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. 1998 Aug;75(2):662–671. doi: 10.1016/S0006-3495(98)77556-3

Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation.

H Lu 1, B Isralewitz 1, A Krammer 1, V Vogel 1, K Schulten 1
PMCID: PMC1299741  PMID: 9675168

Abstract

Titin, a 1-microm-long protein found in striated muscle myofibrils, possesses unique elastic and extensibility properties in its I-band region, which is largely composed of a PEVK region (70% proline, glutamic acid, valine, and lysine residue) and seven-strand beta-sandwich immunoglobulin-like (Ig) domains. The behavior of titin as a multistage entropic spring has been shown in atomic force microscope and optical tweezer experiments to partially depend on the reversible unfolding of individual Ig domains. We performed steered molecular dynamics simulations to stretch single titin Ig domains in solution with pulling speeds of 0.5 and 1.0 A/ps. Resulting force-extension profiles exhibit a single dominant peak for each Ig domain unfolding, consistent with the experimentally observed sequential, as opposed to concerted, unfolding of Ig domains under external stretching forces. This force peak can be attributed to an initial burst of backbone hydrogen bonds, which takes place between antiparallel beta-strands A and B and between parallel beta-strands A' and G. Additional features of the simulations, including the position of the force peak and relative unfolding resistance of different Ig domains, can be related to experimental observations.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Balsera M., Stepaniants S., Izrailev S., Oono Y., Schulten K. Reconstructing potential energy functions from simulated force-induced unbinding processes. Biophys J. 1997 Sep;73(3):1281–1287. doi: 10.1016/S0006-3495(97)78161-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  3. Chan A. W., Hutchinson E. G., Harris D., Thornton J. M. Identification, classification, and analysis of beta-bulges in proteins. Protein Sci. 1993 Oct;2(10):1574–1590. doi: 10.1002/pro.5560021004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Erickson H. P. 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. 1994 Oct 11;91(21):10114–10118. doi: 10.1073/pnas.91.21.10114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Evans E., Ritchie K. Dynamic strength of molecular adhesion bonds. Biophys J. 1997 Apr;72(4):1541–1555. doi: 10.1016/S0006-3495(97)78802-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Granzier H., Helmes M., Trombitás K. Nonuniform elasticity of titin in cardiac myocytes: a study using immunoelectron microscopy and cellular mechanics. Biophys J. 1996 Jan;70(1):430–442. doi: 10.1016/S0006-3495(96)79586-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Granzier H., Kellermayer M., Helmes M., Trombitás K. Titin elasticity and mechanism of passive force development in rat cardiac myocytes probed by thin-filament extraction. Biophys J. 1997 Oct;73(4):2043–2053. doi: 10.1016/S0006-3495(97)78234-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Greaser M. L., Sebestyen M. G., Fritz J. D., Wolff J. A. cDNA sequence of rabbit cardiac titin/connectin. Adv Biophys. 1996;33:13–25. [PubMed] [Google Scholar]
  9. Grubmüller H., Heymann B., Tavan P. Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science. 1996 Feb 16;271(5251):997–999. doi: 10.1126/science.271.5251.997. [DOI] [PubMed] [Google Scholar]
  10. Harpaz Y., Chothia C. Many of the immunoglobulin superfamily 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. 1994 May 13;238(4):528–539. doi: 10.1006/jmbi.1994.1312. [DOI] [PubMed] [Google Scholar]
  11. Honig B., Nicholls A. Classical electrostatics in biology and chemistry. Science. 1995 May 26;268(5214):1144–1149. doi: 10.1126/science.7761829. [DOI] [PubMed] [Google Scholar]
  12. Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996 Feb;14(1):33-8, 27-8. doi: 10.1016/0263-7855(96)00018-5. [DOI] [PubMed] [Google Scholar]
  13. Hünenberger P. H., Mark A. E., van Gunsteren W. F. Computational approaches to study protein unfolding: hen egg white lysozyme as a case study. Proteins. 1995 Mar;21(3):196–213. doi: 10.1002/prot.340210303. [DOI] [PubMed] [Google Scholar]
  14. Improta S., Politou A. S., Pastore A. Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity. Structure. 1996 Mar 15;4(3):323–337. doi: 10.1016/s0969-2126(96)00036-6. [DOI] [PubMed] [Google Scholar]
  15. Isralewitz B., Izrailev S., Schulten K. Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations. Biophys J. 1997 Dec;73(6):2972–2979. doi: 10.1016/S0006-3495(97)78326-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Izrailev S., Stepaniants S., Balsera M., Oono Y., Schulten K. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J. 1997 Apr;72(4):1568–1581. doi: 10.1016/S0006-3495(97)78804-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Karplus M., Sali A. Theoretical studies of protein folding and unfolding. Curr Opin Struct Biol. 1995 Feb;5(1):58–73. doi: 10.1016/0959-440x(95)80010-x. [DOI] [PubMed] [Google Scholar]
  18. Kellermayer M. S., Granzier H. L. Elastic properties of single titin molecules made visible through fluorescent F-actin binding. Biochem Biophys Res Commun. 1996 Apr 25;221(3):491–497. doi: 10.1006/bbrc.1996.0624. [DOI] [PubMed] [Google Scholar]
  19. Kellermayer M. S., Smith S. B., Granzier H. L., Bustamante C. Folding-unfolding transitions in single titin molecules characterized with laser tweezers. Science. 1997 May 16;276(5315):1112–1116. doi: 10.1126/science.276.5315.1112. [DOI] [PubMed] [Google Scholar]
  20. Labeit S., Kolmerer B., Linke W. A. The giant protein titin. Emerging roles in physiology and pathophysiology. Circ Res. 1997 Feb;80(2):290–294. doi: 10.1161/01.res.80.2.290. [DOI] [PubMed] [Google Scholar]
  21. Labeit S., Kolmerer B. Titins: giant proteins in charge of muscle ultrastructure and elasticity. Science. 1995 Oct 13;270(5234):293–296. doi: 10.1126/science.270.5234.293. [DOI] [PubMed] [Google Scholar]
  22. Li A., Daggett V. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Biol. 1996 Mar 29;257(2):412–429. doi: 10.1006/jmbi.1996.0172. [DOI] [PubMed] [Google Scholar]
  23. Linke W. A., Ivemeyer M., Olivieri N., Kolmerer B., Rüegg J. C., Labeit S. Towards a molecular understanding of the elasticity of titin. J Mol Biol. 1996 Aug 9;261(1):62–71. doi: 10.1006/jmbi.1996.0441. [DOI] [PubMed] [Google Scholar]
  24. Maruyama K. Connectin/titin, giant elastic protein of muscle. FASEB J. 1997 Apr;11(5):341–345. doi: 10.1096/fasebj.11.5.9141500. [DOI] [PubMed] [Google Scholar]
  25. Muñoz V., Thompson P. A., Hofrichter J., Eaton W. A. Folding dynamics and mechanism of beta-hairpin formation. Nature. 1997 Nov 13;390(6656):196–199. doi: 10.1038/36626. [DOI] [PubMed] [Google Scholar]
  26. Nayal M., Di Cera E. Predicting Ca(2+)-binding sites in proteins. Proc Natl Acad Sci U S A. 1994 Jan 18;91(2):817–821. doi: 10.1073/pnas.91.2.817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Oberhauser A. F., Marszalek P. E., Erickson H. P., Fernandez J. M. The molecular elasticity of the extracellular matrix protein tenascin. Nature. 1998 May 14;393(6681):181–185. doi: 10.1038/30270. [DOI] [PubMed] [Google Scholar]
  28. Pfuhl M., Gautel M., Politou A. S., Joseph C., Pastore A. Secondary structure determination by NMR spectroscopy of an immunoglobulin-like domain from the giant muscle protein titin. J Biomol NMR. 1995 Jul;6(1):48–58. doi: 10.1007/BF00417491. [DOI] [PubMed] [Google Scholar]
  29. Pfuhl M., Pastore A. Tertiary structure of an immunoglobulin-like domain from the giant muscle protein titin: a new member of the I set. Structure. 1995 Apr 15;3(4):391–401. doi: 10.1016/s0969-2126(01)00170-8. [DOI] [PubMed] [Google Scholar]
  30. Politou A. S., Gautel M., Pfuhl M., Labeit S., Pastore A. Immunoglobulin-type domains of titin: same fold, different stability? Biochemistry. 1994 Apr 19;33(15):4730–4737. doi: 10.1021/bi00181a604. [DOI] [PubMed] [Google Scholar]
  31. Politou A. S., Thomas D. J., Pastore A. The folding and stability of titin immunoglobulin-like modules, with implications for the mechanism of elasticity. Biophys J. 1995 Dec;69(6):2601–2610. doi: 10.1016/S0006-3495(95)80131-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Rief M., Gautel M., Oesterhelt F., Fernandez J. M., Gaub H. E. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science. 1997 May 16;276(5315):1109–1112. doi: 10.1126/science.276.5315.1109. [DOI] [PubMed] [Google Scholar]
  33. Tirado-Rives J., Orozco M., Jorgensen W. L. Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea. Biochemistry. 1997 Jun 17;36(24):7313–7329. doi: 10.1021/bi970096i. [DOI] [PubMed] [Google Scholar]
  34. Tskhovrebova L., Trinick J., Sleep J. A., Simmons R. M. Elasticity and unfolding of single molecules of the giant muscle protein titin. Nature. 1997 May 15;387(6630):308–312. doi: 10.1038/387308a0. [DOI] [PubMed] [Google Scholar]
  35. Wang K., McCarter R., Wright J., Beverly J., Ramirez-Mitchell R. Viscoelasticity of the sarcomere matrix of skeletal muscles. The titin-myosin composite filament is a dual-stage molecular spring. Biophys J. 1993 Apr;64(4):1161–1177. doi: 10.1016/S0006-3495(93)81482-6. [DOI] [PMC free article] [PubMed] [Google Scholar]

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