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Volumn 49, Issue 4, 2002, Pages 560-566

Origins of protein denatured state compactness and hydrophobic clustering in aqueous urea: Inferences from nonpolar potentials of mean force

Author keywords

Compact denatured states; Heat capacity; Hydrophobicity; m value; Solvent accessible surface area; Urea denaturation

Indexed keywords

PROTEIN; UREA; WATER;

EID: 0036891682     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10263     Document Type: Article
Times cited : (90)

References (65)
  • 1
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Protein Chem 1959;14:1-63.
    • (1959) Adv Protein Chem , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 2
    • 0014718113 scopus 로고
    • Protein denaturation
    • Tanford C. Protein denaturation. Adv Protein Chem 1970;24:1-95.
    • (1970) Adv Protein Chem , vol.24 , pp. 1-95
    • Tanford, C.1
  • 3
    • 0028820703 scopus 로고
    • Denaturant m-values and heat capacity changes: Relation to changes in accessible surface area of protein unfolding
    • Myers JK, Pace CN, Scholtz JM. Denaturant m-values and heat capacity changes: Relation to changes in accessible surface area of protein unfolding. Protein Sci 1995;4:2138-2148.
    • (1995) Protein Sci , vol.4 , pp. 2138-2148
    • Myers, J.K.1    Pace, C.N.2    Scholtz, J.M.3
  • 4
    • 20544461199 scopus 로고    scopus 로고
    • Thermodynamics of protein interactions with urea and guanidinium hydrochloride
    • Makhatadze GI. Thermodynamics of protein interactions with urea and guanidinium hydrochloride. J Phys Chem B 1999;103:4781-4785.
    • (1999) J Phys Chem B , vol.103 , pp. 4781-4785
    • Makhatadze, G.I.1
  • 5
    • 78651119214 scopus 로고
    • Solubility of amino acids and related compounds in aqueous urea solutions
    • Nozaki Y, Tanford C. Solubility of amino acids and related compounds in aqueous urea solutions. J Biol Chem 1963;238:4074-4081.
    • (1963) J Biol Chem , vol.238 , pp. 4074-4081
    • Nozaki, Y.1    Tanford, C.2
  • 6
    • 33947485233 scopus 로고
    • Nonpolar group participation in denaturation of proteins by urea + guanidium salts. Model compound studies
    • Wetlaufer DB, Malik SK, Stoller L, Coffin RL. Nonpolar group participation in denaturation of proteins by urea + guanidium salts. Model compound studies. J Am Chem Soc 1964;86:508-514.
    • (1964) J Am Chem Soc , vol.86 , pp. 508-514
    • Wetlaufer, D.B.1    Malik, S.K.2    Stoller, L.3    Coffin, R.L.4
  • 7
    • 0001469974 scopus 로고
    • Calorimetric studies of hydrophobic nature of several protein constituents and ovalumin in water and in aqueous urea
    • Kresheck GC, Benjamin L. Calorimetric studies of hydrophobic nature of several protein constituents and ovalumin in water and in aqueous urea. J Phys Chem 1964;68:2476-2486.
    • (1964) J Phys Chem , vol.68 , pp. 2476-2486
    • Kresheck, G.C.1    Benjamin, L.2
  • 8
    • 33847800736 scopus 로고
    • Interactions of urea and other polar compounds in water
    • Roseman M, Jencks WP. Interactions of urea and other polar compounds in water. J Am Chem Soc 1975;97:631-640.
    • (1975) J Am Chem Soc , vol.97 , pp. 631-640
    • Roseman, M.1    Jencks, W.P.2
  • 9
    • 0021766648 scopus 로고
    • Effects of urea and guanidine-hydrochloride on peptide and nonpolar groups
    • Nandi PK, Robinson DR. Effects of urea and guanidine-hydrochloride on peptide and nonpolar groups. Biochemistry 1984;23:6661-6668.
    • (1984) Biochemistry , vol.23 , pp. 6661-6668
    • Nandi, P.K.1    Robinson, D.R.2
  • 10
    • 0032080534 scopus 로고    scopus 로고
    • Urea effects on protein stability: Hydrogen bonding and the hydrophobic effect
    • Zou Q, Habermann-Rottinghaus SM, Murphy KP. Urea effects on protein stability: Hydrogen bonding and the hydrophobic effect. Proteins 1998;31:107-115.
    • (1998) Proteins , vol.31 , pp. 107-115
    • Zou, Q.1    Habermann-Rottinghaus, S.M.2    Murphy, K.P.3
  • 11
    • 0028862864 scopus 로고
    • The peptide backbone plays a dominant role in protein stabilization by naturally-occurring osmolytes
    • Liu Y, Bolen DW. The peptide backbone plays a dominant role in protein stabilization by naturally-occurring osmolytes. Biochemistry 1995;34:12884-12891.
    • (1995) Biochemistry , vol.34 , pp. 12884-12891
    • Liu, Y.1    Bolen, D.W.2
  • 14
    • 0033772098 scopus 로고    scopus 로고
    • Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: Interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model
    • Courtenay ES, Capp MW, Saecker RM, Record MT. Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: Interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model. Proteins 2000;41(S4):72-85.
    • (2000) Proteins , vol.41 , Issue.S4 , pp. 72-85
    • Courtenay, E.S.1    Capp, M.W.2    Saecker, R.M.3    Record, M.T.4
  • 15
    • 0035936688 scopus 로고    scopus 로고
    • A Gaussian statistical mechanical model for the equilibrium thermodynamics of barnase folding
    • Crippen GM. A Gaussian statistical mechanical model for the equilibrium thermodynamics of barnase folding. J Mol Biol 2001;306:565-573.
    • (2001) J Mol Biol , vol.306 , pp. 565-573
    • Crippen, G.M.1
  • 16
    • 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
  • 17
    • 0026672305 scopus 로고
    • NMR determination of residual structure in a urea-denatured protein, the 434-repressor
    • Neri D, Billeter M, Wider G, Wüthrich K. NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Science 1992;257:1559-1563.
    • (1992) Science , vol.257 , pp. 1559-1563
    • Neri, D.1    Billeter, M.2    Wider, G.3    Wüthrich, K.4
  • 18
    • 0030070225 scopus 로고    scopus 로고
    • Mutagenic and thermodynamic analyses of residual structure in the alpha sub- unit of tryptophan synthase
    • Saab-Rincon G, Gualfetti PJ, Matthews CR. Mutagenic and thermodynamic analyses of residual structure in the alpha sub- unit of tryptophan synthase. Biochemistry 1996;35:1988-1994.
    • (1996) Biochemistry , vol.35 , pp. 1988-1994
    • Saab-Rincon, G.1    Gualfetti, P.J.2    Matthews, C.R.3
  • 20
    • 0035919635 scopus 로고    scopus 로고
    • Persistence of native-like topology in a denatured protein in 8 M urea
    • Shortle D, Ackerman MS. Persistence of native-like topology in a denatured protein in 8 M urea. Science 2001;293:487-489.
    • (2001) Science , vol.293 , pp. 487-489
    • Shortle, D.1    Ackerman, M.S.2
  • 21
    • 0034886552 scopus 로고    scopus 로고
    • Unfolded, yes, but random? Never!
    • Plaxco KW, Gross M. Unfolded, yes, but random? Never! Nature Struct Biol 2001;8:659-660.
    • (2001) Nature Struct Biol , vol.8 , pp. 659-660
    • Plaxco, K.W.1    Gross, M.2
  • 22
    • 0036500833 scopus 로고    scopus 로고
    • Protein folding - Making a network of hydrophobic clusters
    • Baldwin RL. Protein folding - Making a network of hydrophobic clusters. Science 2002;295:1657-1658.
    • (2002) Science , vol.295 , pp. 1657-1658
    • Baldwin, R.L.1
  • 23
    • 0025822867 scopus 로고
    • Solvent denaturation and stabilization of globular proteins
    • Alonso DOV, Dill KA. Solvent denaturation and stabilization of globular proteins. Biochemistry 1991;30:5974-5985.
    • (1991) Biochemistry , vol.30 , pp. 5974-5985
    • Alonso, D.O.V.1    Dill, K.A.2
  • 25
    • 0025017318 scopus 로고
    • Differences between pair and bulk hydrophobic interactions
    • Wood RH, Thompson PT. Differences between pair and bulk hydrophobic interactions. Proc Natl Acad Sci USA 1990;87:8921-8927.
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 8921-8927
    • Wood, R.H.1    Thompson, P.T.2
  • 26
    • 0343274684 scopus 로고    scopus 로고
    • Solvation: How to obtain microscopic energies from partitioning and solvation experiments
    • Chan HS, Dill KA. Solvation: How to obtain microscopic energies from partitioning and solvation experiments. Annu Rev Biophys Biomol Struct 1997;26:425-459.
    • (1997) Annu Rev Biophys Biomol Struct , vol.26 , pp. 425-459
    • Chan, H.S.1    Dill, K.A.2
  • 27
    • 0011737676 scopus 로고
    • Biophysical discussion
    • Karplus M. Biophysical discussion. Biophys J 1980;32:45-46.
    • (1980) Biophys J , vol.32 , pp. 45-46
    • Karplus, M.1
  • 28
    • 0020024242 scopus 로고
    • Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding
    • Kim PS, Baldwin RL. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem 1982;51:459-489.
    • (1982) Annu Rev Biochem , vol.51 , pp. 459-489
    • Kim, P.S.1    Baldwin, R.L.2
  • 29
    • 36749120002 scopus 로고
    • Theory of hydrophobic effect
    • Pratt LR, Chandler D. Theory of hydrophobic effect. J Chem Phys 1977;67:3683-3704.
    • (1977) J Chem Phys , vol.67 , pp. 3683-3704
    • Pratt, L.R.1    Chandler, D.2
  • 30
    • 0011960339 scopus 로고    scopus 로고
    • Hydrophobicity at small and large length scales
    • Lum K, Chandler D, Weeks JD. Hydrophobicity at small and large length scales. J Phys Chem B 1999;103:4570-4577.
    • (1999) J Phys Chem B , vol.103 , pp. 4570-4577
    • Lum, K.1    Chandler, D.2    Weeks, J.D.3
  • 32
    • 10644281621 scopus 로고
    • Molecular-dynamics study of the hydration of Lennard-Jones solutes
    • Geiger A, Rahman A, Stillinger FH. Molecular-dynamics study of the hydration of Lennard-Jones solutes. J Chem Phys 1979;70:263-276.
    • (1979) J Chem Phys , vol.70 , pp. 263-276
    • Geiger, A.1    Rahman, A.2    Stillinger, F.H.3
  • 33
    • 0001153179 scopus 로고
    • Hydrophobic hydration around a pair of apolar species in water
    • Pangali C, Rao M, Berne BJ. Hydrophobic hydration around a pair of apolar species in water. J Chem Phys 1979;71:2982-2990.
    • (1979) J Chem Phys , vol.71 , pp. 2982-2990
    • Pangali, C.1    Rao, M.2    Berne, B.J.3
  • 36
    • 0034272188 scopus 로고    scopus 로고
    • Temperature dependence of hydrophobic interactions: A mean force perspective, effects of water density, and nonadditivity of thermodynamic signatures
    • Erratum: J Chem Phys 2002;116:8636
    • Shimizu S, Chan HS. Temperature dependence of hydrophobic interactions: A mean force perspective, effects of water density, and nonadditivity of thermodynamic signatures. J Chem Phys 2000;113:4683-4700. [Erratum: J Chem Phys 2002;116:8636.]
    • (2000) J Chem Phys , vol.113 , pp. 4683-4700
    • Shimizu, S.1    Chan, H.S.2
  • 37
    • 0035819985 scopus 로고    scopus 로고
    • Configuration-dependent heat capacity of pairwise hydrophobic interactions
    • Shimizu S, Chan HS. Configuration-dependent heat capacity of pairwise hydrophobic interactions. J Am Chem Soc 2001;123:2083-2084.
    • (2001) J Am Chem Soc , vol.123 , pp. 2083-2084
    • Shimizu, S.1    Chan, H.S.2
  • 38
    • 0037040051 scopus 로고    scopus 로고
    • Enthalpy and entropy contributions to the pressure dependence of hydrophobic interactions
    • Ghosh T, García AE, Garde S. Enthalpy and entropy contributions to the pressure dependence of hydrophobic interactions. J Chem Phys 2002;116:2480-2486.
    • (2002) J Chem Phys , vol.116 , pp. 2480-2486
    • Ghosh, T.1    García, A.E.2    Garde, S.3
  • 39
    • 0032554078 scopus 로고    scopus 로고
    • Hydrophobic interactions in aqueous urea solutions with implications for the mechanism of protein denaturation
    • Wallqvist A, Covell DG, Thirumalai D. Hydrophobic interactions in aqueous urea solutions with implications for the mechanism of protein denaturation. J Am Chem Soc 1998;120:427-428.
    • (1998) J Am Chem Soc , vol.120 , pp. 427-428
    • Wallqvist, A.1    Covell, D.G.2    Thirumalai, D.3
  • 40
    • 0035977650 scopus 로고    scopus 로고
    • Molecular dynamics study on hydrophobic effects in aqueous urea solutions
    • Ikeguchi M, Nakamura S, Shimizu K. Molecular dynamics study on hydrophobic effects in aqueous urea solutions. J Am Chem Soc 2001;123:677-682.
    • (2001) J Am Chem Soc , vol.123 , pp. 677-682
    • Ikeguchi, M.1    Nakamura, S.2    Shimizu, K.3
  • 42
    • 0021754413 scopus 로고
    • Molecular-dynamics study of solvation in urea water solution
    • Kuharski RA, Rossky PJ. Molecular-dynamics study of solvation in urea water solution. J Am Chem Soc 1984;106:5794-5800.
    • (1984) J Am Chem Soc , vol.106 , pp. 5794-5800
    • Kuharski, R.A.1    Rossky, P.J.2
  • 43
    • 0035878954 scopus 로고    scopus 로고
    • Anti-cooperativity in hydrophobic interactions: A simulation study of spatial dependence of three-body effects and beyond
    • Shimizu S, Chan HS. Anti-cooperativity in hydrophobic interactions: A simulation study of spatial dependence of three-body effects and beyond. J Chem Phys 2001;115:1414-1421.
    • (2001) J Chem Phys , vol.115 , pp. 1414-1421
    • Shimizu, S.1    Chan, H.S.2
  • 44
    • 0036643497 scopus 로고    scopus 로고
    • Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins
    • Erratum: Proteins 2002;49:294
    • Shimizu S, Chan HS. Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins. Proteins 2002;48:15-30. [Erratum: Proteins 2002;49:294.]
    • (2002) Proteins , vol.48 , pp. 15-30
    • Shimizu, S.1    Chan, H.S.2
  • 45
    • 0000759696 scopus 로고    scopus 로고
    • Computer simulation of cosolvent effects on hydrophobic hydration
    • Smith PE. Computer simulation of cosolvent effects on hydrophobic hydration. J Phys Chem B 1999;103:525-534.
    • (1999) J Phys Chem B , vol.103 , pp. 525-534
    • Smith, P.E.1
  • 46
    • 0000784156 scopus 로고
    • A model for the partial reversal of hydrophobic hydration by addition of a urea-like cosolvent
    • Muller N. A model for the partial reversal of hydrophobic hydration by addition of a urea-like cosolvent. J Phys Chem 1990;94:3856-3859.
    • (1990) J Phys Chem , vol.94 , pp. 3856-3859
    • Muller, N.1
  • 47
    • 0035809977 scopus 로고    scopus 로고
    • On the solubility of aliphatic hydrocarbons in 7 M aqueous urea
    • Graziano G. On the solubility of aliphatic hydrocarbons in 7 M aqueous urea. J Phys Chem B 2001;105:2632-2637.
    • (2001) J Phys Chem B , vol.105 , pp. 2632-2637
    • Graziano, G.1
  • 49
    • 0037133605 scopus 로고    scopus 로고
    • A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins
    • Zhou HX. A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins. Proc Natl Acad Sci USA 2002;99:3569-3574.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 3569-3574
    • Zhou, H.X.1
  • 50
    • 0036304480 scopus 로고    scopus 로고
    • Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: How applicable is the transition state picture to folding and unfolding?
    • Kaya H, Chan HS. Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: How applicable is the transition state picture to folding and unfolding? J Mol Biol 2002;315:899-909.
    • (2002) J Mol Biol , vol.315 , pp. 899-909
    • Kaya, H.1    Chan, H.S.2
  • 51
    • 0026733250 scopus 로고
    • Denatured states of ribonuclease A have compact dimensions and residual secondary structure
    • Sosnick TR, Trewhella J. Denatured states of ribonuclease A have compact dimensions and residual secondary structure. Biochemistry 1992;31:8329-8335.
    • (1992) Biochemistry , vol.31 , pp. 8329-8335
    • Sosnick, T.R.1    Trewhella, J.2
  • 52
    • 0031779708 scopus 로고    scopus 로고
    • Chain- like conformation of heat-denatured ribonuclease A and cytochrome c as evidenced by solution X-ray scattering
    • Hagihara Y, Hoshino M, Hamada D, Kataoka M, Goto Y. Chain- like conformation of heat-denatured ribonuclease A and cytochrome c as evidenced by solution X-ray scattering. Fold Des 1998;3:195-201.
    • (1998) Fold Des , vol.3 , pp. 195-201
    • Hagihara, Y.1    Hoshino, M.2    Hamada, D.3    Kataoka, M.4    Goto, Y.5
  • 53
    • 0014349486 scopus 로고
    • Dimensions of protein random coils
    • Miller WG, Goebel CV. Dimensions of protein random coils. Biochemistry 1968;7:3925-3935.
    • (1968) Biochemistry , vol.7 , pp. 3925-3935
    • Miller, W.G.1    Goebel, C.V.2
  • 54
    • 0035906650 scopus 로고    scopus 로고
    • Calculation of ensembles of structures representing the unfolded state of an SH3 domain
    • Choy WY, Forman-Kay JD. Calculation of ensembles of structures representing the unfolded state of an SH3 domain. J Mol Biol 2001;308:1011-1032.
    • (2001) J Mol Biol , vol.308 , pp. 1011-1032
    • Choy, W.Y.1    Forman-Kay, J.D.2
  • 55
    • 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
  • 56
    • 0036136694 scopus 로고    scopus 로고
    • Composites of local structure propensities: Evidence for local encoding of long-range structure
    • Shortle D. Composites of local structure propensities: Evidence for local encoding of long-range structure. Protein Sci 2002;11:18-26.
    • (2002) Protein Sci , vol.11 , pp. 18-26
    • Shortle, D.1
  • 57
    • 0033730431 scopus 로고    scopus 로고
    • The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding
    • Pappu RV, Srinivasan R, Rose GD. The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding. Proc Natl Acad Sci USA 2000;97:12565-12570.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 12565-12570
    • Pappu, R.V.1    Srinivasan, R.2    Rose, G.D.3
  • 59
    • 0036139188 scopus 로고    scopus 로고
    • Probabilistic sampling of protein conformations: New hope for brute force?
    • Feldman HJ, Hogue CWV. Probabilistic sampling of protein conformations: New hope for brute force? Proteins 2002;46:8-23.
    • (2002) Proteins , vol.46 , pp. 8-23
    • Feldman, H.J.1    Hogue, C.W.V.2
  • 60
    • 0022423920 scopus 로고
    • Theory for the folding and stability of globular-proteins
    • Dill KA. Theory for the folding and stability of globular-proteins. Biochemistry 1985;24:1501-1509.
    • (1985) Biochemistry , vol.24 , pp. 1501-1509
    • Dill, K.A.1
  • 61
    • 0034581327 scopus 로고    scopus 로고
    • Role of the molten globule state in protein folding
    • Arai M, Kuwajima K. Role of the molten globule state in protein folding. Adv Protein Chem 2000;53:209-282.
    • (2000) Adv Protein Chem , vol.53 , pp. 209-282
    • Arai, M.1    Kuwajima, K.2
  • 62
    • 0028243107 scopus 로고
    • Cold denaturation of the molten globule states of apomyoglobin and a profile for protein-folding
    • Nishii I, Kataoka M, Tokunaga F, Goto Y. Cold denaturation of the molten globule states of apomyoglobin and a profile for protein-folding. Biochemistry 1994;33:4903-4909.
    • (1994) Biochemistry , vol.33 , pp. 4903-4909
    • Nishii, I.1    Kataoka, M.2    Tokunaga, F.3    Goto, Y.4
  • 63
    • 0000376855 scopus 로고
    • Importance of heat capacity effects in the association of hydrophobic moieties in aqueous solution
    • Christian SD, Tucker EE. Importance of heat capacity effects in the association of hydrophobic moieties in aqueous solution. J Sol Chem 1982;11:749-754.
    • (1982) J Sol Chem , vol.11 , pp. 749-754
    • Christian, S.D.1    Tucker, E.E.2
  • 64
    • 0023322630 scopus 로고
    • Selective binding and solvent denaturation
    • Schellman JA. Selective binding and solvent denaturation. Biopolymers 1987;26:549-559.
    • (1987) Biopolymers , vol.26 , pp. 549-559
    • Schellman, J.A.1
  • 65
    • 33751132430 scopus 로고
    • The statistical mechanical theory of solutions. 1
    • Kirkwood JG, Buff FP. The statistical mechanical theory of solutions. 1. J Chem Phys 1951;19:774-777.
    • (1951) J Chem Phys , vol.19 , pp. 774-777
    • Kirkwood, J.G.1    Buff, F.P.2


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