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Volumn 129, Issue 2-3, 2007, Pages 242-250

On the NMR analysis of pKa values in the unfolded state of proteins by extrapolation to zero denaturant

Author keywords

Denaturant; NMR analysis; pKa values; Unfolded state of proteins

Indexed keywords

AMIDE; CARBOXYL GROUP; CARBOXYLIC ACID; GLUTAMINE; POLYPEPTIDE; THIOREDOXIN; UREA; GLUTAMIC ACID; PROTEIN;

EID: 34547557897     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2007.06.004     Document Type: Article
Times cited : (16)

References (45)
  • 1
    • 1542320003 scopus 로고    scopus 로고
    • Structural interpretation of pH and salt-dependent processes in proteins with computational methods
    • García-Moreno B.E., and Fitch C.A. Structural interpretation of pH and salt-dependent processes in proteins with computational methods. Methods Enzymol. 380 (2004) 20-51
    • (2004) Methods Enzymol. , vol.380 , pp. 20-51
    • García-Moreno, B.E.1    Fitch, C.A.2
  • 2
    • 33645034410 scopus 로고    scopus 로고
    • Molecular mechanisms of pH-driven conformational transitions of proteins: insights from continuum electrostatics calculations of acid unfolding
    • Fitch C.A., Whitten S.T., Hilser V.J., and García-Moreno B. Molecular mechanisms of pH-driven conformational transitions of proteins: insights from continuum electrostatics calculations of acid unfolding. Proteins 63 (2006) 113-126
    • (2006) Proteins , vol.63 , pp. 113-126
    • Fitch, C.A.1    Whitten, S.T.2    Hilser, V.J.3    García-Moreno, B.4
  • 4
    • 0037432563 scopus 로고    scopus 로고
    • Contribution of surface salt bridges to protein stability: guidelines for protein engineering
    • Makhatadze G.I., Loladze V.V., Ermolenko D.N., Chen X.-F., and Thomas S.T. Contribution of surface salt bridges to protein stability: guidelines for protein engineering. J. Mol. Biol. 327 (2003) 1135-1148
    • (2003) J. Mol. Biol. , vol.327 , pp. 1135-1148
    • Makhatadze, G.I.1    Loladze, V.V.2    Ermolenko, D.N.3    Chen, X.-F.4    Thomas, S.T.5
  • 5
    • 67650040559 scopus 로고
    • Linked functions and reciprocal effects in myoglobin: a second look
    • Wyman J. Linked functions and reciprocal effects in myoglobin: a second look. Adv. Protein Chem. 19 (1964) 223-286
    • (1964) Adv. Protein Chem. , vol.19 , pp. 223-286
    • Wyman, J.1
  • 6
    • 77956727554 scopus 로고
    • The interpretation of hydrogen ion titration curves of proteins
    • Tanford C. The interpretation of hydrogen ion titration curves of proteins. Adv. Protein Chem. 17 (1962) 9-165
    • (1962) Adv. Protein Chem. , vol.17 , pp. 9-165
    • Tanford, C.1
  • 10
    • 0034636803 scopus 로고    scopus 로고
    • a values in the ovomucoid third domain to charge replacement at a neighboring residue
    • a values in the ovomucoid third domain to charge replacement at a neighboring residue. Biochemistry 39 (2000) 8067-8072
    • (2000) Biochemistry , vol.39 , pp. 8067-8072
    • Forsyth, W.R.1    Robertson, A.D.2
  • 11
    • 0037058895 scopus 로고    scopus 로고
    • Charge-charge interactions are the primary determinants of the pK values of the ionizable groups in ribonuclease T1
    • Pace C.N., Huyghues-Despointes B.M.P., Briggs J.M., Grimsley G.R., and Scholtz J.M. Charge-charge interactions are the primary determinants of the pK values of the ionizable groups in ribonuclease T1. Biophys. Chem. 101 (2002) 211-219
    • (2002) Biophys. Chem. , vol.101 , pp. 211-219
    • Pace, C.N.1    Huyghues-Despointes, B.M.P.2    Briggs, J.M.3    Grimsley, G.R.4    Scholtz, J.M.5
  • 12
    • 0041324868 scopus 로고    scopus 로고
    • Rearrangement of charge-charge interactions in variant ubiquitins as detected by double-mutant cycles and NMR
    • Sundd M., and Robertson A.D. Rearrangement of charge-charge interactions in variant ubiquitins as detected by double-mutant cycles and NMR. J. Mol. Biol. 332 (2003) 927-936
    • (2003) J. Mol. Biol. , vol.332 , pp. 927-936
    • Sundd, M.1    Robertson, A.D.2
  • 15
    • 0037452862 scopus 로고    scopus 로고
    • a values for Asp, Glu, His, and Lys mutants at each variable contiguous enzyme-inhibitor contact position of the turkey ovomucoid third domain.
    • a values for Asp, Glu, His, and Lys mutants at each variable contiguous enzyme-inhibitor contact position of the turkey ovomucoid third domain. Biochemistry 42 (2003) 2487-2856
    • (2003) Biochemistry , vol.42 , pp. 2487-2856
    • Song, J.1    Leskowski, M.2    Qasim, M.A.3    Markley, J.L.4
  • 16
    • 33846011386 scopus 로고    scopus 로고
    • a values for side-chain carboxyl groups of a PGB1 variant explain salt and pH-dependent stability
    • 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.A.3    Andre, I.4
  • 18
    • 0033551039 scopus 로고    scopus 로고
    • a values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions
    • a values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions. Biochemistry 38 (1999) 4896-4903
    • (1999) Biochemistry , vol.38 , pp. 4896-4903
    • Kuhlman, B.1    Luisi, D.L.2    Young, P.3    Raleigh, D.P.4
  • 20
    • 4744368929 scopus 로고    scopus 로고
    • Inverse electrostatic effect: electrostatic repulsion in the unfolded state stabilizes a leucine zipper
    • Marti D.N., and Bosshard H.R. Inverse electrostatic effect: electrostatic repulsion in the unfolded state stabilizes a leucine zipper. Biochemistry 43 (2004) 12436-12447
    • (2004) Biochemistry , vol.43 , pp. 12436-12447
    • Marti, D.N.1    Bosshard, H.R.2
  • 21
    • 0028983182 scopus 로고
    • a values of the denatured state are on average 0.4 units lower than those of model compounds
    • a 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
  • 23
    • 0034700307 scopus 로고    scopus 로고
    • pH dependence of stability of staphiloccal nuclease: evidence of substantial electrostatic interactions in the denatured state
    • Whitten S.T., and García-Moreno B.E. pH dependence of stability of staphiloccal nuclease: evidence of substantial electrostatic interactions in the denatured state. Biochemistry 39 (2000) 14292-14304
    • (2000) Biochemistry , vol.39 , pp. 14292-14304
    • Whitten, S.T.1    García-Moreno, B.E.2
  • 24
    • 0041846681 scopus 로고    scopus 로고
    • Aromatic and methyl NOEs highlight hydrophobic clustering in the unfolded state of an SH3 domain
    • Crowhurst K.A., and Forman-Kay J.D. Aromatic and methyl NOEs highlight hydrophobic clustering in the unfolded state of an SH3 domain. Biochemistry 42 (2003) 8687-8695
    • (2003) Biochemistry , vol.42 , pp. 8687-8695
    • Crowhurst, K.A.1    Forman-Kay, J.D.2
  • 25
    • 0037157124 scopus 로고    scopus 로고
    • a values of glutamate and aspartate residues in an unfolded protein by multinuclear NMR spectroscopy
    • a values of glutamate and aspartate residues in an unfolded protein by multinuclear NMR spectroscopy. J. Am. Chem. Soc. 124 (2002) 5714-5717
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 5714-5717
    • Tollinger, M.1    Forman-Kay, J.D.2    Kay, L.E.3
  • 27
    • 0037069354 scopus 로고    scopus 로고
    • Characterization of large peptide fragments derived from the N-terminal domain of the ribosomal protein L9: definition of the minimum folding motif and characterization of local electrostatic interactions
    • Horng J.C., Moroz V., Rigotti D.J., Fairman R., and Raleigh D.P. Characterization of large peptide fragments derived from the N-terminal domain of the ribosomal protein L9: definition of the minimum folding motif and characterization of local electrostatic interactions. Biochemistry 41 (2002) 13360-13369
    • (2002) Biochemistry , vol.41 , pp. 13360-13369
    • Horng, J.C.1    Moroz, V.2    Rigotti, D.J.3    Fairman, R.4    Raleigh, D.P.5
  • 28
    • 84985733652 scopus 로고
    • 1H-NMR parameters for the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH
    • 1H-NMR parameters for the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers 18 (1979) 285-297
    • (1979) Biopolymers , vol.18 , pp. 285-297
    • Bundi, A.1    Wüthrich, K.2
  • 29
    • 84985653913 scopus 로고
    • 1H-NMR titration shifts for studies of polypeptide conformation
    • 1H-NMR titration shifts for studies of polypeptide conformation. Biopolymers 18 (1979) 299-311
    • (1979) Biopolymers , vol.18 , pp. 299-311
    • Bundi, A.1    Wüthrich, K.2
  • 30
    • 27744450628 scopus 로고    scopus 로고
    • pH-dependence of amide chemical shifts in natively disordered polypeptides detects medium-range interactions with ionizable residues
    • Pujato M., Bracken C., Mancusso R., Cataldi M., and Tasayco M.L. pH-dependence of amide chemical shifts in natively disordered polypeptides detects medium-range interactions with ionizable residues. Biophys. J. 89 (2005) 3293-3302
    • (2005) Biophys. J. , vol.89 , pp. 3293-3302
    • Pujato, M.1    Bracken, C.2    Mancusso, R.3    Cataldi, M.4    Tasayco, M.L.5
  • 31
    • 0035193201 scopus 로고    scopus 로고
    • pH corrections and protein ionization in water/guanidinium chloride
    • García-Mira M.M., and Sánchez-Ruiz J.M. pH corrections and protein ionization in water/guanidinium chloride. Biophys. J. 81 (2001) 3489-3502
    • (2001) Biophys. J. , vol.81 , pp. 3489-3502
    • García-Mira, M.M.1    Sánchez-Ruiz, J.M.2
  • 33
    • 27744471390 scopus 로고    scopus 로고
    • a shifts of titratable residues at high denaturant concentration and the impact on protein stability
    • a shifts of titratable residues at high denaturant concentration and the impact on protein stability. Biophys. Chem. 118 (2005) 88-92
    • (2005) Biophys. Chem. , vol.118 , pp. 88-92
    • Marti, D.N.1
  • 34
    • 0032511360 scopus 로고    scopus 로고
    • NMR evidence for the reassembly of an α/β domain after cleavage of an α-helix: Implications for protein design
    • Yang X.-M., Yu W.-F., Li J.-H., Fuchs J.A., Rizo J., and Tasayco M.L. NMR evidence for the reassembly of an α/β domain after cleavage of an α-helix: Implications for protein design. J. Am. Chem. Soc. 120 (1998) 7985-7986
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 7985-7986
    • Yang, X.-M.1    Yu, W.-F.2    Li, J.-H.3    Fuchs, J.A.4    Rizo, J.5    Tasayco, M.L.6
  • 35
    • 0033970021 scopus 로고    scopus 로고
    • NMR analysis of cleaved E. coli thioredoxin (1-73/74-108) and its P76A variant: cis/trans peptide isomerization
    • Yu W.-F., Tung C.-S., Wang H., and Tasayco M.L. NMR analysis of cleaved E. coli thioredoxin (1-73/74-108) and its P76A variant: cis/trans peptide isomerization. Protein Sci. 9 (2000) 20-28
    • (2000) Protein Sci. , vol.9 , pp. 20-28
    • Yu, W.-F.1    Tung, C.-S.2    Wang, H.3    Tasayco, M.L.4
  • 36
    • 0035909078 scopus 로고    scopus 로고
    • Probing the structure and stability of a hybrid protein: the human-E. coli thioredoxin chimera
    • Louis J.M., Georgescu R.E., Tasayco M.L., Tcherkasskaya O., and Gronenborn A.M. Probing the structure and stability of a hybrid protein: the human-E. coli thioredoxin chimera. Biochemistry 40 (2001) 11184-11192
    • (2001) Biochemistry , vol.40 , pp. 11184-11192
    • Louis, J.M.1    Georgescu, R.E.2    Tasayco, M.L.3    Tcherkasskaya, O.4    Gronenborn, A.M.5
  • 37
    • 0003115169 scopus 로고
    • Isotope effects in deuterium oxide solution. I. Acid-base equilibria
    • Bunton C.A., and Shiner V.J. Isotope effects in deuterium oxide solution. I. Acid-base equilibria. J. Am. Chem. Soc. 83 (1961) 42-47
    • (1961) J. Am. Chem. Soc. , vol.83 , pp. 42-47
    • Bunton, C.A.1    Shiner, V.J.2
  • 40
    • 0027568083 scopus 로고
    • A general method for assigning NMR spectra of denatured proteins using 3D HC(CO)NH-TOCSY triple resonance experiments
    • Logan T.M., Olejniczak E.T., Xu R.-X., and Fesik S.W. A general method for assigning NMR spectra of denatured proteins using 3D HC(CO)NH-TOCSY triple resonance experiments. J. Biomol. NMR 3 (1993) 225-231
    • (1993) J. Biomol. NMR , vol.3 , pp. 225-231
    • Logan, T.M.1    Olejniczak, E.T.2    Xu, R.-X.3    Fesik, S.W.4
  • 42
    • 34547600946 scopus 로고    scopus 로고
    • T.D. Goddard, D.G. Kneller, SPARKY 3, University of California at San Francisco.
  • 43
    • 34547604616 scopus 로고    scopus 로고
    • BMRB (BioMagResBank), http://www.bmrb.wisc.edu.
  • 45
    • 0002870406 scopus 로고
    • Observation of histidine residues in proteins by means of nuclear magnetic resonance spectroscopy
    • Markley J.L. Observation of histidine residues in proteins by means of nuclear magnetic resonance spectroscopy. Acc. Chem. Res. 8 (1975) 70-80
    • (1975) Acc. Chem. Res. , vol.8 , pp. 70-80
    • Markley, J.L.1


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