메뉴 건너뛰기




Volumn 293, Issue 4, 1999, Pages 917-951

Folding of a model three-helix bundle protein: A thermodynamic and kinetic analysis

Author keywords

Equilibrium intermediates; Kinetic intermediates; Protein folding; Three helix bundle; Two state cooperativity

Indexed keywords

PROTEIN;

EID: 0033527768     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2936     Document Type: Article
Times cited : (98)

References (136)
  • 1
    • 0028024928 scopus 로고
    • Specific nucleus as the transition state for protein folding. Evidence from the lattice model
    • Abkevich V. I., Gutin A. M., Shakhnovich E. I. Specific nucleus as the transition state for protein folding. Evidence from the lattice model. Biochemistry. 33:1994;10026-10036.
    • (1994) Biochemistry , vol.33 , pp. 10026-10036
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 2
    • 0030342453 scopus 로고    scopus 로고
    • Improved design of stable and fast-folding model proteins
    • Abkevich V. I., Gutin A. M., Shakhnovich E. I. Improved design of stable and fast-folding model proteins. Fold. Des. 1:1996;221-230.
    • (1996) Fold. Des. , vol.1 , pp. 221-230
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 3
    • 0028802181 scopus 로고
    • Initial hydrophobic collapse in the folding of barstar
    • Agashe V. R., Shastry M. C. R., Udgaonkar J. B. Initial hydrophobic collapse in the folding of barstar. Nature. 377:1995;754-757.
    • (1995) Nature , vol.377 , pp. 754-757
    • Agashe, V.R.1    Shastry, M.C.R.2    Udgaonkar, J.B.3
  • 4
    • 36849126204 scopus 로고
    • Studies in molecular dynamics I. General method
    • Alder B. J., Wainwright T. E. Studies in molecular dynamics I. General method. J. Chem. Phys. 31:1959;459-466.
    • (1959) J. Chem. Phys. , vol.31 , pp. 459-466
    • Alder, B.J.1    Wainwright, T.E.2
  • 6
    • 36749107785 scopus 로고
    • Molecular dynamics simulations at constant pressure and/or constant temperature
    • Andersen H. C. Molecular dynamics simulations at constant pressure and/or constant temperature. J. Chem. Phys. 72:1980;2384-2393.
    • (1980) J. Chem. Phys. , vol.72 , pp. 2384-2393
    • Andersen, H.C.1
  • 8
    • 0030755502 scopus 로고    scopus 로고
    • Absence of a stable intermediate on the folding pathway of protein A
    • Bai Y. W., Karimi A., Dyson H. J., Wright P. E. Absence of a stable intermediate on the folding pathway of protein A. Protein Sci. 6:1997;1449-1457.
    • (1997) Protein Sci. , vol.6 , pp. 1449-1457
    • Bai, Y.W.1    Karimi, A.2    Dyson, H.J.3    Wright, P.E.4
  • 9
    • 0029249945 scopus 로고
    • The nature of protein folding pathways - The classical versus the new view
    • Baldwin R. L. The nature of protein folding pathways - the classical versus the new view. J. Biomol. NMR. 5:1995;103-109.
    • (1995) J. Biomol. NMR , vol.5 , pp. 103-109
    • Baldwin, R.L.1
  • 10
    • 0029973119 scopus 로고    scopus 로고
    • Direct observation of fast protein folding: The initial collapse of apomyoglobin
    • Ballew R. M., Sabelko J., Gruebele M. Direct observation of fast protein folding: the initial collapse of apomyoglobin. Proc. Natl Acad. Sci. USA. 93:1996;5759-5764.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 5759-5764
    • Ballew, R.M.1    Sabelko, J.2    Gruebele, M.3
  • 11
    • 84946639640 scopus 로고
    • Molecular dynamics of rigid and non-rigid necklaces of hard discs
    • Bellemans A., Orban J., Belle D. V. Molecular dynamics of rigid and non-rigid necklaces of hard discs. Mol. Phys. 39:1980;781-782.
    • (1980) Mol. Phys. , vol.39 , pp. 781-782
    • Bellemans, A.1    Orban, J.2    Belle, D.V.3
  • 12
    • 0000019441 scopus 로고    scopus 로고
    • Langevin model of protein folding: Cooperativity and stability
    • Berriz G. F., Gutin A. M., Shakhnovich E. I. Langevin model of protein folding: cooperativity and stability. J. Chem. Phys. 106:1997;9276-9285.
    • (1997) J. Chem. Phys. , vol.106 , pp. 9276-9285
    • Berriz, G.F.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 15
    • 0029151245 scopus 로고
    • First principles calculation of the folding free energy of a three-helix bundle protein
    • Boczko E. M., Brooks C. L. III. First principles calculation of the folding free energy of a three-helix bundle protein. Science. 269:1995;393-396.
    • (1995) Science , vol.269 , pp. 393-396
    • Boczko, E.M.1    Brooks C.L. III2
  • 16
    • 0028608099 scopus 로고
    • The stability and unfolding of an IgG binding protein based upon the B domain of protein A from Staphylococcus aureus probed by tryptophan substitution and fluorescence spectroscopy
    • Bottomley S. P., Popplewell A. G., Scawan M., Wan T., Sutton B. J., Gore M. G. The stability and unfolding of an IgG binding protein based upon the B domain of protein A from Staphylococcus aureus probed by tryptophan substitution and fluorescence spectroscopy. Protein Eng. 7:1994;1463-1470.
    • (1994) Protein Eng. , vol.7 , pp. 1463-1470
    • Bottomley, S.P.1    Popplewell, A.G.2    Scawan, M.3    Wan, T.4    Sutton, B.J.5    Gore, M.G.6
  • 18
    • 0024733407 scopus 로고
    • Intermediates and barrier crossing in a random energy model (with applications to protein folding)
    • Bryngelson J. D., Wolynes P. G. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93:1989;6902-6915.
    • (1989) J. Phys. Chem. , vol.93 , pp. 6902-6915
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 19
    • 0031746429 scopus 로고    scopus 로고
    • From coiled coils to small globular proteins - design of a native-like three-helix bundle
    • Bryson J. W., Desjarlais J. R., Handel T. M., Degrado W. F. From coiled coils to small globular proteins - design of a native-like three-helix bundle. Protein Sci. 7:1998;1404-1414.
    • (1998) Protein Sci. , vol.7 , pp. 1404-1414
    • Bryson, J.W.1    Desjarlais, J.R.2    Handel, T.M.3    Degrado, W.F.4
  • 20
    • 0032554626 scopus 로고    scopus 로고
    • Protein folding dynamics. Quantitative comparison between theory and experiment
    • Burton R. E., Myers J. K., Oas T. G. Protein folding dynamics. Quantitative comparison between theory and experiment. Biochemistry. 37:1998;5337-5343.
    • (1998) Biochemistry , vol.37 , pp. 5337-5343
    • Burton, R.E.1    Myers, J.K.2    Oas, T.G.3
  • 21
    • 0026793589 scopus 로고
    • Kinetic resolution of peptide bond and side-chain far-UV circular dichroism during the folding of hen egg-white lysozyme
    • Chaffotte A. F., Guillou Y., Goldberg M. E. Kinetic resolution of peptide bond and side-chain far-UV circular dichroism during the folding of hen egg-white lysozyme. Biochemistry. 31:1992;9694-9702.
    • (1992) Biochemistry , vol.31 , pp. 9694-9702
    • Chaffotte, A.F.1    Guillou, Y.2    Goldberg, M.E.3
  • 22
    • 0025150383 scopus 로고
    • The origins of structure in globular proteins
    • Chan H. S., Dill K. A. The origins of structure in globular proteins. Proc. Natl Acad. Sci. USA. 83:1990;6388-6392.
    • (1990) Proc. Natl Acad. Sci. USA , vol.83 , pp. 6388-6392
    • Chan, H.S.1    Dill, K.A.2
  • 24
    • 0003166498 scopus 로고    scopus 로고
    • Protein folding in the landscape perspective - chevron plots and non-Arrhenius kinetics
    • Chan Y., Dill K. A. Protein folding in the landscape perspective - chevron plots and non-Arrhenius kinetics. Proteins: Struct. Funct. Genet. 30:1998;1-33.
    • (1998) Proteins: Struct. Funct. Genet. , vol.30 , pp. 1-33
    • Chan, Y.1    Dill, K.A.2
  • 26
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill K. A., Chan H. S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4:1997;10-19.
    • (1997) Nature Struct. Biol. , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 28
    • 0345409221 scopus 로고    scopus 로고
    • The thermodynamics and kinetics of protein folding. A lattice model analysis of multiple pathways with intermediates
    • Dinner A. R., Karplus M. The thermodynamics and kinetics of protein folding. A lattice model analysis of multiple pathways with intermediates. J. Mol. Biol. 1999.
    • (1999) J. Mol. Biol
    • Dinner, A.R.1    Karplus, M.2
  • 29
    • 0029781355 scopus 로고    scopus 로고
    • The folding mechanism of larger model proteins: Role of native structure
    • Dinner A. R., Šali A., Karplus M. The folding mechanism of larger model proteins: role of native structure. Proc. Natl Acad. Sci. USA. 93:1996;8356-8361.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 8356-8361
    • Dinner, A.R.1    Šali, A.2    Karplus, M.3
  • 31
    • 0344301982 scopus 로고    scopus 로고
    • Protein folding: A perspective from theory and experiment
    • Dobson C. M., Šali A., Karplus M. Protein folding: a perspective from theory and experiment. Angew Chem. Int. Ed. 37:1998;868-893.
    • (1998) Angew Chem. Int. Ed. , vol.37 , pp. 868-893
    • Dobson, C.M.1    Šali, A.2    Karplus, M.3
  • 32
    • 0032443390 scopus 로고    scopus 로고
    • Discrete molecular dynamics studies of the folding of a protein-like model
    • Dokholyan N. V., Buldyrev S. V., Stanley H. E., Shakhnovich E. I. Discrete molecular dynamics studies of the folding of a protein-like model. Fold. Des. 3:1998;577-587.
    • (1998) Fold. Des. , vol.3 , pp. 577-587
    • Dokholyan, N.V.1    Buldyrev, S.V.2    Stanley, H.E.3    Shakhnovich, E.I.4
  • 34
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y., Kollman P. A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:1998;740-744.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 36
    • 0023140044 scopus 로고
    • Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin
    • Elber R., Karplus M. Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science. 235:1987;318-321.
    • (1987) Science , vol.235 , pp. 318-321
    • Elber, R.1    Karplus, M.2
  • 37
    • 0028352044 scopus 로고
    • Kinetic mechanism of cytochrome c folding: Involvement of the heme and its ligands
    • Elöve G. A., Bhuyan A. K., Roder H. Kinetic mechanism of cytochrome c folding: involvement of the heme and its ligands. Biochemistry. 33:1994;5925-6935.
    • (1994) Biochemistry , vol.33 , pp. 5925-6935
    • Elöve, G.A.1    Bhuyan, A.K.2    Roder, H.3
  • 39
    • 0011875725 scopus 로고
    • Equilibrium electrostatic effects on behavior of polyions in solution: Polyion-mobile ion interaction
    • Ermak D. L., Yeh Y. Equilibrium electrostatic effects on behavior of polyions in solution: polyion-mobile ion interaction. Chem. Phys. Letters. 24:1974;243-248.
    • (1974) Chem. Phys. Letters , vol.24 , pp. 243-248
    • Ermak, D.L.1    Yeh, Y.2
  • 40
    • 0027491027 scopus 로고
    • Thermal motions and functions of bacteriorhodopsin in purple membranes: Effects of temperature and hydration studied by neutron scattering
    • Ferrand M., Dianoux A. J., Petry W., Zaccai G. Thermal motions and functions of bacteriorhodopsin in purple membranes: effects of temperature and hydration studied by neutron scattering. Proc. Natl Acad. Sci. USA. 90:1993;9668-9672.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 9668-9672
    • Ferrand, M.1    Dianoux, A.J.2    Petry, W.3    Zaccai, G.4
  • 42
    • 0031043161 scopus 로고    scopus 로고
    • Nucleation mechanisms in protein folding
    • Fersht A. R. Nucleation mechanisms in protein folding. Curr. Opin. Struct. Biol. 7:1997;3-9.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 3-9
    • Fersht, A.R.1
  • 43
    • 0029157429 scopus 로고
    • Compact intermediate states in protein folding
    • Fink A. L. Compact intermediate states in protein folding. Annu. Rev. Biophys. Biomol. Struct. 24:1995;495-522.
    • (1995) Annu. Rev. Biophys. Biomol. Struct. , vol.24 , pp. 495-522
    • Fink, A.L.1
  • 44
    • 0031933289 scopus 로고    scopus 로고
    • Discrete intermediate versus molten globule models for protein folding - 'characterization' of partially folded intermediates of apomyoglobin
    • Fink A. L., Oberg K. A., Seshadri S. Discrete intermediate versus molten globule models for protein folding - 'characterization' of partially folded intermediates of apomyoglobin. Fold. Des. 3:1998;19-25.
    • (1998) Fold. Des. , vol.3 , pp. 19-25
    • Fink, A.L.1    Oberg, K.A.2    Seshadri, S.3
  • 46
    • 0032574827 scopus 로고    scopus 로고
    • Dynamics and function of proteins: The search for general concepts
    • Frauenfelder H., McMahon B. Dynamics and function of proteins: the search for general concepts. Proc. Natl Acad. Sci. USA. 95:1998;4795-4797.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 4795-4797
    • Frauenfelder, H.1    McMahon, B.2
  • 48
    • 0026801084 scopus 로고
    • Three-dimensional solution structure of the B domain of staphylococcal protein A: Comparisons of the solution and crystal structures
    • Gouda H., Torigoe H., Saito A., Sato M., Arata Y., Shimada I. Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures. Biochemistry. 31:1992;9665.
    • (1992) Biochemistry , vol.31 , pp. 9665
    • Gouda, H.1    Torigoe, H.2    Saito, A.3    Sato, M.4    Arata, Y.5    Shimada, I.6
  • 50
    • 0002689652 scopus 로고    scopus 로고
    • Thermodynamics of protein folding - A statistical mechanical study of a small all-beta protein
    • Guo Z. Y., Brooks C. L. III. Thermodynamics of protein folding - a statistical mechanical study of a small all-beta protein. Biopolymers. 42:1997;745-757.
    • (1997) Biopolymers , vol.42 , pp. 745-757
    • Guo, Z.Y.1    Brooks C.L. III2
  • 51
    • 0029010695 scopus 로고
    • Kinetics of protein folding: Nucleation mechanism, time scales, and pathways
    • Guo Z., Thirumalai D. Kinetics of protein folding: nucleation mechanism, time scales, and pathways. Biopolymers. 36:1995;83-102.
    • (1995) Biopolymers , vol.36 , pp. 83-102
    • Guo, Z.1    Thirumalai, D.2
  • 52
    • 0030601851 scopus 로고    scopus 로고
    • Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein
    • Guo Z., Thirumalai D. Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J. Mol. Biol. 263:1996;323-343.
    • (1996) J. Mol. Biol. , vol.263 , pp. 323-343
    • Guo, Z.1    Thirumalai, D.2
  • 53
    • 0031303354 scopus 로고    scopus 로고
    • The nucleation-collapse mechanism in protein folding: Evidence for the non-uniqueness of the folding nucleus
    • Guo Z., Thirmulai D. The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus. J. Mol. Biol. 2:1997;377-391.
    • (1997) J. Mol. Biol. , vol.2 , pp. 377-391
    • Guo, Z.1    Thirmulai, D.2
  • 54
    • 0030967896 scopus 로고    scopus 로고
    • Exploring the folding free energy surface of a three-helix bundle protein
    • Guo Z. Y., Brooks C. L. III, Boczko E. M. Exploring the folding free energy surface of a three-helix bundle protein. Proc. Natl Acad. Sci. USA. 94:1997;10161-10166.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 10161-10166
    • Guo, Z.Y.1    Brooks C.L. III2    Boczko, E.M.3
  • 55
    • 0028944346 scopus 로고
    • Is burst hydrophobic collapse necessary for protein folding
    • Gutin A. M., Abkevich V. I., Shakhnovich E. I. Is burst hydrophobic collapse necessary for protein folding. Biochemistry. 34:1995;3066-2076.
    • (1995) Biochemistry , vol.34 , pp. 3066-2076
    • Gutin, A.M.1    Abkevich, V.I.2    Shakhnovich, E.I.3
  • 56
    • 0029964867 scopus 로고    scopus 로고
    • Diffusion-limited contact formation in unfolded cytochrome c: Estimating the maximum rate of protein folding
    • Hagen S. J., Hofrichter J., Szabo A., Eaton W. A. Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding. Proc. Natl Acad. Sci. USA. 93:1996;11615-11617.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 11615-11617
    • Hagen, S.J.1    Hofrichter, J.2    Szabo, A.3    Eaton, W.A.4
  • 57
    • 0032502803 scopus 로고    scopus 로고
    • Molecular mechanisms for cooperative folding of proteins
    • Hao M. H., Scheraga H. A. Molecular mechanisms for cooperative folding of proteins. J. Mol. Biol. 277:1998;973-983.
    • (1998) J. Mol. Biol. , vol.277 , pp. 973-983
    • Hao, M.H.1    Scheraga, H.A.2
  • 58
    • 0001043435 scopus 로고
    • Square-well and square-shoulder fluids: Simulation and equations of state
    • Heyes D. M., Aston P. J. Square-well and square-shoulder fluids: simulation and equations of state. J. Chem. Phys. 97:1992;5738-5748.
    • (1992) J. Chem. Phys. , vol.97 , pp. 5738-5748
    • Heyes, D.M.1    Aston, P.J.2
  • 59
    • 0026643094 scopus 로고
    • The nature of folded states of globular proteins
    • Honeycutt J. D., Thirumalai D. The nature of folded states of globular proteins. Biopolymers. 32:1992;695-709.
    • (1992) Biopolymers , vol.32 , pp. 695-709
    • Honeycutt, J.D.1    Thirumalai, D.2
  • 60
    • 0001842441 scopus 로고    scopus 로고
    • Adding backbone to protein folding why proteins are polypeptides
    • Honig B., Cohen F. E. Adding backbone to protein folding why proteins are polypeptides. Fold. Des. 1:1997;R17-R20.
    • (1997) Fold. Des. , vol.1
    • Honig, B.1    Cohen, F.E.2
  • 61
    • 0001538909 scopus 로고
    • Nonequilibrium molecular dynamics
    • Hoover W. G. Nonequilibrium molecular dynamics. Phys. Rev. ser. A. 31:1985;1695.
    • (1985) Phys. Rev. Ser. a , vol.31 , pp. 1695
    • Hoover, W.G.1
  • 62
    • 0027992140 scopus 로고
    • The origins of protein secondary structure. Effects of packing density and hydrogen bonding studied by a fast conformational search
    • Hunt N. G., Gregoret L. M., Cohen F. E. The origins of protein secondary structure. Effects of packing density and hydrogen bonding studied by a fast conformational search. J. Mol. Biol. 241:1994;214-225.
    • (1994) J. Mol. Biol. , vol.241 , pp. 214-225
    • Hunt, N.G.1    Gregoret, L.M.2    Cohen, F.E.3
  • 63
    • 0028868995 scopus 로고
    • The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods. Evidence for a nucleation-condensation mechanism for protein folding
    • Itzhaki L. S., Otzen D. E., Fersht A. R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods. Evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254:1995;260-288.
    • (1995) J. Mol. Biol. , vol.254 , pp. 260-288
    • Itzhaki, L.S.1    Otzen, D.E.2    Fersht, A.R.3
  • 64
    • 0026345750 scopus 로고
    • Folding of chymotrypsin inhibitor 2. I. Evidence for a two-state transition
    • Jackson S. E., Fersht A. R. Folding of chymotrypsin inhibitor 2. I. Evidence for a two-state transition. Biochemistry. 30:1991;10428-10435.
    • (1991) Biochemistry , vol.30 , pp. 10428-10435
    • Jackson, S.E.1    Fersht, A.R.2
  • 65
    • 0030626588 scopus 로고    scopus 로고
    • The Levinthal paradox: Yesterday and today
    • Karplus M. The Levinthal paradox: yesterday and today. Fold. Des. 2:1997;S68-S75.
    • (1997) Fold. Des. , vol.2
    • Karplus, M.1
  • 67
    • 0028949547 scopus 로고
    • Theoretical studies of protein folding and unfolding
    • Karplus M., Šali A. Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5:1995;58-73.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 58-73
    • Karplus, M.1    Šali, A.2
  • 68
    • 84985656311 scopus 로고
    • Diffusion-collision model for protein folding
    • Karplus M., Weaver D. L. Diffusion-collision model for protein folding. Biopolymers. 18:1979;1421-1437.
    • (1979) Biopolymers , vol.18 , pp. 1421-1437
    • Karplus, M.1    Weaver, D.L.2
  • 69
    • 0028327236 scopus 로고
    • Protein folding dynamics - The diffusion-collision model and experimental data
    • Karplus M., Weaver D. L. Protein folding dynamics - the diffusion-collision model and experimental data. Protein Sci. 3:1994;650-668.
    • (1994) Protein Sci. , vol.3 , pp. 650-668
    • Karplus, M.1    Weaver, D.L.2
  • 70
    • 0029025915 scopus 로고
    • Kinetic traps in lysozyme folding
    • Kiefhaber T. Kinetic traps in lysozyme folding. Proc. Natl Acad. Sci. USA. 92:1995;9029-9033.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 9029-9033
    • Kiefhaber, T.1
  • 71
    • 0025345415 scopus 로고
    • Intermediates in the folding reactions of small proteins
    • Kim P. S., Baldwin R. L. Intermediates in the folding reactions of small proteins. Annu. Rev. Biochem. 59:1990;631-660.
    • (1990) Annu. Rev. Biochem. , vol.59 , pp. 631-660
    • Kim, P.S.1    Baldwin, R.L.2
  • 72
    • 0032374086 scopus 로고    scopus 로고
    • Energy landscape of a native protein. Jumping-among-minima model
    • Kitao A., Hayward S., Go N. Energy landscape of a native protein. Jumping-among-minima model. Proteins: Struct. Funct. Genet. 33:1998;496-577.
    • (1998) Proteins: Struct. Funct. Genet. , vol.33 , pp. 496-577
    • Kitao, A.1    Hayward, S.2    Go, N.3
  • 73
    • 0029809182 scopus 로고    scopus 로고
    • On the origin of the cooperativity of protein folding: Implication from model simulations
    • Kolinski A., Galazka W., Skolnick J. On the origin of the cooperativity of protein folding: Implication from model simulations. Proteins: Struct. Funct. Genet. 26:1996;271-287.
    • (1996) Proteins: Struct. Funct. Genet. , vol.26 , pp. 271-287
    • Kolinski, A.1    Galazka, W.2    Skolnick, J.3
  • 74
    • 0000542656 scopus 로고    scopus 로고
    • Monte Carlo studies of the thermodynamics and kinetics of reduced protein models application to small helical, beta, and alpha/beta proteins
    • Kolinski A., Galazka W., Skolnick J. Monte Carlo studies of the thermodynamics and kinetics of reduced protein models application to small helical, beta, and alpha/beta proteins. J. Chem. Phys. 108:1998;2608-2617.
    • (1998) J. Chem. Phys. , vol.108 , pp. 2608-2617
    • Kolinski, A.1    Galazka, W.2    Skolnick, J.3
  • 75
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Applied Crystallog. 24:1991;946-950.
    • (1991) J. Applied Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.1
  • 76
    • 0031311964 scopus 로고    scopus 로고
    • Molten globule as an intermediate on the human prostatic phosphatase folding pathway
    • Kuciel R., Mazurkiewicz A. Molten globule as an intermediate on the human prostatic phosphatase folding pathway. Acta Biochim. Polonica. 44:1997;645-657.
    • (1997) Acta Biochim. Polonica , vol.44 , pp. 645-657
    • Kuciel, R.1    Mazurkiewicz, A.2
  • 77
    • 0031465967 scopus 로고    scopus 로고
    • Multiple unfolding simulations reconcile the "new view" of protein folding with the old
    • Lazaridis T., Karplus M. Multiple unfolding simulations reconcile the "new view" of protein folding with the old. Science. 278:1997;1928-1931.
    • (1997) Science , vol.278 , pp. 1928-1931
    • Lazaridis, T.1    Karplus, M.2
  • 78
    • 0002006297 scopus 로고
    • Are three pathways for protein folding?
    • Levinthal C. Are three pathways for protein folding? J. Chim. Phys. 65:1968;44-45.
    • (1968) J. Chim. Phys. , vol.65 , pp. 44-45
    • Levinthal, C.1
  • 80
    • 0000936038 scopus 로고
    • The calculation of molecular vibration frequencies
    • Lindemann F. A. The calculation of molecular vibration frequencies. Physik, Z. 11:1910;609-612.
    • (1910) Physik, Z. , vol.11 , pp. 609-612
    • Lindemann, F.A.1
  • 81
    • 0028406756 scopus 로고
    • Discontinuous molecular dynamics simulation of hydrogen-bonding systems
    • Liu J., Bowman T. L. II, Elliott J. R. Jr. Discontinuous molecular dynamics simulation of hydrogen-bonding systems. Ind. Eng. Chem. Res. 33:1994;957-964.
    • (1994) Ind. Eng. Chem. Res. , vol.33 , pp. 957-964
    • Liu, J.1    Bowman T.L. II2    Elliott J.R., Jr.3
  • 82
    • 0032584210 scopus 로고    scopus 로고
    • The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-Å resolution
    • Liu Y., Hart P. J., Schlunegger M. P., Eisenberg D. The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-Å resolution. Proc. Natl Acad. Sci. USA. 95:1998;3437-3442.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 3437-3442
    • Liu, Y.1    Hart, P.J.2    Schlunegger, M.P.3    Eisenberg, D.4
  • 83
    • 0031576990 scopus 로고    scopus 로고
    • Fast and slow tracks in lysozyme folding: Insight into the role of domains in the folding process
    • Matagne A., Radford S. E., Dobson C. M. Fast and slow tracks in lysozyme folding: insight into the role of domains in the folding process. J. Mol. Biol. 267:1997;1068-1074.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1068-1074
    • Matagne, A.1    Radford, S.E.2    Dobson, C.M.3
  • 84
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa S., Jernigan R. L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:1985;534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 85
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of beta-hairpin formation
    • Muñnoz V., Thompson P. A., Hofrichter J., Eaton W. A. Folding dynamics and mechanism of beta-hairpin formation. Nature. 390:1997;196-199.
    • (1997) Nature , vol.390 , pp. 196-199
    • Muñnoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 86
    • 0027530219 scopus 로고
    • Termination of right-handed helices in proteins by residues in left-handed helical conformations
    • Nagarajara H. A., Sowdhamini R., Ramakrishnan C., Balaram P. Termination of right-handed helices in proteins by residues in left-handed helical conformations. FEBS Letters. 321:1993;79-83.
    • (1993) FEBS Letters , vol.321 , pp. 79-83
    • Nagarajara, H.A.1    Sowdhamini, R.2    Ramakrishnan, C.3    Balaram, P.4
  • 87
    • 0001849773 scopus 로고
    • Proline isomerization as a rate-limiting step
    • R. H. Pain. Oxford, New York, Tokyo: IRL Press at Oxford University Press
    • Nall B. T. Proline isomerization as a rate-limiting step. Pain R. H. Mechanisms of Protein Folding. 1994;IRL Press at Oxford University Press, Oxford, New York, Tokyo.
    • (1994) Mechanisms of Protein Folding
    • Nall, B.T.1
  • 88
    • 0029908737 scopus 로고    scopus 로고
    • Initial loss of secondary structure in the unfolding of barstar
    • Nath U., Agashe V. R., Udganokar J. B. Initial loss of secondary structure in the unfolding of barstar. Nature Struct. Biol. 3:1996;920-923.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 920-923
    • Nath, U.1    Agashe, V.R.2    Udganokar, J.B.3
  • 89
    • 0000329743 scopus 로고    scopus 로고
    • Symmetry and kinetic optimization of protein like heteropolymers
    • Nelson E. D., Teneyck F., Onuchic J. N. Symmetry and kinetic optimization of protein like heteropolymers. Phys. Rev. Letters. 79:1997;3534-3537.
    • (1997) Phys. Rev. Letters , vol.79 , pp. 3534-3537
    • Nelson, E.D.1    Teneyck, F.2    Onuchic, J.N.3
  • 90
    • 0031777173 scopus 로고    scopus 로고
    • Initial hydrophobic collapse is not necessary for folding RNAse A
    • Nöppert A., Gast K., Zirwer D., Damaschun G. Initial hydrophobic collapse is not necessary for folding RNAse A. Fold. Des. 3:1998;213-221.
    • (1998) Fold. Des. , vol.3 , pp. 213-221
    • Nöppert, A.1    Gast, K.2    Zirwer, D.3    Damaschun, G.4
  • 91
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • Nosé S. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52:1984;255-268.
    • (1984) Mol. Phys. , vol.52 , pp. 255-268
    • Nosé, S.1
  • 92
    • 0032568599 scopus 로고    scopus 로고
    • Folding funnels and frustration in off-lattice minimalist protein landscapes
    • Nymeyer H., García A. E., Onuchic J. N. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc. Natl Acad. Sci. USA. 95:1998;5921-5928.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 5921-5928
    • Nymeyer, H.1    García, A.E.2    Onuchic, J.N.3
  • 95
    • 0032539684 scopus 로고    scopus 로고
    • Is the molten globule a third phase of proteins?
    • Pande V. S., Rokhsar D. S. Is the molten globule a third phase of proteins? Proc. Natl Acad. Sci. USA. 95:1998;1490-1494.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 1490-1494
    • Pande, V.S.1    Rokhsar, D.S.2
  • 97
    • 0031940406 scopus 로고    scopus 로고
    • The early folding kinetics of apomyoglobin
    • Pappu R. V., Weaver D. The early folding kinetics of apomyoglobin. Protein Sci. 7:1998;480-490.
    • (1998) Protein Sci. , vol.7 , pp. 480-490
    • Pappu, R.V.1    Weaver, D.2
  • 98
    • 0030272670 scopus 로고    scopus 로고
    • Time-resolved biophysical methods in the study of protein folding
    • Plaxco K. W., Dobson C. M. Time-resolved biophysical methods in the study of protein folding. Curr. Opin. Struct. Biol. 6:1996;630-636.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 630-636
    • Plaxco, K.W.1    Dobson, C.M.2
  • 99
    • 0007463680 scopus 로고    scopus 로고
    • Statistical mechanics of a correlated energy landscape model for protein folding funnels
    • Plotkin S. S., Wang J., Wolynes P. G. Statistical mechanics of a correlated energy landscape model for protein folding funnels. J. Chem. Phys. 106:1997;2932-2948.
    • (1997) J. Chem. Phys. , vol.106 , pp. 2932-2948
    • Plotkin, S.S.1    Wang, J.2    Wolynes, P.G.3
  • 101
    • 0029124248 scopus 로고
    • Molten globule and protein folding
    • Ptitsyn O. B. Molten globule and protein folding. Advan. Protein Chem. 47:1995;83-230.
    • (1995) Advan. Protein Chem. , vol.47 , pp. 83-230
    • Ptitsyn, O.B.1
  • 103
    • 36149044755 scopus 로고
    • Molecular dynamics simulation of polymer chains with excluded volume
    • Rapaport D. C. Molecular dynamics simulation of polymer chains with excluded volume. J. Phys. A: Math. Gen. 11:1978;L213-L216.
    • (1978) J. Phys. A: Math. Gen. , vol.11
    • Rapaport, D.C.1
  • 104
    • 0000439253 scopus 로고
    • Molecular dynamics study of a polymer chain in solution
    • Rapaport D. C. Molecular dynamics study of a polymer chain in solution. J. Chem. Phys. 71:1979;3299-3303.
    • (1979) J. Chem. Phys. , vol.71 , pp. 3299-3303
    • Rapaport, D.C.1
  • 105
    • 0001412006 scopus 로고
    • The event scheduling problem in molecular dynamics simulation
    • Rapaport D. C. The event scheduling problem in molecular dynamics simulation. J. Comput. Phys. 34:1980;184-201.
    • (1980) J. Comput. Phys. , vol.34 , pp. 184-201
    • Rapaport, D.C.1
  • 106
    • 0027232632 scopus 로고
    • Computer modeling and folding of four helix bundles
    • Rey A., Skolnick J. Computer modeling and folding of four helix bundles. Proteins: Struct. Funct. Genet. 16:1993;199-219.
    • (1993) Proteins: Struct. Funct. Genet. , vol.16 , pp. 199-219
    • Rey, A.1    Skolnick, J.2
  • 107
    • 0029961470 scopus 로고    scopus 로고
    • Equilibrium stability and sub-millisecond refolding of a designed single-chain arc repressor
    • Robinson C. R., Sauer R. T. Equilibrium stability and sub-millisecond refolding of a designed single-chain arc repressor. Biochemistry. 35:1996;13878-13884.
    • (1996) Biochemistry , vol.35 , pp. 13878-13884
    • Robinson, C.R.1    Sauer, R.T.2
  • 108
    • 0002775727 scopus 로고
    • Early stage of protein folding
    • R. H. Pain. Oxford, New York, Tokyo: IRL Press at Oxford University Press
    • Roder H., Elöve g. A. Early stage of protein folding. Pain R. H. Mechanisms of Protein Folding. 1994;26-54 IRL Press at Oxford University Press, Oxford, New York, Tokyo.
    • (1994) Mechanisms of Protein Folding , pp. 26-54
    • Roder, H.1    Elöve, G.A.2
  • 110
    • 0028270634 scopus 로고
    • Kinetics of protein folding: A lattice model study of the requirements for folding to the native state
    • Šali A., Shakhnovich E. I., Karplus M. Kinetics of protein folding: a lattice model study of the requirements for folding to the native state. J. Mol. Biol. 235:1994b;1614-1636.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1614-1636
    • Šali, A.1    Shakhnovich, E.I.2    Karplus, M.3
  • 111
    • 0030770294 scopus 로고    scopus 로고
    • Oligomer formation by 3D domain swapping: A model for protein assembly and misassembly
    • Schlunegger M., Bennett M., Eisenberg D. Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. Advan. Protein Chem. 50:1997;61-122.
    • (1997) Advan. Protein Chem. , vol.50 , pp. 61-122
    • Schlunegger, M.1    Bennett, M.2    Eisenberg, D.3
  • 112
    • 4243114736 scopus 로고
    • Molecular dynamics study of a three-dimensional one-component model for distortive phase transition
    • Schneider T., Stroll E. Molecular dynamics study of a three-dimensional one-component model for distortive phase transition. Phys. Rev. ser. B. 17:1978;1302-1322.
    • (1978) Phys. Rev. Ser. B , vol.17 , pp. 1302-1322
    • Schneider, T.1    Stroll, E.2
  • 113
    • 0002698766 scopus 로고    scopus 로고
    • Modeling protein folding: The beauty and power of simplicity
    • Shakhnovich E. I. Modeling protein folding: the beauty and power of simplicity. Fold. Des. 1:1996;R50-R54.
    • (1996) Fold. Des. , vol.1
    • Shakhnovich, E.I.1
  • 114
    • 0024357911 scopus 로고
    • Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach
    • Shaknovich E. I., Gutin A. M. Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach. Biophys. Chem. 34:1989;187-199.
    • (1989) Biophys. Chem. , vol.34 , pp. 187-199
    • Shaknovich, E.I.1    Gutin, A.M.2
  • 115
    • 0542421561 scopus 로고    scopus 로고
    • Kinetic and structural analysis of submillisecond folding events in cytochrome c
    • Shastry M. C. R., Sauder J. M., Roder H. Kinetic and structural analysis of submillisecond folding events in cytochrome c. Acc. Chem. Res. 31:1998;717-725.
    • (1998) Acc. Chem. Res. , vol.31 , pp. 717-725
    • Shastry, M.C.R.1    Sauder, J.M.2    Roder, H.3
  • 116
    • 0000449653 scopus 로고    scopus 로고
    • Molecular dynamic study of entangled hard-chain fluids
    • Smith S. W., Hall C. K., Freeman B. D. Molecular dynamic study of entangled hard-chain fluids. J. Chem. Phys. 104:1996;5616-5637.
    • (1996) J. Chem. Phys. , vol.104 , pp. 5616-5637
    • Smith, S.W.1    Hall, C.K.2    Freeman, B.D.3
  • 117
    • 0001669870 scopus 로고
    • Kinetic and thermodynamic analysis of protein like heteropolymers: Monte Carlo histogram technique
    • Socci N. D., Onuchic J. N. Kinetic and thermodynamic analysis of protein like heteropolymers: Monte Carlo histogram technique. J. Chem. Phys. 103:1995;4732-4744.
    • (1995) J. Chem. Phys. , vol.103 , pp. 4732-4744
    • Socci, N.D.1    Onuchic, J.N.2
  • 118
    • 0000778705 scopus 로고
    • Properties and origins of protein secondary structure
    • Socci N. D., Bialek W. S., Onuchic J. N. Properties and origins of protein secondary structure. Phys. Rev. ser. A. 49:1994;3440-3443.
    • (1994) Phys. Rev. Ser. a , vol.49 , pp. 3440-3443
    • Socci, N.D.1    Bialek, W.S.2    Onuchic, J.N.3
  • 121
    • 0029940033 scopus 로고    scopus 로고
    • Molecular collapse: The rate-limiting step in two-state cytochrome c folding
    • Sosnick T. R., Mayne L., Englander S. W. Molecular collapse: the rate-limiting step in two-state cytochrome c folding. Proteins: Struct. Funct. Genet. 24:1996;413-426.
    • (1996) Proteins: Struct. Funct. Genet. , vol.24 , pp. 413-426
    • Sosnick, T.R.1    Mayne, L.2    Englander, S.W.3
  • 122
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulations
    • Taketomi H., Ueda Y., Go N. Studies on protein folding, unfolding and fluctuations by computer simulations. Int. J. Pept. Protein Res. 7:1975;445-459.
    • (1975) Int. J. Pept. Protein Res. , vol.7 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 123
    • 0031285905 scopus 로고    scopus 로고
    • Kinetic partitioning mechanism as a unifying theme in the folding of biomolecules
    • Thirumalai D., Klimov D. K., Woodson S. A. Kinetic partitioning mechanism as a unifying theme in the folding of biomolecules. Theoret. Chem. Acc. 96:1997;14-22.
    • (1997) Theoret. Chem. Acc. , vol.96 , pp. 14-22
    • Thirumalai, D.1    Klimov, D.K.2    Woodson, S.A.3
  • 124
    • 0026606219 scopus 로고
    • Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K
    • Tilton R. F. Jr, Dewan J. C., Petsko G. A. Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. Biochemistry. 31:1992;2469-2481.
    • (1992) Biochemistry , vol.31 , pp. 2469-2481
    • Tilton R.F., Jr.1    Dewan, J.C.2    Petsko, G.A.3
  • 125
    • 0017842051 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulations. II. A three-dimensional lattice model of lysozyme
    • Ueda Y., Taketomi H., Go N. Studies on protein folding, unfolding and fluctuations by computer simulations. II. A three-dimensional lattice model of lysozyme. Biopolymers. 17:1978;1531-1548.
    • (1978) Biopolymers , vol.17 , pp. 1531-1548
    • Ueda, Y.1    Taketomi, H.2    Go, N.3
  • 127
    • 0025132269 scopus 로고
    • Nucleation in protein folding - confusion of structure and process
    • Wetlaufer D. B. Nucleation in protein folding - confusion of structure and process. Trends Biochem. Sic. 15:1990;414-415.
    • (1990) Trends Biochem. Sic. , vol.15 , pp. 414-415
    • Wetlaufer, D.B.1
  • 128
    • 0030796986 scopus 로고    scopus 로고
    • Three-state model for lysozyme folding: Triangular folding mechanism with an energetically trapped intermediate
    • Wildegger G., Kiefhaber T. Three-state model for lysozyme folding: triangular folding mechanism with an energetically trapped intermediate. J. Mol. Biol. 270:1997;294-304.
    • (1997) J. Mol. Biol. , vol.270 , pp. 294-304
    • Wildegger, G.1    Kiefhaber, T.2
  • 130
    • 0040994037 scopus 로고
    • Computer studies on fluid systems of hard-core particles
    • Amsterdam, New York: North-Holland/American Elsevier. p. 331
    • Wood W. W. Computer studies on fluid systems of hard-core particles. Fundamental Problems in Statistical Mechanics III. 1975;North-Holland/American Elsevier, Amsterdam, New York. p. 331.
    • (1975) Fundamental Problems in Statistical Mechanics III
    • Wood, W.W.1
  • 131
    • 0028124611 scopus 로고
    • Does compactness induce secondary structure in proteins. A study of polyalanine chains computed by distance geometry
    • Yee D. P., Chan H. S., Havel T. F., Dill K. A. Does compactness induce secondary structure in proteins. A study of polyalanine chains computed by distance geometry. J. Mol. Biol. 241:1994;557-573.
    • (1994) J. Mol. Biol. , vol.241 , pp. 557-573
    • Yee, D.P.1    Chan, H.S.2    Havel, T.F.3    Dill, K.A.4
  • 132
    • 0000519105 scopus 로고    scopus 로고
    • Cytochrome c folding and unfolding: A biphasic mechanism
    • Yeh S., Hun S., Rousseau D. Cytochrome c folding and unfolding: a biphasic mechanism. Acc. Chem. Res. 31:1998;727-736.
    • (1998) Acc. Chem. Res. , vol.31 , pp. 727-736
    • Yeh, S.1    Hun, S.2    Rousseau, D.3
  • 133
    • 0031475159 scopus 로고    scopus 로고
    • Folding thermodynamics of a model three-helix bundle protein
    • Zhou Y., Karplus M. Folding thermodynamics of a model three-helix bundle protein. Proc. Natl Acad. Sci. USA. 94:1997;14429-14432.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 14429-14432
    • Zhou, Y.1    Karplus, M.2
  • 134
    • 0001351693 scopus 로고    scopus 로고
    • A first-order disorder-to-order transition in an isolated homopolymer model
    • Zhou Y., Hall C. K., Karplus M. A first-order disorder-to-order transition in an isolated homopolymer model. Phys. Rev. Letters. 77:1996;2822-2825.
    • (1996) Phys. Rev. Letters , vol.77 , pp. 2822-2825
    • Zhou, Y.1    Hall, C.K.2    Karplus, M.3
  • 135
    • 0001015060 scopus 로고    scopus 로고
    • Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions
    • Zhou Y., Karplus M., Wichert J. M., Hall C. K. Equilibrium thermodynamics of homopolymers and clusters: molecular dynamics and Monte Carlo simulations of systems with square-well interactions. J. Chem. Phys. 107:1997;10691-10708.
    • (1997) J. Chem. Phys. , vol.107 , pp. 10691-10708
    • Zhou, Y.1    Karplus, M.2    Wichert, J.M.3    Hall, C.K.4
  • 136
    • 0033613906 scopus 로고    scopus 로고
    • Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state
    • Zhou Y., Vitkup D., Karplus M. Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. J. Mol. Biol. 285:1999;1371-1377.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1371-1377
    • Zhou, Y.1    Vitkup, D.2    Karplus, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.