Single-molecule experiments in vitro and in silico

Science

Volumn 316, Issue 5828, 2007, Pages 1144-1148

  Sotomayor, Marcos ^a   Schulten, Klaus ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANKYRIN; CONNECTIN; CYTOSKELETON PROTEIN; FIBRONECTIN; MUSCLE PROTEIN; SCLEROPROTEIN; SPECTRIN;

COMPUTER SIMULATION; EXPERIMENTAL STUDY; MOLECULAR ANALYSIS; PROTEIN; SILICON;

CELL FUNCTION; COMPUTER ANALYSIS; COMPUTER MODEL; ELASTICITY; HUMAN; IN VITRO STUDY; MACROMOLECULE; MECHANICS; MOLECULAR DYNAMICS; MOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; REVIEW; SIMULATION;

ANKYRIN REPEAT; COMPUTER SIMULATION; ELASTICITY; FIBRONECTINS; HUMANS; MODELS, BIOLOGICAL; MUSCLE PROTEINS; PROTEIN KINASES; SPECTRIN; SPECTRUM ANALYSIS;

EID: 34249930159     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1137591     Document Type: Review

References (72)

1. Molecular dynamics (MD) simulations have their bases in theoretical models describing interactions between atoms through so-called force fields (66-68). In a typical MD simulation, initial coordinates of the atoms in a macromolecule are obtained from crystallographic or NMR structures. The structure is then solvated in water, and the motion of atoms in time is determined through integration of Newton's equations (68) assuming the mentioned force field. Current simulation packages, such as NAMD (68), use standardized force fields and provide the source code of the simulation engine. The widespread use and availability of the software and force fields ensures constant verification and reproducibility of results.
2. SMD simulations apply, in addition to indigenous forces, external forces to biomolecules (17). There are two typical protocols for SMD simulations: constant force and constant velocity. In constant force SMD simulations, a force is directly applied to one or more atoms, and extension or displacement is monitored throughout dynamics. Customized time-dependent forces may be applied as well, in constant velocity SMD simulations, a moving harmonic potential (spring) is used to induce motion along a reaction coordinate. The free end of the spring is moved at constant velocity, while the protein atoms attached to the other end of the spring are subject to the steering force. The force applied is determined by the extension of the spring and can be monitored throughout the entire simulation.
3. A. D. Mehta, M. Rief, J. A. Spudich, D. A. Smith, R. M. Simmons, Science 283, 1689 (1999).
4. J. Zlatanova, K. van Holde, Mol. Cell 24, 317 (2006).
5. D. Leckband, A. Prakasam, Annu. Rev. Biomed. Eng. 8, 259 (2006).
6. M. Gao, M. Sotomayor, E. Villa, E. Lee, K. Schulten, Phys. Chem. Chem. Phys. 8, 3692 (2006).
7. V. Vogel, Annu. Rev. Biophys. Biomol. Struct. 35, 459 (2006).
8. H. Lu, B. Isralewitz, A. Krammer, V. Vogel, K. Schulten, Biophys. J. 75, 662 (1998).
9. H. Lu, K. Schulten, Biophys. J. 79, 51 (2000).
10. M. Gao, H. Lu, K. Schulten, J. Muscle Res. Cell Motil. 23, 513 (2002).
11. M. Gao et al., Proc. Natl. Acad. Sci. U.S.A. 100, 14784 (2003).
12. V. Ortiz, S. O. Nielsen, M. L. Klein, D. E. Discher, J. Mol. Biol. 349, 638 (2005).
13. S. Paramore, G. A. Voth, Biophys. J. 91, 3436 (2006).
14. M. Sotomayor, D. P. Corey, K. Schulten, Structure 13, 669 (2005).
15. Z. Lu, H. Hu, W. Yang, P. E. Marszalek, Biophys. J. 91, L57 (2006).
16. M. Carrion-Vazquez et al., Nat. Struct. Biol. 10, 738 (2003).
17. B. Isralewitz, M. Gao, K. Schulten, Curr. Opin. Struct. Biol. 11, 224 (2001).
18. H. Grubmüller, Methods Mol. Biol. 305, 493 (2005).
19. E.-L. Florin, V. T. Moy, H. E. Gaub, Science 264, 415 (1994).
20. H. Grubmüller, B. Heymann, P. Tavan, Science 271, 997 (1996).
21. S. Izrallev, S. Stepaniants, M. Balsera, Y. Oono, K. Schulten, Biophys. J. 72, 1568 (1997).
22. E. Evans, K. Ritchie, Biophys. J. 72, 1541 (1997).
23. L. Tskhovrebova, J. Trinick, Nat. Rev. Mol. Cell Biol. 4, 679 (2003).
24. S. Improta, A. Politou, A. Pastore, Structure 4, 323 (1996).
25. M. Rief, M. Gautel, F. Oesterhelt, J. M. Fernandez, H. E. Gaub, Science 276, 1109 (1997).
26. M. S. Z. Kellermayer, S. Smith, H. Granzier, C. Bustamante, Science 276, 1112 (1997).
27. L. Tskhovrebova, J. Trinick, J. Sleep, R. Simmons, Nature 387, 308 (1997).
28. P. E. Marszalek et al., Nature 402, 100 (1999).
29. S. B. Fowler et al., J. Mol. Biol. 322, 841 (2002).
30. P. M. Williams et al., Nature 422, 446 (2003).
31. R. B. Best et al., J. Mol. Biol. 330, 867 (2003).
32. H. Lu, K. Schulten, Proteins Struct. Funct. Genet. 35, 453 (1999).
33. D. Craig, M. Gao, K. Schulten, V. Vogel, Structure 12, 21 (2004).
34. F. Gráter, J. Shen, H. Jiang, M. Gautel, H. Grubmüller, Biophys. J. 88, 790 (2005).
35. A. F. Oberhauser, C. Badilla-Fernandez, M. Carrion-Vazquez, J. Fernandez, J. Mol. Biol. 319, 433 (2002).
36. D. Craig, A. Krammer, K. Schulten, V. Vogel, Proc. Natl. Acad. Sci. U.S.A. 98, 5590 (2001).
37. R. W. S. Rounsevell, J. Clarke, Structure 12, 4 (2004).
38. E. Paci, M. Karplus, J. Mol. Biol. 288, 441 (1999).
39. M. Gao, D. Craig, V. Vogel, K. Schulten, J. Mol. Biol. 323, 939 (2002).
40. L. Li, H. H. Huang, C. L. Badilla, J. M. Fernandez, J. Mol. Biol. 345, 817 (2005).
41. M. Yi, E. Ruoslahti, Proc. Natl. Acad. Sci. U.S.A. 98, 620 (2001).
42. V. Bennett, A. J. Baines, Physiol. Rev. 81, 1353 (2001).
43. D. E. Discher, P. Carl, Cell. Mol. Biol. Lett. 6, 593 (2001).
44. C. P. Johnson et al., Blood 109, 3538 (2007).
45. H. Kusunoki, R. I. MacDonald, A. Mondragón, Structure 12, 645 (2004).
46. M. Rief, J. Pascual, M. Saraste, H. Gaub, J. Mol. Biol. 286, 553 (1999).
47. S. M. Altmann et al., Structure 10, 1085 (2002).
48. R. Law et al., Biophys. J. 84, 533 (2003).
49. L. G. Randles, R. W. S. Rounsevell, J. Clarke, Biophys. J. 92, 571 (2007).
50. The magnitude and fluctuations of the monitored forces in constant-velocity SMD simulations will depend on the stretching velocity and spring constant used (21, 22). The smaller the velocity used, the less drastic the perturbation of the system is, and more details along the reaction coordinate are likely to be captured. Because of limitations in computational resources, even the slowest stretching velocities used in simulations are orders of magnitude faster than those used in equivalent AFM stretching experiments. The force peak values observed will then be larger than those recorded in experiments (Fig. 1D). The dependence of the monitored force on the stretching velocity is more relevant for secondary structure elasticity than for tertiary structure elasticity, because in the latter case solvent effects due to friction and hydrogen bond attack play a less important role.
51. P. J. Mohler, A. O. Gramolini, V. Bennett, J. Cell Sci. 115, 1565 (2002).
52. L. K. Mosavi, T. J. Cammett, D. C. Desrosiers, Z. Peng, Protein Sci. 13, 1435 (2004).
53. L. K. Mosavi, D. L. Minor, Z. Peng, Proc. Natl. Acad. Sci. U.S.A. 99, 16029 (2002).
54. P. Michaely, D. R. Tomchick, M. Machlus, R. G. W. Anderson, EMBO J. 21, 6387 (2002).
55. J. Howard, S. Bechstedt, Curr. Biol. 14, R224 (2004).
56. D. P. Corey, M. Sotomayor, Nature 428, 901 (2004).
57. G. Lee et al., Nature 440, 246 (2006).
58. L. Li, S. Wetzel, A. Pluckthun, J. M. Fernandez, Biophys. J. 90, L30 (2006).
59. It is often noticed that SMD simulations yield "wrong" unfolding force values when compared with AFM measurements. Such a statement is obviously ilogical, because SMD simulations must yield stronger forces because of the faster pulling velocity. Faster pulling may alter the nature of the protein's elastic response, but AFM extensions can be directly compared with SMD extensions, offering a test of the concern.
60. M. Takeichi, Annu. Rev. Biochem. 59, 237 (1990).
61. T. J. Boggon et al., Science 296, 1308 (2002); published online 18 April 2002 (10.1126/science.1071559).
62. F. Cailliez, R. Lavery, Biophys. J. 89, 3895 (2005).
63. C. Söllner et al., Nature 428, 955 (2004).
64. J. Siemens et al., Nature 428, 950 (2004).
65. M. Marino et al., Structure 14, 1437 (2006).
66. A. MacKerell Jr. et al., J. Phys. Chem. B 102, 3586 (1998).
67. S. A. Adcock, J. A. McCammon, Chem. Rev. 106, 1589(2006).
68. J. C. Phillips et al., J. Comput. Chem. 26, 1781 (2005).
69. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph. 14, 33 (1996).
70. H. Lu, K. Schulten, Chem. Phys. 247, 141 (1999).
71. M. Rief, H. Grubmüller, ChemPhysChem 3, 255 (2002).
72. The work reviewed here involved many researchers from our own and other groups. We apologize to all researchers whose pioneering work could not be reviewed because of space limitation. We thank M. Gao, B. Isralewitz, S. Izrailev, H. Lu, J. C. Gumbart, and members of the Theoretical and Computational Biophysics Group for their contributions and helpful discussions; our long-time collaborator, V. Vogel, for guidance and Inspirations; collaborators D. P. Corey, D. Craig, A. Krammer, O. Mayans, and M. Wilmanns; and J. Fernandez and P. Marszalek for a wonderful experimental-theoretical collaboration. The molecular images in this paper were created with the molecular graphics program VMD (69) and Tachyon. This work was supported by funds of the NIH (grant no. P41 RR05969 and grant no. 1 R01 GM073655) and the Humboldt Foundation (K.S.). The authors also acknowledge computer time provided by the NSF through the Large Resource Allocations Committee grant MCA93S02B.