Theoretical Chemistry Accounts

, Volume 125, Issue 3–6, pp 397–405 | Cite as

Interplay of mechanical and binding properties of Fibronectin type I

  • Jiankuai Diao
  • Andrew J. Maniotis
  • Robert Folberg
  • Emad Tajkhorshid
Regular Article


Fibronectins (FNs) are a major component of the extracellular matrix (ECM), and provide important binding sites for a variety of ligands outside and on the surface of the cell. Similar to other ECM proteins, FNs are consistently subject to mechanical stress in the ECM. Therefore, it is important to study their structure and binding properties under mechanical stress and understand how their binding and mechanical properties might affect each other. Although certain FN modules have been extensively investigated, no simulation studies have been reported for the FN type I (Fn1) domains, despite their prominent role in binding of various protein modules to FN polymers in the ECM. Using equilibrium and steered molecular dynamics simulations, we have studied mechanical properties of Fn1 modules in the presence or the absence of a specific FN-binding peptide (FnBP). We have also investigated how the binding of the FnBP peptide to Fn1 might be affected by tensile force. Despite the presence of disulfide bonds within individual Fn1 modules that are presumed to prevent their extension, it is found that significant internal structural changes within individual modules are induced by the forces applied in our simulations. These internal structural changes result in significant variations in the accessibility of different residues of the Fn1 modules, which affect their exposure, and, thus, the binding properties of the Fn1 modules. Binding of the FnBP appears to reduce the flexibility of the linker region connecting individual Fn1 modules (exhibited in the form of reduced fluctuation and motion of the linker region), both with regard to bending and stretching motions, and hence stabilizes the inter-domain configuration under force. Under large tensile forces, the FnBP peptide unbinds from Fn1. The results suggest that Fn1 modules in FN polymers do contribute to the overall extension caused by force-induced stretching of the polymer in the ECM, and that binding properties of Fn1 modules can be affected by mechanically induced internal protein conformational changes in spite of the presence of disulfide bonds which were presumed to completely abolish the capacity of Fn1 modules to undergo extension in response to external forces.


Molecular dynamics Fibronectin binding protein Extracellular matrix Steered molecular dynamics Mechanical proteins 



This work was supported by grants from NIH [P41-RR05969 (ET) and EY10457 (RF)]. The authors acknowledge computer time provided at TeraGrid resources (grant number MCA06N060), as well as computer time from the DoD High Performance Computing Modernization Program at the Arctic Region Supercomputing Center, University of Alaska at Fairbanks.


  1. 1.
    Ingber D (1998) The architecure of life. Scientific American January:48–57Google Scholar
  2. 2.
    Maniotis A, Chen C, Ingber D (1997) Demonstration of mechanical interconnections between integrins, cytoskeletal filaments, and nuclear scaffolds that stabilize nuclear structure. Proc Natl Acad Sci USA 94:849–854CrossRefGoogle Scholar
  3. 3.
    Humphries MJ, Obara M, Yamada KOKM (1989) Role of Fibronectin in addhesion, migration, and metastasis. Cancer Invest 7:373–393CrossRefGoogle Scholar
  4. 4.
    Mosher DF (1989) Fibronectin. Academic Press, New YorkGoogle Scholar
  5. 5.
    Hynes RO (1990) Fibronectins. Springer, New YorkGoogle Scholar
  6. 6.
    Ohashi T, Kiehart DP, Erickson HP (1999) Dynamics and elasticity of the fibronectin matrix in living cell culture visualized by fibronectin-green fluorescent protein. Proc Natl Acad Sci USA 96:2153–2158CrossRefGoogle Scholar
  7. 7.
    Baneyx G, Baugh L, Vogel V (2002) Supramolecular chemistry and self-assembly special feature: fibronectin extension and unfolding within cell matrix fibrils controlled by cytoskeletal tension. Proc Natl Acad Sci USA 99:5139–5143CrossRefGoogle Scholar
  8. 8.
    Hocking DC, Sottile J, McKeown-Longo PJ (1994) Fibronectin’s III-1 module contains a conformation-dependent binding site for the amino-terminal region of fibronectin. J Biol Chem 269:19183–19187Google Scholar
  9. 9.
    Zhong C, Chrzanowska-Wodnicka M, Brown J, Shaub A, Belkin AM, Burridge K (1998) Rho-mediated contractility exposes a cryptic site in fibronectin and induces fibronectin matrix assembly. J Cell Biol 141:539–551CrossRefGoogle Scholar
  10. 10.
    Langenbach KJ, Sottile J (1999) Identification of protein-disulfide isomerase activity in fibronectin. J Biol Chem 274:7032–7038CrossRefGoogle Scholar
  11. 11.
    Gao M, Craig D, Vogel V, Schulten K (2002) Identifying unfolding intermediates of FN-III10 by steered molecular dynamics. J Mol Biol 323:939–950CrossRefGoogle Scholar
  12. 12.
    Gao M, Craig D, Lequin O, Campbell ID, Vogel V, Schulten K (2003) Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates. Proc Natl Acad Sci USA 100:14784–14789CrossRefGoogle Scholar
  13. 13.
    Vogel V (2006) Mechanotransduction involving multimodular proteins: converting force into biochemical signals. Annu Rev Biophys Biomol Struct 35:459–488CrossRefGoogle Scholar
  14. 14.
    Gao M, Sotomayor M, Villa E, Lee E, Schulten K (2006) Molecular mechanisms of cellular mechanics. Phys Chem Chem Phys 8:3692–3706CrossRefGoogle Scholar
  15. 15.
    Magnusson MK, Mosher DF (1998) Role of fibronectin in addhesion, migration, and metastasis. Artheroscler Thromb Vasc Biol 18:1363–1370Google Scholar
  16. 16.
    Mao Y, Schwarzbauer JE (2005) Fibronectin fibrillogenesis, a cell-mediated matrix assembly process. Matrix Biol 24:389–399CrossRefGoogle Scholar
  17. 17.
    Wierzbicka-Patynowski I, Schwarzbauer JE (2003) The ins and outs of fibronectin matrix assembly. J Cell Sci 116:3269–3276CrossRefGoogle Scholar
  18. 18.
    Rostagno AA, Schwarzbauer JE, Gold LI (1999) Comparison of the fibrin-binding activities in the N- and C-termini of fibronectin. Biochem J 338:375–386CrossRefGoogle Scholar
  19. 19.
    Lin H, Lai R, Clegg DO (2000) Comparison of the fibrin-binding activities in the N- and C-termini of fibronectin. Biochemistry 39:3192–3196CrossRefGoogle Scholar
  20. 20.
    Ingham KC, Brew SA, Erickson HP (2004) Localization of a cryptic binding site for tenascin on fibronectin. J Biol Chem 279:28132–28135CrossRefGoogle Scholar
  21. 21.
    Schwarz-Linek U, Werner JM, Pickford AR, Gurusiddappa S, Kim JH, Pilka ES, Briggs JAG, Gough TS, Hook M, Campbell ID, Potts JR (2003) Pathogenic bacteria attach to human fibronectin through a tandem beta-zipper. Nature 423:177–181CrossRefGoogle Scholar
  22. 22.
    Schwarz-Linek U, Hook M, Potts JR (2004) The molecular basis of fibronectin-mediated bacterial adherence to host cells. Mol Microbiol 52:631–641CrossRefGoogle Scholar
  23. 23.
    Isralewitz B, Gao M, Schulten K (2001) Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol 11:224–230CrossRefGoogle Scholar
  24. 24.
    Sotomayor M, Schulten K (2007) Single-molecule experiments in vitro and in silico. Science 316:1144–1148CrossRefGoogle Scholar
  25. 25.
    Lu H, Isralewitz B, Krammer A, Vogel V, Schulten K (1998) Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J 75:662–671CrossRefGoogle Scholar
  26. 26.
    Marszalek PE, Lu H, Li H, Carrion-Vazquez M, Oberhauser AF, Schulten K, Fernandez JM (1999) Mechanical unfolding intermediates in titin modules. Nature 402:100–103CrossRefGoogle Scholar
  27. 27.
    Lu H, Schulten K (2000) The key event in force-induced unfolding of titin’s immunoglobulin domains. Biophys J 79:51–65CrossRefGoogle Scholar
  28. 28.
    Lu H, Krammer A, Isralewitz B, Vogel V, Schulten K (2000) Computer modeling of force-induced titin domain unfolding. In: Pollack J, Granzier H (eds) Elastic filaments of the cell, chap 1. Kluwer Academic/Plenum Publishers, New York, pp 143–162Google Scholar
  29. 29.
    Gao M, Lu H, Schulten K (2001) Simulated refolding of stretched titin immunoglobulin domains. Biophys J 81:2268–2277CrossRefGoogle Scholar
  30. 30.
    Gao M, Wilmanns M, Schulten K (2002) Steered molecular dynamics studies of titin I1 domain unfolding. Biophys J 83:3435–3445CrossRefGoogle Scholar
  31. 31.
    Gao M, Lu H, Schulten K (2002) Unfolding of titin domains studied by molecular dynamics simulations. J Muscle Res Cell Mot 23:513–521CrossRefGoogle Scholar
  32. 32.
    Lee EH, Gao M, Pinotsis N, Wilmanns M, Schulten K (2006) Mechanical strength of the titin Z1Z2/telethonin complex. Structure 14:497–509CrossRefGoogle Scholar
  33. 33.
    Lee EH, Hsin J, Mayans O, Schulten K (2007) Secondary and tertiary structure elasticity of titin Z1Z2 and a titin chain model. Biophys J 93:1719–1735CrossRefGoogle Scholar
  34. 34.
    Krammer A, Lu H, Isralewitz B, Schulten K, Vogel V (1999) Forced unfolding of the fibronectin Type III module reveals a tensile molecular recognition switch. Proc Natl Acad Sci USA 96:1351–1356CrossRefGoogle Scholar
  35. 35.
    Craig D, Krammer A, Schulten K, Vogel V (2001) Comparison of the early stages of forced unfolding of fibronectin type III modules. Proc Natl Acad Sci USA 98:5590–5595CrossRefGoogle Scholar
  36. 36.
    Craig D, Gao M, Schulten K, Vogel V (2004) Tuning the mechanical stability of fibronectin type III modules through sequence variation. Structure 12:21–30CrossRefGoogle Scholar
  37. 37.
    Krammer A, Craig D, Thomas WE, Schulten K, Vogel V (2002) A structural model for force regulated integrin binding to fibronectin’s RGD-synergy site. Matrix Biol 21:139–147CrossRefGoogle Scholar
  38. 38.
    Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comp Chem 26:1781–1802CrossRefGoogle Scholar
  39. 39.
    MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck J, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher IWE, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616CrossRefGoogle Scholar
  40. 40.
    Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935CrossRefGoogle Scholar
  41. 41.
    Darden T, York D, Pedersen L (1993) Particle mesh Ewald. An N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092CrossRefGoogle Scholar
  42. 42.
    Feller SE, Zhang YH, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation—the Langevin piston method. J Chem Phys 103:4613–4621CrossRefGoogle Scholar
  43. 43.
    Martyna GJ, Tobias DJ, Klein ML (1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101:4177–4189CrossRefGoogle Scholar
  44. 44.
    Shrake A, Rupley JA (1973) Enviroment and exposure to solvent of protein atoms—lysozyme and insulin. J Mol Biol 79:351–371CrossRefGoogle Scholar
  45. 45.
    Humphrey W, Dalke A, Schulten K (1996) VMD—visual molecular dynamics. J. Mol. Graphics 14:33–38CrossRefGoogle Scholar
  46. 46.
    Rudino-Pinera E, Ravelli RBG, Sheldrick GM, Nanao MH, Korostelev VV, Werner JM, Schwarz-Linek U, Potts JR, Garman EF (2007) The solution and crystal structures of a module pair from the Staphylococcus aureus-binding site of human fibronectin—a tale with a twist. J Mol Biol 368:833–844CrossRefGoogle Scholar
  47. 47.
    Pilka ES, Werner JM, Schwarz-Linek U, Pickford AR, Meenan NAG, Campbell ID, Potts JR (2006) Structural insight into binding of Staphylococcus aureus to human fibronectin. FEBS Lett 580:273–277CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Jiankuai Diao
    • 1
  • Andrew J. Maniotis
    • 3
  • Robert Folberg
    • 3
  • Emad Tajkhorshid
    • 2
  1. 1.Department of Biochemistry, Beckman Institute, Center for Biophysics and Computational BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Beckman InstituteUrbanaUSA
  3. 3.Department of PathologyUniversity of Illinois at ChicagoChicagoUSA

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