Atomistically informed mesoscale model of alpha-helical protein domains

International Journal for Multiscale Computational Engineering

Volumn 7, Issue 3, 2009, Pages 237-250

  Bertaud, Jeremie ^a   Qin, Zhao ^a   Buehler, Markus J ^a  

^a USA   (United States)

Author keywords

Biological protein materials; Deformation; Experiment; Fracture; Hierarchical material; Materiomics; Multiscale modeling; Nanomechanics; Simulation

Indexed keywords

BIOLOGICAL PROTEIN MATERIALS; HIERARCHICAL MATERIAL; MATERIOMICS; MULTISCALE MODELING; SIMULATION;

DEFORMATION; EXPERIMENTS; FRACTURE; FRACTURE MECHANICS; MECHANICAL PROPERTIES; NANOMECHANICS; SHEAR STRENGTH; SIMULATORS; TENSILE STRENGTH;

BIOLOGICAL MATERIALS;

EID: 68349087878     PISSN: 15431649     EISSN: None     Source Type: Journal    
DOI: 10.1615/IntJMultCompEng.v7.i3.70     Document Type: Article

References (36)

1. Alberts, B., et al., Molecular Biology of the Cell. Taylor & Francis, New York, 2002.
2. Astbury, W. T., and Street, A., X-ray studies of the structures of hair, wool and related fibres. I. General. Trans. R. Soc. London, Ser. A. 230:75-101, 1931.
3. Weiner, S., and Wagner, H. D., The material bone: Structure mechanical function relations. Annu. Rev. Mater. Sci. 28:271-298, 1998.
4. Vincent, J. F. V., Structural Biomaterials. Princeton University Press, Princeton, NJ, 1990.
5. Fratzl, P., and Weinkamer, R., Nature's hierarchical materials. Prog. Mater. Sci. 52:1263-1334, 2007.
6. Courtney, T. H., Mechanical Behavior of Materials. McGraw-Hill, New York, 1990.
7. Broberg, K. B., Cracks and Fracture. Academic Press, San Diego, 1990.
8. Hirth, J. P., and Lothe, J., Theory of Dislocations. Wiley-Interscience, New York, 1982.
9. Engler, A. J., Sen, S., Sweeney, H. L., and Discher, D. E., Matrix elasticity directs stem cell lineage specification. Cell. 126:677-689, 2006.
10. Gautieri, A., Vesentini, S., Redaelli, A., and Buehler, M. J., Single molecule effects of osteogenesis imperfecta mutations in tropocollagen protein domains. Protein Sci. 18(1):161-168, 2009.
11. Suresh, S., Spatz, J., Mills, J. P., Micoulet, A., Dao, M., Lim, C. T., Beil, M., and Seufferlein, T., Connections between single-cell biomechanics and human disease states: Gastrointestinal cancer and malaria. Acta Biomater. 1:15-30, 2005.
12. Jin, Y.-S., Rao, J., and Gimzewski, J. K., Nanomechanical analysis of cells from cancer patients. Nature Nanotechnol. 2:780-783, 2007.
13. Tirion, M., Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908, 1996.
14. Haliloglu, T., Bahar, I., and Erman, B., Gaussian dynamics of folded proteins. Phys. Rev. Lett. 79:3090-3093, 1997.
15. Hayward, S., and Go, N., Collective variable description of native protein dynamics. Annu. Rev. Phys. Chem. 46:223-250, 1995.
16. Tozzini, V., Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15:144-150, 2005.
17. West, D. K., Brockwell, D. J., Olmsted, P. D., Radford, S. E., and Paci, E., Mechanical resistance of proteins explained using simple molecular models. Biophys. J. 90:287-297, 2006.
18. Dietz, H., and Rief, M., Elastic bond network model for protein unfolding mechanics. Phys. Rev. Lett. 100(9): paper 098101, 2008.
19. Sulkowska, J. I., and Cieplak, M., Mechanical stretching of proteins-a theoretical survey of the Protein Data Bank. J. Phys. Condens. Matter. 19:283201, 2007.
20. Bathe, M., A finite element framework for computation of protein normal modes and mechanical response. Proteins Struct. Function Bioinformatics. 70:1595-1609, 2008.
21. Bahar, I., and Jernigan, R., Inter-residue poten- tials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266:195-214, 1997.
22. Nguyen, H., and Hall, C., Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl. Acad. Sci. U. S. A. 101:16180-16185, 2004.
23. Nguyen, H., and Hall, C., Spontaneous fibril formation by polyalanines: Discontinuous molecular dynamics simulations. J. Am. Chem. Soc. 128:1890-1901, 2006.
24. Freddolino, P., Arkhipov, A., and Schulten, K., Coarse-grained molecular dynamics simulations of rotation-induced structural transitions in the bacterial flagellum. Biophys. J. 91: 4589-4597, 2007.
25. Buehler, M. J., Nature designs tough collagen: Explaining the nanostructure of collagen fibrils. Proc. Natl. Acad. Sci. U. S. A. 103:12285-12290, 2006.
26. Buehler, M., Molecular nanomechanics of nascent bone: Fibrillar toughening by mineralization. Nanotechnology. 18:295102, 2007.
27. Ackbarow, T., Chen, X., Keten, S., and 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. U. S. A. 104:16410-16415, 2007.
28. Ackbarow, T., and Buehler, M. J., Superelasticity, energy dissipation and strain hardening of vimentin coiled-coil intermediate filaments: Atomistic and continuum studies. J. Mater. Sci. 42:8771-8787, 2007.
29. Karcher, H., Lee, S. E., Kaazempur- Mofrad, M. R., and Kamm, R. D., A coarsegrained model for force-induced protein deformation and kinetics. Biophys. J. 90:2686-2697, 2006.
30. Lazaridis, T., and Karplus, M., Effective energy function for proteins in solution. Proteins Struct. Function Genet. 35:133-152, 1999.
31. Lazaridis, T., and Karplus, M., "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science. 278:1928-1931, 1997.
32. Bell, G. I., Models for the specific adhesion of cells to cells. Science. 200:618-627, 1978.
33. Hanggi, P., Talkner, P., and Borkovec, M., Reaction-rate theory: Fifty years after Kramers. Rev. Mod. Phys. 62:251-341, 1990.
34. Zhurkov, S. N., Kinetic concept of the strength of solids. Int. J. Fract. Mech. 1:311-323, 1965.
35. Lantz, M. A., Jarvis, S. P., Tokumoto, H., Martynski, T., Kusumi, T., Nakamura, C., and Miyake, J., Stretching the alpha-helix: A direct measure of the hydrogen-bond energy of a single-peptide molecule. Chem. Phys. Lett. 315:61-68, 1999.
36. Kageshima, M., Lantz, M. A., Jarvis, S. P., Tokumoto, H., Takeda, S., Ptak, A., Nakamura, C., and Miyake, J., Insight into conformational changes of a single alpha-helix peptide molecule through stiffness measurements. Chem. Phys. Lett. 343:77-82, 2001.