Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation

Biophysical Journal

Volumn 75, Issue 2, 1998, Pages 662-671

  Lu, Hui ^a,b   Isralewitz, Barry ^a   Krammer, André ^c   Vogel, Viola ^c   Schulten, Klaus ^a  

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

^b University of Illinois at Urbana Champaign   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONNECTIN;

AMINO ACID COMPOSITION; ARTICLE; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PROTEIN CONFORMATION; PROTEIN DOMAIN; SIMULATION; STRUCTURE ACTIVITY RELATION;

EID: 0031848099     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77556-3     Document Type: Article

References (45)

1. Balsera, M., S. Stepaniants, S. Izrailev, Y. Oono, and K. Schulten. 1997. Reconstructing potential energy functions from simulated force-induced unbinding processes. Biophys. J. 73:1281-1287.
2. Bernstein, F. C., T. F. Koetzle, G. J. Williams, E. F. Meyer, M. D. Brice, J. R. Rogers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
3. Brown, I., and K. Wu. 1976. Empirical parameters for calculating cation-oxygen bond valences. Acta Crystallogr. B. 32:1957-1959.
4. Brünger, A. T. 1992. X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
5. Chan, A., E. Hutchinson, D. Harris, and J. Thornton. 1993. Identification, classification, and analysis of beta-bulges in proteins. Protein Sci. 2:1574-1590.
6. Erickson, H. 1994. Reversible unfolding of fibronectin type III and immunoglobulin domains provides the structural basis for stretch and elasticity of titin and fibronectin. Proc. Natl. Acad. Sci. USA. 91:10114-10118.
7. Evans, E., and K. Ritchie. 1997. Dynamic strength of molecular adhesion bonds. Biophys. J. 72:1541-1555.
8. Granzier, H., M. Helmes, and K. Trombitas. 1996. Nonuniform elasticity of titin in cardiac myocytes: a study using immunoelectron microscopy and cellular mechanics. Biophys. J. 70:430-442.
9. Granzier, H., M. Kellermayer, M. Helmes, and K. Trombitas. 1997. Titin elasticity and mechanism of passive force development in rat cardiac myocytes probed by thin-film extraction. Biophys. J. 73:2043-2053.
10. Greaser, M., M. Sebestyen, J. Fritz, and J. Wolff. 1996. cDNA sequence of rabbit cardiac titin/connectin. Adv. Biophys. 33:13-25.
11. Grubmüller, H., B. Heymann, and P. Tavan. 1996. Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force. Science. 271:997-999.
12. Harpaz, Y., and C. Chothia. 1994. Many of the immunoglobulin super-family domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains J. Mol. Biol. 238:528-539.
13. Honig, B., and A. Nicholls. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
14. Humphrey, W. F., A. Dalke, and K. Schulten. 1996. VMD - visual molecular dynamics. J. Mol. Graph. 14:33-38.
15. Hunenberger, P. H., A. E. Mark, and W. van Gunsteren. 1995. Computational approaches to study protein unfolding: hen egg white lysozyme as a case study. Proteins Struct. Funct. Genet. 21:196-213.
16. Improta, S., A. Politou, and A. Pastore. 1996. Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity. Structure. 4:323-337.
17. Isralewitz, B., S. Izrailev, and K. Schulten. 1997. Binding pathway of retinal to bacterioopsin: a prediction by molecular dynamics simulations. Biophys. J. 73:2972-2979.
18. Izrailev, S., S. Stepaniants, M. Baisera, Y. Oono, and K. Schulten. 1997. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J. 72:1568-1581.
19. Izrailev, S., S. Stepaniants, B. Isralewitz, D. Kosztin, H. Lu, F. Molnar, W. Wriggers and K. Schulten. 1998. Steered molecular dynamics. In Algorithms for Macromolecular Modelling, Lecture Notes in Computational Science and Engineering. P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, R. D. Skeel, and S. Reich, editors. Springer-Verlag, New York (in press).
20. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
21. Karplus, M., and A. Sali. 1995. Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5:58-73.
22. Kellermayer, M., and H. Granzier. 1996. Elastic properties of single titin molecules made visible through fluorescent F-actin binding. Biochem. Biophys. Res. Commun. 221:491-497.
23. Kellermayer, M., S. Smith, H. Granzier, and C. Bustamante. 1997. Folding-unfolding transition in single titin modules characterized with laser tweezers. Science. 276:1112-1116.
24. Labeit, S., and B. Kolmerer. 1995. Titins, giant proteins in charge of muscle ultrastructure and elasticity. Science. 270:293-296.
25. Labeit, S., B. Kolmerer, and W. Linke. 1997. The giant protein titin: emerging roles in physiology and pathophysiology. Circ. Res. 80: 290-294.
26. Leech, J., J. Prins, and J. Hermans. 1996. SMD: visual steering of molecular dynamics for protein design. IEEE Comp. Sci. Eng. 3:38-45.
27. Li, A., and V. Daggett. 1996. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J. Mol. Biol. 257:412-429.
28. Linke, W., M. Ivemeyer, N. Olivieri, B. Kolmerer, J. Ruegg, and S. Lebeit. 1996. Towards a molecular understanding of the elasticity of titin. J. Mol. Biol. 261:62-71.
29. Maruyama, K. 1997. Connectin/titin, a giant elastic protein of muscle. FASEB J. 11:341-345.
30. Munoz, V., P. Thompson, J. Hofrichter, and W. Eaton. 1997. Folding dynamics and mechanism of beta-hairpin formation. Nature. 390: 196-199.
31. 2+-binding sites in proteins. Proc. Natl. Acad. Sci. USA. 91:817-821.
32. Nelson, M., W. Humphrey, A. Gursoy, A. Dalke, L. Kalé, R. D. Skeel, and K. Schulten. 1996. NAMD - a parallel, object-oriented molecular dynamics program. J. Supercomputing Appl. 10:251-268.
33. Oberhauser, A. F., P. E. Marszalek, H. Erickson, and J. Fernandez. 1998. The molecular elasticity of tenascin, an extracellular matrix protein. Nature. 393:181-185.
34. Pearlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, D. M. Ferguson, G. L. Seibel, U. C. Singh, P. K. Weiner, and P. A. Kollman. 1995. AMBER4.1. University of California, San Francisco.
35. Pfuhl, M., M. Gautel, A. Politou, C. Joseph, and A. Pastore. 1995. Secondary structure determination by NMR spectroscopy of an immunoglobulin-like domain from the giant muscle protein titin. J. Biomol. NMR. 5:48-58.
36. Pfuhl, M., and A. Pastore. 1995. Tertiary structure of an immunoglobulin-like domain from the giant muscle protein titin: a new member of the I set. Structure. 3:391-401.
37. Politou, A., M. Gautel, M. Pfuhl, S. Labeit, and A. Pastore. 1994. Immunoglobulin-type domains of titin: same fold, different stability? Biochemistry. 33:4730-4737.
38. Politou, A. S., D. Thomas, and A. Pastore. 1995. The folding and the stability of titin immunoglobulin-like modules, with implications for mechanism of elasticity. Biophys. J. 69:2601-2610.
39. Rief, M., M. Gautel, F. Oesterhelt, J. M. Fernandez, and H. E. Gaub. 1997. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science. 276:1109-1112.
40. Stepaniants, S., S. Izrailev, and K. Schulten. 1997. Extraction of lipids from phospholipid membranes by steered molecular dynamics. J. Mol. Model. 3:473-475.
41. Swanson, E. 1996. PSSHOW User's Guide, Version 2.2. University of Washington, Seattle, WA.
42. Tirado-Rives, J., M. Orozco, and W. Jorgensen. 1997. Molecular dynamics simulations of the unfolding of barnase in water and 8M aqueous urea. Biochemistry. 36:7313-7329.
43. Tskhovrebova, L., J. Trinick, J. Sleep, and R. Simmons. 1997. Elasticity and unfolding of single molecules of the giant protein titin. Nature. 387:308-312.
44. Varshnev, A., F. P. Brooks, and W. V. Wright. 1994. Linearly scalable computation of smooth molecular surfaces. IEEE Comp. Graph. Appl. 14:19-25.
45. Wang, K., R. McCarter, J. Wright, J. severly, and R. Ramirez-Mitchell. 1993. Viscoelasticity of the sarcomere matrix of skeletal muscles. Biophys. J. 64:1161-1177.