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Volumn 85, Issue 3, 2003, Pages 1492-1502

Similarity of force-induced unfolding of apomyoglobin to its chemical-induced unfolding: An atomistic molecular dynamics simulation approach

Author keywords

[No Author keywords available]

Indexed keywords

APOMYOGLOBIN;

EID: 0042322478     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74582-2     Document Type: Article
Times cited : (16)

References (38)
  • 1
    • 0029973119 scopus 로고    scopus 로고
    • Direct observation of fast protein folding: The initial collapse of apomyoglobin
    • Ballew, R. M., J. Sabelko, and M. Gruebele. 1996. Direct observation of fast protein folding: the initial collapse of apomyoglobin. Proc. Natl. Acad. Sci. USA. 93:5759-5764.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 5759-5764
    • Ballew, R.M.1    Sabelko, J.2    Gruebele, M.3
  • 2
    • 0027245421 scopus 로고
    • Three-state analysis of sperm whale apomyoglobin folding
    • Barrick, D., and R. L. Baldwin. 1993. Three-state analysis of sperm whale apomyoglobin folding. Biochemistry. 32:3790-3796.
    • (1993) Biochemistry , vol.32 , pp. 3790-3796
    • Barrick, D.1    Baldwin, R.L.2
  • 3
    • 0034804341 scopus 로고    scopus 로고
    • Can nonmechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation
    • Best, R. B., B. Li, A. Steward, V. Daggett, and J. Clarke. 2001. Can nonmechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophys. J. 81:2344-2356.
    • (2001) Biophys. J. , vol.81 , pp. 2344-2356
    • Best, R.B.1    Li, B.2    Steward, A.3    Daggett, V.4    Clarke, J.5
  • 4
    • 0037126019 scopus 로고    scopus 로고
    • A simple method for probing the mechanical unfolding pathway of proteins in detail
    • Best, R. B., S. B. Fowler, J. L. Toca-Herrera, and J. Clarke. 2002. A simple method for probing the mechanical unfolding pathway of proteins in detail. Proc. Natl. Acad. Sci. USA. 99:12143-12148.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 12143-12148
    • Best, R.B.1    Fowler, S.B.2    Toca-Herrera, J.L.3    Clarke, J.4
  • 6
    • 0026731467 scopus 로고
    • Characterization of native apomyoglobin by molecular dynamics simulation
    • Brooks, C. L. 1992. Characterization of native apomyoglobin by molecular dynamics simulation. J. Mol. Biol. 227:375-380.
    • (1992) J. Mol. Biol. , vol.227 , pp. 375-380
    • Brooks, C.L.1
  • 7
    • 0034081255 scopus 로고    scopus 로고
    • Mechanical unfolding of a β-hairpin using molecular dynamics
    • Bryant, Z., V. S. Pande, and D. S. Rokhsar. 2000. Mechanical unfolding of a β-hairpin using molecular dynamics. Biophys. J. 78:584-589.
    • (2000) Biophys. J. , vol.78 , pp. 584-589
    • Bryant, Z.1    Pande, V.S.2    Rokhsar, D.S.3
  • 9
    • 0033534586 scopus 로고    scopus 로고
    • Effect of H helix destabilizing mutations on the kinetic and equilibrium folding of apomyoglobin
    • Cavagnero, S., H. J. Dyson, and P. E. Wright. 1999. Effect of H helix destabilizing mutations on the kinetic and equilibrium folding of apomyoglobin. J. Mol. Biol. 285:269-282.
    • (1999) J. Mol. Biol. , vol.285 , pp. 269-282
    • Cavagnero, S.1    Dyson, H.J.2    Wright, P.E.3
  • 10
    • 0035807845 scopus 로고    scopus 로고
    • Conformational and dynamic characterization of the molten globule state of an apomyoglobin mutant with an altered folding pathway
    • Cavagnero, S., C. Nishimura, S. Schwarzinger, H. J. Dyson, and P. E. Wright. 2001. Conformational and dynamic characterization of the molten globule state of an apomyoglobin mutant with an altered folding pathway. Biochemistry. 40:14459-14467.
    • (2001) Biochemistry , vol.40 , pp. 14459-14467
    • Cavagnero, S.1    Nishimura, C.2    Schwarzinger, S.3    Dyson, H.J.4    Wright, P.E.5
  • 11
    • 0033614784 scopus 로고    scopus 로고
    • Ultraviolet resonance Raman examination of horse apomyoglobin acid unfolding intermediates
    • Chi, Z., and S. A. Asher. 1999. Ultraviolet resonance Raman examination of horse apomyoglobin acid unfolding intermediates. Biochemistry. 38:8196-8203.
    • (1999) Biochemistry , vol.38 , pp. 8196-8203
    • Chi, Z.1    Asher, S.A.2
  • 12
    • 0026525048 scopus 로고
    • Molecular dynamics simulations of helix denaturation
    • Daggett, V., and M. Levitt. 1992. Molecular dynamics simulations of helix denaturation. J. Mol. Biol. 223:1121-1138.
    • (1992) J. Mol. Biol. , vol.223 , pp. 1121-1138
    • Daggett, V.1    Levitt, M.2
  • 13
    • 0030575785 scopus 로고    scopus 로고
    • Is apomyoglobin a molten globule? Structural characterization by NMR
    • Eliezer, D., and P. E. Wright. 1996. Is apomyoglobin a molten globule? Structural characterization by NMR. J. Mol. Biol. 263:531-538.
    • (1996) J. Mol. Biol. , vol.263 , pp. 531-538
    • Eliezer, D.1    Wright, P.E.2
  • 15
    • 0036389817 scopus 로고    scopus 로고
    • Mechanical unfolding of a titin Ig domain: Structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering
    • Fowler, S. B., R. B. Best, J. L. Toca-Herrera, T. J. Rutherford, A. Steward, E. Paci, M. Karplus, and J. Clarke. 2002. Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J. Mol. Biol. 322:841-849.
    • (2002) J. Mol. Biol. , vol.322 , pp. 841-849
    • Fowler, S.B.1    Best, R.B.2    Toca-Herrera, J.L.3    Rutherford, T.J.4    Steward, A.5    Paci, E.6    Karplus, M.7    Clarke, J.8
  • 16
    • 0035339911 scopus 로고    scopus 로고
    • Core formation in apomyoglobin: Probing the upper reaches of the folding energy landscape
    • Gulotta, C., R. Gilmanshin, T. C. Buscher, R. H. Callender, and R. B. Dyer. 2001. Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape. Biochemistry. 40:5137-5143.
    • (2001) Biochemistry , vol.40 , pp. 5137-5143
    • Gulotta, C.1    Gilmanshin, R.2    Buscher, T.C.3    Callender, R.H.4    Dyer, R.B.5
  • 17
    • 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
  • 18
    • 0025891257 scopus 로고
    • Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis
    • Hughson, F. M., D, Barrick, and R. L. Baldwin. 1991. Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis. Biochemistry. 30:4113-4118.
    • (1991) Biochemistry , vol.30 , pp. 4113-4118
    • Hughson, F.M.1    Barrick, D.2    Baldwin, R.L.3
  • 19
    • 0025186451 scopus 로고
    • Structural characterization of a partly folded apomyoglobin intermediate
    • Hughson, F. M., P. E. Wright, and R. L. Baldwin. 1990. Structural characterization of a partly folded apomyoglobin intermediate. Science. 249:1544-1548.
    • (1990) Science , vol.249 , pp. 1544-1548
    • Hughson, F.M.1    Wright, P.E.2    Baldwin, R.L.3
  • 20
    • 0027749370 scopus 로고
    • Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin
    • Jennings, P. A., and P. E. Wright. 1993. Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. Science. 262:892-896.
    • (1993) Science , vol.262 , pp. 892-896
    • Jennings, P.A.1    Wright, P.E.2
  • 21
    • 0033514920 scopus 로고    scopus 로고
    • Specificity of native-like interhelical hydrophobic contacts in the apomyoglobin intermediate
    • Kay, M. S., C. H. I. Ramos, and R. L. Baldwin. 1999. Specificity of native-like interhelical hydrophobic contacts in the apomyoglobin intermediate. Proc. Natl. Acad. Sci. USA. 96:2007-2012.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 2007-2012
    • Kay, M.S.1    Ramos, C.H.I.2    Baldwin, R.L.3
  • 22
    • 0031002460 scopus 로고    scopus 로고
    • Folding-unfolding transition in single titin modules characterized with laser tweezers
    • Kellermayer, M., S. Smith, H. Granzier, and C. Bustamante. 1997. Folding-unfolding transition in single titin modules characterized with laser tweezers. Science. 276:1112-1116.
    • (1997) Science , vol.276 , pp. 1112-1116
    • Kellermayer, M.1    Smith, S.2    Granzier, H.3    Bustamante, C.4
  • 23
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for protein dynamics and thermodynamics
    • Lazaridis, T., and M. Karplus. 1999. Effective energy function for protein dynamics and thermodynamics. Proteins Struct. Funct. Genet. 35:133-152.
    • (1999) Proteins Struct. Funct. Genet. , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 24
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 25
    • 0031848099 scopus 로고    scopus 로고
    • Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
    • Lu, H., B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten. 1998. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys. J. 75:662-671.
    • (1998) Biophys. J. , vol.75 , pp. 662-671
    • Lu, H.1    Isralewitz, B.2    Krammer, A.3    Vogel, V.4    Schulten, K.5
  • 26
    • 0033917135 scopus 로고    scopus 로고
    • The key event in force-induced unfolding of titin's immunoglobulin domains
    • Lu, H., and K. Schulten. 2000. The key event in force-induced unfolding of titin's immunoglobulin domains. Biophys. J. 79:51-65.
    • (2000) Biophys. J. , vol.79 , pp. 51-65
    • Lu, H.1    Schulten, K.2
  • 27
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular dynamics system
    • Neria, E., S. Fischer, and M. Karplus. 1996. Simulation of activation free energies in molecular dynamics system. J. Chem. Phys. 105:1902-1921.
    • (1996) J. Chem. Phys. , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 28
    • 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
  • 29
    • 0033531973 scopus 로고    scopus 로고
    • Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulation
    • Paci, E., and M. Karplus. 1999. Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulation. J. Mol. Biol. 288:441-459.
    • (1999) J. Mol. Biol. , vol.288 , pp. 441-459
    • Paci, E.1    Karplus, M.2
  • 30
    • 0034612284 scopus 로고    scopus 로고
    • Unfolding proteins by external forces and temperature: The importance of topology and energetics
    • Paci, E., and M. Karplus. 2000. Unfolding proteins by external forces and temperature: the importance of topology and energetics. Proc. Natl. Acad. Sci. USA. 97:6521-6526.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 6521-6526
    • Paci, E.1    Karplus, M.2
  • 31
    • 0031011695 scopus 로고    scopus 로고
    • Reversible unfolding of individual titin immunoglobulin domains by AFM
    • Rief, M., M. Gautel, F. Oesterhelt, J. M. Fernandez, and H. E. Gaub. 1997. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science. 276:1109-1112.
    • (1997) Science , vol.276 , pp. 1109-1112
    • Rief, M.1    Gautel, M.2    Oesterhelt, F.3    Fernandez, J.M.4    Gaub, H.E.5
  • 32
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 33
    • 0000864144 scopus 로고    scopus 로고
    • Cold-denatured ensemble of apomyoglobin: Implications for the early steps of folding
    • Sabelko, J., Ervin, and M. Gruebele. 1998. Cold-denatured ensemble of apomyoglobin: implications for the early steps of folding. J. Phys. Chem. 102:1806-1819.
    • (1998) J. Phys. Chem. , vol.102 , pp. 1806-1819
    • Sabelko, J.1    Ervin2    Gruebele, M.3
  • 35
    • 0027248899 scopus 로고
    • Peptide models of proteins folding initiation sites. 3. The G-H helical hairpin of myoglobin
    • Shin, H. C., G. Merutka, J. P. Waltho, L. L. Tennant, H. J. Dyson, and P. E. Wright. 1993. Peptide models of proteins folding initiation sites. 3. The G-H helical hairpin of myoglobin. Biochemistry. 32:6356-6364.
    • (1993) Biochemistry , vol.32 , pp. 6356-6364
    • Shin, H.C.1    Merutka, G.2    Waltho, J.P.3    Tennant, L.L.4    Dyson, H.J.5    Wright, P.E.6
  • 36
    • 0004155427 scopus 로고
    • W. H. Freeman and Company, New York
    • Stryer, L. 1995. Biochemistry, 4th ed. W. H. Freeman and Company, New York. 423-424.
    • (1995) Biochemistry, 4th Ed. , pp. 423-424
    • Stryer, L.1
  • 37
    • 0027316216 scopus 로고
    • Molecular dynamics simulations of the unfolding of apomyoglobin in water
    • Tirado-Rives, J., and W. L. Jorgensen. 1993. Molecular dynamics simulations of the unfolding of apomyoglobin in water. Biochemistry. 32:4175-4184.
    • (1993) Biochemistry , vol.32 , pp. 4175-4184
    • Tirado-Rives, J.1    Jorgensen, W.L.2
  • 38
    • 0028958953 scopus 로고
    • Structure determination of the biliverdin apomyoglobin complex: Crystal structure analysis of two crystal forms at 1.4- and 1.5-Å resolution
    • Wagner, U. G., N. Moeiler, W. Schmitzberger, H. Falk, and C. Kratky. 1995. Structure determination of the biliverdin apomyoglobin complex: crystal structure analysis of two crystal forms at 1.4- and 1.5-Å resolution. J. Mol. Biol. 247:326-337.
    • (1995) J. Mol. Biol. , vol.247 , pp. 326-337
    • Wagner, U.G.1    Moeiler, N.2    Schmitzberger, W.3    Falk, H.4    Kratky, C.5


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