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Volumn 51, Issue 2, 2003, Pages 245-257

Kinetics of cytochrome C folding: Atomically detailed simulations

Author keywords

Computer simulations; Molecular dynamics; Protein folding; Stochastic difference equation

Indexed keywords

CYTOCHROME C;

EID: 0344407048     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10349     Document Type: Article
Times cited : (57)

References (57)
  • 2
    • 0022423920 scopus 로고
    • Theory for the folding stability of globular proteins
    • Dill KA. Theory for the folding stability of globular proteins. Biochemistry 1985;24:1501-1509.
    • (1985) Biochemistry , vol.24 , pp. 1501-1509
    • Dill, K.A.1
  • 3
    • 0020024242 scopus 로고
    • Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding
    • Kim PS, Baldwin RL. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem 1982;51:459-489.
    • (1982) Annu Rev Biochem , vol.51 , pp. 459-489
    • Kim, P.S.1    Baldwin, R.L.2
  • 4
    • 0029151245 scopus 로고
    • First-principles calculation of the folding free-energy of a 3-helix bundle protein
    • Boczko EM, Brooks CL III. First-principles calculation of the folding free-energy of a 3-helix bundle protein. Science 1995;269:393-396.
    • (1995) Science , vol.269 , pp. 393-396
    • Boczko, E.M.1    Brooks C.L. III2
  • 5
    • 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
  • 6
    • 0034610360 scopus 로고    scopus 로고
    • Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
    • Mayor U, Johnson CM, Daggett V, Fersht AR. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc Natl Acad Sci USA 2000;97:13518-13522.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 13518-13522
    • Mayor, U.1    Johnson, C.M.2    Daggett, V.3    Fersht, A.R.4
  • 7
    • 0025007598 scopus 로고
    • High-resolution threedimensional structure of horse heart cytochrome c
    • Bushnell GW, Louie GV, Brayer, GD. High-resolution threedimensional structure of horse heart cytochrome c. J Mol Biol 1990;214:585-595.
    • (1990) J Mol Biol , vol.214 , pp. 585-595
    • Bushnell, G.W.1    Louie, G.V.2    Brayer, G.D.3
  • 9
    • 0034714154 scopus 로고    scopus 로고
    • Two-state expansion and collapse of a polypeptide
    • Hagen SJ, Eaton WA. Two-state expansion and collapse of a polypeptide. J Mol Biol 2000;301:1019-1027.
    • (2000) J Mol Biol , vol.301 , pp. 1019-1027
    • Hagen, S.J.1    Eaton, W.A.2
  • 10
    • 0026781019 scopus 로고
    • Early steps in cytochrome c folding probed by time-resolved circular dichroism and fluorescence spectroscopy
    • Elöve GA, Chaffotte AF, Roder H, Goldberg ME. Early steps in cytochrome c folding probed by time-resolved circular dichroism and fluorescence spectroscopy. Biochemistry 1992;31:6876-6883.
    • (1992) Biochemistry , vol.31 , pp. 6876-6883
    • Elöve, G.A.1    Chaffotte, A.F.2    Roder, H.3    Goldberg, M.E.4
  • 12
    • 0023705432 scopus 로고
    • Structural characterization of folding intermediates in cytochrome c by H-exchange labeling and proton NMR
    • Roder H, Elöve GA, Englander SW. Structural characterization of folding intermediates in cytochrome c by H-exchange labeling and proton NMR. Nature 1988;335:700-704.
    • (1988) Nature , vol.335 , pp. 700-704
    • Roder, H.1    Elöve, G.A.2    Englander, S.W.3
  • 16
    • 0028352044 scopus 로고
    • Kinetic mechanism of cytochrome c folding: Involvement of the heme and its ligands
    • Elöve GA, Bhuyan AK, Roder H. Kinetic mechanism of cytochrome c folding: involvement of the heme and its ligands. Biochemistry 1994;33:6925-6935.
    • (1994) Biochemistry , vol.33 , pp. 6925-6935
    • Elöve, G.A.1    Bhuyan, A.K.2    Roder, H.3
  • 19
    • 0542421561 scopus 로고    scopus 로고
    • Kinetic and structural analysis of submillisecond folding events in cytochrome c
    • Shastry MCR, Sauder JM, Roder H. Kinetic and structural analysis of submillisecond folding events in cytochrome c. Acc Chem Res 1998;31:717-725.
    • (1998) Acc Chem Res , vol.31 , pp. 717-725
    • Shastry, M.C.R.1    Sauder, J.M.2    Roder, H.3
  • 20
    • 0037192146 scopus 로고    scopus 로고
    • Rapid intrachain binding of histidine-26 and histidine-33 to heme in unfolded ferrocytochrome c
    • Hagen SJ, Latypov RM, Dolgikh DA, Roder H. Rapid intrachain binding of histidine-26 and histidine-33 to heme in unfolded ferrocytochrome c. Biochemistry 2002;41:1372-1380.
    • (2002) Biochemistry , vol.41 , pp. 1372-1380
    • Hagen, S.J.1    Latypov, R.M.2    Dolgikh, D.A.3    Roder, H.4
  • 21
    • 0031919973 scopus 로고    scopus 로고
    • Evidence for barrier-limited protein folding kinetics on the microsecond time scale
    • Shastry MCR, Roder H. Evidence for barrier-limited protein folding kinetics on the microsecond time scale. Nat Struct Biol 1998;5:385-392.
    • (1998) Nat Struct Biol , vol.5 , pp. 385-392
    • Shastry, M.C.R.1    Roder, H.2
  • 22
    • 0031059496 scopus 로고    scopus 로고
    • Theoretical studies of protein folding thermodynamics and kinetics
    • Shaknovich EI. Theoretical studies of protein folding thermodynamics and kinetics. Curr Opin Struct Biol 1997;7:29-40.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 29-40
    • Shaknovich, E.I.1
  • 23
    • 0027318781 scopus 로고
    • Kinetics and thermodynamics of folding in model proteins
    • Camacho CJ, Thirumalai D. Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci USA 1993;90:6369-6372.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 6369-6372
    • Camacho, C.J.1    Thirumalai, D.2
  • 25
    • 0036280655 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the protein unfolding/folding reaction
    • Daggett V. Molecular dynamics simulations of the protein unfolding/folding reaction. Acc Chem Res 2002;35:422-429.
    • (2002) Acc Chem Res , vol.35 , pp. 422-429
    • Daggett, V.1
  • 26
    • 0036280693 scopus 로고    scopus 로고
    • Protein and peptide folding explored with molecular simulations
    • Brooks III CL. Protein and peptide folding explored with molecular simulations. Acc Chem Res 2002;35:447-454.
    • (2002) Acc Chem Res , vol.35 , pp. 447-454
    • Brooks C.L. III1
  • 27
    • 16444370098 scopus 로고    scopus 로고
    • Stochastic path approach to compute atomically detailed trajectories: Application to the folding of C peptide
    • Elber R, Meller J, Olender R. Stochastic path approach to compute atomically detailed trajectories: application to the folding of C peptide. J Phys Chem 1999;103:899-911.
    • (1999) J Phys Chem , vol.103 , pp. 899-911
    • Elber, R.1    Meller, J.2    Olender, R.3
  • 28
    • 0034625276 scopus 로고    scopus 로고
    • Parallel computations of molecular dynamics trajectories using stochastic path approach
    • Zalov V, Elber R. Parallel computations of molecular dynamics trajectories using stochastic path approach. Comput Phys Commun 2000;128:118-127.
    • (2000) Comput Phys Commun , vol.128 , pp. 118-127
    • Zalov, V.1    Elber, R.2
  • 29
    • 0035874109 scopus 로고    scopus 로고
    • The enzymatic circularization of a malto-octaose linear chain studied by stochastic reaction path calculations on cyclodextrin glycosyltransferase
    • Uitdehaag JCM, van der Veen BA, Dijkhuizen L, Elber R, Dijkstra BW. The enzymatic circularization of a malto-octaose linear chain studied by stochastic reaction path calculations on cyclodextrin glycosyltransferase. Proteins 2001;43:327-335.
    • (2001) Proteins , vol.43 , pp. 327-335
    • Uitdehaag, J.C.M.1    Van der Veen, B.A.2    Dijkhuizen, L.3    Elber, R.4    Dijkstra, B.W.5
  • 30
    • 0037233422 scopus 로고    scopus 로고
    • Ion permeation through the gramicidin channel: Atomically detailed modeling by the stochastic difference equation
    • Siva K, Elber R. Ion permeation through the gramicidin channel: atomically detailed modeling by the stochastic difference equation. Proteins 2003;50:63-80.
    • (2003) Proteins , vol.50 , pp. 63-80
    • Siva, K.1    Elber, R.2
  • 31
    • 0036678831 scopus 로고    scopus 로고
    • An atomically detailed study of the folding pathways of protein A with the stochastic difference equation
    • Ghosh A, Elber R, Scheraga HA. An atomically detailed study of the folding pathways of protein A with the stochastic difference equation. Proc Natl Acad Sci USA 2002;99:10394-10398.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 10394-10398
    • Ghosh, A.1    Elber, R.2    Scheraga, H.A.3
  • 32
    • 0002636134 scopus 로고
    • Pairwise solute descreening of solute charges from a dielectric medium
    • Hawkins GD, Cramer CJ, Truhlar DG. Pairwise solute descreening of solute charges from a dielectric medium. Chem Phys Lett 1995;246:122-129.
    • (1995) Chem Phys Lett , vol.246 , pp. 122-129
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 33
    • 14244273182 scopus 로고    scopus 로고
    • Theory and applications of the generalized Born solvation model in macromolecular simulations
    • Tsui V, Case DA. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 2000;56:275-291.
    • (2000) Biopolymers , vol.56 , pp. 275-291
    • Tsui, V.1    Case, D.A.2
  • 34
    • 0012021417 scopus 로고    scopus 로고
    • Calculation of classical trajectories with a very large time step: Formalism and numerical examples
    • Olender R, Elber R. Calculation of classical trajectories with a very large time step: Formalism and numerical examples. J Chem Phys 1996;105:9299-9315.
    • (1996) J Chem Phys , vol.105 , pp. 9299-9315
    • Olender, R.1    Elber, R.2
  • 35
    • 0345421087 scopus 로고    scopus 로고
    • Bridging the gap between reaction pathways, long time dynamics and calculation of rates
    • in press
    • Elber R, Ghosh A, Cárdenas A, Stern H. Bridging the gap between reaction pathways, long time dynamics and calculation of rates. Adv Chem Phys (in press).
    • Adv Chem Phys
    • Elber, R.1    Ghosh, A.2    Cárdenas, A.3    Stern, H.4
  • 36
    • 4243606192 scopus 로고
    • Unified approach for density functional theory and molecular dynamics
    • Carr R, Parrinello M. Unified approach for density functional theory and molecular dynamics. Phys Rev Lett 1985;55:2471-2474.
    • (1985) Phys Rev Lett , vol.55 , pp. 2471-2474
    • Carr, R.1    Parrinello, M.2
  • 37
    • 0036286652 scopus 로고    scopus 로고
    • Long time dynamics of complex systems
    • Elber R, Ghosh A, Cárdenas A. Long time dynamics of complex systems. Acc Chem Res 2002;35:396-403.
    • (2002) Acc Chem Res , vol.35 , pp. 396-403
    • Elber, R.1    Ghosh, A.2    Cárdenas, A.3
  • 38
    • 36449008311 scopus 로고
    • Shadowing, rare events, and rubber bands: A variational Verlet algorithm for molecular dynamics
    • Gillilan RE, Wilson KR. Shadowing, rare events, and rubber bands: a variational Verlet algorithm for molecular dynamics. J Chem Phys 1992;97:1757-1772.
    • (1992) J Chem Phys , vol.97 , pp. 1757-1772
    • Gillilan, R.E.1    Wilson, K.R.2
  • 39
    • 0001210312 scopus 로고
    • The construction of double-ended classical trajectories
    • Cho AE, Doll JD, Freeman DL. The construction of double-ended classical trajectories. Chem Phys Lett 1994;229:218-224.
    • (1994) Chem Phys Lett , vol.229 , pp. 218-224
    • Cho, A.E.1    Doll, J.D.2    Freeman, D.L.3
  • 40
    • 0002911251 scopus 로고
    • Classical-limit quantum mechanics and the theory of molecular collisions
    • Miller WH. Classical-limit quantum mechanics and the theory of molecular collisions. Adv Chem Phys 1974;25:69-177.
    • (1974) Adv Chem Phys , vol.25 , pp. 69-177
    • Miller, W.H.1
  • 41
    • 84963146276 scopus 로고
    • Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions
    • Grubmüller H, Heller H, Windemuth A, Shulten K. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol Sim 1991;6:121-142.
    • (1991) Mol Sim , vol.6 , pp. 121-142
    • Grubmüller, H.1    Heller, H.2    Windemuth, A.3    Shulten, K.4
  • 42
    • 0000504254 scopus 로고
    • A multiple time step molecular dynamics algorithm for macromolecules
    • Humphreys DD, Friesner RA, Berne BJ. A multiple time step molecular dynamics algorithm for macromolecules. J Chem Phys 1994;98:6885-6892.
    • (1994) J Chem Phys , vol.98 , pp. 6885-6892
    • Humphreys, D.D.1    Friesner, R.A.2    Berne, B.J.3
  • 43
    • 0035449971 scopus 로고    scopus 로고
    • Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations
    • Batcho PF, Case DA, Schlick T. Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations. J Chem Phys 2001;115:4003-4018.
    • (2001) J Chem Phys , vol.115 , pp. 4003-4018
    • Batcho, P.F.1    Case, D.A.2    Schlick, T.3
  • 45
    • 0002197305 scopus 로고    scopus 로고
    • Reaction path studies of biomolecules
    • Elber R, editor. Singapore: World Scientific
    • Elber R. Reaction path studies of biomolecules. In: Elber R, editor. Recent developments in theoretical studies of proteins. Singapore: World Scientific; 1996. p 65-136.
    • (1996) Recent Developments in Theoretical Studies of Proteins , pp. 65-136
    • Elber, R.1
  • 46
    • 39249083909 scopus 로고    scopus 로고
    • Action-derived molecular dynamics in the study of rare events
    • Passerone D, Parrinello M. Action-derived molecular dynamics in the study of rare events. Phys Rev Lett 2001;87:108-302.
    • (2001) Phys Rev Lett , vol.87 , pp. 108-302
    • Passerone, D.1    Parrinello, M.2
  • 50
    • 33645941402 scopus 로고
    • The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin
    • Jorgensen WL, Tirado-Rives J. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
    • (1988) J Am Chem Soc , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 51
    • 84987058840 scopus 로고
    • Self avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems
    • Czerminski R, Elber R. Self avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems. Int J Quantum Chem 1990;24:167-186.
    • (1990) Int J Quantum Chem , vol.24 , pp. 167-186
    • Czerminski, R.1    Elber, R.2
  • 52
    • 13044284157 scopus 로고    scopus 로고
    • Kinetic evidence for an on-pathway intermediate in the folding of cytochrome c
    • Bai Y. Kinetic evidence for an on-pathway intermediate in the folding of cytochrome c. Proc Nat Acad Sci USA 1999;96:477-480.
    • (1999) Proc Nat Acad Sci USA , vol.96 , pp. 477-480
    • Bai, Y.1
  • 55
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer-simulation. 1. Effect of specific amino-acid sequence represented by specific inter-unit interactions
    • Taketomi H, Ueda Y, Go N. Studies on protein folding, unfolding and fluctuations by computer-simulation. 1. Effect of specific amino-acid sequence represented by specific inter-unit interactions. Int J Pept Prot Res 1975;7:445-459.
    • (1975) Int J Pept Prot Res , vol.7 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 57
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein folding dynamics
    • Snow CD, Nguyen N, Pande VS, Gruebele M. Absolute comparison of simulated and experimental protein folding dynamics. Nature 2002;420:102-106.
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.D.1    Nguyen, N.2    Pande, V.S.3    Gruebele, M.4


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