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Volumn 44, Issue 4, 2011, Pages 630-636

Biomechanics of actin filaments: A computational multi-level study

Author keywords

Actin; Bending; Biomechanics; Biopolymer; Coarse grain; Cytoskeleton; Elastic modulus; Elastic network; Fluctuations; Mechanical properties; Mechanics; Molecular dynamics; Normal mode analysis; Persistence length; Stiffness; Stretching; Torsion

Indexed keywords

ACTIN; BENDING; COARSE GRAINS; CYTOSKELETONS; ELASTIC NETWORK; FLUCTUATIONS; NORMAL MODE ANALYSIS; PERSISTENCE LENGTH; TORSION;

EID: 79951720598     PISSN: 00219290     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiomech.2010.11.014     Document Type: Article
Times cited : (36)

References (65)
  • 1
    • 36749062973 scopus 로고    scopus 로고
    • Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains
    • Ackbarow T., Chen X., Keten S., Buehler M.J. Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains. Proc. Natl. Acad. Sci. USA 2007, 104:16410-16415.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 16410-16415
    • Ackbarow, T.1    Chen, X.2    Keten, S.3    Buehler, M.J.4
  • 2
    • 33845381177 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum
    • Arkhipov A., Freddolino P.L., Imada K., Namba K., Schulten K. Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophys. J. 2006, 91:4589-4597.
    • (2006) Biophys. J. , vol.91 , pp. 4589-4597
    • Arkhipov, A.1    Freddolino, P.L.2    Imada, K.3    Namba, K.4    Schulten, K.5
  • 5
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I., Atilgan A.R., Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des. 1997, 2:173-181.
    • (1997) Fold Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 6
    • 25844431698 scopus 로고    scopus 로고
    • Coarse-grained normal mode analysis in structural biology
    • Bahar I., Rader A.J. Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol. 2005, 15:586-592.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 586-592
    • Bahar, I.1    Rader, A.J.2
  • 7
    • 0028905547 scopus 로고
    • Dynamic and elastic properties of F-actin: a normal-modes analysis
    • ben-Avraham D., Tirion M.M. Dynamic and elastic properties of F-actin: a normal-modes analysis. Biophys. J. 1995, 68:1231-1245.
    • (1995) Biophys. J. , vol.68 , pp. 1231-1245
    • ben-Avraham, D.1    Tirion, M.M.2
  • 9
    • 33847242278 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of membrane proteins and peptides
    • Bond P.J., Holyoake J., Ivetac A., Khalid S., Sansom M.S. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J. Struct. Biol. 2007, 157:593-605.
    • (2007) J. Struct. Biol. , vol.157 , pp. 593-605
    • Bond, P.J.1    Holyoake, J.2    Ivetac, A.3    Khalid, S.4    Sansom, M.S.5
  • 11
    • 33744940504 scopus 로고    scopus 로고
    • Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model
    • Chang C.E., Shen T., Trylska J., Tozzini V., McCammon J.A. Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys. J. 2006, 90:3880-3885.
    • (2006) Biophys. J. , vol.90 , pp. 3880-3885
    • Chang, C.E.1    Shen, T.2    Trylska, J.3    Tozzini, V.4    McCammon, J.A.5
  • 12
    • 25844440811 scopus 로고    scopus 로고
    • Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies
    • Chennubhotla C., Rader A.J., Yang L.W., Bahar I. Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies. Phys. Biol. 2005, 2:S173-S180.
    • (2005) Phys. Biol. , vol.2
    • Chennubhotla, C.1    Rader, A.J.2    Yang, L.W.3    Bahar, I.4
  • 13
    • 73949129925 scopus 로고    scopus 로고
    • Coarse-grained models reveal functional dynamics - II. molecular dynamics simulation at the coarse-grained level - theories and biological applications
    • Chng C.-P., Yang L.-W. Coarse-grained models reveal functional dynamics - II. molecular dynamics simulation at the coarse-grained level - theories and biological applications. Bioinform. Biol. Insights 2008, 2008.
    • (2008) Bioinform. Biol. Insights , vol.2008
    • Chng, C.-P.1    Yang, L.-W.2
  • 14
    • 33746606875 scopus 로고    scopus 로고
    • The multiscale challenge for biomolecular systems: coarse-grained modeling
    • Chu J.W., Izveko S., Voth G.A. The multiscale challenge for biomolecular systems: coarse-grained modeling. Mol. Simulation 2006, 32:211-218.
    • (2006) Mol. Simulation , vol.32 , pp. 211-218
    • Chu, J.W.1    Izveko, S.2    Voth, G.A.3
  • 15
    • 24944541377 scopus 로고    scopus 로고
    • Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis
    • Chu J.W., Voth G.A. Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. Proc. Natl. Acad. Sci. USA 2005, 102:13111-13116.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 13111-13116
    • Chu, J.W.1    Voth, G.A.2
  • 16
    • 33646123091 scopus 로고    scopus 로고
    • Coarse-grained modeling of the actin filament derived from atomistic-scale simulations
    • Chu J.W., Voth G.A. Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys. J. 2006, 90:1572-1582.
    • (2006) Biophys. J. , vol.90 , pp. 1572-1582
    • Chu, J.W.1    Voth, G.A.2
  • 17
    • 36849057606 scopus 로고    scopus 로고
    • Coarse-grained free energy functions for studying protein conformational changes: a double-well network model
    • Chu J.W., Voth G.A. Coarse-grained free energy functions for studying protein conformational changes: a double-well network model. Biophys. J. 2007, 93:3860-3871.
    • (2007) Biophys. J. , vol.93 , pp. 3860-3871
    • Chu, J.W.1    Voth, G.A.2
  • 20
    • 77958497931 scopus 로고    scopus 로고
    • b. Anisotropic elastic network modeling of entire microtubules. Biophys. J. 99
    • Deriu, M.A., Soncini, M., Orsi, M., Patel, M., Essex, J.W., Montevecchi, F.M., Redaelli, A., 2010b. Anisotropic elastic network modeling of entire microtubules. Biophys. J. 99 (7), 2190-2199.
    • (2010) , Issue.7 , pp. 2190-2199
    • Deriu, M.A.1    Soncini, M.2    Orsi, M.3    Patel, M.4    Essex, J.W.5    Montevecchi, F.M.6    Redaelli, A.7
  • 21
    • 0034663710 scopus 로고    scopus 로고
    • Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor
    • Doruker P., Atilgan A.R., Bahar I. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor. Proteins 2000, 40:512-524.
    • (2000) Proteins , vol.40 , pp. 512-524
    • Doruker, P.1    Atilgan, A.R.2    Bahar, I.3
  • 22
    • 0015243824 scopus 로고
    • Dynamic study of F-actin by quasielastic scattering of laser light
    • Fujime S., Ishiwata S. Dynamic study of F-actin by quasielastic scattering of laser light. J. Mol. Biol. 1971, 62:251-265.
    • (1971) J. Mol. Biol. , vol.62 , pp. 251-265
    • Fujime, S.1    Ishiwata, S.2
  • 24
    • 68949144886 scopus 로고    scopus 로고
    • Molecular and mesoscale mechanisms of osteogenesis imperfecta disease in collagen fibrils
    • Gautieri A., Uzel S., Vesentini S., Redaelli A., Buehler M.J. Molecular and mesoscale mechanisms of osteogenesis imperfecta disease in collagen fibrils. Biophys. J. 2009, 97:857-865.
    • (2009) Biophys. J. , vol.97 , pp. 857-865
    • Gautieri, A.1    Uzel, S.2    Vesentini, S.3    Redaelli, A.4    Buehler, M.J.5
  • 25
    • 0027533269 scopus 로고
    • Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape
    • Gittes F., Mickey B., Nettleton J., Howard J. Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape. J. Cell Biol. 1993, 120:923-934.
    • (1993) J. Cell Biol. , vol.120 , pp. 923-934
    • Gittes, F.1    Mickey, B.2    Nettleton, J.3    Howard, J.4
  • 26
    • 33244462037 scopus 로고    scopus 로고
    • Dynamics of membranes driven by actin polymerization
    • Gov N.S., Gopinathan A. Dynamics of membranes driven by actin polymerization. Biophys. J. 2006, 90:454-469.
    • (2006) Biophys. J. , vol.90 , pp. 454-469
    • Gov, N.S.1    Gopinathan, A.2
  • 27
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B., Kutzner C., van der Spoel D., Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory. Comput. 2008, 4:435-447.
    • (2008) J. Chem. Theory. Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    van der Spoel, D.3    Lindahl, E.4
  • 28
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998, 33:417-429.
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 30
    • 79951725774 scopus 로고    scopus 로고
    • Mechanics of Motor Proteins and The Cyto-Skeleton. Sinauer, Sunderland
    • Howard, J., 2001. Mechanics of Motor Proteins and The Cyto-Skeleton. Sinauer, Sunderland, pp. 119-134.
    • (2001) , pp. 119-134
    • Howard, J.1
  • 31
    • 0029046139 scopus 로고
    • Flexibility of actin filaments derived from thermal fluctuations. effect of bound nucleotide, phalloidin, and muscle regulatory proteins
    • Isambert H., Venier P., Maggs A.C., Fattoum A., Kassab R., Pantaloni D., Carlier M.F. Flexibility of actin filaments derived from thermal fluctuations. effect of bound nucleotide, phalloidin, and muscle regulatory proteins. J. Biol. Chem. 1995, 270:11437-11444.
    • (1995) J. Biol. Chem. , vol.270 , pp. 11437-11444
    • Isambert, H.1    Venier, P.2    Maggs, A.C.3    Fattoum, A.4    Kassab, R.5    Pantaloni, D.6    Carlier, M.F.7
  • 33
    • 52149113093 scopus 로고    scopus 로고
    • Protrusion of a virtual model lamellipodium by actin polymerization: a coarse-grained langevin dynamics model. J. Stat. Phys. 133
    • Jeon, J., Alexander, N., Weaver, A., Cummings, P., 2008. Protrusion of a virtual model lamellipodium by actin polymerization: a coarse-grained langevin dynamics model. J. Stat. Phys. 133, 79-100.
    • (2008) , pp. 79-100
    • Jeon, J.1    Alexander, N.2    Weaver, A.3    Cummings, P.4
  • 36
    • 0028607563 scopus 로고
    • Direct measurement of stiffness of single actin filaments with and without tropomyosin by in vitro nanomanipulation
    • Kojima H., Ishijima A., Yanagida T. Direct measurement of stiffness of single actin filaments with and without tropomyosin by in vitro nanomanipulation. Proc. Natl. Acad. Sci. USA 1994, 91:12962-12966.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12962-12966
    • Kojima, H.1    Ishijima, A.2    Yanagida, T.3
  • 38
    • 0030339738 scopus 로고    scopus 로고
    • AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
    • Laskowski R.A., Rullmannn J.A., MacArthur M.W., Kaptein R., Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 1996, 8:477-486.
    • (1996) J. Biomol. NMR , vol.8 , pp. 477-486
    • Laskowski, R.A.1    Rullmannn, J.A.2    MacArthur, M.W.3    Kaptein, R.4    Thornton, J.M.5
  • 39
    • 0036841235 scopus 로고    scopus 로고
    • Mechanics of F-actin characterized with microfabricated cantilevers
    • Liu X., Pollack G.H. Mechanics of F-actin characterized with microfabricated cantilevers. Biophys. J. 2002, 83:2705-2715.
    • (2002) Biophys. J. , vol.83 , pp. 2705-2715
    • Liu, X.1    Pollack, G.H.2
  • 40
    • 58149161251 scopus 로고    scopus 로고
    • Systematic multiscale parameterization of heterogeneous elastic network models of proteins
    • Lyman E., Pfaendtner J., Voth G.A. Systematic multiscale parameterization of heterogeneous elastic network models of proteins. Biophys. J. 2008, 95:4183-4192.
    • (2008) Biophys. J. , vol.95 , pp. 4183-4192
    • Lyman, E.1    Pfaendtner, J.2    Voth, G.A.3
  • 41
    • 48049098171 scopus 로고    scopus 로고
    • Cofilin increases the bending flexibility of actin filaments: implications for severing and cell mechanics
    • McCullough B.R., Blanchoin L., Martiel J.L., De la Cruz E.M. Cofilin increases the bending flexibility of actin filaments: implications for severing and cell mechanics. J. Mol. Biol. 2008, 381:550-558.
    • (2008) J. Mol. Biol. , vol.381 , pp. 550-558
    • McCullough, B.R.1    Blanchoin, L.2    Martiel, J.L.3    De la Cruz, E.M.4
  • 42
    • 58749091822 scopus 로고    scopus 로고
    • The nature of the globular- to fibrous-actin transition
    • Oda T., Iwasa M., Aihara T., Maeda Y., Narita A. The nature of the globular- to fibrous-actin transition. Nature 2009, 457:441-445.
    • (2009) Nature , vol.457 , pp. 441-445
    • Oda, T.1    Iwasa, M.2    Aihara, T.3    Maeda, Y.4    Narita, A.5
  • 44
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6
    • Oostenbrink C., Villa A., Mark A.E., van Gunsteren W.F. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 2004, 25:1656-1676.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    van Gunsteren, W.F.4
  • 47
    • 0035958757 scopus 로고    scopus 로고
    • The crystal structure of uncomplexed actin in the ADP state
    • Otterbein L.R., Graceffa P., Dominguez R. The crystal structure of uncomplexed actin in the ADP state. Science 2001, 293:708-711.
    • (2001) Science , vol.293 , pp. 708-711
    • Otterbein, L.R.1    Graceffa, P.2    Dominguez, R.3
  • 48
    • 0034866072 scopus 로고    scopus 로고
    • Viscoelastic dynamics of actin filaments coupled to rotary F-ATPase: angular torque profile of the enzyme
    • Panke O., Cherepanov D.A., Gumbiowski K., Engelbrecht S., Junge W. Viscoelastic dynamics of actin filaments coupled to rotary F-ATPase: angular torque profile of the enzyme. Biophys. J. 2001, 81:1220-1233.
    • (2001) Biophys. J. , vol.81 , pp. 1220-1233
    • Panke, O.1    Cherepanov, D.A.2    Gumbiowski, K.3    Engelbrecht, S.4    Junge, W.5
  • 50
    • 0028454915 scopus 로고
    • A new approach for determining low-frequency normal modes in macromolecules
    • Durand Philippe, Trinquier Georges, Sanejouand Yves-Henri A new approach for determining low-frequency normal modes in macromolecules. Biopolymers 1994, 34:759-771.
    • (1994) Biopolymers , vol.34 , pp. 759-771
    • Durand, P.1    Trinquier, G.2    Sanejouand, Y.-H.3
  • 52
    • 72449133271 scopus 로고    scopus 로고
    • A multi-scale approach to understand the mechanobiology of intermediate filaments
    • Qin Z., Buehler M.J., Kreplak L. A multi-scale approach to understand the mechanobiology of intermediate filaments. J. Biomech. 2010, 43:15-22.
    • (2010) J. Biomech. , vol.43 , pp. 15-22
    • Qin, Z.1    Buehler, M.J.2    Kreplak, L.3
  • 53
    • 0028811138 scopus 로고
    • Mg- and Ca-actin filaments appear virtually identical in steady-state as determined by dynamic light scattering
    • Scharf R.E., Newman J. Mg- and Ca-actin filaments appear virtually identical in steady-state as determined by dynamic light scattering. Biochim. Biophys. Acta 1995, 1253:129-132.
    • (1995) Biochim. Biophys. Acta , vol.1253 , pp. 129-132
    • Scharf, R.E.1    Newman, J.2
  • 55
    • 0034308140 scopus 로고    scopus 로고
    • Building-block approach for determining low-frequency normal modes of macromolecules
    • Tama F., Gadea F.X., Marques O., Sanejouand Y.H. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000, 41:1-7.
    • (2000) Proteins , vol.41 , pp. 1-7
    • Tama, F.1    Gadea, F.X.2    Marques, O.3    Sanejouand, Y.H.4
  • 56
  • 57
    • 17044393884 scopus 로고    scopus 로고
    • Coarse-grained models for proteins
    • Tozzini V. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 2005, 15:144-150.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 58
    • 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., Yasutake H., Ishijima A., Yanagida T. 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 1996, 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
  • 60
    • 0030883755 scopus 로고    scopus 로고
    • Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
    • Wriggers W., Schulten K. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 1997, 29:1-14.
    • (1997) Proteins , vol.29 , pp. 1-14
    • Wriggers, W.1    Schulten, K.2
  • 61
    • 0030787462 scopus 로고    scopus 로고
    • Stability and dynamics of G-actin: back-door water diffusion and behavior of a subdomain 3/4 loop
    • Wriggers W., Schulten K. Stability and dynamics of G-actin: back-door water diffusion and behavior of a subdomain 3/4 loop. Biophys. J. 1997, 73:624-639.
    • (1997) Biophys. J. , vol.73 , pp. 624-639
    • Wriggers, W.1    Schulten, K.2
  • 62
    • 77952750301 scopus 로고    scopus 로고
    • Alzheimer's abeta(1-40) amyloid fibrils feature size-dependent mechanical properties
    • Xu Z., Paparcone R., Buehler M.J. Alzheimer's abeta(1-40) amyloid fibrils feature size-dependent mechanical properties. Biophys. J. 2010, 98:2053-2062.
    • (2010) Biophys. J. , vol.98 , pp. 2053-2062
    • Xu, Z.1    Paparcone, R.2    Buehler, M.J.3
  • 63
    • 0021261156 scopus 로고
    • Direct observation of motion of single F-actin filaments in the presence of myosin
    • Yanagida T., Nakase M., Nishiyama K., Oosawa F. Direct observation of motion of single F-actin filaments in the presence of myosin. Nature 1984, 307:58-60.
    • (1984) Nature , vol.307 , pp. 58-60
    • Yanagida, T.1    Nakase, M.2    Nishiyama, K.3    Oosawa, F.4
  • 64
    • 61449160619 scopus 로고    scopus 로고
    • Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives
    • Yang L.W., Chng C.P. Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives. Bioinform. Biol. Insights 2008, 2:25-45.
    • (2008) Bioinform. Biol. Insights , vol.2 , pp. 25-45
    • Yang, L.W.1    Chng, C.P.2
  • 65
    • 0030601791 scopus 로고    scopus 로고
    • Direct measurement of the torsional rigidity of single actin filaments
    • Yasuda R., Miyata H., Kinosita K. Direct measurement of the torsional rigidity of single actin filaments. J. Mol. Biol. 1996, 263:227-236.
    • (1996) J. Mol. Biol. , vol.263 , pp. 227-236
    • Yasuda, R.1    Miyata, H.2    Kinosita, K.3


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