메뉴 건너뛰기




Volumn 100, Issue 6, 2011, Pages 1526-1533

Backbone and side-chain contributions in protein denaturation by urea

Author keywords

[No Author keywords available]

Indexed keywords


EID: 79953858621     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.01.028     Document Type: Article
Times cited : (99)

References (54)
  • 1
    • 0027310845 scopus 로고
    • The control of protein stability and association by weak interactions with water: How do solvents affect these processes?
    • Timasheff, S. N. 1993. The control of protein stability and association by weak interactions with water: how do solvents affect these processes? Annu. Rev. Biophys. Biomol. Struct. 22:67-97. (Pubitemid 23180317)
    • (1993) Annual Review of Biophysics and Biomolecular Structure , vol.22 , pp. 67-97
    • Timasheff, S.N.1
  • 2
    • 0020336190 scopus 로고
    • Living with water stress: evolution of osmolyte systems.
    • Yancey, P. H., M. E. Clark, ., G. N. Somero. 1982. Living with water stress: evolution of osmolyte systems. Science. 217:1214-1222. (Pubitemid 13283134)
    • (1982) Science , vol.217 , Issue.4566 , pp. 1214-1222
    • Yancey, P.H.1    Clark, M.E.2    Hand, S.C.3    Bowlus, R.D.4    Somero, G.N.5
  • 3
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein dena- turation
    • Kauzmann, W. 1959. Some factors in the interpretation of protein dena- turation. Adv. Protein Chem. 14:1-63.
    • (1959) Adv. Protein Chem. , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 4
    • 0022555885 scopus 로고
    • Determination and analysis of urea and guanidine hydrochloride denaturation curves
    • Pace, C. N. 1986. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 131:266-280. (Pubitemid 16002205)
    • (1986) Methods in Enzymology , vol.131 , pp. 266-280
    • Pace, C.N.1
  • 5
    • 33749541104 scopus 로고
    • Structural approach to solvent power of water for hydrocarbons-urea as a structure breaker
    • Frank, H. S., and F. Franks. 1968. Structural approach to solvent power of water for hydrocarbons-urea as a structure breaker. J. Chem. Phys. 48:4746-4757.
    • (1968) J. Chem. Phys. , vol.48 , pp. 4746-4757
    • Frank, H.S.1    Franks, F.2
  • 6
    • 70349289438 scopus 로고    scopus 로고
    • Urea-mediated protein denatur- ation: A consensus view
    • Das, A., and C. Mukhopadhyay. 2009. Urea-mediated protein denatur- ation: a consensus view. J. Phys. Chem. B. 113:12816-12824.
    • (2009) J. Phys. Chem. B. , vol.113 , pp. 12816-12824
    • Das, A.1    Mukhopadhyay, C.2
  • 7
    • 75649108542 scopus 로고    scopus 로고
    • Effects of urea, tetramethyl urea, and trimethylamine N-oxide on aqueous solution structure and solvation of protein backbones: A molecular dynamics simulation study
    • Wei, H. Y., Y. B. Fan, and Y. Q. Gao. 2010. Effects of urea, tetramethyl urea, and trimethylamine N-oxide on aqueous solution structure and solvation of protein backbones: a molecular dynamics simulation study. J. Phys. Chem. B. 114:557-568.
    • (2010) J. Phys. Chem. B. , vol.114 , pp. 557-568
    • Wei, H.Y.1    Fan, Y.B.2    Gao, Y.Q.3
  • 8
    • 77956512505 scopus 로고    scopus 로고
    • Mutation of charged residues to neutral ones accelerates urea denaturation of HP-35
    • Wei, H. Y., L. J. Yang, and Y. Q. Gao. 2010. Mutation of charged residues to neutral ones accelerates urea denaturation of HP-35. J. Phys. Chem. B. 114:11820-11826.
    • (2010) J. Phys. Chem. B. , vol.114 , pp. 11820-11826
    • Wei, H.Y.1    Yang, L.J.2    Gao, Y.Q.3
  • 9
    • 0141560450 scopus 로고    scopus 로고
    • Impact of urea on water structure: A clue to its properties as a denaturant?
    • DOI 10.1016/S0301-4622(03)00095-4
    • Soper, A. K., E. W. Castner, and A. Luzar. 2003. Impact of urea on water structure: a clue to its properties as a denaturant? Biophys. Chem. 105:649-666. (Pubitemid 37123089)
    • (2003) Biophysical Chemistry , vol.105 , Issue.2-3 , pp. 649-666
    • Soper, A.K.1    Castner, E.W.2    Luzar, A.3
  • 11
    • 34249806047 scopus 로고    scopus 로고
    • Preferential solvation in urea solutions at different concentrations: Properties from simulation studies
    • DOI 10.1021/jp067659x
    • Kokubo, H., and B. M. Pettitt. 2007. Preferential solvation in urea solutions at different concentrations: properties from simulation studies. J. Phys. Chem. B. 111:5233-5242. (Pubitemid 46854511)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.19 , pp. 5233-5242
    • Kokubo, H.1    Pettitt, B.M.2
  • 12
    • 55949132427 scopus 로고    scopus 로고
    • Protein denaturation by urea: Slash and bond
    • Rossky, P. J. 2008. Protein denaturation by urea: slash and bond. Proc. Natl. Acad. Sci. USA. 105:16825-16826.
    • (2008) Proc. Natl. Acad. Sci. USA. , vol.105 , pp. 16825-16826
    • Rossky, P.J.1
  • 13
    • 0001664170 scopus 로고
    • Effect of compounds of ureaguanidinium class on activity coefficient of acetyltetraglycine ethyl ester and related compounds
    • Robinson, D. R., and W. P. Jencks. 1965. Effect of compounds of ureaguanidinium class on activity coefficient of acetyltetraglycine ethyl ester and related compounds. J. Am. Chem. Soc. 87:2462-2470.
    • (1965) J. Am. Chem. Soc. , vol.87 , pp. 2462-2470
    • Robinson, D.R.1    Jencks, W.P.2
  • 14
    • 0026729426 scopus 로고
    • Protein interactions with urea and guanidinium chloride. A calorimetric study
    • Makhatadze, G. I., and P. L. Privalov. 1992. Protein interactions with urea and guanidinium chloride. A calorimetric study. J. Mol. Biol. 226:491-505.
    • (1992) J. Mol. Biol. , vol.226 , pp. 491-505
    • Makhatadze, G.I.1    Privalov, P.L.2
  • 15
    • 37549043949 scopus 로고    scopus 로고
    • Interaction of urea with amino acids: Implications for urea-induced protein denaturation
    • Stumpe, M. C., and H. Grubmüller. 2007. Interaction of urea with amino acids: implications for urea-induced protein denaturation. J. Am. Chem. Soc. 129:16126-16131.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 16126-16131
    • Stumpe, M.C.1    Grubmüller, H.2
  • 16
    • 55949131241 scopus 로고    scopus 로고
    • Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding
    • Hua, L., R. H. Zhou, B. J. Berne. 2008. Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc. Natl. Acad. Sci. USA. 105:16928-16933.
    • (2008) Proc. Natl. Acad. Sci. USA. , vol.105 , pp. 16928-16933
    • Hua, L.1    Zhou, R.H.2    Berne, B.J.3
  • 17
    • 77749285768 scopus 로고    scopus 로고
    • Equilibrium study of protein denaturation by urea
    • Canchi, D. R., D. Paschek, and A. E. Garcia. 2010. Equilibrium study of protein denaturation by urea. J. Am. Chem. Soc. 132:2338-2344.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 2338-2344
    • Canchi, D.R.1    Paschek, D.2    Garcia, A.E.3
  • 18
    • 77956142105 scopus 로고    scopus 로고
    • Urea interactions with protein groups: A volumetric study
    • Lee, S., Y. L. Shek, and T. V. Chalikian. 2010. Urea interactions with protein groups: a volumetric study. Biopolymers. 93:866-879.
    • (2010) Biopolymers , vol.93 , pp. 866-879
    • Lee, S.1    Shek, Y.L.2    Chalikian, T.V.3
  • 21
    • 34548270876 scopus 로고    scopus 로고
    • Urea-amide preferential interactions in water: Quantitative comparison of model compound data with biopolymer results using water accessible surface areas
    • DOI 10.1021/jp072037c
    • Cannon, J. G., C. F. Anderson, and M. T. Record, Jr. 2007. Urea-amide preferential interactions in water: quantitative comparison of model compound data with biopolymer results using water accessible surface areas. J. Phys. Chem. B. 111:9675-9685. (Pubitemid 47317896)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.32 , pp. 9675-9685
    • Cannon, J.G.1    Anderson, C.F.2    Record Jr., M.T.3
  • 22
    • 0037162456 scopus 로고    scopus 로고
    • Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components
    • DOI 10.1073/pnas.122225399
    • Timasheff, S. N. 2002. Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components. Proc. Natl. Acad. Sci. USA. 99:9721-9726. (Pubitemid 34831114)
    • (2002) Proceedings of the National Academy of Sciences of the United States of America , vol.99 , Issue.15 , pp. 9721-9726
    • Timasheff, S.N.1
  • 23
    • 0020477047 scopus 로고
    • Preferential interactions of proteins with salts in concentrated solutions
    • Arakawa, T., and S. N. Timasheff. 1982. Preferential interactions of proteins with salts in concentrated solutions. Biochemistry. 21:6545-6552.
    • (1982) Biochemistry , vol.21 , pp. 6545-6552
    • Arakawa, T.1    Timasheff, S.N.2
  • 24
    • 0034681955 scopus 로고    scopus 로고
    • Vapor pressure osmometry studies of osmolyte-protein interactions: Implications for the action of osmoprotectants in vivo and for the interpretation of 'osmotic stress' experiments in vitro
    • DOI 10.1021/bi992887l
    • Courtenay, E. S., M. W. Capp, . , M. T. Record, Jr. 2000. Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of ''osmotic stress'' experiments in vitro. Biochemistry. 39:4455-4471. (Pubitemid 30212662)
    • (2000) Biochemistry , vol.39 , Issue.15 , pp. 4455-4471
    • Courtenay, E.S.1    Capp, M.W.2    Anderson, C.F.3    Record Jr., M.T.4
  • 25
    • 0028962012 scopus 로고
    • Interpretation of preferential interaction coefficients of nonelectrolytes and of electrolyte ions in terms of a two-domain model
    • Record, Jr., M. T., and C. F. Anderson. 1995. Interpretation of preferential interaction coefficients of nonelectrolytes and of electrolyte ions in terms of a two-domain model. Biophys. J. 68:786-794.
    • (1995) Biophys. J. , vol.68 , pp. 786-794
    • Record Jr., M.T.1    Anderson, C.F.2
  • 26
    • 0346936517 scopus 로고    scopus 로고
    • Proteins in mixed solvents: A molecular-level perspective
    • Baynes, B. M., and B. L. Trout. 2003. Proteins in mixed solvents: a molecular-level perspective. J. Phys. Chem. B. 107:14058-14067.
    • (2003) J. Phys. Chem. B. , vol.107 , pp. 14058-14067
    • Baynes, B.M.1    Trout, B.L.2
  • 27
    • 70349099268 scopus 로고    scopus 로고
    • Molecular computations of preferential interaction coefficients of proteins
    • Shukla, D., C. Shinde, and B. L. Trout. 2009. Molecular computations of preferential interaction coefficients of proteins. J. Phys. Chem. B. 113:12546-12554.
    • (2009) J. Phys. Chem. B. , vol.113 , pp. 12546-12554
    • Shukla, D.1    Shinde, C.2    Trout, B.L.3
  • 28
    • 23244459863 scopus 로고    scopus 로고
    • Osmolyte trimethylamine-N-oxide does not affect the strength of hydrophobic interactions: Origin of osmolyte compatibility
    • DOI 10.1529/biophysj.104.056671
    • Athawale, M. V., J. S. Dordick, and S. Garde. 2005. Osmolyte trime- thylamine-N-oxide does not affect the strength of hydrophobic interactions: origin of osmolyte compatibility. Biophys. J. 89:858-866. (Pubitemid 41098972)
    • (2005) Biophysical Journal , vol.89 , Issue.2 , pp. 858-866
    • Athawale, M.V.1    Dordick, J.S.2    Garde, S.3
  • 29
    • 77949878597 scopus 로고    scopus 로고
    • Trimethylamine N-oxide influence on the backbone of proteins: An oligoglycine model
    • Hu, C. Y., G. C. Lynch, B. M. Pettitt. 2010. Trimethylamine N-oxide influence on the backbone of proteins: an oligoglycine model. Proteins. 78:695-704.
    • (2010) Proteins. , vol.78 , pp. 695-704
    • Hu, C.Y.1    Lynch, G.C.2    Pettitt, B.M.3
  • 30
    • 77749259034 scopus 로고    scopus 로고
    • Preferential interactions between small solutes and the protein backbone: A computational analysis
    • Ma, L., L. Pegram, . , Q. Cui. 2010. Preferential interactions between small solutes and the protein backbone: a computational analysis. Biochemistry. 49:1954-1962.
    • (2010) Biochemistry , vol.49 , pp. 1954-1962
    • Ma, L.1    Pegram, L.2    Cui, Q.3
  • 31
    • 77958451843 scopus 로고    scopus 로고
    • Interaction of arginine with proteins and the mechanism by which it inhibits aggregation
    • Shukla, D., and B. L. Trout. 2010. Interaction of arginine with proteins and the mechanism by which it inhibits aggregation. J. Phys. Chem. B. 114:13426-13438.
    • (2010) J. Phys. Chem. B. , vol.114 , pp. 13426-13438
    • Shukla, D.1    Trout, B.L.2
  • 33
    • 33947209951 scopus 로고    scopus 로고
    • Unfolding thermodynamics of Trp-cage, a 20 residue miniprotein, studied by differential scanning calorimetry and circular dichroism spectroscopy
    • DOI 10.1021/bi602424x
    • Streicher, W. W., and G. I. Makhatadze. 2007. Unfolding thermodynamics of Trp-cage, a 20 residue miniprotein, studied by differential scanningcalorimetryandcirculardichroismspectroscopy. Biochemistry. 46:2876-2880. (Pubitemid 46417925)
    • (2007) Biochemistry , vol.46 , Issue.10 , pp. 2876-2880
    • Streicher, W.W.1    Makhatadze, G.I.2
  • 34
    • 56649083699 scopus 로고    scopus 로고
    • Computing the stability diagram of the Trp-cage miniprotein
    • Paschek, D., S. Hempel, and A. E. Garcia. 2008. Computing the stability diagram of the Trp-cage miniprotein. Proc. Natl. Acad. Sci. USA. 105:17754-17759.
    • (2008) Proc. Natl. Acad. Sci. USA. , vol.105 , pp. 17754-17759
    • Paschek, D.1    Hempel, S.2    Garcia, A.E.3
  • 35
    • 77951243667 scopus 로고    scopus 로고
    • Thermodynamics of the Trp-cage miniprotein unfolding in urea
    • Wafer, L. N. R., W. W. Streicher, and G. I. Makhatadze. 2010. Thermodynamics of the Trp-cage miniprotein unfolding in urea. Proteins. 78:1376-1381.
    • (2010) Proteins , vol.78 , pp. 1376-1381
    • Wafer, L.N.R.1    Streicher, W.W.2    Makhatadze, G.I.3
  • 36
    • 0029011701 scopus 로고
    • A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic- molecules
    • Cornell, W. D., P. Cieplak, P. A. Kollman. 1995. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic- molecules. J. Am. Chem. Soc. 117:5179-5197.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Kollman, P.A.3
  • 38
    • 77953508894 scopus 로고    scopus 로고
    • Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein
    • Day, R., D. Paschek, and A. E. Garcia. 2010. Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein. Proteins. 78:1889-1899.
    • (2010) Proteins , vol.78 , pp. 1889-1899
    • Day, R.1    Paschek, D.2    Garcia, A.E.3
  • 39
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • PII S0009261499011239
    • Sugita, Y., and Y. Okamoto. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314:141-151. (Pubitemid 129556751)
    • (1999) Chemical Physics Letters , vol.314 , Issue.1-2 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 40
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen, W. L., J. Chandrasekhar, M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Klein, M.L.3
  • 41
    • 0037997632 scopus 로고    scopus 로고
    • A Kirkwood-Buff derived force field for mixtures of urea and water
    • DOI 10.1021/jp022049s
    • Weerasinghe, S., and P. E. Smith. 2003. A Kirkwood-Buff derived force field for mixtures of urea and water. J. Phys. Chem. B. 107:3891-3898. (Pubitemid 43677182)
    • (2003) Journal of Physical Chemistry B , vol.107 , Issue.16 , pp. 3891-3898
    • Weerasinghe, S.1    Smith, P.E.2
  • 42
    • 34247279285 scopus 로고    scopus 로고
    • Simulations of temperature and pressure unfolding of peptides and proteins with replica exchange molecular dynamics
    • Garcia, A., H. Herce, and D. Paschek. 2006. Simulations of temperature and pressure unfolding of peptides and proteins with replica exchange molecular dynamics. Annu. Rep. Comput. Chem. 2:83-96.
    • (2006) Annu. Rep. Comput. Chem. , vol.2 , pp. 83-96
    • Garcia, A.1    Herce, H.2    Paschek, D.3
  • 43
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B., C. Kutzner, E. Lindahl. 2008. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4:435-447.
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Lindahl, E.3
  • 44
    • 84943502952 scopus 로고
    • A molecular-dynamics method for simulations in the canonical ensemble
    • Nose, S. 1984. A molecular-dynamics method for simulations in the canonical ensemble. Mol. Phys. 52:255-268.
    • (1984) Mol. Phys. , vol.52 , pp. 255-268
    • Nose, S.1
  • 45
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. 1985. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 31:1695-1697.
    • (1985) Phys. Rev. A. , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 46
    • 84986440341 scopus 로고
    • SETTLE-an analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto, S., and P. A. Kollman. 1992. SETTLE-an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13:952-962.
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 49
    • 33748619519 scopus 로고    scopus 로고
    • Entropy of hydrophobic hydration: Extension to hydrophobic chains
    • Ashbaugh, H. S., and M. E. Paulaitis. 1996. Entropy of hydrophobic hydration: extension to hydrophobic chains. J. Phys. Chem. 100:1900-1913. (Pubitemid 126790014)
    • (1996) Journal of Physical Chemistry , vol.100 , Issue.5 , pp. 1900-1913
    • Ashbaugh, H.S.1    Paulaitis, M.E.2
  • 50
    • 0000293654 scopus 로고
    • aq at 25°C
    • Mehrotra, P. K., and D. L. Beveridge. 1980. Structural-analysis of molecular solutions based on quasi-component distribution-functions-application to [H2CO]aq at 25°C. J. Am. Chem. Soc. 102:4287-4294.
    • (1980) J. Am. Chem. Soc. , vol.102 , pp. 4287-4294
    • Mehrotra, P.K.1    Beveridge, D.L.2
  • 51
    • 0141783830 scopus 로고    scopus 로고
    • Preferential interactions of urea with lysozyme and their linkage to protein denaturation
    • DOI 10.1016/S0301-4622(03)00106-6
    • Timasheff, S. N., and G. Xie. 2003. Preferential interactions of urea with lysozyme and their linkage to protein denaturation. Biophys. Chem. 105:421-448. (Pubitemid 37123076)
    • (2003) Biophysical Chemistry , vol.105 , Issue.2-3 , pp. 421-448
    • Timasheff, S.N.1    Xie, G.2
  • 52
    • 0028820703 scopus 로고
    • Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding
    • Myers, J. K., C. N. Pace, and J. M. Scholtz. 1995. Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4:2138-2148.
    • (1995) Protein Sci. , vol.4 , pp. 2138-2148
    • Myers, J.K.1    Pace, C.N.2    Scholtz, J.M.3
  • 54
    • 0030762556 scopus 로고    scopus 로고
    • A naturally occurring protective system in urea-rich cells: Mechanism of osmolyte protection of proteins against urea denaturation
    • DOI 10.1021/bi970247h
    • Wang, A., and D. W. Bolen. 1997. A naturally occurring protective system in urea-rich cells: mechanism of osmolyte protection of proteins against urea denaturation. Biochemistry. 36:9101-9108. (Pubitemid 27329494)
    • (1997) Biochemistry , vol.36 , Issue.30 , pp. 9101-9108
    • Wang, A.1    Bolen, D.W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.