Mesoscopic model for mechanical characterization of biological protein materials

Journal of Computational Chemistry

Volumn 30, Issue 6, 2009, Pages 873-880

  Yoon, Gwonchan ^a   Park, Hyeong Jin ^a   Na, Sungsoo ^a   Eom, Kilho ^b  

^a Korea University   (South Korea)

^b Korea Institute of Science and Technology   (South Korea)

Author keywords

Go model; Mechanical property; Protein crystal; Virial stress; Young's modulus

Indexed keywords

ATOMISTIC SIMULATIONS; BIOLOGICAL FUNCTIONS; BIOLOGICAL PROTEINS; ELASTIC BEHAVIOR; GAINING INSIGHTS; GO MODEL; MECHANICAL CHARACTERIZATIONS; MECHANICAL FUNCTIONS; MESOSCOPIC MODELS; NATIVE TOPOLOGY; NON-LINEAR ELASTIC BEHAVIOR; NORMAL STRAIN; PROTEIN CRYSTAL; PROTEIN MOLECULES; REPRESENTATIVE VOLUME ELEMENTS; STRESS THEORY; STRESS-STRAIN RELATIONSHIPS; VIRIAL STRESS; YOUNG'S MODULUS;

BIOLOGICAL MATERIALS; CRYSTALS; DROP FORMATION; ELASTIC MODULI; ELASTICITY; HYDROGEN; HYDROGEN BONDS; MECHANICAL PROPERTIES; PROTEINS; STRAIN; STRESS-STRAIN CURVES; SUPERCONDUCTING MATERIALS; VOLUME MEASUREMENT;

STRESSES;

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELASTICITY; MECHANICAL STRESS; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; ELASTICITY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; STRESS, MECHANICAL;

EID: 65449162336     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21107     Document Type: Article

References (61)

1. Oberhauser, A. F.; Marszalek, P. E.; Erickson, H. P.; Fernandez, J. M. Nature 1998, 393, 181.
2. Smith, B. L.; Schaffer, T. E.; Viani, M.; Thompson, J. B.; Frederick, N. A.; Kindt, J.; Belcher, A.; Stucky, G. D.; Morse, D. E.; Hansma, P. K. Nature 1999, 399, 761.
3. Marszalek, P. E.; Lu, H.; Li, H. B.; Carrionvazquez, M.; Oberhauser, A. F.; Schulten, K.; Fernandez, J. M. Nature 1999, 402, 100.
4. Becker, N.; Oroudjev, E.; Mutz, S.; Cleveland, J. P.; Hansma, P. K.; Hayashi, C. Y.; Makarov, D. E.; Hansma, H. G. Nat Mater 2003, 2, 278.
5. Oroudjev, E.; Soares, J.; Arcidiacono, S.; Thompson, J. B.; Fossey, S. A.; Hansma, H. G. Proc Natl Acad Sci USA 2002, 99, 6460.
6. Shao, Z.; Vollrath, F. Nature 2002, 418, 741.
7. Li, X.; Gao, H.; Murphy, C. J.; Caswell, K. K. Nano Lett 2003, 3, 1495.
8. Stephane, C.; Christian, F.; Sophie, D.-C.; Bernard, N. Phys Rev B 2004, 69, 165410.
9. Wu, B.; Heidelberg, A.; Boland, J. J. Nat Mater 2005, 4, 525.
10. Kis, A.; Kasas, S.; Babic, B.; Kulik, A. J.; Beno, W.; Briggs, G. A. D.; Schonenberger, C.; Catsicas, S.; Forro, L. Phys Rev Lett 2002, 89, 248101.
11. Pampaloni, F.; Lattanzi, G.; Jonas, A.; Surrey, T.; Frey, E.; Florin, E. -L. Proc Natl Acad Sci USA 2006, 103, 10248.
12. Wilhelm, J.; Frey, E. Phys Rev Lett 1996, 77, 2581.
13. Bustamante, C.; Marko, J. F.; Siggia, E. D.; Smith, S. Science 1994, 265, 1599.
14. Bustamante, C.; Bryant, Z.; Smith, S. B. Nature 2003, 421, 423.
15. Rief, M.; Gautel, M.; Oesterhelt, F.; Fernandez, J. M.; Gaub, H. E. Science 1997, 276, 1109.
16. Schafer, L. V.; Muller, E. M.; Gaub, H. E.; Grubmuller, H. Angew Chem Int Ed 2007, 46, 2232.
17. Liphardt, J.; Dumont, S.; Smith, S. B.; Tinoco, I.; Bustamante, C. Science 2002, 296, 1832.
18. Collin, D.; Ritort, F.; Jarzynski, C.; Smith, S. B.; Tinoco, I.; Bustamante, C. Nature 2005, 437, 231.
19. Sotomayor, M.; Schulten, K. Science 2007, 316, 1144.
20. Cieplak, M.; Pastore, A.; Hoang, T. X. J Chem Phys 2005, 122, 054906.
21. Lu, H.; Isralewitz, B.; Krammer, A.; Vogel, V.; Schulten, K. Bio-phys J 1998, 75, 662.
22. Cieplak, M.; Hoang, T. X.; Robbins, M. O. Proteins: Struct Funct Genet 2002, 49, 114.
23. Cieplak, M.; Hoang, T. X.; Robbins, M. O. Proteins: Struct Funct Bioinfo 2004, 56, 285.
24. Eom, K.; Li, P. C.; Makarov, D. E.; Rodin, G. J. J Phys Chem B 2003, 107, 8730.
25. Eom, K.; Makarov, D. E.; Rodin, G. J. Phys Rev E 2005, 71, 021904.
26. Buehler, M. J.; Ackbarow, T. Mater Today 2007, 10, 46.
27. Buehler, M. J. J Comput Theor Nanosci 2006, 3, 603.
28. Buehler, M. J. J Comput Theor Nanosci 2006, 3, 670.
29. Termonia, Y. Macromolecules 1994, 27, 7378.
30. van Beek, J. D.; Hess, S.; Vollrath, F.; Meier, B. H. Proc Natl Acad Sci USA 2002, 99, 10266.
31. Zhou, H.; Zhang, Y. Phys Rev Lett 2005, 94, 028104.
32. Kasas, S.; Kis, A.; Riederer, B. M.; Forro, L.; Dietler, G.; Catsicas, S. ChemPhysChem 2004, 5, 252.
33. Wagner, O.; Zinke, J.; Dancker, P.; Grill, W.; Bereiter-Hahn, J. Bio-phys J 1999, 76, 2784.
34. Knowles, T. P.; Fitzpatrick, A. W.; Meehan, S.; Mott, H. R.; Vendruscolo, M.; Dobson, C. M.; Welland, M. E. Science 2007, 318, 1900.
35. Makarov, D. E.; Hansma, P. K.; Metiu, H. J Chem Phys 2001, 114, 9663.
36. Ackbarow, T.; Chen, X.; Keten, S.; Buehler, M. J. Proc Natl Acad Sci USA 2007, 104, 16410.
37. Weiner, J. H. Statistical Mechanics of Elasticity; Dover: New York, 1983.
38. Zhou, M. Proc R Soc Lond A 2003, 459, 2347.
39. Timoshenko, S. P.; Goodier, J. N. Theory of Elasticity; McGraw-Hill: New York, 1970.
40. Landau, L. D.; Lifshitz, E. M. Theory of Elasticity; Butterworth- Heinemann: St. Louis, 1986.
41. Hayward, S.; Go, N. Annu Rev Phys Chem 1995, 46, 223.
42. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J Am Chem Soc 1984, 106, 765.
43. Tirion, M. M. Phys Rev Lett 1996, 77, 1905.
44. Atilgan, A. R.; Durell, S. R.; Jernigan, R. L.; Demirel, M. C.; Keskin, O.; Bahar, I. Biophys J 2001, 80, 505.
45. Tama, F.; Brooks, C. L. Annu Rev Biophys Biomol Struct 2006, 35, 115.
46. Nicolay, S.; Sanejouand, Y. H. Phys Rev Lett 2006, 96, 078104.
47. Eom, K.; Baek, S.-C.; Ahn, J.-H.; Na, S. J Comput Chem 2007, 28, 1400.
48. Eom, K.; Ahn, J. H.; Baek, S. C.; Kim, J. I.; Na, S. CMC: Comput Mater Continua 2007, 6, 35.
49. Juanico, B.; Sanejouand, Y. H.; Piazza, F.; Rios, P. D. L. Phys Rev Lett 2007, 99, 238104.
50. Paci, E.; Karplus, M. Proc Natl Acad Sci USA 2000, 97, 6521.
51. Christensen, R. M. Theory of Viscoelasticity; Dover: New York, 2003.
52. Makarov, D. E. Biophys J 2007, 92, 4135.
53. Tskhovrebova, L.; Trinick, J. J Biol Chem 2004, 279, 46351.
54. Keten, S.; Buehler, M. J. Nano Lett 2008, 8, 743.
55. Plaxco, K. W.; Simons, K. T.; Baker, D. J Mol Biol 1998, 277, 985.
56. Bell, G. I. Science 1978, 200, 618.
57. Seifert, U. Phys Rev Lett 2000, 84, 2750.
58. Dietz, H.; Rief, M. Phys Rev Lett 2008, 100, 098101.
59. Klimov, D. K.; Thirumalai, D. Proc Natl Acad Sci USA 2000, 97, 7254.
60. Brockwell, D. J.; Beddard, G. S.; Paci, E.; West, D. K.; Olmsted, P. D.; Smith, D. A.; Radford, S. E. Biophys J 2005, 89, 506.
61. Li, M. S. Biophys J 2007, 93, 2644.