Steered molecular dynamics studies of titin I1 domain unfolding

Biophysical Journal

Volumn 83, Issue 6, 2002, Pages 3435-3445

  Gao, Mu ^a   Wilmanns, Matthias ^b   Schulten, Klaus ^a,c  

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

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

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

Author keywords

[No Author keywords available]

Indexed keywords

CONNECTIN; DISULFIDE; IMMUNOGLOBULIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; BETA CHAIN; DISULFIDE BOND; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR MODEL; OXIDATION; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; SIMULATION; STRESS; VELOCITY;

EID: 0036924186     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)75343-5     Document Type: Article

References (33)

1. Brünger, A. T. 1992. X-PLOR, Version 3.1: A System of X-ray Crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University.
2. Carrion-Vazquez, M., A. Oberhauser, S. Fowler, P. Marszalek, S. Broedel, J. Clarke, and J. Fernandez. 1999. Mechanical and chemical unfolding of a single protein: A comparison. Proc. Natl. Acad. Sci. U.S.A. 96:3694-3699.
3. Consortium, 2001. Initial sequencing and analysis of the human genome. Nature. 409:860-921.
4. 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. U.S.A. 91:10114-10118.
5. Erickson, H. 1997. Stretching single protein modules: Titin is a weird spring. Science. 276:1090-1093.
6. Freiburg, A., K. Trombitas, W. Hell, O. Cazorla, F. Fougerousse, T. Centner, B. Kolmerer, C. Witt, J. Beckmann, C. Gregorio, H. Granzier, and S. Labeit. 2000. Series of exon-skipping events in the elastic spring region of titin as the structural basis for myofibrillar elastic diversity. Circ. Res. 86:1114-1121.
7. Gao, M., H. Lu, and K. Schulten. 2001. Simulated refolding of stretched titin immunoglobulin domains. Biophys. J. 81:2268-2277.
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., and S. Labeit. 2002. Cardiac titin: An adjustable multifunctional spring. J. Physiol. 541:335-342.
10. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD - Visual molecular dynamics. J. Mol. Graphics. 14:33-38.
11. Isralewitz, B., M. Gao, and K. Schulten. 2001. Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11:224-230.
12. Izrailev, S., S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten. 1997. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J. 72:1568-1581.
13. 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.
14. Kalé, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. 1999. NAMD2: Greater scalability for parallel molecular dynamics. J. Comp. Phys. 151:283-312.
15. 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.
16. Klimov, D. K., and D. Thirumalai. 1999. Stretching single-domain proteins: Phase diagram and kinetics of force-induced unfolding. Proc. Natl. Acad. Sci. U.S.A. 96:1306-1315.
17. Klimov, D. K., and D. Thirumalai. 2000. Native topology determines force-induced unfolding pathways in globular proteins. Proc. Natl. Acad. Sci. U.S.A. 97:7254-7259.
18. Li, H., C. V. Mariano, A. F. Oberhauser, P. E. Marszalek, and J. M. Fernandez. 2001b. Point mutations alter the mechanical stability of immunoglobulin modules. Nature Struct. Biol. 7:1117-1120.
19. Li, H. B., A. F. Oberhauser, S. B. Fowler, J. Clarke, and J. M. Fernandez. 2000. Atomic force microscopy reveals the mechanical design of a modular protein. Proc. Natl. Acad. Sci. U.S.A. 97:6527-6531.
20. Li, H., A. F. Oberhauser, S. D. Redick, M. Carrion-Vazquez, H. Erikson, and J. M. Fernandez. 2001a. Multiple conformations of PEVK proteins detected by single-molecule techniques. Proc. Natl. Acad. Sci. U.S.A. 98:10682-10686.
21. Linke, W. A. 2000. Stretching molecular springs: Elasticity of titin filaments in vertebrate striated muscle. Histol. Histopathol. 15:799-811.
22. Linke, W. A., M. Ivemeyer, P. Mundel, M. R. Stockmeier, and B. Kolmerer. 1998. Nature of PEVK-titin elasticity in skeletal muscle. Proc. Natl. Acad. Sci. U.S.A. 95:8052-8057.
23. Linke, W. A., D. E. Rudy, T. Centner, M. Gautel, C. Witt, S. Labeit, and C. C. Gregorio. 1999. I-band titin in cardiac muscle is a three-element molecular spring and is critical for maintaining thin filament structure. J. Cell Biol. 146:631-644.
24. Lu, H., B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten. 1998. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys. J. 75:662-671.
25. Lu, H., and K. Schulten. 1999. Steered molecular dynamics simulation of conformational changes of immunoglobulin domain 127 interpret atomic force microscopy observations. Chem. Phys. 247:141-153.
26. Lu, H., and K. Schulten. 2000. The key event in force-induced unfolding of titin's immunoglobulin domains. Biophys. J. 79:51-65.
27. Ma, K., L. Kan, and K. Wang. 2001. Polyproline II helix is a key structural motif of the elastic PEVK segment of titin. Biochemistry. 40:3427-38.
28. MacKerell Jr., A. D., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. Evanseck, M. J. Field, S. Fischer, 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-hydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field. J. Phys. Chem. B. 102:3586-3616.
29. Marszalek, P. E., H. Lu, H. Li, M. Carrion-Vazquez, A. F. Oberhauser, K. Schulten, and J. M. Fernandez. 1999. Mechanical unfolding intermediates in titin modules. Nature. 402:100-103.
30. Maruyama, K. 1997. Connectin/titin, a giant elastic protein of muscle. FASEB J. 11:341-345.
31. Mayans, O., J. Wuerges, S. Canela, M. Gautel, and M. Wilmanns. 2001. Structural Evidence
32. 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.
33. Wang, K. 1996. Titin/connectin and nebulin: Giant protein ruler of muscle structure and function. Adv. Biophys. 33:123-134.