Simulation of the mechanical strength of a single collagen molecule

Biophysical Journal

Volumn 95, Issue 1, 2008, Pages 33-39

  In 't Veld, Pieter J ^a   Stevens, Mark J ^a  

^a SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COLLAGEN TYPE 3;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELASTICITY; HUMAN; MECHANICAL STRESS; METHODOLOGY; MICROMANIPULATION; TENSILE STRENGTH; ULTRASTRUCTURE;

COLLAGEN TYPE III; COMPUTER SIMULATION; ELASTICITY; HUMANS; MICROMANIPULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; STRESS, MECHANICAL; TENSILE STRENGTH;

EID: 46749084254     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.120659     Document Type: Article

References (26)

1. Lodish, H., D. Baltimore, A. Berk, S. L. Zipursky, P. Matsudaira, and J. Darnell. 2000. Molecular Cell Biology, 4th ed. W. H. Freeman and Co., New York.
2. Holmes, D. F., C. J. Gilpin, C. Baldock, U. Ziese, A. J. Koster, and K. E. Kadler. 2001. Corneal collagen fibril structure in three dimensions: structural insights into fibril assembly, mechanical properties, and tissue organization. Proc. Nat. Acad. Sci. 98:7307-7312.
3. Fratzl, P. 2003. Cellulose and collagen: from fibers to tissues. Current Op. Coll. Inter. Sci. 8:32-39.
4. Tinoco, I., Jr. 2004. Force as a useful variable in reactions: unfolding RNA. Annu. Rev. Biophys. Biomol. Struct. 33:363-385.
5. Bockelmann, U., Ph. Thomen, B. Essevaz-Roulet, V. Viasnoff, and F. Heslot. 2002. Unzipping DNA with optical tweezers: high sequence sensitivity and force flips. Biophys. J. 82:1537-1553.
6. Sun, Y. L., Z. P. Luo, and K. N. An. 2001. Stretching short biopolymers using optical tweezers. Biochem. Biophys. Res. Commun. 286:826-830.
7. Gutsmann, T., G. E. Fantner, J. H. Kindt, M. Venturoni, S. Danielsen, and P. K. Hansma. 2004. Force spectroscopy of collagen fibers to investigate their mechanical properties and structural organization. Biophys. J. 86:3186-3193.
8. Gutsmann, T., G. E. Fantner, M. Venturoni, A. Ekani-Nkodo, J. B. Thompson, J. H. Kindt, D. E. Morse, D. K. Fygenson, and P. K. Hansma. 2003. Evidence that collagen fibrils in tendons are inhomogeneously structured in a tubelike manner. Biophys. J. 84:2593-2598.
9. Bozec, L., and M. Horton. 2005. Topography and mechanical properties of single molecules of type I collagen using atomic force microscopy. Biophys. J. 88:4223-4231.
10. Wenger, M. P. E., L. Bozec, M. A. Horton, and P. Mesquida. 2007. Mechanical properties of collagen fibrils. Biophys. J. 93:1255-1263.
11. Zhuang, X., and M. Rief. 2003. Single-molecule folding. Curr. Opin. Struct. Biol. 13:88-97.
12. Bustamante, C., S. B. Smith, J. Lipardt, and D. Smith. 2000. Single-molecule studies of DNA mechanics. Curr. Op. Struct. Biol. 10:279-285.
13. Mooney, S., P. Kollman, and T. Klein. 2002. Conformational preferences of substituted prolines in the collagen triple helix. Biopolymers 64:63-71.
14. Lorenzo, A., and E. Caffarena. 2005. Elastic properties, Young's modulus determination and structural stability of the tropocollagen molecule: a computational study by steered molecular dynamics. J. Biomech. 38:1527-1533.
15. Buehler, M. J., and S. Y. Wong. 2007. Entropic elasticity controls nanomechanics of single tropocollagen molecules. Biophys. J. 93:37-43.
16. Konrad, M. W., and J. I. Bolonick. 1996. Molecular dynamics simulation of DNA stretching is consistent with the tension observed for extension and strand separation and predicts a novel ladder structure. J. Am. Chem. Soc. 118:10989-10994.
17. MacKerell, A. D., Jr., and G. U. Lee. 1999. Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads. Eur. Biophys. J. 28:415-426.
18. Lohikoski, R., J. Timonen, and A. Laaksonen, 2005. Molecular dynamics simulation of single DNA stretching reveals a novel structure. Chem. Phys. Lett. 407:23-29.
19. Harris, S. A., Z. A. Sands, and C. A. Laughton. 2005. Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. Biophys. J. 88:1684-1691.
20. Piana, S. 2005. Structure and energy of a DNA dodecamer under tensile load. Nucleic Acids Res. 33:7029-7038.
21. Strick, T. R., M.-N. Dessinges, G. Charvin, N. H. Dekker, J. F. Allemand, D. Bensimon, and V. Croquette. 2003. Stretching of macromolecules and proteins. Rep. Prog. Phys. 66:1-45.
22. Hugel, T., M. Rief, M. Seitz, H. E. Gaub, and R. R. Netz, 2005. Highly stretched single polymers: atomic-force-microscope experiments versus ab initio theory. Phys. Rev. Lett. 94:048301.
23. Kramer, R. Z., J. Bella, P. Mayville, B. Brodsky, and H. M. Berman. 1999. Sequence dependent conformational variations of collagen triplehelical structure. Nat. Struct. Biol. 6:454-457.
24. MacKerell, A. D., Jr., D. Bashford, M. Belott, R. L. Dunbrack, Jr., J. Evanseck, M. J. Field, S. Fisher, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, I. W. E. Reiher, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
25. Plimpton, S. J. 1995. Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117:1-19.
26. in 't Veld, P. J., and M. J. Stevens. Translation script for LAMMPS Molecular Dynamics Simulator. Available at http://lammps.sandia.gov/.