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Volumn 93, Issue 12, 2007, Pages 4116-4127

A water-explicit lattice model of heat-, cold-, and pressure-induced protein unfolding

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; WATER;

EID: 37349103161     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.107.108530     Document Type: Article
Times cited : (44)

References (56)
  • 1
    • 0015236387 scopus 로고
    • Reversible pressure-temperature denaturation of chymotrypsinogen
    • Hawley, S. A. 1971. Reversible pressure-temperature denaturation of chymotrypsinogen. Biochemistry. 10:2436-2442.
    • (1971) Biochemistry , vol.10 , pp. 2436-2442
    • Hawley, S.A.1
  • 2
    • 0031714901 scopus 로고    scopus 로고
    • Protein structure and dynamics at high pressure
    • Heremans, K., and L. Smeller. 1998. Protein structure and dynamics at high pressure. Biochim. Biophys. Acta. 1386:353-370.
    • (1998) Biochim. Biophys. Acta , vol.1386 , pp. 353-370
    • Heremans, K.1    Smeller, L.2
  • 3
    • 0037437224 scopus 로고    scopus 로고
    • On the temperature-pressure freeenergy landscape of proteins
    • Ravindra, R., and R. Winter. 2003. On the temperature-pressure freeenergy landscape of proteins. ChemPhysChem. 4:359-365.
    • (2003) ChemPhysChem , vol.4 , pp. 359-365
    • Ravindra, R.1    Winter, R.2
  • 4
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill, K. A. 1990. Dominant forces in protein folding. Biochemistry. 29: 7133-7155.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 5
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann, W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14:1-63.
    • (1959) Adv. Protein Chem , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 6
    • 0022412192 scopus 로고
    • Hydrophobicity of amino-acid residues in globular-proteins
    • Rose, G. D., A. R. Geselowitz, G. J. Lesser, R. H. Lee, and M. H. Zehfus. 1985. Hydrophobicity of amino-acid residues in globular-proteins. Science. 229:834-838.
    • (1985) Science , vol.229 , pp. 834-838
    • Rose, G.D.1    Geselowitz, A.R.2    Lesser, G.J.3    Lee, R.H.4    Zehfus, M.H.5
  • 7
    • 77956714255 scopus 로고
    • The properties of proteins in nonaqueous solvents
    • Singer, S. J. 1962. The properties of proteins in nonaqueous solvents. Adv. Protein Chem. 17:1-68.
    • (1962) Adv. Protein Chem , vol.17 , pp. 1-68
    • Singer, S.J.1
  • 8
    • 0000180763 scopus 로고
    • Temperature-dependence of the hydrophobic interaction in protein folding
    • Baldwin, R. L. 1986. Temperature-dependence of the hydrophobic interaction in protein folding. Proc. Natl. Acad. Sci. USA. 83:8069-8072.
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 8069-8072
    • Baldwin, R.L.1
  • 9
    • 36849150819 scopus 로고
    • Protein stabilization - thermodynamics of unfolding
    • Kauzmann, W. 1987. Protein stabilization - thermodynamics of unfolding. Nature. 325:763-764.
    • (1987) Nature , vol.325 , pp. 763-764
    • Kauzmann, W.1
  • 10
    • 0032539604 scopus 로고    scopus 로고
    • The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins
    • Hummer, G., S. Garde, A. E. Garcia, M. E. Paulaitis, and L. R. Pratt. 1998. The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. Proc. Natl. Acad. Sci. USA. 95:1552-1555.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 1552-1555
    • Hummer, G.1    Garde, S.2    Garcia, A.E.3    Paulaitis, M.E.4    Pratt, L.R.5
  • 12
    • 0011960339 scopus 로고    scopus 로고
    • Hydrophobicity at small and large length scales
    • Lum, K., D. Chandler, and J. D. Weeks. 1999. Hydrophobicity at small and large length scales. J. Phys. Chem. B. 103:4570-4577.
    • (1999) J. Phys. Chem. B , vol.103 , pp. 4570-4577
    • Lum, K.1    Chandler, D.2    Weeks, J.D.3
  • 13
    • 0037078482 scopus 로고    scopus 로고
    • Hydrophobic interactions: An overview
    • ten Wolde, P. R. 2002. Hydrophobic interactions: an overview. J. Phys. Cond. Matt. 14:9445-9460.
    • (2002) J. Phys. Cond. Matt , vol.14 , pp. 9445-9460
    • ten Wolde, P.R.1
  • 14
    • 0037076337 scopus 로고    scopus 로고
    • Drying-induced hydrophobic polymer collapse
    • ten Wolde, P. R., and D. Chandler. 2002. Drying-induced hydrophobic polymer collapse. Proc. Natl. Acad. Sci. USA. 99:6539-6543.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 6539-6543
    • ten Wolde, P.R.1    Chandler, D.2
  • 15
    • 33846512404 scopus 로고    scopus 로고
    • Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water
    • Athawale, M. V., G. Goel, T. Ghosh, T. M. Truskett, and S. Garde. 2007. Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water. Proc. Natl. Acad. Sci. USA. 104: 733-738.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 733-738
    • Athawale, M.V.1    Goel, G.2    Ghosh, T.3    Truskett, T.M.4    Garde, S.5
  • 16
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan, Y., and P. A. Kollman. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:740-744.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 17
    • 4344619300 scopus 로고    scopus 로고
    • All-atom folding simulations of the villin headpiece from stochastically selected coarse-grained structures
    • De Mori, G. M. S., C. Micheletti, and G. Colombo. 2004. All-atom folding simulations of the villin headpiece from stochastically selected coarse-grained structures. J. Phys. Chem. B. 108:12267-12270.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 12267-12270
    • De Mori, G.M.S.1    Micheletti, C.2    Colombo, G.3
  • 18
    • 1942519803 scopus 로고    scopus 로고
    • beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water
    • Wu, X. W., and B. R. Brooks. 2004. beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water. Biophys. J. 86:1946-1958.
    • (2004) Biophys. J , vol.86 , pp. 1946-1958
    • Wu, X.W.1    Brooks, B.R.2
  • 20
    • 4644236471 scopus 로고    scopus 로고
    • Hydrophobic collapse in multidomain protein folding
    • Zhou, R. H., X. H. Huang, C. J. Margulis, and B. J. Berne. 2004. Hydrophobic collapse in multidomain protein folding. Science. 305:1605-1609.
    • (2004) Science , vol.305 , pp. 1605-1609
    • Zhou, R.H.1    Huang, X.H.2    Margulis, C.J.3    Berne, B.J.4
  • 21
    • 2542633488 scopus 로고    scopus 로고
    • Protein-water interactions in ribonuclease A and angiogenin: A molecular dynamics study
    • Sanjeev, B. S., and S. Vishveshwara. 2004. Protein-water interactions in ribonuclease A and angiogenin: a molecular dynamics study. Proteins. 55:915-923.
    • (2004) Proteins , vol.55 , pp. 915-923
    • Sanjeev, B.S.1    Vishveshwara, S.2
  • 22
    • 16344381007 scopus 로고    scopus 로고
    • Pressure denaturation of staphylococcal nuclease studied by neutron small-angle scattering and molecular simulation
    • Paliwal, A., D. Asthagiri, D. P. Bossev, and M. E. Paulaitis. 2004. Pressure denaturation of staphylococcal nuclease studied by neutron small-angle scattering and molecular simulation. Biophys. J. 87:3479-3492.
    • (2004) Biophys. J , vol.87 , pp. 3479-3492
    • Paliwal, A.1    Asthagiri, D.2    Bossev, D.P.3    Paulaitis, M.E.4
  • 23
    • 0036892356 scopus 로고    scopus 로고
    • All-atom fast protein folding simulations: The villin headpiece
    • Shen, M. Y., and K. F. Freed. 2002. All-atom fast protein folding simulations: the villin headpiece. Proteins. 49:439-445.
    • (2002) Proteins , vol.49 , pp. 439-445
    • Shen, M.Y.1    Freed, K.F.2
  • 24
    • 0038133195 scopus 로고    scopus 로고
    • Folding and misfolding of the papillomavirus E6 interacting peptide E6ap
    • Cui, B. X., M. Y. Shen, and K. F. Freed. 2003. Folding and misfolding of the papillomavirus E6 interacting peptide E6ap. Proc. Natl. Acad. Sci. USA. 100:7087-7092.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 7087-7092
    • Cui, B.X.1    Shen, M.Y.2    Freed, K.F.3
  • 25
    • 4544223597 scopus 로고    scopus 로고
    • Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations
    • Chowdhury, S., M. C. Lee, and Y. Duan. 2004. Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations. J. Phys. Chem. B. 108:13855-13865.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 13855-13865
    • Chowdhury, S.1    Lee, M.C.2    Duan, Y.3
  • 26
    • 21244495332 scopus 로고    scopus 로고
    • Folding thermodynamics of peptides
    • Irback, A., and S. Mohanty. 2005. Folding thermodynamics of peptides. Biophys. J. 88:1560-1569.
    • (2005) Biophys. J , vol.88 , pp. 1560-1569
    • Irback, A.1    Mohanty, S.2
  • 27
    • 1542375359 scopus 로고    scopus 로고
    • Temperature-dependent conformational transitions and hydrogen-bond dynamics of the elastin-like octapeptide GVG(VPGVG): A molecula-rdynamics study
    • Rousseau, R., E. Schreiner, A. Kohlmeyer, and D. Marx. 2004. Temperature-dependent conformational transitions and hydrogen-bond dynamics of the elastin-like octapeptide GVG(VPGVG): a molecula-rdynamics study. Biophys. J. 86:1393-1407.
    • (2004) Biophys. J , vol.86 , pp. 1393-1407
    • Rousseau, R.1    Schreiner, E.2    Kohlmeyer, A.3    Marx, D.4
  • 28
    • 18144364015 scopus 로고    scopus 로고
    • In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field
    • Herges, T., and W. Wenzel. 2005. In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field. Phys. Rev. Lett. 94:018101.
    • (2005) Phys. Rev. Lett , vol.94 , pp. 018101
    • Herges, T.1    Wenzel, W.2
  • 29
    • 11244302065 scopus 로고    scopus 로고
    • An all-atom force field for tertiary structure prediction of helical proteins
    • Herges, T., and W. Wenzel. 2004. An all-atom force field for tertiary structure prediction of helical proteins. Biophys. J. 87:3100-3109.
    • (2004) Biophys. J , vol.87 , pp. 3100-3109
    • Herges, T.1    Wenzel, W.2
  • 30
    • 18744415073 scopus 로고    scopus 로고
    • Simulations of the pressure and temperature unfolding of an alpha-helical peptide
    • Paschek, D., S. Gnanakaran, and A. E. Garcia. 2005. Simulations of the pressure and temperature unfolding of an alpha-helical peptide. Proc. Natl. Acad. Sci. USA. 102:6765-6770.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6765-6770
    • Paschek, D.1    Gnanakaran, S.2    Garcia, A.E.3
  • 31
    • 37649031797 scopus 로고    scopus 로고
    • Reversible temperature and pressure denaturation of a protein fragment: A replica exchange molecular dynamics simulation study
    • Paschek, D., and A. E. Garcia. 2004. Reversible temperature and pressure denaturation of a protein fragment: A replica exchange molecular dynamics simulation study. Phys. Rev. Lett. 93:238105.
    • (2004) Phys. Rev. Lett , vol.93 , pp. 238105
    • Paschek, D.1    Garcia, A.E.2
  • 32
    • 0024750637 scopus 로고
    • A lattice statistical-mechanics model of the conformational and sequence-spaces of proteins
    • Lau, K. F., and K. A. Dill. 1989. A lattice statistical-mechanics model of the conformational and sequence-spaces of proteins. Macromolecules. 22:3986-3997.
    • (1989) Macromolecules , vol.22 , pp. 3986-3997
    • Lau, K.F.1    Dill, K.A.2
  • 33
    • 33744825406 scopus 로고
    • Sequence space soup of proteins and copolymers
    • Chan, H. S., and K. A. Dill. 1991. Sequence space soup of proteins and copolymers. J. Chem. Phys. 95:3775-3787.
    • (1991) J. Chem. Phys , vol.95 , pp. 3775-3787
    • Chan, H.S.1    Dill, K.A.2
  • 34
    • 0034516064 scopus 로고    scopus 로고
    • Putting proteins back into water
    • De Los Rios, P., and G. Caldarelli. 2000. Putting proteins back into water. Phys. Rev. E. 62:8449-8452.
    • (2000) Phys. Rev. E , vol.62 , pp. 8449-8452
    • De Los Rios, P.1    Caldarelli, G.2
  • 35
    • 0035684441 scopus 로고    scopus 로고
    • Cold and warm denaturation of proteins
    • Caldarelli, G., and P. De Los Rios. 2001. Cold and warm denaturation of proteins. J. Biol. Phys. 27:229-241.
    • (2001) J. Biol. Phys , vol.27 , pp. 229-241
    • Caldarelli, G.1    De Los Rios, P.2
  • 36
    • 41349094523 scopus 로고    scopus 로고
    • Design of lattice proteins with explicit solvent
    • Salvi, G., S. Molbert, and P. De Los Rios. 2002. Design of lattice proteins with explicit solvent. Phys. Rev. E. 66:061911.
    • (2002) Phys. Rev. E , vol.66 , pp. 061911
    • Salvi, G.1    Molbert, S.2    De Los Rios, P.3
  • 37
    • 17644446703 scopus 로고    scopus 로고
    • Effective interactions cannot replace solvent effects in a lattice model of proteins
    • Salvi, G., and P. De Los Rios. 2003. Effective interactions cannot replace solvent effects in a lattice model of proteins. Phys. Rev. Lett. 91:258102.
    • (2003) Phys. Rev. Lett , vol.91 , pp. 258102
    • Salvi, G.1    De Los Rios, P.2
  • 38
    • 0001843048 scopus 로고
    • Search for a realistic view of hydrophobic effects
    • Muller, N. 1990. Search for a realistic view of hydrophobic effects. Accounts Chem. Res. 23:23-28.
    • (1990) Accounts Chem. Res , vol.23 , pp. 23-28
    • Muller, N.1
  • 39
    • 0029939483 scopus 로고    scopus 로고
    • A two-state model of hydrophobic hydration that produces compensating enthalpy and entropy changes
    • Lee, B., and G. Graziano. 1996. A two-state model of hydrophobic hydration that produces compensating enthalpy and entropy changes. J. Am. Chem. Soc. 118:5163-5168.
    • (1996) J. Am. Chem. Soc , vol.118 , pp. 5163-5168
    • Lee, B.1    Graziano, G.2
  • 40
    • 0022423920 scopus 로고
    • Theory for the folding and stability of globular-proteins
    • Dill, K. A. 1985. Theory for the folding and stability of globular-proteins. Biochemistry. 24:1501-1509.
    • (1985) Biochemistry , vol.24 , pp. 1501-1509
    • Dill, K.A.1
  • 41
    • 0024359551 scopus 로고
    • Thermal stabilities of globular-proteins
    • Dill, K. A., D. O. V. Alonso, and K. Hutchinson. 1989. Thermal stabilities of globular-proteins. Biochemistry. 28:5439-5449.
    • (1989) Biochemistry , vol.28 , pp. 5439-5449
    • Dill, K.A.1    Alonso, D.O.V.2    Hutchinson, K.3
  • 42
    • 33749453423 scopus 로고    scopus 로고
    • Heteropolymer collapse theory for protein folding in the pressure-temperature plane
    • Cheung, J. K., P. Shah, and T. M. Truskett. 2006. Heteropolymer collapse theory for protein folding in the pressure-temperature plane. Biophys. J. 91:2427-2435.
    • (2006) Biophys. J , vol.91 , pp. 2427-2435
    • Cheung, J.K.1    Shah, P.2    Truskett, T.M.3
  • 43
  • 44
    • 0034724564 scopus 로고    scopus 로고
    • The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by H-1 NMR
    • Lassalle, M. W., H. Yamada, and K. Akasaka. 2000. The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by H-1 NMR. J. Mol. Biol. 298:293-302.
    • (2000) J. Mol. Biol , vol.298 , pp. 293-302
    • Lassalle, M.W.1    Yamada, H.2    Akasaka, K.3
  • 45
    • 36849117971 scopus 로고
    • Free volume and entropy in condensed systems. 3. Entropy in binary liquid mixtures - partial molal entropy in dilute solutions - structure and thermodynamics in aqueous electrolytes
    • Frank, H. S., and M. W. Evans. 1945. Free volume and entropy in condensed systems. 3. Entropy in binary liquid mixtures - partial molal entropy in dilute solutions - structure and thermodynamics in aqueous electrolytes. J. Chem. Phys. 13:507-532.
    • (1945) J. Chem. Phys , vol.13 , pp. 507-532
    • Frank, H.S.1    Evans, M.W.2
  • 46
    • 0001101089 scopus 로고    scopus 로고
    • Singularity-free interpretation of the thermodynamics of supercooled water
    • Sastry, S., P. G. Debenedetti, F. Sciortino, and H. E. Stanley. 1996. Singularity-free interpretation of the thermodynamics of supercooled water. Phys. Rev. E. 53:6144-6154.
    • (1996) Phys. Rev. E , vol.53 , pp. 6144-6154
    • Sastry, S.1    Debenedetti, P.G.2    Sciortino, F.3    Stanley, H.E.4
  • 47
    • 0000204784 scopus 로고    scopus 로고
    • Singularity-free interpretation of the thermodynamics of supercooled water. II. Thermal and volumetric behavior
    • Rebelo, L. P. N., P. G. Debenedetti, and S. Sastry. 1998. Singularity-free interpretation of the thermodynamics of supercooled water. II. Thermal and volumetric behavior. J. Chem. Phys. 109:626-633.
    • (1998) J. Chem. Phys , vol.109 , pp. 626-633
    • Rebelo, L.P.N.1    Debenedetti, P.G.2    Sastry, S.3
  • 48
    • 0037717183 scopus 로고    scopus 로고
    • Intramolecular coupling as a mechanism for a liquid-liquid phase transition
    • Franzese, G., M. I. Marques, and H. E. Stanley. 2003. Intramolecular coupling as a mechanism for a liquid-liquid phase transition. Phys. Rev. E. 67:011103.
    • (2003) Phys. Rev. E , vol.67 , pp. 011103
    • Franzese, G.1    Marques, M.I.2    Stanley, H.E.3
  • 50
    • 37049097878 scopus 로고
    • Molecular librations and solvent orientational correlations in hydrophobic phenomena
    • Rossky, P. J., and D. A. Zichi. 1982. Molecular librations and solvent orientational correlations in hydrophobic phenomena. Faraday Symp. Chem. Soc. 17:69-78.
    • (1982) Faraday Symp. Chem. Soc , vol.17 , pp. 69-78
    • Rossky, P.J.1    Zichi, D.A.2
  • 51
    • 39749147672 scopus 로고    scopus 로고
    • Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
    • Wang, F. G., and D. P. Landau. 2001. Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram. Phys. Rev. E. 64:056101.
    • (2001) Phys. Rev. E , vol.64 , pp. 056101
    • Wang, F.G.1    Landau, D.P.2
  • 52
    • 0038333434 scopus 로고    scopus 로고
    • Temperature range of thermodynamic stability for the native state of reversible two-state proteins
    • Kumar, S., C. J. Tsai, and R. Nussinov. 2003. Temperature range of thermodynamic stability for the native state of reversible two-state proteins. Biochemistry. 42:4864-4873.
    • (2003) Biochemistry , vol.42 , pp. 4864-4873
    • Kumar, S.1    Tsai, C.J.2    Nussinov, R.3
  • 53
    • 36849117243 scopus 로고
    • Partial molal volumes of hydrocarbons in water solution
    • Masterton, W. L. 1954. Partial molal volumes of hydrocarbons in water solution. J. Chem. Phys. 22:1830-1833.
    • (1954) J. Chem. Phys , vol.22 , pp. 1830-1833
    • Masterton, W.L.1
  • 54
    • 0030356081 scopus 로고    scopus 로고
    • Volumes of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 298.15 K to 705 K and pressures to 35 MPa
    • Hnedkovsky, L., R. H. Wood, and V. Majer. 1996. Volumes of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 298.15 K to 705 K and pressures to 35 MPa. J. Chem. Therm. 28:125-142.
    • (1996) J. Chem. Therm , vol.28 , pp. 125-142
    • Hnedkovsky, L.1    Wood, R.H.2    Majer, V.3
  • 55
    • 0000189181 scopus 로고
    • Effect of pressure on the solubilities of benzene and alkylbenzenes in water
    • Sawamura, S., K. Kitamura, and Y. Taniguchi. 1989. Effect of pressure on the solubilities of benzene and alkylbenzenes in water. J. Phys. Chem. 93:4931-4935.
    • (1989) J. Phys. Chem , vol.93 , pp. 4931-4935
    • Sawamura, S.1    Kitamura, K.2    Taniguchi, Y.3
  • 56
    • 16444374355 scopus 로고    scopus 로고
    • Extending the pressure-temperature state diagram of myoglobin
    • Meersman, F., L. Smeller, and K. Heremans. 2005. Extending the pressure-temperature state diagram of myoglobin. Helv. Chim. Acta. 88:546-556.
    • (2005) Helv. Chim. Acta , vol.88 , pp. 546-556
    • Meersman, F.1    Smeller, L.2    Heremans, K.3


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