메뉴 건너뛰기




Volumn 85, Issue 1, 2003, Pages 27-35

Simulation of F-actin filaments of several microns

Author keywords

[No Author keywords available]

Indexed keywords

F ACTIN; PROTEIN SUBUNIT;

EID: 0037636333     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74451-8     Document Type: Article
Times cited : (27)

References (57)
  • 3
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-181.
    • (1997) Fold. Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 4
    • 0028905547 scopus 로고
    • Dynamic and elastic properties of F-actin: A normal-modes analysis
    • ben-Avraham, D., and M. M. Tirion. 1995. Dynamic and elastic properties of F-actin: a normal-modes analysis. Biophys. J. 68:1231-1245.
    • (1995) Biophys. J. , vol.68 , pp. 1231-1245
    • Ben-Avraham, D.1    Tirion, M.M.2
  • 5
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks, B. R., D. Janezic, and M. Karplus. 1995. Harmonic analysis of large systems. I. Methodology. J. Comp. Chem. 16:1522-1542.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 6
    • 0001031179 scopus 로고
    • Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
    • Brooks III, C. L., M. Karplus, and B. M. Pettitt. 1988. Proteins: a theoretical perspective of dynamics, structure, and thermodynamics. Adv. Chem. Phys. 71:1-249.
    • (1988) Adv. Chem. Phys. , vol.71 , pp. 1-249
    • Brooks C.L. III1    Karplus, M.2    Pettitt, B.M.3
  • 7
    • 0037436340 scopus 로고    scopus 로고
    • Mega-dalton biomolecular motion captured from electron microscopy reconstructions
    • Chacon, P., F. Tama, and W. Wriggers. 2003. Mega-dalton biomolecular motion captured from electron microscopy reconstructions. J. Mol. Biol. 326:485-492.
    • (2003) J. Mol. Biol. , vol.326 , pp. 485-492
    • Chacon, P.1    Tama, F.2    Wriggers, W.3
  • 8
    • 0033977699 scopus 로고    scopus 로고
    • Regulating actin-filament dynamics in vivo
    • Chen, H., B. W. Bernstein, and J. R. Bamburg. 2000. Regulating actin-filament dynamics in vivo. TIBS. 25:19-23.
    • (2000) TIBS , vol.25 , pp. 19-23
    • Chen, H.1    Bernstein, B.W.2    Bamburg, J.R.3
  • 9
    • 0037079578 scopus 로고    scopus 로고
    • Dynamic of large proteins through hierarchical levels of coarse-grained structures
    • Doruker, P., R. L. Jernigan, and I. Bahar. 2002. Dynamic of large proteins through hierarchical levels of coarse-grained structures. J. Comp. Chem. 23:119-127.
    • (2002) J. Comp. Chem. , vol.23 , pp. 119-127
    • Doruker, P.1    Jernigan, R.L.2    Bahar, I.3
  • 11
    • 0034870406 scopus 로고    scopus 로고
    • Actin allostery again?
    • Egelman, E. H. 2001. Actin allostery again? Nat. Struct. Biol. 8:735-736.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 735-736
    • Egelman, E.H.1
  • 12
    • 0020477574 scopus 로고
    • F-actin is a helix with a random variable twist
    • Egelman, E. H., N. Francis, and D. J. DeRosier. 1982. F-actin is a helix with a random variable twist. Nature. 298:131-135.
    • (1982) Nature , vol.298 , pp. 131-135
    • Egelman, E.H.1    Francis, N.2    DeRosier, D.J.3
  • 13
    • 0028988935 scopus 로고
    • New insights into actin filament dynamics
    • Egelman, E. H., and A. Orlova. 1995. New insights into actin filament dynamics. Curr. Opin. Struct. Biol. 5:172-180.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 172-180
    • Egelman, E.H.1    Orlova, A.2
  • 14
    • 0037006805 scopus 로고    scopus 로고
    • A new internal mode in F-actin helps explain the remarkable evolutionary conservation of actin's sequence and structure
    • Galkin, V. E., M. S. VanLoock, A. Orlova, and E. H. Egelman. 2002. A new internal mode in F-actin helps explain the remarkable evolutionary conservation of actin's sequence and structure. Curr. Biol. 12:570-575.
    • (2002) Curr. Biol. , vol.12 , pp. 570-575
    • Galkin, V.E.1    VanLoock, M.S.2    Orlova, A.3    Egelman, E.H.4
  • 15
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • Go, N., T. Noguti, and T. Nishikawa. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA. 80:3696-3700.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 16
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen, K. 1998. Analysis of domain motions by approximate normal mode calculations. Proteins. 33:417-429.
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 17
  • 18
    • 0027496917 scopus 로고
    • A comparison of the atomic model of F-actin with cryo-electron micrographs of actin and decorated actin
    • Holmes, K. C., M. Tirion, D. Popp, M. Lorenz, W. Kabsch, and R. A. Milligan. 1993. A comparison of the atomic model of F-actin with cryo-electron micrographs of actin and decorated actin. Adv. Exp. Med. Biol. 332:15-22.
    • (1993) Adv. Exp. Med. Biol. , vol.332 , pp. 15-22
    • Holmes, K.C.1    Tirion, M.2    Popp, D.3    Lorenz, M.4    Kabsch, W.5    Milligan, R.A.6
  • 19
    • 0028081493 scopus 로고
    • X-ray diffraction measurements of the extensibility of actin and myosin filaments in contracting muscle
    • Huxley, H. E., A. Stewart, H. Sosa, and T. Irving. 1994. X-ray diffraction measurements of the extensibility of actin and myosin filaments in contracting muscle. Biophys. J. 67:2411-2421.
    • (1994) Biophys. J. , vol.67 , pp. 2411-2421
    • Huxley, H.E.1    Stewart, A.2    Sosa, H.3    Irving, T.4
  • 20
    • 84986473952 scopus 로고
    • Harmonic analysis of large systems. III. Comparison with molecular dynamics
    • Janezic, D., R. M. Venable, and B. R. Brooks. 1995. Harmonic analysis of large systems. III. Comparison with molecular dynamics. J. Comp. Chem. 16:1554-1566.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1554-1566
    • Janezic, D.1    Venable, R.M.2    Brooks, B.R.3
  • 23
    • 0028607563 scopus 로고
    • Direct measurement of stiffness of single actin filaments with and without tropomyosin by in vitro nanomanipulation
    • Kojima, H., A. Ishijima, and T. Yanagida. 1994. Direct measurement of stiffness of single actin filaments with and without tropomyosin by in vitro nanomanipulation. Proc. Natl. Acad. Sci. USA. 91:12962-12966.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12962-12966
    • Kojima, H.1    Ishijima, A.2    Yanagida, T.3
  • 24
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 25
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt, M., C. Sander, and P. S. Stem. 1985. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181:423-447.
    • (1985) J. Mol. Biol. , vol.181 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stem, P.S.3
  • 27
    • 0036841235 scopus 로고    scopus 로고
    • Mechanics of F-actin characterized with microfabricated cantilevers
    • Liu, X., and G. H. Pollack. 2002. Mechanics of F-actin characterized with microfabricated cantilevers. Biophys. J. 83:2705-2715.
    • (2002) Biophys. J. , vol.83 , pp. 2705-2715
    • Liu, X.1    Pollack, G.H.2
  • 28
    • 0028940312 scopus 로고
    • An atomic model of the unregulated thin filament obtained by x-ray fiber diffraction on oriented actin-tropomyosin gels
    • Lorenz, M., K. J. Poole, D. Popp, G. Rosenbaum, and K. C. Holmes. 1995. An atomic model of the unregulated thin filament obtained by x-ray fiber diffraction on oriented actin-tropomyosin gels. J. Mol. Biol. 246:108-119.
    • (1995) J. Mol. Biol. , vol.246 , pp. 108-119
    • Lorenz, M.1    Poole, K.J.2    Popp, D.3    Rosenbaum, G.4    Holmes, K.C.5
  • 29
    • 0027131941 scopus 로고
    • Refinement of the F-actin model against x-ray fiber diffraction data by the use of a directed mutation algorithm
    • Lorenz, M., D. Popp, and K. C. Holmes. 1993. Refinement of the F-actin model against x-ray fiber diffraction data by the use of a directed mutation algorithm. J. Mol. Biol. 234:826-836.
    • (1993) J. Mol. Biol. , vol.234 , pp. 826-836
    • Lorenz, M.1    Popp, D.2    Holmes, K.C.3
  • 30
    • 0030700726 scopus 로고    scopus 로고
    • Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis
    • Ma, J., and M. Karplus. 1997. Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. J. Mol. Biol. 274:114-131.
    • (1997) J. Mol. Biol. , vol.274 , pp. 114-131
    • Ma, J.1    Karplus, M.2
  • 31
    • 0032555216 scopus 로고    scopus 로고
    • The allosteric mechanism of the chaperonin GroEL: A dynamic analysis
    • Ma, J., and M. Karplus. 1998. The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proc. Natl. Acad. Sci. USA. 95:8502-8507.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 8502-8507
    • Ma, J.1    Karplus, M.2
  • 33
    • 0027251071 scopus 로고
    • Structure of gelsolin segment 1-actin complex and the mechanism of filament severing
    • McLaughlin, P. J., J. T. Gooch, H. G. Mannherz, and A. G. Weeds. 1993. Structure of gelsolin segment 1-actin complex and the mechanism of filament severing. Nature. 364:685-692.
    • (1993) Nature , vol.364 , pp. 685-692
    • McLaughlin, P.J.1    Gooch, J.T.2    Mannherz, H.G.3    Weeds, A.G.4
  • 36
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino-acid sequence and atomic coordinates
    • Ming, D., Y. Kong, M. Lambert, Z. Huang, and J. Ma. 2002a. How to describe protein motion without amino-acid sequence and atomic coordinates. Proc. Natl. Acad. Sci. USA. 99:8620-8625.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 8620-8625
    • Ming, D.1    Kong, Y.2    Lambert, M.3    Huang, Z.4    Ma, J.5
  • 37
    • 0037062479 scopus 로고    scopus 로고
    • Domain movements in human fatty acid synthase by quantized elastic deformational model
    • Ming, D., Y. Kong, S. J. Wakil, J. Brink, and J. Ma. 2002b. Domain movements in human fatty acid synthase by quantized elastic deformational model. Proc. Natl. Acad. Sci. USA. 99:7895-7899.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 7895-7899
    • Ming, D.1    Kong, Y.2    Wakil, S.J.3    Brink, J.4    Ma, J.5
  • 38
    • 0037422581 scopus 로고    scopus 로고
    • Substructure synthesis method for simulating large molecular complexes
    • Ming, D., Y. Kong, Y. Wu, and J. Ma. 2003. Substructure synthesis method for simulating large molecular complexes. Proc. Natl. Acad. Sci. USA. 100:104-109.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 104-109
    • Ming, D.1    Kong, Y.2    Wu, Y.3    Ma, J.4
  • 39
    • 0035143042 scopus 로고    scopus 로고
    • Distinct structural changes detected by x-ray fiber diffraction in stabilization of F-actin by lowering pH and increasing ionic strength
    • Oda, T., K. Makino, I. Yamashita, K. Namba, and Y. Maeda. 2001. Distinct structural changes detected by x-ray fiber diffraction in stabilization of F-actin by lowering pH and increasing ionic strength. Biophys. J. 80:841-851.
    • (2001) Biophys. J. , vol.80 , pp. 841-851
    • Oda, T.1    Makino, K.2    Yamashita, I.3    Namba, K.4    Maeda, Y.5
  • 40
    • 0019023530 scopus 로고
    • The flexibility of F-actin
    • Oosawa, F. 1980. The flexibility of F-actin. Biophys. Chem. 11:443-446.
    • (1980) Biophys. Chem. , vol.11 , pp. 443-446
    • Oosawa, F.1
  • 41
  • 42
    • 0035958757 scopus 로고    scopus 로고
    • The crystal structure of uncomplexed actin in the ADP state
    • Otterbein, L. R., P. Graceffa, and R. Dominguez. 2001. The crystal structure of uncomplexed actin in the ADP state. Science. 293:708-711.
    • (2001) Science , vol.293 , pp. 708-711
    • Otterbein, L.R.1    Graceffa, P.2    Dominguez, R.3
  • 45
    • 0025163070 scopus 로고
    • Deoxymyoglobin studied by the conformational normal mode analysis. II. The conformational change upon oxygenation
    • Seno, Y., and N. Go. 1990. Deoxymyoglobin studied by the conformational normal mode analysis. II. The conformational change upon oxygenation. J. Mol. Biol. 216:111-126.
    • (1990) J. Mol. Biol. , vol.216 , pp. 111-126
    • Seno, Y.1    Go, N.2
  • 46
    • 0026650567 scopus 로고
    • Normal modes of symmetric protein assemblies. Application to the tobacco mosaic virus protein disk
    • Simonson, T., and D. Perahia. 1992. Normal modes of symmetric protein assemblies. Application to the tobacco mosaic virus protein disk. Biophys. J. 61:410-427.
    • (1992) Biophys. J. , vol.61 , pp. 410-427
    • Simonson, T.1    Perahia, D.2
  • 47
    • 0036307741 scopus 로고    scopus 로고
    • The mechanism and pathway of pH-induced swelling in Cowpea Chlorotic Mottle virus
    • Tama, F., and C. L. Brooks III. 2002. The mechanism and pathway of pH-induced swelling in Cowpea Chlorotic Mottle virus. J. Mol. Biol. 318:733-747.
    • (2002) J. Mol. Biol. , vol.318 , pp. 733-747
    • Tama, F.1    Brooks C.L. III2
  • 48
    • 0034308140 scopus 로고    scopus 로고
    • Building-block approach for determining low-frequency normal modes of macromolecules
    • Tama, F., F. X. Gadea, O. Marques, and Y. H. Sanejouand. 2000. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins. 41:1-7.
    • (2000) Proteins , vol.41 , pp. 1-7
    • Tama, F.1    Gadea, F.X.2    Marques, O.3    Sanejouand, Y.H.4
  • 49
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama, F., and Y. H. Sanejouand. 2001. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:1-6.
    • (2001) Protein Eng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 50
    • 0036382958 scopus 로고    scopus 로고
    • Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
    • Tama, F., W. Wriggers, and C. L. Brooks. 2002. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol. 321:297-305.
    • (2002) J. Mol. Biol. , vol.321 , pp. 297-305
    • Tama, F.1    Wriggers, W.2    Brooks, C.L.3
  • 52
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 53
    • 0028861589 scopus 로고
    • Normal modes as refinement parameters for the F-actin model
    • Tirion, M. M., D. ben-Avraham, M. Lorenz, and K. C. Holmes. 1995. Normal modes as refinement parameters for the F-actin model. Biophys. J. 681:5-12.
    • (1995) Biophys. J. , vol.681 , pp. 5-12
    • Tirion, M.M.1    Ben-Avraham, D.2    Lorenz, M.3    Holmes, K.C.4
  • 54
    • 0029822651 scopus 로고    scopus 로고
    • Torsional rigidity of single actin filaments and actin-actin bond breaking force under torsion measured directly by in vitro micromanipulation
    • Tsuda, Y., H. Yasutake, A. Ishijima, and T. Yanagida. 1996. Torsional rigidity of single actin filaments and actin-actin bond breaking force under torsion measured directly by in vitro micromanipulation. Proc. Natl. Acad. Sci. USA. 93:12937-12942.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 12937-12942
    • Tsuda, Y.1    Yasutake, H.2    Ishijima, A.3    Yanagida, T.4
  • 56
    • 0028081494 scopus 로고
    • X-ray diffraction evidence for the extensibility of actin and myosin filaments during muscle contraction
    • Wakabayashi, K., Y. Sugimoto, H. Tanaka, Y. Ueno, Y. Takezawa, and Y. Amemiya. 1994. X-ray diffraction evidence for the extensibility of actin and myosin filaments during muscle contraction. Biophys. J. 67:2422-2435.
    • (1994) Biophys. J. , vol.67 , pp. 2422-2435
    • Wakabayashi, K.1    Sugimoto, Y.2    Tanaka, H.3    Ueno, Y.4    Takezawa, Y.5    Amemiya, Y.6
  • 57
    • 0030601791 scopus 로고    scopus 로고
    • Direct measurement of the torsional rigidity of single actin filaments
    • Yasuda, R., H. Miyata, and K. Kinosita, Jr. 1996. Direct measurement of the torsional rigidity of single actin filaments. J. Mol. Biol. 263:227-236.
    • (1996) J. Mol. Biol. , vol.263 , pp. 227-236
    • Yasuda, R.1    Miyata, H.2    Kinosita K., Jr.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.