Coarse-grained model of collagen molecules using an extended MARTINI force field

Journal of Chemical Theory and Computation

Volumn 6, Issue 4, 2010, Pages 1210-1218

  Gautieri, Alfonso ^a,b   Russo, Antonio ^a   Vesentini, Simone ^a   Redaelli, Alberto ^a   Buehler, Markus J ^b  

^a POLITECNICO DI MILANO   (Italy)

^b Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77951113751     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct100015v     Document Type: Article

References (52)

1. Kadler, K. E.; Baldock, C.; Bella, J.; Boot-Handford, R. P. Collagens at a glance J. Cell Sci. 2007, 120, 1955
2. Hyde, T. J.; Bryan, M. A.; Brodsky, B.; Baum, J. Sequence dependence of renucleation after a Gly mutation in model collagen peptides J. Biol. Chem. 2006, 281, 36937-36943
3. Hoffmann, D.; Voss, T.; Kuhn, K.; Engel, J. Localization of flexible sites in thread-like molecules from electron micrographs. Comparison of interstitial, basement membrane and intima collagens J. Mol. Biol. 1984, 172
4. Cowin, S. C. The mechanical and stress adaptive properties of bone Ann. Biomed. Eng. 1983, 11, 263-95
5. Srinivasan, M.; Uzel, S. G. M.; Gautieri, A.; Keten, S.; Buehler, M. J. Alport Syndrome mutations in type IV tropocollagen alter molecular structure and nanomechanical properties J. Struct. Biol. 2009, 168, 503-510
6. Beck, K.; Chan, V. C.; Shenoy, N.; Kirkpatrick, A.; Ramshaw, J. A. M.; Brodsky, B. Destabilization of osteogenesis imperfecta collagen-like model peptides correlates with the identity of the residue replacing glycine P. Natl. Acad. Sci. U.S.A. 2000, 97, 4273-4278
7. Sasaki, N.; Odajima, S. Stress-strain curve and Youngs modulus of a collagen molecule as determined by the X-ray diffraction technique J Biomech. 1996, 29, 655-658
8. Bozec, L.; Horton, M. Topography and mechanical properties of single molecules of type I collagen using atomic force microscopy Biophys. J. 2005, 88, 4223-4231
9. Sun, Y.; Luo, Z.; Fertala, A.; An, K. Direct quantification of the flexibility of type I collagen monomer Biochem. Biophys. Res. Commun. 2002, 295, 382-386
10. Fratzl, P.; Weinkamer, R. Natures hierarchical materials Prog. Mater. Sci. 2007, 52, 1263-1334
11. Persikov, A. V.; Ramshaw, J. A.; Brodsky, B. Collagen model peptides: Sequence dependence of triple-helix stability Biopolymers 2000, 55, 436-450
12. Vesentini, S.; Fitie, C. F. C.; Montevecchi, F. M.; Redaelli, A. Molecular assessment of the elastic properties of collagen-like homotrimer sequences Biomech. Model Mechanobiol. 2005, 3, 224-234
13. Lorenzo, A. C.; Caffarena, E. R. Elastic properties, Youngs modulus determination and structural stability of the tropocollagen molecule: a computational study by steered molecular dynamics J. Biomech. 2005, 38, 1527-1533
14. Buehler, M. J. Atomistic and continuum modeling of mechanical properties of collagen: Elasticity, fracture and self-assembly J. Mater. Res. 2006, 21, 1947-1961
15. Buehler, M. J. Nature designs tough collagen: Explaining the nanostructure of collagen fibrils P. Natl. Acad. Sci. U.S.A. 2006, 103, 12285-12290
16. Buehler, M. J.; Wong, S. Y. Entropic elasticity controls nanomechanics of single tropocollagen molecules Biophys. J. 2007, 93, 37-43
17. Gautieri, A.; Vesentini, S.; Montevecchi, F. M.; Redaelli, A. Mechanical properties of physiological and pathological models of collagen peptides investigated via steered molecular dynamics simulations J. Biomech. 2008, 41, 3073-3077 DOI: 10.1016/j.jbiomech.2008.06.028
18. Ayton, G. S.; Noid, W. G.; Voth, G. A. Multiscale modeling of biomolecular systems: in serial and in parallel Curr. Opin. Struct. Biol. 2007, 17, 192-198
19. Noid, W. G.; Chu, J. W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A.; Andersen, H. C. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models J. Chem. Phys. 2008, 128
20. Wang, Y.; Noid, W. G.; Liu, P.; Voth, G. A. Effective force coarse-graining Phys. Chem. Chem. Phys. 2009, 11, 2002-15
21. Tozzini, V. Coarse-grained models for proteins Curr. Opin. Struct. Biol. 2005, 15, 144-150
22. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H. The MARTINI force field: Coarse grained model for biomolecular simulations J. Phys. Chem. B 2007, 111, 7812-7824
23. Monticelli, L.; Kandasamy, S. K.; Periole, X.; Larson, R. G.; Tieleman, D. P.; Marrink, S. J. The MARTINI coarse-grained force field: Extension to proteins J. Chem. Theory Comput. 2008, 4, 819-834
24. Lopez, C. A.; Rzepiela, A. J.; de Vries, A. H.; Dijkhuizen, L.; Hunenberger, P. H.; Marrink, S. J. Martini Coarse-Grained Force Field: Extension to Carbohydrates J. Chem. Theory Comput. 2009, 5, 3195-3210
25. Chetwynd, A. P.; Scott, K. A.; Mokrab, Y.; Sansom, M. S. CGDB: a database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations Mol. Membr. Biol. 2008, 25, 662-9
26. Sansom, M. S.; Scott, K. A.; Bond, P. J. Coarse-grained simulation: a high-throughput computational approach to membrane proteins Biochem. Soc. Trans. 2008, 36, 27-32
27. Treptow, W.; Marrink, S. J.; Tarek, M. Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations J. Phys. Chem. B 2008, 112, 3277-82
28. Risselada, H. J.; Marrink, S. J. Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations Phys. Chem. Chem. Phys. 2009, 11, 2056-67
29. Berendsen, H. J. C.; Vanderspoel, D.; Vandrunen, R. Gromacs-a message-passing parallel molecular-dynamics implementation Comput. Phys. Commun. 1995, 91, 43-56
30. Vandrunen, R.; Vanderspoel, D.; Berendsen, H. J. C. Gromacs-a software package and a parallel computer for molecular-dynamics Abstr. Pap. Am. Chem. Soc. 1995, 209, 49
31. Gautieri, A.; Buehler, M. J.; Redaelli, A. Deformation rate controls elasticity and unfolding pathway of single tropocollagen molecules J. Mech. Behav. Biomed. Mater. 2009, 2, 130-137
32. Rainey, J.; Goh, M. An interactive triple-helical collagen builder Bioinformatics 2004, 20, 2458-2459
33. Black, S. D.; Mould, D. R. Development of hydrophobicity parameters to analyze proteins which bear posttranslational or cotranslational modifications Anal. Biochem. 1991, 193, 72-82
34. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242
35. Chu, J. W.; Voth, G. A. Coarse-grained modeling of the actin filament derived from atomistic-scale simulations Biophys. J. 2006, 90, 1572-1582
36. Hofmann, H.; Voss, T.; Kuhn, K.; Engel, J. Localization Of Flexible Sites In Thread-Like Molecules From Electron-Micrographs-Comparison Of Interstitial, Basement-Membrane And Intima Collagens J. Mol. Biol. 1984, 172, 325-343
37. Utiyama, H.; Sakato, K.; Ikehara, K.; Setsuiye, T.; Kurata, M. Flexibility Of Tropocollagen From Sedimentation And Viscosity Biopolymers 1973, 12, 53-64
38. Saito, T.; Iso, N.; Mizuno, H.; Onda, N.; Yamato, H.; Odashima, H. Semi-Flexibility Of Collagens In Solution Biopolymers. 1982, 21, 715-728
39. Nestler, F. H. M.; Hvidt, S.; Ferry, J. D.; Veis, A. Flexibility Of Collagen Determined From Dilute-Solution Viscoelastic Measurements Biopolymers 1983, 22, 1747-1758
40. Bustamante, C.; Marko, J. F.; Siggia, E. D.; Smith, S. Entropic Elasticity Of Lambda-Phage Dna Science. 1994, 265, 1599-1600
41. Pampaloni, F.; Lattanzi, G.; Jonas, A.; Surrey, T.; Frey, E.; Florin, E. L. Thermal fluctuations of grafted microtubules provide evidence of a length-dependent persistence length Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 10248-10253
42. Mogilner, A.; Oster, G. Cell motility driven by actin polymerization Biophys. J. 1996, 71, 3030-3045
43. Buehler, M. J. Atomistic modeling of elasticity, plasticity and fracture of protein crystals J. Comput. Theor. Nanosci. 2006, 3, 670-683
44. Sasaki, N.; Odajima, S. Elongation mechanism of collagen fibrils and force-strain relations of tendon at each level of structural hierarchy J Biomech. 1996, 29, 1131-1136
45. Cusack, S.; Miller, A. Determination Of The Elastic-Constants Of Collagen By Brillouin Light-Scattering J. Mol. Biol. 1979, 135, 39-51
46. Higuchi, H.; Nakauchi, Y.; Maruyama, K.; Fujime, S. Characterization of beta-connectin (titin-2) from striated-muscle by dynamic light-scattering Biophys. J. 1993, 65, 1906-1915
47. Svoboda, K.; Schmidt, C. F.; Branton, D.; Block, S. M. Conformation and elasticity of the isolated red-blood-cell membrane skeleton Biophys. J. 1992, 63, 784-793
48. Sun, Y. L.; Luo, Z. P.; Fertala, A.; An, K. N. Direct quantification of the flexibility of type I collagen monomer Biochem. Biophys. Res. Commun. 2002, 295, 382-386
49. Saito, T.; Iso, N.; Mizuno, H.; Onda, N.; Yamato, H.; Odashima, H. Semiflexibility of collagens in solution Biopolymers. 1982, 21, 715-28
50. McCauley, M. J.; Williams, M. C. Mechanisms of DNA binding determined in optical tweezers experiments Biopolymers. 2007, 85, 154-168
51. Mucke, N.; Kreplak, L.; Kirmse, R.; Wedig, T.; Herrmann, H.; Aebi, U.; Langowski, J. Assessing the flexibility of intermediate filaments by atomic force microscopy J. Mol. Biol. 2004, 335, 1241-1250
52. Kikumoto, M.; Kurachi, M.; Tosa, V.; Tashiro, H. Flexural rigidity of individual Microtubules measured by a buckling force with optical traps Biophys. J. 2006, 90, 1687-1696