuclear correlation experiment for simultaneous determination of 15N longitudinal decay and chemical exchange rates of systems in slow equilibrium. J Biomol NMR 4(5):727-734
    • (1994) J Biomol NMR , vol.4 , Issue.5 , pp. 727-734
    • Farrow, N.A.1    Zhang, O.2    Forman-Kay, J.D.3    Kay, L.E.4
  • 10
    • 0001559701 scopus 로고
    • The effects of intermediate exchange processes on the estimation of equilibrium constants by NMR
    • Feeney J, Batchelor JG, Albrand JP, Roberts GCK (1979) The effects of intermediate exchange processes on the estimation of equilibrium constants by NMR. J Magn Reson 33:519
    • (1979) J Magn Reson , vol.33 , pp. 519
    • Feeney, J.1    Batchelor, J.G.2    Albrand, J.P.3    Gck, R.4
  • 11
    • 0001289724 scopus 로고
    • Einfluss der Configuration auf die Wirkung der Enzyme
    • Fischer E (1894) Einfluss der Configuration auf die Wirkung der Enzyme (Influence of configuration on the effect of enzymes). Ber Dtsch Chem Ges 27:2984-2993
    • (1894) Ber Dtsch Chem Ges , vol.27 , pp. 2984-2993
    • Fischer, E.1
  • 12
    • 79955634085 scopus 로고    scopus 로고
    • Measuring low levels of protein aggregation by sedimentation velocity
    • doi:10.1016/j.ymeth.2010.12.030
    • Gabrielson JP, Arthur KK (2011) Measuring low levels of protein aggregation by sedimentation velocity. Methods 54(1):83-91. doi:10.1016/j.ymeth. 2010.12.030
    • (2011) Methods , vol.54 , Issue.1 , pp. 83-91
    • Gabrielson, J.P.1    Arthur, K.K.2
  • 13
    • 80755168127 scopus 로고    scopus 로고
    • Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis
    • doi:10.1007/s10858-011-9538-9
    • Greenwood A, Rogals M, De S, Lu K, Kovrigin E, Nicholson J (2011) Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis. J Biomol NMR 51(1):21-34. doi:10.1007/s10858-011-9538-9
    • (2011) J Biomol NMR , vol.51 , Issue.1 , pp. 21-34
    • Greenwood, A.1    Rogals, M.2    De S Lu, K.3    Kovrigin, E.4    Nicholson, J.5
  • 14
    • 0345306309 scopus 로고    scopus 로고
    • Disulfide Bond Isomerization in Basic Pancreatic Trypsin Inhibitor: Multisite Chemical Exchange Quantified by CPMG Relaxation Dispersion and Chemical Shift Modeling
    • DOI 10.1021/ja0367389
    • Grey MJ, Wang C, Palmer AG (2003) Disulfide bond isomerization in basic pancreatic trypsin inhibitor: multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modeling. J Am Chem Soc 125(47):14324-14335. doi:10.1021/ ja0367389 (Pubitemid 37452371)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.47 , pp. 14324-14335
    • Grey, M.J.1    Wang, C.2    Palmer III, A.G.3
  • 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(3):201-209 (Pubitemid 34296105)
    • (2002) Journal of Biomolecular NMR , vol.22 , Issue.3 , pp. 201-209
    • Gunther, U.L.1    Schaffhausen, B.2
  • 17
    • 0036785230 scopus 로고    scopus 로고
    • Probing Src homology 2 domain ligand interactions by differential line broadening
    • Gunther UL, Mittag T, Schaffhausen B (2002) Probing Src homology 2 domain ligand interactions by differential line broadening. Biochemistry 41(39):11658-11669
    • (2002) Biochemistry , vol.41 , Issue.39 , pp. 11658-11669
    • Gunther, U.L.1    Mittag, T.2    Schaffhausen, B.3
  • 19
    • 0035814889 scopus 로고    scopus 로고
    • Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein
    • DOI 10.1021/bi002078y
    • Henkels CH, Kurz JC, Fierke CA, Oas TG (2001) Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein. Biochemistry 40(9):2777-2789 (Pubitemid 32198279)
    • (2001) Biochemistry , vol.40 , Issue.9 , pp. 2777-2789
    • Henkels, C.H.1    Kurz, J.C.2    Fierke, C.A.3    Oas, T.G.4
  • 21
    • 14844361989 scopus 로고    scopus 로고
    • NMR studies of protein structure and dynamics
    • DOI 10.1016/j.jmr.2004.11.021, PII S1090780704003854
    • Kay LE (2005) NMR studies of protein structure and dynamics. J Magn Reson 173(2):193-207 (Pubitemid 40352443)
    • (2005) Journal of Magnetic Resonance , vol.173 , Issue.2 , pp. 193-207
    • Kay, L.E.1
  • 23
    • 0028877264 scopus 로고
    • Kinetic analysis of cyclophilin-catalyzed prolyl cis/trans isomerization by dynamic NMR spectroscopy
    • 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(41):13594-13602
    • (1995) Biochemistry , vol.34 , Issue.41 , pp. 13594-13602
    • Kern, D.1    Kern, G.2    Scherer, G.3    Fischer, G.4    Drakenberg, T.5
  • 24
    • 59149097809 scopus 로고    scopus 로고
    • Alternate binding modes for a ubiquitin-SH3 domain interaction studied by NMR spectroscopy
    • Korzhnev DM, Bezsonova I, Lee S, Chalikian TV, Kay LE (2009) Alternate binding modes for a ubiquitin-SH3 domain interaction studied by NMR spectroscopy. J Mol Biol 386(2):391-405
    • (2009) J Mol Biol , vol.386 , Issue.2 , pp. 391-405
    • Korzhnev, D.M.1    Bezsonova, I.2    Lee, S.3    Chalikian, T.V.4    Kay, L.E.5
  • 25
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland DE (1958) Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci U S A 44:98-104
    • (1958) Proc Natl Acad Sci U S A , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 26
    • 33750639677 scopus 로고
    • The key-lock theory and the induced fit theory
    • Koshland DE (1994) The key-lock theory and the induced fit theory. Angewandte Chemie Int Ed Engl 33:2375-2378
    • (1994) Angewandte Chemie Int Ed Engl , vol.33 , pp. 2375-2378
    • Koshland, D.E.1
  • 27
    • 33644556820 scopus 로고    scopus 로고
    • Enzyme dynamics along the reaction coordinate: Critical role of a conserved residue
    • Kovrigin EL, Loria JP (2006) Enzyme dynamics along the reaction coordinate: critical role of a conserved residue. Biochemistry 45(8):2636-2647
    • (2006) Biochemistry , vol.45 , Issue.8 , pp. 2636-2647
    • Kovrigin, E.L.1    Loria, J.P.2
  • 28
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar S, Ma BY, Tsai CJ, Sinha N, Nussinov R (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 9(1):10-19 (Pubitemid 30070934)
    • (2000) Protein Science , vol.9 , Issue.1 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.-J.3    Sinha, N.4    Nussinov, R.5
  • 29
    • 77957754309 scopus 로고    scopus 로고
    • Enzyme dynamics point to stepwise conformational selection in catalysis
    • Ma B, Nussinov R (2010) Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol 14(5):652-659
    • (2010) Curr Opin Chem Biol , vol.14 , Issue.5 , pp. 652-659
    • Ma, B.1    Nussinov, R.2
  • 30
    • 0002870406 scopus 로고
    • Observation of histidine residues in proteins by means of nuclear magnetic resonance spectroscopy
    • Markley JL (1975) Observation of histidine residues in proteins by means of nuclear magnetic resonance spectroscopy. Acc Chem Res 8:70
    • (1975) Acc Chem Res , vol.8 , pp. 70
    • Markley, J.L.1
  • 31
    • 0010957050 scopus 로고
    • Reaction rates by nuclear magnetic resonance
    • McConnell H (1958) Reaction rates by nuclear magnetic resonance. J Chem Phys 28:430-431
    • (1958) J Chem Phys , vol.28 , pp. 430-431
    • McConnell, H.1
  • 32
    • 0141791271 scopus 로고    scopus 로고
    • Direct observation of protein-ligand interaction kinetics
    • DOI 10.1021/bi0347499
    • Mittag T, Schaffhausen B, Gunther UL (2003) Direct observation of protein-ligand interaction kinetics. Biochemistry 42(38):11128-11136 (Pubitemid 37158880)
    • (2003) Biochemistry , vol.42 , Issue.38 , pp. 11128-11136
    • Mittag, T.1    Schaffhausen, B.2    Gunther, U.L.3
  • 34
    • 33747830489 scopus 로고    scopus 로고
    • Quantitative Modeling in Cell Biology: What Is It Good for?
    • DOI 10.1016/j.devcel.2006.08.004, PII S1534580706003509
    • Mogilner A, Wollman R, Marshall WF (2006) Quantitative modeling in cell biology: what is it good for? Dev Cell 11(3):279-287. doi: 10.1016/j.devcel. 2006.08.004 (Pubitemid 44283949)
    • (2006) Developmental Cell , vol.11 , Issue.3 , pp. 279-287
    • Mogilner, A.1    Wollman, R.2    Marshall, W.F.3
  • 35
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: A plausible model
    • Monod J, Wyman J, Changeux JP (1965) On the nature of allosteric transitions: a plausible model. J Mol Biol 12:88-118
    • (1965) J Mol Biol , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 36
    • 79955573066 scopus 로고    scopus 로고
    • Global fit and structure optimization of flexible and rigid macromolecules and nanoparticles from analytical ultracentrifugation and other dilute solution properties
    • doi:10.1016/j.ymeth.2010.12.004
    • Ortega A, Amoros D, de la Torre JG (2011) Global fit and structure optimization of flexible and rigid macromolecules and nanoparticles from analytical ultracentrifugation and other dilute solution properties. Methods 54(1):115-123. doi:10.1016/j.ymeth.2010.12.004
    • (2011) Methods , vol.54 , Issue.1 , pp. 115-123
    • Ortega, A.1    Amoros, D.2    De La Torre, J.G.3
  • 37
    • 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. Methods 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
  • 38
    • 0024404656 scopus 로고
    • Nuclear magnetic resonance line-shape analysis and determination of exchange rates
    • edn Academic Press, USA
    • Rao BDN (1989) Nuclear magnetic resonance line-shape analysis and determination of exchange rates. In: Methods in enzymology, vol 176 edn. Academic Press, USA, pp 279-311
    • (1989) Methods in Enzymology , vol.176 , pp. 279-311
    • Bdn, R.1
  • 39
    • 58249085344 scopus 로고    scopus 로고
    • Fluorescence approaches to quantifying biomolecular interactions
    • doi:10.1016/S0076-6879(08)03405-8
    • Royer CA, Scarlata SF (2008) Fluorescence approaches to quantifying biomolecular interactions. Methods Enzymol 450:79-106. doi:10.1016/S0076- 6879(08)03405-8
    • (2008) Methods Enzymol , vol.450 , pp. 79-106
    • Royer, C.A.1    Scarlata, S.F.2
  • 40
    • 78650945739 scopus 로고    scopus 로고
    • Structural and thermodynamic analysis of PDZ-ligand interactions
    • doi:10.1016/B978-0-12-381268-1.00004-5
    • Shepherd TR, Fuentes EJ (2011) Structural and thermodynamic analysis of PDZ-ligand interactions. Methods Enzymol 488:81-100. doi:10.1016/B978-0-12- 381268-1.00004-5
    • (2011) Methods Enzymol , vol.488 , pp. 81-100
    • Shepherd, T.R.1    Fuentes, E.J.2
  • 41
    • 0000337195 scopus 로고
    • Dependence of NMR lineshape analysis upon chemical rates and mechanisms: Implications for enzyme histidine titrations
    • Sudmeier JL, Evelhoch JL, Jonsson NBH (1980) Dependence of NMR lineshape analysis upon chemical rates and mechanisms: implications for enzyme histidine titrations. J Magn Reson 40(2):377-390
    • (1980) J Magn Reson , vol.40 , Issue.2 , pp. 377-390
    • Sudmeier, J.L.1    Evelhoch, J.L.2    Nbh, J.3
  • 42
    • 34250821717 scopus 로고    scopus 로고
    • Mechanism of coupled folding and binding of an intrinsically disordered protein
    • DOI 10.1038/nature05858, PII NATURE05858
    • Sugase K, Dyson HJ, Wright PE (2007a) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447:1021-1025 (Pubitemid 46975749)
    • (2007) Nature , vol.447 , Issue.7147 , pp. 1021-1025
    • Sugase, K.1    Dyson, H.J.2    Wright, P.E.3
  • 43
    • 35948933151 scopus 로고    scopus 로고
    • Tailoring relaxation dispersion experiments for fast-associating protein complexes
    • DOI 10.1021/ja0762238
    • Sugase K, Lansing JC, Dyson HJ, Wright PE (2007b) Tailoring relaxation dispersion experiments for fast-associating protein complexes. J Am Chem Soc 129(44):13406-13407. doi: 10.1021/ja0762238 (Pubitemid 350071766)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.44 , pp. 13406-13407
    • Sugase, K.1    Lansing, J.C.2    Dyson, H.J.3    Wright, P.E.4
  • 44
    • 32344434479 scopus 로고    scopus 로고
    • The changing landscape of protein allostery
    • DOI 10.1016/j.sbi.2006.01.003, PII S0959440X06000042
    • Swain JF, Gierasch LM (2006) The changing landscape of protein allostery. Curr Opin Struct Biol 16(1):102-108 (Pubitemid 43221878)
    • (2006) Current Opinion in Structural Biology , vol.16 , Issue.1 , pp. 102-108
    • Swain, J.F.1    Gierasch, L.M.2
  • 45
    • 41149104308 scopus 로고    scopus 로고
    • Allostery: Absence of a change in shape does not imply that allostery is not at play
    • Tsai CJ, del Sol A, Nussinov R (2008) Allostery: absence of a change in shape does not imply that allostery is not at play. J Mol Biol 378(1):1-11
    • (2008) J Mol Biol , vol.378 , Issue.1 , pp. 1-11
    • Tsai, C.J.1    Del Sol, A.2    Nussinov, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.