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Volumn 13, Issue 1, 2013, Pages 90-106

Modeling the influence of salt on the hydrophobic effect and protein fold stability

Author keywords

Cold shock protein; Electrostatic stability; Halophile; HIV 1 protease; Hydrophobic effect

Indexed keywords


EID: 84866339186     PISSN: 18152406     EISSN: 19917120     Source Type: Journal    
DOI: 10.4208/cicp.290711.121011s     Document Type: Conference Paper
Times cited : (24)

References (50)
  • 1
    • 0013822867 scopus 로고
    • Dependence of the melting temperature of DNA on salt concentration
    • C. Schildkraut and S. Lifson, Dependence of the melting temperature of DNA on salt concentration, Biopolymers, 3 (1965), 195-208.
    • (1965) Biopolymers , vol.3 , pp. 195-208
    • Schildkraut, C.1    Lifson, S.2
  • 2
    • 0025143777 scopus 로고
    • Halophilic proteins and the influence of solvent on protein stabilization
    • G. Zaccai and H. Eisenberg, Halophilic proteins and the influence of solvent on protein stabilization, Trends in Biochemical Sciences, 15 (1990), 333-337. (Pubitemid 20255490)
    • (1990) Trends in Biochemical Sciences , vol.15 , Issue.9 , pp. 333-337
    • Zaccai, G.1    Eisenberg, H.2
  • 3
    • 0019877658 scopus 로고
    • Structural stability of halophilic proteins
    • J. K. M. Rao and P. Argos, Structural stability of halophilic proteins, Biochemistry, 20 (1981), 6536-6543.
    • (1981) Biochemistry , vol.20 , pp. 6536-6543
    • Rao, J.K.M.1    Argos, P.2
  • 4
    • 0035831544 scopus 로고    scopus 로고
    • Co-crystal of escherichia coli rnase hi with mn2+ ions reveals two divalent metals bound in the active site
    • E. R. Goedken and S. Marqusee, Co-crystal of escherichia coli rnase hi with mn2+ ions reveals two divalent metals bound in the active site, Journal of Biological Chemistry, 276 (2001), 7266-7271.
    • (2001) Journal of Biological Chemistry , vol.276 , pp. 7266-7271
    • Goedken, E.R.1    Marqusee, S.2
  • 5
    • 0031776135 scopus 로고    scopus 로고
    • Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: Apractical guide to recognizing and interpreting polyelectrolyte effects, hofmeister effects, and osmotic effects of salts
    • D. S. E. Frederic, M. Richards and S. K. Peter (Eds.), Academic Press
    • M. T. Record Jr, W. Zhang and C. F. Anderson, Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: Apractical guide to recognizing and interpreting polyelectrolyte effects, hofmeister effects, and osmotic effects of salts, in: D. S. E. Frederic, M. Richards and S. K. Peter (Eds.) Advances in Protein Chemistry, Academic Press, 1998, pp. 281-353.
    • (1998) Advances in Protein Chemistry , pp. 281-353
    • Record Jr., M.T.1    Zhang, W.2    Anderson, C.F.3
  • 6
    • 0032563113 scopus 로고    scopus 로고
    • Electrostatic contributions to the stability of halophilic proteins
    • DOI 10.1006/jmbi.1998.1904
    • A. H. Elcock and J. A. McCammon, Electrostatic contributions to the stability of halophilic proteins, Journal of Molecular Biology, 280 (1998), 731-748. (Pubitemid 28336377)
    • (1998) Journal of Molecular Biology , vol.280 , Issue.4 , pp. 731-748
    • Elcock, A.H.1    McCammon, J.A.2
  • 7
    • 0029792830 scopus 로고    scopus 로고
    • How Hofmeister ion interactions affect protein stability
    • R. L. Baldwin, How hofmeister ion interactions affect protein stability, Biophysical Journal, 71 (1996), 2056-2063. (Pubitemid 26325984)
    • (1996) Biophysical Journal , vol.71 , Issue.4 , pp. 2056-2063
    • Baldwin, R.L.1
  • 8
    • 0032096837 scopus 로고    scopus 로고
    • Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
    • PII S0010465598000162
    • W. Im, D. Beglov and B. Roux, Continuum solvation model: Computation of electrostatic forces from numerical solutions to the poisson-boltzmann equation, Computer Physics Communications, 111 (1998), 59-75. (Pubitemid 128400465)
    • (1998) Computer Physics Communications , vol.111 , Issue.1-3 , pp. 59-75
    • Im, W.1    Beglov, D.2    Roux, B.3
  • 9
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm, utilizing successive overrelaxation to solve the poisson-boltzmann equation
    • A. Nicholls and B. Honig, A rapid finite difference algorithm, utilizing successive overrelaxation to solve the poisson-boltzmann equation, Journal of Computational Chemistry, 12 (1991), 435-445.
    • (1991) Journal of Computational Chemistry , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 10
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of macromolecular solvation effects
    • D. Bashford and D. A. Case, Generalized born models of macromolecular solvation effects, Annual Review of Physical Chemistry, 51 (2000), 129-152.
    • (2000) Annual Review of Physical Chemistry , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.A.2
  • 11
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • D. Sitkoff, K. A. Sharp and B. Honig, Accurate calculation of hydration free energies using macroscopic solvent models, The Journal of Physical Chemistry, 98 (1994), 1978-1988.
    • (1994) The Journal of Physical Chemistry , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 12
    • 0027936280 scopus 로고
    • Correlating solvation free energies and surface tensions of hydrocarbon solutes
    • DOI 10.1016/0301-4622(94)00062-X
    • D. Sitkoff, K. A. Sharp and B.Honig, Correlating solvation free energies and surface tensions of hydrocarbon solutes, Biophysical Chemistry, 51 (1994), 397-409. (Pubitemid 24244015)
    • (1994) Biophysical Chemistry , vol.51 , Issue.2-3 , pp. 397-409
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 13
    • 33744822783 scopus 로고    scopus 로고
    • Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
    • DOI 10.1073/pnas.0600118103
    • J. A. Wagoner and N. A. Baker, Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms, Proceedings of the National Academy of Sciences, 103 (2006), 8331-8336. (Pubitemid 43838455)
    • (2006) Proceedings of the National Academy of Sciences of the United States of America , vol.103 , Issue.22 , pp. 8331-8336
    • Wagoner, J.A.1    Baker, N.A.2
  • 14
    • 0034227795 scopus 로고    scopus 로고
    • Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation
    • E. Gallicchio, M. M. Kubo and R. M. Levy, Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation, The Journal of Physical Chemistry B, 104 (2000), 6271-6285.
    • (2000) The Journal of Physical Chemistry B , vol.104 , pp. 6271-6285
    • Gallicchio, E.1    Kubo, M.M.2    Levy, R.M.3
  • 16
    • 0029913459 scopus 로고    scopus 로고
    • Conformational stability and catalytic activity of HIV-1 protease are both enhanced at high salt concentration
    • DOI 10.1074/jbc.271.10.5458
    • Z. Szeltner and L. Polg'ar, Conformational stability and catalytic activity of hiv-1 protease are both enhanced at high salt concentration, Journal of Biological Chemistry, 271 (1996), 5458-5463. (Pubitemid 26083878)
    • (1996) Journal of Biological Chemistry , vol.271 , Issue.10 , pp. 5458-5463
    • Szeltner, Z.1    Polgar, L.2
  • 17
    • 0035914477 scopus 로고    scopus 로고
    • Electrostatic Stabilization of a Thermophilic Cold Shock Protein
    • DOI 10.1006/jmbi.2001.5050, PII S0022283601950508
    • D. Perl and F. X. Schmid, Electrostatic stabilization of a thermophilic cold shock protein, Journal of Molecular Biology, 313 (2001), 343-357. (Pubitemid 33587192)
    • (2001) Journal of Molecular Biology , vol.313 , Issue.2 , pp. 343-357
    • Perl, D.1    Schmid, F.X.2
  • 18
    • 0027296211 scopus 로고
    • Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein
    • DOI 10.1038/364164a0
    • H. Schindelin, M. A. Marahiel and U. Heinemann, Universal nucleic acid-binding domain revealed by crystal structure of the b. Subtilis major cold-shock protein, Nature, 364 (1993), 164-168. (Pubitemid 23238202)
    • (1993) Nature , vol.364 , Issue.6433 , pp. 164-168
    • Schindelin, H.1    Marahlel, M.A.2    Helnemann, U.3
  • 19
    • 0034615784 scopus 로고    scopus 로고
    • Thermal stability and atomic-resolution crystal structure of the bacillus caldolyticus cold shock protein
    • U.Mueller, D. Perl, F. X. Schmid and U.Heinemann, Thermal stability and atomic-resolution crystal structure of the bacillus caldolyticus cold shock protein, Journal ofMolecular Biology, 297 (2000), 975-988.
    • (2000) Journal OfMolecular Biology , vol.297 , pp. 975-988
    • Mueller, U.1    Perl, D.2    Schmid, F.X.3    Heinemann, U.4
  • 21
    • 0034567210 scopus 로고    scopus 로고
    • A, Comparative protein structure modeling. Introduction and practical examples with modeller
    • S'anchez R and S. A, Comparative protein structure modeling. Introduction and practical examples with modeller, Methods in Molecular Biology, 143 (2000), 97-129.
    • (2000) Methods in Molecular Biology , vol.143 , pp. 97-129
    • S'Anchez, R.S.1
  • 22
    • 0026344399 scopus 로고
    • The three-dimensional structure of the aspartyl protease from the hiv-1 isolate bru
    • S. Spinelli, Q. Z. Liu, P.M.Alzari, P.H.Hirel and R. J. Poljak, The three-dimensional structure of the aspartyl protease from the hiv-1 isolate bru, Biochimie, 73 (1991), 1391-1396.
    • (1991) Biochimie , vol.73 , pp. 1391-1396
    • Spinelli, S.1    Liu, Q.Z.2    Alzari, P.M.3    Hirel, P.H.4    Poljak, R.J.5
  • 24
    • 0034602373 scopus 로고    scopus 로고
    • Free energy calculations on dimer stability of the hiv protease using molecular dynamics and a continuum solvent model
    • W. Wang and P. A. Kollman, Free energy calculations on dimer stability of the hiv protease using molecular dynamics and a continuum solvent model, Journal of Molecular Biology, 303 (2000), 567-582.
    • (2000) Journal of Molecular Biology , vol.303 , pp. 567-582
    • Wang, W.1    Kollman, P.A.2
  • 25
    • 65249108700 scopus 로고    scopus 로고
    • Conformational motions of hiv-1 protease identified using reversible digitally filtered molecular dynamics
    • A. P. Wiley, S. L.Williams and J.W. Essex, Conformational motions of hiv-1 protease identified using reversible digitally filtered molecular dynamics, Journal of Chemical Theory and Computation, 5 (2009), 1117-1128.
    • (2009) Journal of Chemical Theory and Computation , vol.5 , pp. 1117-1128
    • Wiley, A.P.1    Williams, S.L.2    Essex, J.W.3
  • 26
    • 0029859529 scopus 로고    scopus 로고
    • Ionization states of the catalytic residues in HIV-1 protease
    • DOI 10.1038/nsb1196-946
    • R. Smith, I.M. Brereton, R. Y. Chai and S. B.H. Kent, Ionization states of the catalytic residues in hiv-1 protease, Nature Structural & Molecular Biology, 3 (1996), 946-950. (Pubitemid 26398328)
    • (1996) Nature Structural Biology , vol.3 , Issue.11 , pp. 946-950
    • Smith, R.1    Brereton, I.M.2    Chai, R.Y.3    Kent, S.B.H.4
  • 27
    • 0036303785 scopus 로고    scopus 로고
    • The effects of ionic strength on protein stability: The cold shock protein family
    • DOI 10.1016/S0022-2836(02)00259-0
    • B. N. Dominy, D. Perl, F. X. Schmid and C. L. Brooks, The effects of ionic strength on protein stability: The cold shock protein family, Journal of Molecular Biology, 319 (2002), 541-554. (Pubitemid 34729478)
    • (2002) Journal of Molecular Biology , vol.319 , Issue.2 , pp. 541-554
    • Dominy, B.N.1    Perl, D.2    Schmid, F.X.3    Brooks III, C.L.4
  • 28
    • 0032561137 scopus 로고    scopus 로고
    • The structural stability of the HIV-1 protease
    • DOI 10.1006/jmbi.1998.2090
    • M. J. Todd, N. Semo and E. Freire, The structural stability of the hiv-1 protease, Journal of Molecular Biology, 283 (1998), 475-488. (Pubitemid 28470423)
    • (1998) Journal of Molecular Biology , vol.283 , Issue.2 , pp. 475-488
    • Todd, M.J.1    Semo, N.2    Freire, E.3
  • 29
    • 2942615093 scopus 로고    scopus 로고
    • The folding and dimerization of HIV-1 protease: Evidence for a stable monomer from simulations
    • DOI 10.1016/j.jmb.2004.04.028, PII S0022283604004425
    • Y. Levy, A. Caflisch, J. N. Onuchic and P. G. Wolynes, The folding and dimerization of hiv-1 protease: Evidence for a stable monomer from simulations, Journal of Molecular Biology, 340 (2004), 67-79. (Pubitemid 38739438)
    • (2004) Journal of Molecular Biology , vol.340 , Issue.1 , pp. 67-79
    • Levy, Y.1    Caflisch, A.2    Onuchic, J.N.3    Wolynes, P.G.4
  • 30
    • 0028361968 scopus 로고
    • Structural origins of ph and ionic strength effects on protein stability: Acid denaturation of sperm whale apomyoglobin
    • A. Yang and B. Honig, Structural origins of ph and ionic strength effects on protein stability: Acid denaturation of sperm whale apomyoglobin, Journal of Molecular Biology, 237 (1994), 602-614.
    • (1994) Journal of Molecular Biology , vol.237 , pp. 602-614
    • Yang, A.1    Honig, B.2
  • 31
    • 0035451052 scopus 로고    scopus 로고
    • What are the dielectric "constants" of proteins and how to validate electrostatic models?
    • DOI 10.1002/prot.1106
    • C. N. Schutz and A. Warshel, What are the dielectric " Constants" Of proteins and how to validate electrostatic models?, Proteins: Structure, Function, and Genetics, 44 (2001), 400- 417. (Pubitemid 32768578)
    • (2001) Proteins: Structure, Function and Genetics , vol.44 , Issue.4 , pp. 400-417
    • Schutz, C.N.1    Warshel, A.2
  • 32
    • 0033544710 scopus 로고    scopus 로고
    • Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability
    • DOI 10.1006/jmbi.1999.3305
    • A. H. Elcock, Realistic modeling of the denatured states of proteins allows accurate calculations of the ph-dependence of protein stability, Journal of Molecular Biology, 294 (1999), 1051-1062. (Pubitemid 30000394)
    • (1999) Journal of Molecular Biology , vol.294 , Issue.4 , pp. 1051-1062
    • Elcock, A.H.1
  • 33
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • DOI 10.1006/jmbi.1994.1301
    • J. Antosiewicz, J. A. McCammon and M. K. Gilson, Prediction of ph-dependent properties of proteins, Journal of Molecular Biology, 238 (1994), 415-436. (Pubitemid 24154721)
    • (1994) Journal of Molecular Biology , vol.238 , Issue.3 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.A.2    Gilson, M.K.3
  • 34
    • 22144448052 scopus 로고    scopus 로고
    • Interactions of macromolecules with salt ions: An electrostatic theory for the Hofmeister effect
    • DOI 10.1002/prot.20500
    • H.-X. Zhou, Interactions of macromolecules with salt ions: An electrostatic theory for the hofmeister effect, Proteins: Structure, Function, and Bioinformatics, 61 (2005), 69-78. (Pubitemid 41262918)
    • (2005) Proteins: Structure, Function and Genetics , vol.61 , Issue.1 , pp. 69-78
    • Zhou, H.-X.1
  • 35
    • 0037380834 scopus 로고    scopus 로고
    • Electrostatic contributions to the stability of a thermophilic cold shock protein
    • H.-X. Zhou and F. Dong, Electrostatic contributions to the stability of a thermophilic cold shock protein, Biophysical Journal, 84 (2003), 2216-2222. (Pubitemid 36373544)
    • (2003) Biophysical Journal , vol.84 , Issue.4 , pp. 2216-2222
    • Zhou, H.-X.1    Dong, F.2
  • 36
    • 0013525220 scopus 로고
    • A theory of surface tension of debye-hückel electrolyte
    • K. Ariyama, A theory of surface tension of debye-hückel electrolyte, Bulletin of the Chemical Society of Japan, 12 (1937), 32-37.
    • (1937) Bulletin of the Chemical Society of Japan , vol.12 , pp. 32-37
    • Ariyama, K.1
  • 37
    • 17144366296 scopus 로고
    • The surface tension of debye-huückel electrolyte
    • L. Onsager and N. Samaras, The surface tension of debye-huückel electrolyte, The Journal of Chemical Physics, 2 (1934), 528-536.
    • (1934) The Journal of Chemical Physics , vol.2 , pp. 528-536
    • Onsager, L.1    Samaras, N.2
  • 38
    • 37049168362 scopus 로고
    • The theory of surface tension of electrolytes
    • J. Belton, The theory of surface tension of electrolytes, Transactions of the Faraday Society, 33 (1937), 1449-1454.
    • (1937) Transactions of the Faraday Society , vol.33 , pp. 1449-1454
    • Belton, J.1
  • 39
    • 0001348172 scopus 로고
    • Continuum based calculations of hydration entropies and the hydrophobic effect
    • A. A. Rashin and M. A. Bukatin, Continuum based calculations of hydration entropies and the hydrophobic effect, The Journal of Physical Chemistry, 95 (1991), 2942-2944.
    • (1991) The Journal of Physical Chemistry , vol.95 , pp. 2942-2944
    • Rashin, A.A.1    Bukatin, M.A.2
  • 40
    • 0026416668 scopus 로고
    • Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
    • K. Sharp, A. Nicholls, R. Fine and B. Honig, Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects, Science, 252 (1991), 106-109. (Pubitemid 21916946)
    • (1991) Science , vol.252 , Issue.5002 , pp. 106-109
    • Sharp, K.A.1    Nicholls, A.2    Fine, R.F.3    Honig, B.4
  • 41
    • 0026076664 scopus 로고
    • Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models
    • K. A. Sharp, A. Nicholls, R. Friedman and B. Honig, Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models, Biochemistry, 30 (1991), 9686-9697.
    • (1991) Biochemistry , vol.30 , pp. 9686-9697
    • Sharp, K.A.1    Nicholls, A.2    Friedman, R.3    Honig, B.4
  • 42
    • 33645903407 scopus 로고
    • Solvation thermodynamics of nonionic solutes
    • A. Ben-Naim, Solvation thermodynamics of nonionic solutes, The Journal of Chemical Physics, 81 (1984), 2016-2027.
    • (1984) The Journal of Chemical Physics , vol.81 , pp. 2016-2027
    • Ben-Naim, A.1
  • 43
    • 0000831520 scopus 로고
    • Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment
    • T. Simonson and A. T. Bruenger, Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment, The Journal of Physical Chemistry, 98 (1994), 4683- 4694.
    • (1994) The Journal of Physical Chemistry , vol.98 , pp. 4683-4694
    • Simonson, T.1    Bruenger, A.T.2
  • 44
    • 77955923537 scopus 로고    scopus 로고
    • Predicting the surface tension of aqueous 1:1 electrolyte solutions at high salinity
    • P. Leroy, A. Lassin, M. Azaroual and L. Andr'e, Predicting the surface tension of aqueous 1:1 electrolyte solutions at high salinity, Geochimica et Cosmochimica Acta, 74 (2010), 5427- 5442.
    • (2010) Geochimica et Cosmochimica Acta , vol.74 , pp. 5427-5442
    • Leroy, P.1    Lassin, A.2    Azaroual, M.3    Andr'E, L.4
  • 45
    • 0020477047 scopus 로고
    • Preferential interactions of proteins with salts in concentrated solutions
    • T. Arakawa and S. N. Timasheff, Preferential interactions of proteins with salts in concentrated solutions, Biochemistry, 21 (1982), 6545-6552.
    • (1982) Biochemistry , vol.21 , pp. 6545-6552
    • Arakawa, T.1    Timasheff, S.N.2
  • 46
    • 0034100848 scopus 로고    scopus 로고
    • Two exposed amino acid residues confer thermostability on a cold shock protein
    • DOI 10.1038/75151
    • D. Perl, U. Mueller, U. Heinemann and F. X. Schmid, Two exposed amino acid residues confer thermostability on a cold shock protein, Nature Structural Biology, 7 (2000), 380-383. (Pubitemid 30250000)
    • (2000) Nature Structural Biology , vol.7 , Issue.5 , pp. 380-383
    • Perl, D.1    Mueller, U.2    Heinemann, U.3    Schmid, F.X.4
  • 47
    • 0028070285 scopus 로고
    • Substrate-dependent mechanisms in the catalysis of human immunodeficiency virus protease
    • L. Polgar, Z. Szeltner and I. Boros, Substrate-dependent mechanisms in the catalysis of human immunodeficiency virus protease, Biochemistry, 33 (1994), 9351-9357. (Pubitemid 24272888)
    • (1994) Biochemistry , vol.33 , Issue.31 , pp. 9351-9357
    • Polgar, L.1    Szeltner, Z.2    Boros, I.3
  • 49
    • 0034483901 scopus 로고    scopus 로고
    • Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance
    • DOI 10.1016/S0969-2126(00)00537-2, PII S0969212600005372
    • W. R. P. Scott and C. A. Schiffer, Curling of flap tips in hiv-1 protease as a mechanism for substrate entry and tolerance of drug resistance, Structure (London, England: 1993), 8 (2000), 1259-1265. (Pubitemid 32149752)
    • (2000) Structure , vol.8 , Issue.12 , pp. 1259-1265
    • Scott, W.R.P.1    Schiffer, C.A.2
  • 50
    • 1842454635 scopus 로고    scopus 로고
    • HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs
    • DOI 10.1110/ps.03468904
    • A. L. Perryman, J.-H. Lin and J. A. McCammon, Hiv-1 protease molecular dynamics of a wild-type and of the v82f/i84v mutant: Possible contributions to drug resistance and a potential new target site for drugs, Protein Science, 13 (2004), 1108-1123. (Pubitemid 38429231)
    • (2004) Protein Science , vol.13 , Issue.4 , pp. 1108-1123
    • Perryman, A.L.1    Lin, J.-H.2    McCammon, J.A.3


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