Computational and theoretical modeling of intermediate filament networks: Structure, mechanics and disease

Acta Mechanica Sinica/Lixue Xuebao

Volumn 28, Issue 4, 2012, Pages 941-950

  Qin, Zhao ^a   Buehler, Markus J ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

Disease mechanism; Intermediate filament network; Mechanics; Molecular mechanics; Multiple scale method; Nanoscopic structure

Indexed keywords

ACTIN MICROFILAMENTS; BIOMECHANICAL PROPERTIES; CHEMICAL COMPOSITIONS; CYTOSKELETONS; EUKARYOTIC CELLS; FILAMENT NETWORKS; INTERFACIAL PROPERTY; INTERMEDIATE FILAMENTS; MATERIAL PROPERTY; MICROTUBULES; MULTIPLE SCALE METHOD; NANOMECHANICAL PROPERTY; NANOSCOPIC STRUCTURE; PROTEIN MOLECULES; RECENT PROGRESS; THEORETICAL MODELING; THEORETICAL STUDY;

BIOLOGICAL MATERIALS; MECHANICAL PROPERTIES; MECHANICS; MOLECULAR MECHANICS; PROTEINS; SIGNAL TRANSDUCTION;

BIOMECHANICS;

EID: 84870381102     PISSN: 05677718     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10409-012-0124-5     Document Type: Conference Paper

References (62)

1. Ishikawa, H., Bischoff, R., Holtzer, H.: Mitosis and intermediate-sized filaments in developing skeletal muscle. Journal of Cell Biology 38, 538-555 (1968)
2. Herrmann, H., Bar, H., Kreplak, L., et al.: Intermediate filaments: from cell architecture to nanomechanics. Nature Reviews Molecular Cell Biology 8, 562-573 (2007)
3. Omary, M. B., Coulombe, P. A., McLean, W. H. I.: Mechanisms of disease: Intermediate filament proteins and their associated diseases. New England Journal of Medicine 351, 2087- 2100 (2004)
4. Hearle, J. W. S.: A critical review of the structural mechanics of wool and hair fibres. International Journal of Biological Macromolecules 27, 123-138 (2000)
5. Kreplak, L., Fudge, D.: Biomechanical properties of intermediate filaments: from tissues to single filaments and back. Bioessays 29, 26-35 (2007)
6. Chang, L., Goldman, R. D.: Intermediate filaments mediate cytoskeletal crosstalk. Nature ReviewsMolecular Cell Biology 5, 601-613 (2004)
7. Strelkov, S. V., Herrmann, H., Aebi, U.: Molecular architecture of intermediate filaments. Bioessays 25, 243-251 (2003)
8. Moll, R., Divo, M., Langbein, L.: The human keratins: biology and pathology. Histochemistry and Cell Biology 129, 705-733 (2008)
9. Jafari, S. S., Maxwell, W. L., Neilson, M., et al.: Axonal cytoskeletal changes after non-disruptive axonal injury. Journal of Neurocytology 26, 207-221 (1997)
10. Dahl, K. N., Kahn, S. M., Wilson, K. L., et al.: The nuclear envelope lamina network has elasticity and a compressibility limit suggestive of a molecular shock absorber. J. Cell. Sci. 117, 4779-4786 (2004)
11. Wilson, K. L., Zastrow, M. S., Lee, K. K.: Lamins and disease: Insights into nuclear infrastructure. Cell 104, 647-650 (2001)
12. Wang, N., Stamenovic, D.: Mechanics of vimentin intermediate filaments. J. Muscle Res. Cell. Motil. 23, 535-540 (2002)
13. Buehler, M. J., Yung, Y. C.: Deformation and failure of protein materials in physiologically extreme conditions and disease. Nature Materials 8, 175-188 (2009)
14. Eriksson, M., Brown, W. T., Gordon, L. B., et al.: Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome. Nature 423, 293-298 (2003)
15. Dahl, K. N., Scaffidi, P., Islam, M. F., et al.: Distinct structural and mechanical properties of the nuclear lamina in Hutchinson-Gilford progeria syndrome. Proceedings of the National Academy of Sciences of the United States of America 103, 10271-10276 (2006)
16. Lin, Y. C., Broedersz, C. P., Rowat, A. C., et al.: Divalent cations crosslink vimentin intermediate filament tail domains to regulate network mechanics. Journal of Molecular Biology 399, 637-644 (2010)
17. Zhang, H., Ackbarow, T., Buehler, M. J.: Muscle dystrophy single point mutation in the 2B segment of lamin A does not affect the mechanical properties at the dimer level. Journal of Biomechanics 41, 1295-1301 (2008)
18. Nicolet, S., Herrmann, H., Aebi, U., et al.: Atomic structure of vimentin coil 2. Journal of Structural Biology 170, 369-376 (2010)
19. Luca, S., Yau, W. M., Leapman, R., et al.: Peptide conformation and supramolecular organization in amylin fibrils: Constraints from solid-state NMR. Biochemistry 46, 13505-13522 (2007)
20. Goldie, K. N., Wedig, T., Mitra, A. K., et al.: Dissecting the 3-D structure of vimentin intermediate filaments by cryoelectron tomography. Journal of Structural Biology 158, 378- 385 (2007)
21. Lee, H. L. D., Sahl, S. J., Lew, M. D., et al.: The doublehelix microscope super-resolves extended biological structures by localizing single blinking molecules in three dimensions with nanoscale precision. Applied Physics Letters 100, 153701 (2012)
22. Zagrovic, B., Snow, C. D., Shirts, M. R., et al.: Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. Journal of Molecular Biology 323, 927-937 (2002)
23. Khatib, F., DiMaio, F., Cooper, S., et al.: Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural&Molecular Biology 18, 1175-1177 (2011)
24. Buehler, M. J., Keten, S.: Colloquium: Failure of molecules, bones, and the Earth itself. Reviews of Modern Physics 82, 1459-1487 (2010)
25. Rauscher, S., Pomes, R.: Molecular simulations of protein disorder. Biochemistry and Cell Biology-Biochimie Et Biologie Cellulaire 88, 269-290 (2010)
26. Zwanzig, R., Szabo, A., Bagchi, B.: Levinthal's paradox. Proc Natl Acad Sci USA 89, 20-22 (1992)
27. del Rio, A., Perez-Jimenez, R., Liu, R. C., et al.: Stretching single talin rod molecules activates vinculin binding. Science 323, 638-641 (2009)
28. Keten, S., Buehler, M. J.: Nanostructure and molecular mechanics of spider dragline silk protein assemblies. J. R. Soc. Interface 7, 1709-1721 (2010)
29. Bates, G.: Huntingtin aggregation and toxicity in Huntington's disease. Lancet 361, 1642-1644 (2003)
30. Qin, Z., Kalinowski, A., Dahl, K. N., et al.: Structure and stability of the lamin A tail domain and HGPS mutant. Journal of Structural Biology 175, 425-433 (2011)
31. Sugita, Y., Okamoto, Y.: Replica-exchange molecular dynamics method for protein folding. Chemical Physics Letters 314, 141-151 (1999)
32. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., et al.: Charmm - a program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry 4, 187-217 (1983)
33. Ackbarow, T., Buehler, M. J.: Superelasticity, energy dissipation and strain hardening of vimentin coiled-coil intermediate filaments: atomistic and continuum studies. Journal of Materials Science 42, 8771-8787 (2007)
34. Sotomayor, M., Schulten, K.: Single-molecule experiments in vitro and in silico. Science 316, 1144-1148 (2007)
35. Qin, Z., Kreplak, L., Buehler, M. J.: Hierarchical structure controls nanomechanical properties of vimentin intermediate filaments. PLoS One 4, e7294 (2009)
36. Qin, Z., Buehler, M. J.: Molecular dynamics simulation of the alpha-helix to beta-sheet transition in coiled protein filaments: evidence for a critical filament length scale. Phys. Rev. Lett. 104, 198304 (2010)
37. Keten, S., Buehler, M. J.: Asymptotic strength limit of hydrogen-bond assemblies in proteins at vanishing pulling rates. Phys. Rev. Lett. 100, 198301 (2008)
38. Kreplak, L., Bar, H.: Severe myopathy mutations modify the nanomechanics of desmin intermediate filaments. J. Mol. Biol. 385, 1043-1051 (2009)
39. Parbhu, A. N., Bryson, W. G., Lal, R.: Disulfide bonds in the outer layer of keratin fibers confer higher mechanical rigidity: Correlative nano-indentation and elasticity measurement with an AFM. Biochemistry 38, 11755-11761 (1999)
40. Wiita, A. P., Ainavarapu, S. R. K., Huang, H. H., et al.: Forcedependent chemical kinetics of disulfide bond reduction observed with single-molecule techniques. Proceedings of the National Academy of Sciences of the United States of America 103, 7222-7227 (2006)
41. Wiche, G.: Role of plectin in cytoskeleton organization and dynamics. Journal of Cell Science 111, 2477-2486 (1998)
42. Keten, S., Chou, C. C., van Duin, A. C. T., et al.: Tunable nanomechanics of protein disulfide bonds in redox microenvironments. Journal of the Mechanical Behavior of Biomedical Materials 5, 32-40 (2012)
43. Aryanpour, M., van Duin, A. C. T., Kubicki, J. D.: Development of a reactive force field for iron-oxyhydroxide systems. Journal of Physical Chemistry A 114, 6298-6307 (2010)
44. Chenoweth, K., van Duin, A. C. T, Goddard,W. A.: ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation. Journal of Physical Chemistry A 112, 1040- 1053 (2008)
45. Buehler, M. J.: Atomistic and continuum modeling of mechanical properties of collagen: Elasticity, fracture, and selfassembly. Journal ofMaterials Research 21, 1947-1961 (2006)
46. Buehler, M. J., Tang, H., van Duin, A. C. T., et al.: Threshold crack speed controls dynamical fracture of silicon single crystals. Physical Review Letters 99, 165502 (2007)
47. Goldberg, M. W., Fiserova, J., Huttenlauch, I., et al.: A new model for nuclear lamina organization. Biochemical Society Transactions 36, 1339-1343 (2008)
48. Krimm, I., Ostlund, C., Gilquin, B., et al.: The Ig-like structure of the c-terminal domain of lamin A/C, mutated in muscular dystrophies, cardiomyopathy, and partial lipodystrophy. Structure 10, 811-823 (2002)
49. Tama, F., Gadea, F. X., Marques, O., et al.: Building-block approach for determining low-frequency normal modes of macromolecules. Proteins-Structure Function and Genetics 41, 1-7 (2000)
50. Xu, Z. P., Paparcone, R., Buehler, M. J.: Alzheimer's a beta(1- 40) amyloid fibrils feature size-dependent mechanical properties. Biophysical Journal 98, 2053-2062 (2010)
51. Barducci, A., Bussi, G., Parrinello, M.: Well-tempered metadynamics: A smoothly converging and tunable free-energy method. Physical Review Letters 100, 020603 (2008)
52. Wilhelmsen, K., Litjens, S. H. M., Kuikman, I., et al.: Nesprin- 3, a novel outer nuclear membrane protein, associates with the cytoskeletal linker protein plectin. Journal of Cell Biology 171, 799-810 (2005)
53. Ostlund, C., Folker, E. S., Choi, J. C., et al.: Dynamics and molecular interactions of linker of nucleoskeleton and cytoskeleton (LINC) complex proteins. Journal of Cell Science 122, 4099-4108 (2009)
54. Kim, H., Nakamura, F., Lee, W., et al.: Filamin A is required for vimentin-mediated cell adhesion and spreading. American Journal of Physiology-Cell Physiology 298, C221-C236 (2010)
55. Lindstrom, S. B., Vader, D. A., Kulachenko, A., et al.: Biopolymer network geometries: Characterization, regeneration, and elastic properties. Physical Review E 82, 051905 (2010)
56. Lin, Y. C., Yao, N. Y., Broedersz, C. P., et al.: Origins of elasticity in intermediate filament networks. Physical Review Letters 104, 058101 (2010)
57. Panorchan, P., Schafer, B. W., Wirtz, D., et al.: Nuclear envelope breakdown requires overcoming the mechanical integrity of the nuclear lamina. J. Biol. Chem. 279, 43462-43467 (2004)
58. Qin, Z., Buehler, M. J.: Mechanical properties of crosslinks controls failure mechanism of hierarchical intermediate filament networks. Theoretical and Applied Mechanics Letters 2, 014005 (2012)
59. Cranford, S. W., Tarakanova, A., Pugno, N. M., et al.: Nonlinear material behaviour of spider silk yields robust webs. Nature 482, 72-76 (2012)
60. Kreplak, L., Herrmann, H., Aebi, U.: Tensile properties of single desmin intermediate filaments. Biophysical Journal 94, 2790-2799 (2008)
61. Qin, Z., Buehler, M. J.: Flaw tolerance of nuclear intermediate filament lamina under extreme mechanical deformation. ACS Nano 5, 3034-3042 (2011)
62. Cotter, L., Allen, T. D., Kiseleva, E., et al.: Nuclear membrane disassembly and rupture. Journal of Molecular Biology 369, 683-695 (2007)