Multiscale modeling and mechanics of filamentous actin cytoskeleton

Biomechanics and Modeling in Mechanobiology

Volumn 11, Issue 3-4, 2012, Pages 291-302

  Yamaoka, Hidetaka ^a,b   Matsushita, Shinji ^a,b,c   Shimada, Yoshitaka ^a,c   Adachi, Taiji ^a,b,c  

^a RIKEN   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c KYOTO UNIVERSITY   (Japan)

Author keywords

Actin filament; Biomechanics; Coarse grained modeling; Computational biomechanics; Continuum dynamics; Mechanobiology; Molecular dynamics; Multiscale modeling and simulation

Indexed keywords

BIOMECHANICS; COARSE-GRAINED MODELING; COMPUTATIONAL CHEMISTRY; PROTEINS;

ACTIN FILAMENT; COARSE-GRAINED MODELING; COMPUTATIONAL BIOMECHANICS; CONTINUUM DYNAMICS; FILAMENTOUS ACTIN CYTOSKELETON; MECHANICAL BEHAVIOR; MECHANO-BIOLOGY; MULTI-SCALE MODELLING AND SIMULATIONS; TEMPORAL AND SPATIAL SCALE;

MOLECULAR DYNAMICS;

ACTIN; ACTIN BINDING PROTEIN; SOLVENT;

ANIMAL; BIOMECHANICS; BIOPHYSICS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; CYTOSKELETON; DIMERIZATION; HUMAN; MECHANICAL STRESS; METABOLISM; METHODOLOGY; MOLECULAR DYNAMICS; REVIEW; THEORETICAL MODEL; TIME;

ACTINS; ANIMALS; BIOMECHANICS; BIOPHYSICS; COMPUTER SIMULATION; CYTOSKELETON; DIMERIZATION; HUMANS; MICROFILAMENT PROTEINS; MODELS, MOLECULAR; MODELS, THEORETICAL; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; SOLVENTS; STRESS, MECHANICAL; TIME FACTORS;

EID: 84861093686     PISSN: 16177959     EISSN: 16177940     Source Type: Journal    
DOI: 10.1007/s10237-011-0317-z     Document Type: Review

References (95)

1. Adachi T et al (2010) Approach behavior of binding proteins toward actin filament: Brownian dynamics simulation. Trans Japan Soc Mech Eng A Sol Mech Mater Eng 76:1119-1127 (in Japanese)
2. Alder BJ, Wainwright TE (1957) Phase transition for a hard sphere system. J Chem Phys 27:1208-1209
3. Ayton GS et al (2007) Multiscale modeling of biomolecular systems: in serial and in parallel. Curr Opin Struct Biol 17:192-198 (Pubitemid 46584804)
4. BatheM (2008) A finite element framework for computation of protein normal modes and mechanical response. Proteins 70:1595-1609 (Pubitemid 351304116)
5. ben-Avraham D, Tirion MM (1995) Dynamic and elastic properties of F-actin: a normal-mode analysis. Biophys J 68:1231-1245
6. ben-Avraham D, Tirion MM (1998) Normal modes analyses of macromolecules. Physica A 249:415-423 (Pubitemid 128427264)
7. Bossis G et al (1982) Brownian dynamics and the fluctuation dissipation theorem. Mol Phys 45:191-196
8. Burton DA, Gould T (2007) Dynamical model of Cosserat nanotubes. J Phys 62:23-33
9. Carlsson AE (2006) Stimulation of actin polymerization by filament severing. Biophys J 90:413-422
10. CascellaMet al (2008) Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins. J Chem Theory Comput 4:1378-1385
11. Chen LF et al (2002) Molecular modeling of averaged rigor crossbridges from tomograms of insect flight muscle. J Struct Biol 138: 92-104 (Pubitemid 35300751)
12. Chu JW, Voth GA (2005) Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. Proc Natl Acad Sci USA 102:13111-13116 (Pubitemid 41324987)
13. Chu JW, VothGA (2006) Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys J 90:1572-1582
14. Cosserat E, Cosserat F (1909) Théorie des corps deformable. Hermann et Fils, Paris
15. Dalhaimer P, Pollard TD (2008) Nucleotide-mediated conformational changes of monomeric actin and Arp3 studied by molecular dynamics simulations. J Mol Biol 376:166-183
16. Das M et al (2007) Effective medium theory of semiflexible filamentous networks. Phys Rev Lett 99:038101
17. Deriu MA et al (2011) Biomechanics of actin filaments: a computational multi-level study. J Biomech 44:630-636
18. Espanol P, Warren P (1995) Statistical mechanics of dissipative particle dynamics. Europhys Lett 30:191-196
19. Gardel ML et al (2004) Elastic behavior of cross-linked and bundled actin networks. Science 304:1301-1305 (Pubitemid 38697422)
20. Geiger B, Bershadsky A (2001) Assembly and mechanosensory function of focal contacts. Curr Opin Cell Biol 13:584-592 (Pubitemid 32817017)
21. Gittes F et al (1993) Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape. J Cell Biol 120:923-934 (Pubitemid 23056298)
22. Goldberg MB (2001) Actin-based motility of intracellular microbial pathogens. Microbiol Mol Biol Rev 65:595-626 (Pubitemid 33123519)
23. Graceffa P, Dominguez R (2003) Crystal structure of monomeric actin in the ATP state-structural basis of nucleotide-dependent actin dynamics. J Biol Chem 278:34172-34180 (Pubitemid 37553259)
24. Hale AL, Meirovitch L (1980) Ageneral substructure synthesismethod for the dynamic simulation of complex structures. J Sound Vib 69:309-326 (Pubitemid 11430331)
25. Hayakawa K et al (2008) Actin stress fibers transmit and focus force to activate mechanosensitive channels. J Cell Sci 121:496-503 (Pubitemid 351405058)
26. Head DA et al (2003) Distinct regimes of elastic response and deformation modes of cross-linked cytoskeletal and semiflexible polymer networks. Phys Rev E 68:061907
27. Hoffman KA et al (2003) Link, twist, energy and the stability of DNA minicircles. Biopolymers 70:145-157 (Pubitemid 37229319)
28. Holmes KC et al (1990) Atomic model of the actin filament. Nature 347:44-49
29. Hoogerbrugge PJ, Koelman JMVA (1992) Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhys Lett 19:155-160
30. Huisman EM et al (2007) Three-dimensional cross-linked F-actin networks: relation between network architecture and mechanical behavior. Phys Rev Lett 99:298193
31. Ingber DE (2003) Tensegrity I. Cell structure and hierarchical systems biology. J Cell Sci 116:157-173
32. Inoue Y et al (2010) Simulations of dynamics of actin filaments by remodeling them in shear flows. Comput Biol Med 40:876-882
33. Inoue Y, Adachi T (2011) Coarse-grained Brownian rachet model of membrane protrusion on cellular scale. Biomech ModelMechanobiol. doi:10.1007/s10237-010- 0250-6
34. Isambert H, Maggs AC (1996) Dynamics and Rheology of actin solutions. Macromol 29:1036-1040 (Pubitemid 126531454)
35. IsambertHet al (1995) Flexibility of actin-filaments derived from thermal fluctuations. J Biol Chem 270:11437-11444
36. Isralewitz B, Gao M, Schulten K (2001) Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol 11:224-230 (Pubitemid 32289426)
37. Janmey PJ et al (2007) Negative normal stress in semiflexible biopolymer gels. Nat Mater 6:48-51
38. Kim T et al (2009) Computational analysis of a cross-linked actin like networks. Exp Mech 49:91-104
39. Kojima H et al (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
40. Kroy K, Frey E (1996) Force-extension relation and plateau modulus for wormlike chains. Phys Rev Lett 77:306-309 (Pubitemid 126624481)
41. Lauffenburger DA, Horwitz AF (1996) Cell migration: a physically integrated molecular process. Cell 84:359-369 (Pubitemid 26058561)
42. Lee J et al (1994) Traction forces generated by locomoting keratocytes. J Cell Biol 127:1957-1964
43. Levine AJ et al (2004) The deformations field in semiflexible networks. J Phys Condens Matter 16:S2079-S2088
44. Liu J et al (2007) Visualizing the strain field in semiflexible polymer networks: strain fluctuations and nonlinear Rheology of F-actin gels. Phys Rev Lett 98:198304
45. Lu H et al (1998) Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J 75:662-671 (Pubitemid 28357508)
46. Lyman et al (2008) Systematic multiscale parameterization of heterogeneous elastic networkmodels of proteins.Biophys J 95:4183-4192
47. MacKintosh FC et al (1995) Elasticity of semiflexible biopolymer networks. Phys Rev Lett 75:4425-4428
48. Maggs AC (1997) Two plateau moduli for actin gels. Phys Rev E 55:7396-7400 (Pubitemid 127736438)
49. Marko JF (1997) Stretching must twist DNA. Europhys Lett 38: 183-188
50. Matsushita S et al (2010a) Evaluation of extensional and torsional stiffness of single actin filaments by molecular dynamics analysis. J Biomech 43:3162-3167
51. Matsushita S et al (2010b) Quantitative evaluation of mechanical behaviors of actin filament under different mechanical conditions. In: Proceeding of the 6th world congress of biomechanics
52. McCammon JA et al (1977) Dynamics of folded proteins. Nature 267:585-590
53. Ming D et al (2003a) Substructure synthesis method for simulating large molecular complexes. Proc Natl Acad Sci USA 100:104-109 (Pubitemid 36078037)
54. Ming D et al (2003b) Simulation of F-actin filaments of several microns. Biophys J 85:27-35 (Pubitemid 36753614)
55. Mitchison TJ, Cramer LP (1996) Actin-based cell motility and cell locomotion. Cell 84:371-379 (Pubitemid 26058562)
56. Mizuno D et al (2007) Nonequilibrium mechanics of active cytoskeletal networks. Science 315:370-373 (Pubitemid 46175516)
57. Mogilner A, Oster G (1996) Cell motility driven by actin polymerization. Biophys J 71:3030-3045 (Pubitemid 26422346)
58. Morse DC (1998a) Viscoelasticity of concentrated isotropic solutions of semiflexible polymers. 1. Model and stress tensor. Macromolecules 31:7030-7043 (Pubitemid 128568011)
59. Morse DC (1998b) Viscoelasticity of concentrated isotropic solutions of semiflexible polymers. 2. Linear response. Macromolecules 31:7044-7067 (Pubitemid 128568012)
60. Morse DC (1998c) Viscoelasticity of tightly entangled solutions of semiflexible polymers. Phys Rev E 58:R1237-R1240 (Pubitemid 128596171)
61. Morse DC et al (2001) Tube diameter in tightly entangled solutions of semiflexible polymers. Phys Rev E 63:031502
62. Narita A, MaedaY (2007) Molecular determination by electronmicroscopy of the actin filament end structure. J Mol Biol 365:480-501 (Pubitemid 44838706)
63. Nemethova M et al (2008) Bundling the actin cytoskeleton: filopodia contribute to the construction of contractile bundles in the lamella. J Cell Biol 180:1233-1244 (Pubitemid 351468477)
64. Oda T et al (2009) The nature of the globular-to fibrous-actin transition. Nature 457:441-445
65. Okeyo KO et al (2010) Mechanical regulation of actin network dynamics in migrating cells. J Biomech Sci Eng 5:186-207
66. Otterbein LR et al (2001) The crystal structure of uncomplexed actin in the ADP state. Science 293:708-711 (Pubitemid 32728675)
67. Padding JT et al (2009) Efficient simulation of noncrossing fibers and chains in a hydrodynamic solvent. J Chem Phys 130:144903
68. Palmer JS, Boyce MC (2008) Constitutive modeling of the stress-strain behavior of F-actin filament networks. Acta Biomater 4:597-612
69. Park et al (2006) Atomistic simulation approach to a continuum description of self-assembled β-sheet filaments. Biophys J 90:2510-2524
70. Pfaendtner J et al (2009) Nucleotide-dependent conformational states of actin. Proc Natl Acad Sci USA 106:12723-12728
71. Pollard TD et al (2000) Molecular mechanisms controlling actin filament dynamics in nonmuscle cells. Annu Rev Biophys Biomol Struct 29:545-576 (Pubitemid 30599604)
72. Pollard TD, Berro J (2009) Mathematical models and simulations of cellular processes based on actin filaments. J Biol Chem 284: 5433-5437
73. Pollard TD, BorisyGG (2003) Cellularmotility driven by assembly and disassembly of actin filaments. Cell 112:453-465 (Pubitemid 36263079)
74. Pollard TD, Cooper JA (1986) Actin and actin-binding proteins. A critical evaluation of mechanisms and functions. Ann Rev Biochem 55:987-1035 (Pubitemid 16070793)
75. Prochniewiez E et al (2009) Cofilin increases the torsional flexibility and dynamics of actin filaments. J Mol Biol 353:990-1000
76. Riveline D et al (2001) Focal contacts as mechanosensors: externally applied local mechanical force induces growth of focal contacts by an mDia1-dependent and ROCK-independent mechanism. J Cell Biol 153:1175-1185 (Pubitemid 34289257)
77. Satcher RL Jr, Dewey CF Jr (1996) Theoretical estimates of mechanical properties of the endothelial cell cytoskeleton. Biophys J 71: 109-118 (Pubitemid 26227297)
78. Schmidt A, Hall MN (1998) Signaling to the actin cytoskeleton. Annu Rev Cell Dev Biol 14:305-338 (Pubitemid 29001457)
79. Sept D, McCammon JA (2001) Thermodynamics and kinetics of actin filament mucleation. Biophys J 81:667-674 (Pubitemid 32721442)
80. Shimada Y et al (2009) Coarse-grained modeling and simulation of actin filament behavior based on Brownian dynamics method. Mol Cell Biomech 6:161-173
81. SmithML, Healey TJ (2008) Predicting the onset of DNA supercoiling using a non-linear hemitropic elastic rod. Int J Non-Linear Mech 43:1020-1028
82. Stricker J et al (2010) Mechanics of the F-actin cytoskeleton. J Biomech 43:9-14
83. Suda H, Saito M (1994) Molecular-dynamics simulations for actin monomers in solution. J Theor Biol 171:347-349
84. Sultan C et al (2004) A computational tensegrity model predicts dynamic rheological behaviors in living cells. Ann Biomed Eng 32:520-530
85. Ter-Oganessian N et al (2005) Active microrheology of networks composed of semiflexible polymers: computer simulation of magnetic tweezers. Phys Rev E 72:041510
86. Theriot JA, Mitchson TJ (1991) Actin microfilament dynamics in locomoting cells. Nature 352:126-131 (Pubitemid 21896707)
87. Tsuda Y et al (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 (Pubitemid 26382747)
88. Vogel V, Sheetz M (2006) Local force and geometry sensing regulate cell functions. Nat Rev Mol Cell Biol 7:265-275
89. WangNet al (2001) Mechanical behavior in living cells consistent with the tensegrity model. Proc Natl Acad Sci USA 98:7765-7770 (Pubitemid 32642635)
90. Winder SJ, Ayscough KR (2005) Actin-binding proteins. J Cell Sci 118:651-654 (Pubitemid 40372573)
91. Wriggers W, Schulten K (1997) Stability and dynamics of G-actin: back-door water diffusion and behavior of a subdomain 3/4 loop. Biophys J 73:624-639 (Pubitemid 27337600)
92. Wriggers W, Schulten K (1999) Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Proteins 35:262-273 (Pubitemid 29165138)
93. Yamaoka H, Adachi T (2010a) Coupling between axial stretch and bending/twisting deformation of actin filaments caused by a mismatched centroid from the center axis. Int J Mech Sci 52:329-333
94. Yamaoka H, Adachi T (2010b) Continuum dynamics on a vector bundle for a directed medium. J Phys A Math Theor 43:325209
95. Zigmond SH (1993) Recent quantitative studies of actin filament turnover during cell locomotion. Cell Motil Cytoskelet 25:309-316 (Pubitemid 23225031)