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Volumn 39, Issue 3, 2000, Pages 252-260

Computer simulations of protein folding by targeted molecular dynamics

Author keywords

Chymotrypsin inhibitor 2; Implicit solvation model; Molecular dynamics simulation; Protein folding

Indexed keywords

CHYMOTRYPSIN INHIBITOR;

EID: 0034657550     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000515)39:3<252::AID-PROT80>3.0.CO;2-3     Document Type: Article
Times cited : (70)

References (40)
  • 2
    • 1842298212 scopus 로고    scopus 로고
    • From levinthal to pathways to funnels
    • Dill K, Chan H. From Levinthal to pathways to funnels. Nat Struct Biol 1997;4:10-19.
    • (1997) Nat Struct Biol , vol.4 , pp. 10-19
    • Dill, K.1    Chan, H.2
  • 3
    • 0344301982 scopus 로고    scopus 로고
    • Protein folding: A perspective from theory and experiment
    • Dobson CM, Sali A, Karplus M. Protein folding: A perspective from theory and experiment. Angew Chem Int Ed 1998;37:869-893.
    • (1998) Angew Chem Int Ed , vol.37 , pp. 869-893
    • Dobson, C.M.1    Sali, A.2    Karplus, M.3
  • 4
    • 0032842870 scopus 로고    scopus 로고
    • The fundamentals of protein folding: Bringing together theory and experiment
    • Dobson CM, Karplus M. The fundamentals of protein folding: bringing together theory and experiment. Curr Opin Struct Biol 1999;9:92-101.
    • (1999) Curr Opin Struct Biol , vol.9 , pp. 92-101
    • Dobson, C.M.1    Karplus, M.2
  • 5
    • 0033117763 scopus 로고    scopus 로고
    • Matching theory and experiment in protein folding
    • Alm E, Baker D. Matching theory and experiment in protein folding. Curr Opin Struct Biol 1999;9:189-196.
    • (1999) Curr Opin Struct Biol , vol.9 , pp. 189-196
    • Alm, E.1    Baker, D.2
  • 7
    • 0028929556 scopus 로고
    • Principles of protein folding - A perspective from simple exact models
    • Dill KA, Bromberg S, Yue K, et al. Principles of protein folding - a perspective from simple exact models. Protein Sci 1995;4:561-601.
    • (1995) Protein Sci , vol.4 , pp. 561-601
    • Dill, K.A.1    Bromberg, S.2    Yue, K.3
  • 8
    • 0025608908 scopus 로고
    • Simulations of the folding of a globular protein
    • Skolnick J, Kolinski A. Simulations of the folding of a globular protein. Science 1990;250:1121-1125.
    • (1990) Science , vol.250 , pp. 1121-1125
    • Skolnick, J.1    Kolinski, A.2
  • 9
    • 0030775114 scopus 로고    scopus 로고
    • Can protein unfolding simulate protein folding?
    • Finkelstein AV. Can protein unfolding simulate protein folding? Protein Eng 1997;10:843-845.
    • (1997) Protein Eng , vol.10 , pp. 843-845
    • Finkelstein, A.V.1
  • 10
    • 0029151245 scopus 로고
    • First-principles calculation of the folding free energy of a three-helix bundle protein
    • Boczko EM, Brooks III CL. First-principles calculation of the folding free energy of a three-helix bundle protein. Science 1995; 269:393-396.
    • (1995) Science , vol.269 , pp. 393-396
    • Boczko, E.M.1    Brooks C.L. III2
  • 11
    • 0032080053 scopus 로고    scopus 로고
    • Calculations on folding of segment B1 of streptococcal protein G
    • Sheinermann FB, Brooks III CL. Calculations on folding of segment B1 of streptococcal protein G. J Mol Biol 1998;278:439-456.
    • (1998) J Mol Biol , vol.278 , pp. 439-456
    • Sheinermann, F.B.1    Brooks C.L. III2
  • 12
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998;282:740-744.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 13
    • 0027794972 scopus 로고
    • Targeted molecular dynamics simulation of conformational change: Application to the T ↔ R transition in insulin
    • Schlitter J, Engels M, Krüger P, Jacoby E, Wollmer A. Targeted molecular dynamics simulation of conformational change: Application to the T ↔ R transition in insulin. Mol Simul 1993;10:291-309.
    • (1993) Mol Simul , vol.10 , pp. 291-309
    • Schlitter, J.1    Engels, M.2    Krüger, P.3    Jacoby, E.4    Wollmer, A.5
  • 14
    • 0242618314 scopus 로고    scopus 로고
    • Calculation of pathways for the conformational transition between the GTP-and GDP-bound states of the Ha-ras-p21 protein: Calculations with explicit solvent simulations and comparison with calculations in vacuum
    • Diaz J, Wroblowski B, Schlitter J, Engelborghs Y. Calculation of pathways for the conformational transition between the GTP-and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum. Proteins 1997;28:434-451.
    • (1997) Proteins , vol.28 , pp. 434-451
    • Diaz, J.1    Wroblowski, B.2    Schlitter, J.3    Engelborghs, Y.4
  • 15
    • 0030711616 scopus 로고    scopus 로고
    • Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21
    • Ma J, Karplus M. Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proc Natl Acad Sci USA 1997;94:11905-11910.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 11905-11910
    • Ma, J.1    Karplus, M.2
  • 16
    • 0001568871 scopus 로고    scopus 로고
    • Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water
    • Apostolakis J, Ferrara P, Caflisch A. Calculation of conformational transitions and barriers in solvated systems: application to the alanine dipeptide in water. J Chem Phys 1999;110:2099-2108.
    • (1999) J Chem Phys , vol.110 , pp. 2099-2108
    • Apostolakis, J.1    Ferrara, P.2    Caflisch, A.3
  • 17
    • 0026345750 scopus 로고
    • Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
    • Jackson SE, Fersht AR. Folding of chymotrypsin inhibitor 2. 1. evidence for a two-state transition. Biochemistry 1991;30:10248-10435.
    • (1991) Biochemistry , vol.30 , pp. 10248-10435
    • Jackson, S.E.1    Fersht, A.R.2
  • 18
    • 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 LS, Otzen DE, Fersht AR. 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 1995;254:260-288.
    • (1995) J Mol Biol , vol.254 , pp. 260-288
    • Itzhaki, L.S.1    Otzen, D.E.2    Fersht, A.R.3
  • 19
    • 0029963345 scopus 로고    scopus 로고
    • Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
    • Li A, Daggett V. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Biol 1996;257:412-429.
    • (1996) J Mol Biol , vol.257 , pp. 412-429
    • Li, A.1    Daggett, V.2
  • 20
    • 0031465967 scopus 로고    scopus 로고
    • "New view" of protein folding reconciled with the old through multiple unfolding simulations
    • Lazaridis T, Karplus M. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 1997;278:1928-1931.
    • (1997) Science , vol.278 , pp. 1928-1931
    • Lazaridis, T.1    Karplus, M.2
  • 22
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • Neria E, Fischer S, Karplus M. Simulation of activation free energies in molecular systems. J Chem Phys 1996;105:1902-1921.
    • (1996) J Chem Phys , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 23
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 24
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199-203.
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 25
    • 0001308921 scopus 로고
    • A rapid approximation to the solvent accessible surface areas of atoms
    • Hasel W, Hendrickson TF, Still WC. A rapid approximation to the solvent accessible surface areas of atoms. Tetrahedron Comput Methodol 1988;1:103-116.
    • (1988) Tetrahedron Comput Methodol , vol.1 , pp. 103-116
    • Hasel, W.1    Hendrickson, T.F.2    Still, W.C.3
  • 26
    • 0029970351 scopus 로고    scopus 로고
    • An efficient mean solvation force model for use molecular dynamics simulations of proteins in aqueous solution
    • Fraternali F, van Gunsteren WF. An efficient mean solvation force model for use molecular dynamics simulations of proteins in aqueous solution. J Mol Biol 1996;256:939-948.
    • (1996) J Mol Biol , vol.256 , pp. 939-948
    • Fraternali, F.1    Van Gunsteren, W.F.2
  • 27
    • 36149010019 scopus 로고
    • Some studies concerning rotating axes and polyatomic molecules
    • Eckart C. Some studies concerning rotating axes and polyatomic molecules. Phys Rev 1935;47:552-558.
    • (1935) Phys Rev , vol.47 , pp. 552-558
    • Eckart, C.1
  • 28
    • 0033531973 scopus 로고    scopus 로고
    • Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations
    • Paci E, Karplus M. Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J Mol Biol 1999;288:441-459.
    • (1999) J Mol Biol , vol.288 , pp. 441-459
    • Paci, E.1    Karplus, M.2
  • 29
    • 0001160648 scopus 로고    scopus 로고
    • Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems
    • Marchi M, Ballone P. Adiabatic bias molecular dynamics: a method to navigate the conformational space of complex molecular systems. J Chem Phys 1999;110:3697-3702.
    • (1999) J Chem Phys , vol.110 , pp. 3697-3702
    • Marchi, M.1    Ballone, P.2
  • 30
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Protein Chem 1959;14:1-64.
    • (1959) Adv Protein Chem , vol.14 , pp. 1-64
    • Kauzmann, W.1
  • 31
    • 0032544002 scopus 로고    scopus 로고
    • The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation
    • Duan Y, Wang L, Kollman PA. The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proc Natl Acad Sci USA 1998;95: 9897-9902.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 9897-9902
    • Duan, Y.1    Wang, L.2    Kollman, P.A.3
  • 32
    • 0030626588 scopus 로고    scopus 로고
    • The levinthal paradox: Yesterday and today
    • Karplus M. The Levinthal paradox: yesterday and today. Folding and Design 1997;2:S69-S75.
    • (1997) Folding and Design , vol.2
    • Karplus, M.1
  • 33
    • 0029124248 scopus 로고
    • Molten globule and protein folding
    • Ptitsyn OB. Molten globule and protein folding. Advan Protein Chem 1995;47:83-230.
    • (1995) Advan Protein Chem , vol.47 , pp. 83-230
    • Ptitsyn, O.B.1
  • 34
    • 0022423920 scopus 로고
    • Theory for the folding and stability of globular proteins
    • Dill KA. Theory for the folding and stability of globular proteins. Biochemistry 1985;24:1501-1509.
    • (1985) Biochemistry , vol.24 , pp. 1501-1509
    • Dill, K.A.1
  • 35
    • 0031853167 scopus 로고    scopus 로고
    • Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain
    • Grantcharova VP, Riddle DS, Santiago JV, Baker D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nat Struct Biol 1998;5:714-720.
    • (1998) Nat Struct Biol , vol.5 , pp. 714-720
    • Grantcharova, V.P.1    Riddle, D.S.2    Santiago, J.V.3    Baker, D.4
  • 36
    • 0031825181 scopus 로고    scopus 로고
    • Obligatory steps in protein folding and the conformational diversity of the transition state
    • Martinez JC, Pisabarro MT, Serrano L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol 1998;5:721-729.
    • (1998) Nat Struct Biol , vol.5 , pp. 721-729
    • Martinez, J.C.1    Pisabarro, M.T.2    Serrano, L.3
  • 37
    • 0345411345 scopus 로고    scopus 로고
    • Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
    • Tsai J, Levitt M, Baker D. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J Mol Biol 1999;291:215-225.
    • (1999) J Mol Biol , vol.291 , pp. 215-225
    • Tsai, J.1    Levitt, M.2    Baker, D.3
  • 38
    • 18344391877 scopus 로고    scopus 로고
    • Protein structures and optimal folding from a geometrical variational principle
    • Micheletti C, Banavar JR, Maritan A, Seno F. Protein structures and optimal folding from a geometrical variational principle. Phys Rev Lett 1999;82:3372-3375.
    • (1999) Phys Rev Lett , vol.82 , pp. 3372-3375
    • Micheletti, C.1    Banavar, J.R.2    Maritan, A.3    Seno, F.4
  • 39
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 40
    • 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 Appl Crystallogr 1991;24: 946-950.
    • (1991) J Appl Crystallogr , vol.24 , pp. 946-950
    • Kraulis, P.1


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