메뉴 건너뛰기




Volumn 79, Issue 12, 2011, Pages 3500-3510

Analysis of electrostatic interactions in the denatured state ensemble of the N-terminal domain of L9 under native conditions

Author keywords

Denatured state ensemble; Electrostatic interactions; PK a; Protein stability; Ribosomal protein L9, pH titration; Unfolded state

Indexed keywords

ASPARAGINE; GLUTAMIC ACID; N TERMINAL DOMAIN OF L9; PROTEIN; UNCLASSIFIED DRUG; VALINE;

EID: 81055156798     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23145     Document Type: Article
Times cited : (19)

References (61)
  • 1
    • 0014718113 scopus 로고
    • Protein denaturation. C. Theoretical models for the mechanism of denaturation
    • Tanford C. Protein denaturation. C. Theoretical models for the mechanism of denaturation. Adv Protein Chem 1970; 24: 1-95.
    • (1970) Adv Protein Chem , vol.24 , pp. 1-95
    • Tanford, C.1
  • 2
    • 0027231258 scopus 로고
    • On the pH dependence of protein stability
    • Yang AS, Honig B. On the pH dependence of protein stability. J Mol Biol 1993; 231: 459-474.
    • (1993) J Mol Biol , vol.231 , pp. 459-474
    • Yang, A.S.1    Honig, B.2
  • 3
    • 0028904906 scopus 로고
    • Hydrogen bonds and the pH dependence of ovomucoid third domain stability
    • Swint-Kruse L, Robertson AD. Hydrogen bonds and the pH dependence of ovomucoid third domain stability. Biochemistry 1995; 34: 4724-4732.
    • (1995) Biochemistry , vol.34 , pp. 4724-4732
    • Swint-Kruse, L.1    Robertson, A.D.2
  • 4
    • 36749004330 scopus 로고    scopus 로고
    • Electrostatic interactions in the denatured state ensemble: their effect upon protein folding and protein stability
    • Cho JH, Sato S, Horng JC, Anil B, Raleigh DP. Electrostatic interactions in the denatured state ensemble: their effect upon protein folding and protein stability. Arch Biochem Biophys 2008; 469: 20-28.
    • (2008) Arch Biochem Biophys , vol.469 , pp. 20-28
    • Cho, J.H.1    Sato, S.2    Horng, J.C.3    Anil, B.4    Raleigh, D.P.5
  • 5
    • 0034700307 scopus 로고    scopus 로고
    • pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state
    • Whitten ST, Garcia-Moreno EB. pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state. Biochemistry 2000; 39: 14292-14304.
    • (2000) Biochemistry , vol.39 , pp. 14292-14304
    • Whitten, S.T.1    Garcia-Moreno, E.B.2
  • 6
    • 0033852796 scopus 로고    scopus 로고
    • Charge-charge interactions influence the denatured state ensemble and contribute to protein stability
    • Pace CN, Alston RW, Shaw KL. Charge-charge interactions influence the denatured state ensemble and contribute to protein stability. Protein Sci 2000; 9: 1395-1398.
    • (2000) Protein Sci , vol.9 , pp. 1395-1398
    • Pace, C.N.1    Alston, R.W.2    Shaw, K.L.3
  • 7
    • 0026602704 scopus 로고
    • Urea denaturation of barnase: pH dependence and characterization of the unfolded state
    • Pace CN, Laurents DV, Erickson RE. Urea denaturation of barnase: pH dependence and characterization of the unfolded state. Biochemistry 1992; 31: 2728-2734.
    • (1992) Biochemistry , vol.31 , pp. 2728-2734
    • Pace, C.N.1    Laurents, D.V.2    Erickson, R.E.3
  • 8
    • 25144470141 scopus 로고    scopus 로고
    • Mutational analysis demonstrates that specific electrostatic interactions can play a key role in the denatured state ensemble of proteins
    • Cho JH, Raleigh DP. Mutational analysis demonstrates that specific electrostatic interactions can play a key role in the denatured state ensemble of proteins. J Mol Biol 2005; 353: 174-185.
    • (2005) J Mol Biol , vol.353 , pp. 174-185
    • Cho, J.H.1    Raleigh, D.P.2
  • 9
    • 33845918456 scopus 로고    scopus 로고
    • Denatured state effects and the origin of nonclassical Φ-values in protein folding
    • Cho JH, Raleigh DP. Denatured state effects and the origin of nonclassical Φ-values in protein folding. J Am Chem Soc 2006; 128: 16492-16493.
    • (2006) J Am Chem Soc , vol.128 , pp. 16492-16493
    • Cho, J.H.1    Raleigh, D.P.2
  • 10
    • 22244458003 scopus 로고    scopus 로고
    • Charge-charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa
    • Trefethen JM, Pace CN, Scholtz JM, Brems DN. Charge-charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa. Protein Sci 2005; 14: 1934-1938.
    • (2005) Protein Sci , vol.14 , pp. 1934-1938
    • Trefethen, J.M.1    Pace, C.N.2    Scholtz, J.M.3    Brems, D.N.4
  • 11
    • 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 1999; 38: 4896-4903.
    • (1999) Biochemistry , vol.38 , pp. 4896-4903
    • Kuhlman, B.1    Luisi, D.L.2    Young, P.3    Raleigh, D.P.4
  • 12
    • 0034674156 scopus 로고    scopus 로고
    • pH-dependent interactions and the stability and folding kinetics of the n-terminal domain of L9. Electrostatic interactions are only weakly formed in the transition state for folding
    • Luisi DL, Raleigh DP. pH-dependent interactions and the stability and folding kinetics of the n-terminal domain of L9. Electrostatic interactions are only weakly formed in the transition state for folding. J Mol Biol 2000; 299: 1091-1100.
    • (2000) J Mol Biol , vol.299 , pp. 1091-1100
    • Luisi, D.L.1    Raleigh, D.P.2
  • 13
    • 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 2002; 124: 5714-5717.
    • (2002) J Am Chem Soc , vol.124 , pp. 5714-5717
    • Tollinger, M.1    Forman-Kay, J.D.2    Kay, L.E.3
  • 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 2007; 92: 257-266.
    • (2007) Biophys J , vol.92 , pp. 257-266
    • Lindman, S.1    Linse, S.2    Mulder, F.A.A.3    Andre, I.4
  • 20
    • 4644259437 scopus 로고    scopus 로고
    • Using NMRView to visualize and analyze NMR spectra of macromolecules
    • Johnson BA. Using NMRView to visualize and analyze NMR spectra of macromolecules. Methods Mol Biol 2004; 278: 313-352.
    • (2004) Methods Mol Biol , vol.278 , pp. 313-352
    • Johnson, B.A.1
  • 21
    • 44949291986 scopus 로고
    • Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins
    • Kay LE, Ikura M, Tschudin R, Bax A. Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins. J Magn Reson 1990; 89: 496-514.
    • (1990) J Magn Reson , vol.89 , pp. 496-514
    • Kay, L.E.1    Ikura, M.2    Tschudin, R.3    Bax, A.4
  • 22
    • 0027310404 scopus 로고
    • Complete assignments of magnetic resonances of ribonuclease H from Escherichia coli by double-resonance and triple-resonance 2D and 3D NMR spectroscopies
    • Yamazaki T, Yoshida M, Nagayama K. Complete assignments of magnetic resonances of ribonuclease H from Escherichia coli by double-resonance and triple-resonance 2D and 3D NMR spectroscopies. Biochemistry 1993; 32: 5656-5669.
    • (1993) Biochemistry , vol.32 , pp. 5656-5669
    • Yamazaki, T.1    Yoshida, M.2    Nagayama, K.3
  • 23
    • 81055138052 scopus 로고    scopus 로고
    • Folding of ribosomal protein L9 and its isolated N- and C-terminal domains. Ph.D. thesis, Stony Brook University, Stony Brook, NY
    • Sato S. Folding of ribosomal protein L9 and its isolated N- and C-terminal domains. Ph.D. thesis, Stony Brook University, Stony Brook, NY, 2002.
    • (2002)
    • Sato, S.1
  • 24
    • 27744452242 scopus 로고    scopus 로고
    • Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing
    • Anil B, Sato S, Cho JH, Raleigh DP. Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing. J Mol Biol 2005; 354: 693-705.
    • (2005) J Mol Biol , vol.354 , pp. 693-705
    • Anil, B.1    Sato, S.2    Cho, J.H.3    Raleigh, D.P.4
  • 25
    • 0025222978 scopus 로고
    • A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino-acids
    • Oneil KT, Degrado WF. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino-acids. Science 1990; 250: 646-651.
    • (1990) Science , vol.250 , pp. 646-651
    • Oneil, K.T.1    Degrado, W.F.2
  • 26
    • 0028222235 scopus 로고
    • Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
    • Chakrabartty A, Kortemme T, Baldwin RL. Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci 1994; 3: 843-852.
    • (1994) Protein Sci , vol.3 , pp. 843-852
    • Chakrabartty, A.1    Kortemme, T.2    Baldwin, R.L.3
  • 27
    • 0028873081 scopus 로고
    • Elucidating the folding problem of helical peptides using empirical parameters. 2. Helix macrodipole effects and rational modification of the helical content of natural peptides
    • Munoz V, Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. 2. Helix macrodipole effects and rational modification of the helical content of natural peptides. J Mol Biol 1995; 245: 275-296.
    • (1995) J Mol Biol , vol.245 , pp. 275-296
    • Munoz, V.1    Serrano, L.2
  • 28
    • 0028834210 scopus 로고
    • Elucidating the folding problem of helical peptides using empirical parameters. 3. Temperature and pH-dependence
    • Munoz V, Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. 3. Temperature and pH-dependence. J Mol Biol 1995; 245: 297-308.
    • (1995) J Mol Biol , vol.245 , pp. 297-308
    • Munoz, V.1    Serrano, L.2
  • 30
    • 0001229341 scopus 로고    scopus 로고
    • Calculation of hydrodynamic properties of globular proteins from their atomic-level structure
    • Garcia De La Torre J, Huertas ML, Carrasco B. Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys J 2000; 78: 719-730.
    • (2000) Biophys J , vol.78 , pp. 719-730
    • Garcia De La Torre, J.1    Huertas, M.L.2    Carrasco, B.3
  • 34
    • 0030032461 scopus 로고    scopus 로고
    • The denatured state (the other half of the folding equation) and its role in protein stability
    • Shortle D. The denatured state (the other half of the folding equation) and its role in protein stability. FASEB J 1996; 10: 27-34.
    • (1996) FASEB J , vol.10 , pp. 27-34
    • Shortle, D.1
  • 35
    • 0036401140 scopus 로고    scopus 로고
    • Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins
    • Millet IS, Doniach S, Plaxco KW. Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. Adv Protein Chem 2002; 62: 241-262.
    • (2002) Adv Protein Chem , vol.62 , pp. 241-262
    • Millet, I.S.1    Doniach, S.2    Plaxco, K.W.3
  • 36
    • 0036400348 scopus 로고    scopus 로고
    • A new perspective on unfolded proteins
    • Baldwin RL. A new perspective on unfolded proteins. Adv Protein Chem 2002; 62: 361-367.
    • (2002) Adv Protein Chem , vol.62 , pp. 361-367
    • Baldwin, R.L.1
  • 37
    • 0036300690 scopus 로고    scopus 로고
    • Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques
    • Choy WY, Mulder FAA, Crowhurst KA, Muhandiram DR, Millett IS, Doniach S, Forman-Kay JD, Kay LE. Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques. J Mol Biol 2002; 316: 101-112.
    • (2002) J Mol Biol , vol.316 , pp. 101-112
    • Choy, W.Y.1    Mulder, F.A.A.2    Crowhurst, K.A.3    Muhandiram, D.R.4    Millett, I.S.5    Doniach, S.6    Forman-Kay, J.D.7    Kay, L.E.8
  • 38
    • 1942521649 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of non-native interactions in protein folding: a single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state
    • Cho JH, Sato S, Raleigh DP. Thermodynamics and kinetics of non-native interactions in protein folding: a single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state. J Mol Biol 2004; 338: 827-837.
    • (2004) J Mol Biol , vol.338 , pp. 827-837
    • Cho, J.H.1    Sato, S.2    Raleigh, D.P.3
  • 39
    • 33846498387 scopus 로고    scopus 로고
    • Thermodynamics of protein denatured states
    • Bowler BE. Thermodynamics of protein denatured states. Mol Biosyst 2007; 3: 88-99.
    • (2007) Mol Biosyst , vol.3 , pp. 88-99
    • Bowler, B.E.1
  • 40
    • 0025856806 scopus 로고
    • Denatured states of proteins
    • Dill KA, Shortle D. Denatured states of proteins. Annu Rev Biochem 1991; 60: 795-825.
    • (1991) Annu Rev Biochem , vol.60 , pp. 795-825
    • Dill, K.A.1    Shortle, D.2
  • 41
    • 0033546123 scopus 로고    scopus 로고
    • NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions
    • Mok YK, Kay CM, Kay LE, Forman-Kay J. NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions. J Mol Biol 1999; 289: 619-638.
    • (1999) J Mol Biol , vol.289 , pp. 619-638
    • Mok, Y.K.1    Kay, C.M.2    Kay, L.E.3    Forman-Kay, J.4
  • 42
    • 3242789489 scopus 로고    scopus 로고
    • Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings
    • Mohana-Borges R, Goto NK, Kroon GJ, Dyson HJ, Wright PE. Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings. J Mol Biol 2004; 340: 1131-1142.
    • (2004) J Mol Biol , vol.340 , pp. 1131-1142
    • Mohana-Borges, R.1    Goto, N.K.2    Kroon, G.J.3    Dyson, H.J.4    Wright, P.E.5
  • 44
    • 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 1995; 34: 9424-9433.
    • (1995) Biochemistry , vol.34 , pp. 9424-9433
    • Oliveberg, M.1    Arcus, V.L.2    Fersht, A.R.3
  • 45
    • 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 JC, Moroz V, Rigotti DJ, Fairman R, Raleigh DP. 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 2002; 41: 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
  • 46
    • 67650089623 scopus 로고    scopus 로고
    • Charge neutralization and collapse of the C-terminal tail of alpha-synuclein at low pH
    • McClendon S, Rospigliosi CC, Eliezer D. Charge neutralization and collapse of the C-terminal tail of alpha-synuclein at low pH. Protein Sci 2009; 18: 1531-1540.
    • (2009) Protein Sci , vol.18 , pp. 1531-1540
    • McClendon, S.1    Rospigliosi, C.C.2    Eliezer, D.3
  • 48
    • 0033544710 scopus 로고    scopus 로고
    • Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability
    • Elcock AH. Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability. J Mol Biol 1999; 294: 1051-1062.
    • (1999) J Mol Biol , vol.294 , pp. 1051-1062
    • Elcock, A.H.1
  • 49
    • 0036927473 scopus 로고    scopus 로고
    • Residual charge interations in unfolded staphylococcal nuclease can be explained by the Gaussian-chain model
    • Zhou HX. Residual charge interations in unfolded staphylococcal nuclease can be explained by the Gaussian-chain model. Biophy J 2002; 83: 2981-2986.
    • (2002) Biophy J , vol.83 , pp. 2981-2986
    • Zhou, H.X.1
  • 50
    • 77952858860 scopus 로고    scopus 로고
    • a values from analysis of stability changes in single mutant cycles
    • a values from analysis of stability changes in single mutant cycles. J Am Chem Soc 2010; 132: 7258-7259.
    • (2010) J Am Chem Soc , vol.132 , pp. 7258-7259
    • Shen, J.K.1
  • 51
    • 0038392707 scopus 로고    scopus 로고
    • Energetic evidence for formation of a pH-dependent hydrophobic cluster in the denatured state of Thermus thermophilus ribonuclease H
    • Guzman-Casado M, Parody-Morreale A, Robic S, Marqusee S, Sanchez-Ruiz JM. Energetic evidence for formation of a pH-dependent hydrophobic cluster in the denatured state of Thermus thermophilus ribonuclease H. J Mol Biol 2003; 329: 731-743.
    • (2003) J Mol Biol , vol.329 , pp. 731-743
    • Guzman-Casado, M.1    Parody-Morreale, A.2    Robic, S.3    Marqusee, S.4    Sanchez-Ruiz, J.M.5
  • 52
    • 4744368929 scopus 로고    scopus 로고
    • Inverse electrostatic effect: electrostatic repulsion in the unfolded state stabilizes a leucine zipper
    • Marti DN, Bosshard HR. Inverse electrostatic effect: electrostatic repulsion in the unfolded state stabilizes a leucine zipper. Biochemistry 2004; 43: 12436-12447.
    • (2004) Biochemistry , vol.43 , pp. 12436-12447
    • Marti, D.N.1    Bosshard, H.R.2
  • 53
    • 0029859858 scopus 로고    scopus 로고
    • Surface point mutations that significantly alter the structure and stability of a protein's denatured state
    • Smith CK, Bu ZM, Anderson KS, Sturtevant JM, Engelman DM, Regan L. Surface point mutations that significantly alter the structure and stability of a protein's denatured state. Protein Sci 1996; 5: 2009-2019.
    • (1996) Protein Sci , vol.5 , pp. 2009-2019
    • Smith, C.K.1    Bu, Z.M.2    Anderson, K.S.3    Sturtevant, J.M.4    Engelman, D.M.5    Regan, L.6
  • 54
    • 0036081435 scopus 로고    scopus 로고
    • Modeling of denatured state for calculation of the electrostatic contribution to protein stability
    • Kundrotas PJ, Karshikoff A. Modeling of denatured state for calculation of the electrostatic contribution to protein stability. Protein Sci 2002; 11: 1681-1686.
    • (2002) Protein Sci , vol.11 , pp. 1681-1686
    • Kundrotas, P.J.1    Karshikoff, A.2
  • 55
    • 0037150077 scopus 로고    scopus 로고
    • Residual electrostatic effects in the unfolded state of the N-terminal domain of L9 can be attributed to nonspecific nonlocal charge-charge interactions
    • Zhou HX. Residual electrostatic effects in the unfolded state of the N-terminal domain of L9 can be attributed to nonspecific nonlocal charge-charge interactions. Biochemistry 2002; 41: 6533-6538.
    • (2002) Biochemistry , vol.41 , pp. 6533-6538
    • Zhou, H.X.1
  • 57
    • 9644303208 scopus 로고    scopus 로고
    • Analysis of the pH-dependent folding and stability of histidine point mutants allows characterization of the denatured state and transition state for protein folding
    • Horng JC, Cho JH, Raleigh DP. Analysis of the pH-dependent folding and stability of histidine point mutants allows characterization of the denatured state and transition state for protein folding. J Mol Biol 2005; 345: 163-173.
    • (2005) J Mol Biol , vol.345 , pp. 163-173
    • Horng, J.C.1    Cho, J.H.2    Raleigh, D.P.3
  • 59
    • 34548423250 scopus 로고    scopus 로고
    • a values, ion pairs, hydrogen bonding, and the pH-dependence of folding the hyperthermophile proteins Sac7d and Sso7d
    • a values, ion pairs, hydrogen bonding, and the pH-dependence of folding the hyperthermophile proteins Sac7d and Sso7d. J Mol Biol 2007; 372: 992-1008.
    • (2007) J Mol Biol , vol.372 , pp. 992-1008
    • Clark, A.T.1    Smith, K.2    Muhandiram, R.3    Edmondson, S.P.4    Shriver, J.W.5
  • 60
    • 33846586937 scopus 로고    scopus 로고
    • Role of the charge-charge interactions in defining stability and halophilicity of the CspB proteins
    • Gribenko AV, Makhatadze GI. Role of the charge-charge interactions in defining stability and halophilicity of the CspB proteins. J Mol Biol 2007; 366: 842-856.
    • (2007) J Mol Biol , vol.366 , pp. 842-856
    • Gribenko, A.V.1    Makhatadze, G.I.2
  • 61
    • 22144469126 scopus 로고    scopus 로고
    • Effects of pH, salt, and macromolecular crowding on the stability of FK506-binding protein: an integrated experimental and theoretical study
    • Spencer DS, Xu K, Logan TM, Zhou HX. Effects of pH, salt, and macromolecular crowding on the stability of FK506-binding protein: an integrated experimental and theoretical study. J Mol Biol 2005; 351: 219-232.
    • (2005) J Mol Biol , vol.351 , pp. 219-232
    • Spencer, D.S.1    Xu, K.2    Logan, T.M.3    Zhou, H.X.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.