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Volumn 35, Issue 4, 1999, Pages 453-463

Steered molecular dynamics simulations of force-induced protein domain unfolding

Author keywords

Domain classification; Fibronectin type III domain; Immunoglobulin domain; Protein folding; Steered molecular dynamics

Indexed keywords

FIBRONECTIN;

EID: 0033151955     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990601)35:4<453::AID-PROT9>3.0.CO;2-M     Document Type: Article
Times cited : (259)

References (46)
  • 5
    • 0032053619 scopus 로고    scopus 로고
    • Simulations of protein folding and unfolding
    • Brooks C. Simulations of protein folding and unfolding. Curr Opin Struct Biol 1998;8:222-226.
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 222-226
    • Brooks, C.1
  • 6
    • 0028949547 scopus 로고
    • Theoretical studies of protein folding and unfolding
    • Karplus M, Sali A. Theoretical studies of protein folding and unfolding. Curr Opin Struct Biol 1995;5:58-73.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 58-73
    • Karplus, M.1    Sali, A.2
  • 7
    • 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
  • 8
    • 0030939289 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the unfolding of barnase in water and 8M aqueous urea
    • Tirado-Rives J, Orozco M, Jorgensen W. Molecular dynamics simulations of the unfolding of barnase in water and 8M aqueous urea. Biochemistry 1997;36:7313-7329.
    • (1997) Biochemistry , vol.36 , pp. 7313-7329
    • Tirado-Rives, J.1    Orozco, M.2    Jorgensen, W.3
  • 9
    • 0032555115 scopus 로고    scopus 로고
    • Synergy between simulation and experiment in describing the energy landscape of protein folding
    • Ladurner A, Itzhaki L, Daggett V, Fersht A. Synergy between simulation and experiment in describing the energy landscape of protein folding. Proc Natl Acad Sci USA 1998;95:8473-8478.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 8473-8478
    • Ladurner, A.1    Itzhaki, L.2    Daggett, V.3    Fersht, A.4
  • 10
    • 0032516205 scopus 로고    scopus 로고
    • The molecular elasticity of tenascin, an extracellular matrix protein
    • Oberhauser AF, Marszalek PE, Erickson H, Fernandez J. The molecular elasticity of tenascin, an extracellular matrix protein. Nature 1998;393:181-185.
    • (1998) Nature , vol.393 , pp. 181-185
    • Oberhauser, A.F.1    Marszalek, P.E.2    Erickson, H.3    Fernandez, J.4
  • 11
    • 0031767965 scopus 로고    scopus 로고
    • The mechanical stability of immunoglobulin and fibronectin III domains in the muscle protein titin measured by AFM
    • Rief M, Gautel M, Schemmel A, Gaub H. The mechanical stability of immunoglobulin and fibronectin III domains in the muscle protein titin measured by AFM. Biophys J 1998;75:3008-3014.
    • (1998) Biophys J , vol.75 , pp. 3008-3014
    • Rief, M.1    Gautel, M.2    Schemmel, A.3    Gaub, H.4
  • 12
    • 0031011695 scopus 로고    scopus 로고
    • Reversible unfolding of individual titin immunoglobulin domains by AFM
    • Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 1997;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
  • 13
    • 0033573912 scopus 로고    scopus 로고
    • Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch
    • Krammer A, Lu H, Isralewitz B, Schulten K, Vogel V. Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch. Proc Natl Acad Sci USA 1999;96:1351-1356.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 1351-1356
    • Krammer, A.1    Lu, H.2    Isralewitz, B.3    Schulten, K.4    Vogel, V.5
  • 14
    • 0030982846 scopus 로고    scopus 로고
    • Connectin/titin, a giant elastic protein of muscle
    • Maruyama K. Connectin/titin, a giant elastic protein of muscle. FASEB J 1997;11:341-345.
    • (1997) FASEB J , vol.11 , pp. 341-345
    • Maruyama, K.1
  • 15
    • 0027172919 scopus 로고
    • Mechanotransduction across the cell surface and through the cytoskeleton
    • Wang N, Butler JP, Ingber DE. Mechanotransduction across the cell surface and through the cytoskeleton. Science 1993;260:1124-1127.
    • (1993) Science , vol.260 , pp. 1124-1127
    • Wang, N.1    Butler, J.P.2    Ingber, D.E.3
  • 16
    • 0032550178 scopus 로고    scopus 로고
    • Human autoantibodies reveal titin as a chromosomal protein
    • Machado C, Sunkel CE, Andrew DJ. Human autoantibodies reveal titin as a chromosomal protein. J Cell Biol 1998;141:321-333.
    • (1998) J Cell Biol , vol.141 , pp. 321-333
    • Machado, C.1    Sunkel, C.E.2    Andrew, D.J.3
  • 17
    • 0031002460 scopus 로고    scopus 로고
    • Folding-unfolding transition in single titin modules characterized with laser tweezers
    • Kellermayer M, Smith S, Granzier H, Bustamante C. Folding-unfolding transition in single titin modules characterized with laser tweezers. Science 1997;276:1112-1116.
    • (1997) Science , vol.276 , pp. 1112-1116
    • Kellermayer, M.1    Smith, S.2    Granzier, H.3    Bustamante, C.4
  • 18
    • 0031006659 scopus 로고    scopus 로고
    • Elasticity and unfolding of single molecules of the giant protein titin
    • Tskhovrebova L, Trinick J, Sleep JA, Simmons RM. Elasticity and unfolding of single molecules of the giant protein titin. Nature 1997;387:308-312.
    • (1997) Nature , vol.387 , pp. 308-312
    • Tskhovrebova, L.1    Trinick, J.2    Sleep, J.A.3    Simmons, R.M.4
  • 20
    • 0030378980 scopus 로고    scopus 로고
    • SMD: Visual steering of molecular dynamics for protein design
    • Leech J, Prins J, Hermans J. SMD: visual steering of molecular dynamics for protein design. IEEE Comp Sci Eng 1996;3:38-45.
    • (1996) IEEE Comp Sci Eng , vol.3 , pp. 38-45
    • Leech, J.1    Prins, J.2    Hermans, J.3
  • 21
    • 0030059225 scopus 로고    scopus 로고
    • Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force
    • Grubmüller H, Heymann B, Tavan P. Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force. Science 1996;271:997-999.
    • (1996) Science , vol.271 , pp. 997-999
    • Grubmüller, H.1    Heymann, B.2    Tavan, P.3
  • 22
    • 0030987036 scopus 로고    scopus 로고
    • Molecular dynamics study of unbinding of the avidin-biotin complex
    • Izrailev S, Stepaniants S, Balsera M, Oono Y, Schulten K. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J 1997;72:1568-1581.
    • (1997) Biophys J , vol.72 , pp. 1568-1581
    • Izrailev, S.1    Stepaniants, S.2    Balsera, M.3    Oono, Y.4    Schulten, K.5
  • 23
    • 0030834853 scopus 로고    scopus 로고
    • Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations
    • Isralewitz B, Izrailev S, Schulten K. Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations. Biophys J 1997;73:2972-2979.
    • (1997) Biophys J , vol.73 , pp. 2972-2979
    • Isralewitz, B.1    Izrailev, S.2    Schulten, K.3
  • 24
    • 0001068789 scopus 로고    scopus 로고
    • Extraction of lipids from phospholipid membranes by steered molecular dynamics
    • Stepaniants S, Izrailev S, Schulten K. Extraction of lipids from phospholipid membranes by steered molecular dynamics. J Mol Model 1997;3:473-475.
    • (1997) J Mol Model , vol.3 , pp. 473-475
    • Stepaniants, S.1    Izrailev, S.2    Schulten, K.3
  • 25
    • 0032906662 scopus 로고    scopus 로고
    • Unbinding of retinoic acid from its receptor studied by steered molecular dynamics
    • Kosztin D, Izrailev S, Schulten K. Unbinding of retinoic acid from its receptor studied by steered molecular dynamics. Biophys J 1999;76:188-197.
    • (1999) Biophys J , vol.76 , pp. 188-197
    • Kosztin, D.1    Izrailev, S.2    Schulten, K.3
  • 26
    • 0033136019 scopus 로고    scopus 로고
    • Investigating a back door mechanism of actin phosphate release by steered molecular dynamics
    • Wriggers W, Schulten K. Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Proteins 1999;35:262-273.
    • (1999) Proteins , vol.35 , pp. 262-273
    • Wriggers, W.1    Schulten, K.2
  • 27
    • 0031848099 scopus 로고    scopus 로고
    • Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
    • Lu H, Isralewitz B, Krammer A, Vogel V, Schulten K. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J 1998;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
  • 28
    • 0029980542 scopus 로고    scopus 로고
    • Structural basis of calcium-induced e-cadherin rigidification and dimerization
    • Nagar B, Overdulin M, Ikura M, Rini J. Structural basis of calcium-induced e-cadherin rigidification and dimerization. Nature 1996;380:360-364.
    • (1996) Nature , vol.380 , pp. 360-364
    • Nagar, B.1    Overdulin, M.2    Ikura, M.3    Rini, J.4
  • 29
    • 0029046132 scopus 로고
    • The crystal structure of an n-terminal two-domain fragment of vascular cell adhesion molecule 1 (vcam-1)
    • Wang JH, Pepinsky RB, Stehle T, et al. The crystal structure of an n-terminal two-domain fragment of vascular cell adhesion molecule 1 (vcam-1). Proc Natl Acad Sci USA 1995;92:5714-5718.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 5714-5718
    • Wang, J.H.1    Pepinsky, R.B.2    Stehle, T.3
  • 30
    • 0030050396 scopus 로고    scopus 로고
    • 2.0 angstroms crystal structure of a four-domain segment of human fibronectin encompassing the rgd loop and synergy region
    • Leahy DJ, Aukhil I, Erickson HP. 2.0 angstroms crystal structure of a four-domain segment of human fibronectin encompassing the rgd loop and synergy region. Cell 1996;84:155-164.
    • (1996) Cell , vol.84 , pp. 155-164
    • Leahy, D.J.1    Aukhil, I.2    Erickson, H.P.3
  • 31
    • 0029154240 scopus 로고    scopus 로고
    • The structure of chloroplast cytochrome c6 at 1.9 angstroms resolution: Evidence for functional oligomerization
    • Kerfeld C, Anwar H, Interrante R, Merchant S, Yeates T. The structure of chloroplast cytochrome c6 at 1.9 angstroms resolution: evidence for functional oligomerization. J Mol Biol 1996;250: 627.
    • (1996) J Mol Biol , vol.250 , pp. 627
    • Kerfeld, C.1    Anwar, H.2    Interrante, R.3    Merchant, S.4    Yeates, T.5
  • 32
    • 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 1992;31:9665-9672.
    • (1992) Biochemistry , vol.31 , pp. 9665-9672
    • Gouda, H.1    Torigoe, H.2    Saito, A.3    Sato, M.4    Arata, Y.5    Shimada, I.6
  • 33
    • 0028986240 scopus 로고
    • Structure of the first C2 domain of synaptotagmin I: A novel Ca2+/phospholipid-binding fold
    • Brayn Sutton R, Davletov RA, Berghuis AM, Sudhof TC, Sprang SR. Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold. Cell 1995;80:929-938.
    • (1995) Cell , vol.80 , pp. 929-938
    • Brayn Sutton, R.1    Davletov, R.A.2    Berghuis, A.M.3    Sudhof, T.C.4    Sprang, S.R.5
  • 34
    • 0017411710 scopus 로고
    • The Protein Data Bank: A computer-based archival file for macromolecular structures
    • Bernstein FC, Koetzle TF, Williams GJ, et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
    • (1977) J Mol Biol , vol.112 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.3
  • 35
    • 8344276781 scopus 로고    scopus 로고
    • NAMD - A parallel, object-oriented molecular dynamics program
    • Nelson M, Humphrey W, Gursoy A, et al. NAMD - A parallel, object-oriented molecular dynamics program. J Supercomputing App 1996;10:251-268.
    • (1996) J Supercomputing App , vol.10 , pp. 251-268
    • Nelson, M.1    Humphrey, W.2    Gursoy, A.3
  • 36
    • 0003769049 scopus 로고
    • New Haven: The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University
    • Brünger AT. X-PLOR, Version 3.1: a system for x-ray crystallography and NMR. New Haven: The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University; 1992.
    • (1992) X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR
    • Brünger, A.T.1
  • 37
    • 0041784950 scopus 로고    scopus 로고
    • All-hydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field
    • MacKerell Jr AD, Bashford D, Bellott M, et al. All-hydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field. J Phys Chem B 1998;102:3586-3616.
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell A.D., Jr.1    Bashford, D.2    Bellott, M.3
  • 38
    • 0030584660 scopus 로고    scopus 로고
    • Immunoglobulin-like modules from titin I-band: Extensible components of muscle elasticity
    • Improta S, Politou A, Pastore A. Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity. Structure 1996;4:323-337.
    • (1996) Structure , vol.4 , pp. 323-337
    • Improta, S.1    Politou, A.2    Pastore, A.3
  • 40
    • 0032508555 scopus 로고    scopus 로고
    • The dependence of chemical exchange on boundary selection in a fibronectin type III domain from human tenascin
    • Meekhof A, Hamill S, Arcus V, Clarke J, Freund S. The dependence of chemical exchange on boundary selection in a fibronectin type III domain from human tenascin. J Mol Biol 1998;282:181-194.
    • (1998) J Mol Biol , vol.282 , pp. 181-194
    • Meekhof, A.1    Hamill, S.2    Arcus, V.3    Clarke, J.4    Freund, S.5
  • 41
    • 0030962748 scopus 로고    scopus 로고
    • Stretching single protein modules: Titin is a weird spring
    • Erickson H. Stretching single protein modules: titin is a weird spring. Science 1997;276:1090-1093.
    • (1997) Science , vol.276 , pp. 1090-1093
    • Erickson, H.1
  • 42
    • 0033445338 scopus 로고    scopus 로고
    • Steered molecular dynamics simulation of conformational changes of immunoglobulin domain 127 interprete atomic force microscopy observations
    • In press
    • Lu H, Schulten K. Steered molecular dynamics simulation of conformational changes of immunoglobulin domain 127 interprete atomic force microscopy observations. Chem Phys 1999: In press.
    • (1999) Chem Phys
    • Lu, H.1    Schulten, K.2
  • 43
    • 0004043397 scopus 로고
    • New York: Springer-Verlag
    • Hynes RO. Fibronectins. New York: Springer-Verlag; 1990.
    • (1990) Fibronectins
    • Hynes, R.O.1
  • 44
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1 microsecond simulation in aqueous solution
    • Duan Y, Kollman P. 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.2
  • 45
    • 0042852135 scopus 로고    scopus 로고
    • Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations
    • In press
    • Gullingsrud J, Braun R, Schulten K. Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. J Comp Phys Special Issue on Computational Biophysics, 1999. In press.
    • (1999) J Comp Phys Special Issue on Computational Biophysics
    • Gullingsrud, J.1    Braun, R.2    Schulten, K.3


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