Advertisement

Journal of Molecular Modeling

, Volume 18, Issue 6, pp 2823–2829 | Cite as

Computational investigation of the effect of thermal perturbation on the mechanical unfolding of titin I27

  • Navneet Bung
  • U. Deva PriyakumarEmail author
Original Paper

Abstract

The emergence of single-molecule force measurement experiments has facilitated a better understanding of protein folding pathways and the thermodynamics involved. Computational methods such as steered molecular dynamics (SMD) simulations are helpful in providing atomistic level information on the unfolding pathways. Recent experimental studies have showed that combinations of single-molecule experiments with traditional methods such as chemical and/or thermal denaturation yield additional insights into the folding phenomenon. In this study, we report results from extensive computations (a total of about 60 SMD simulations with a total length of about 0.4 μs) that address the effect of thermal perturbation on the mechanical stability of the I27 domain of the protein titin. A wide range of temperatures (280–340 K) were considered for the pulling, which was done at both constant velocity and constant force using SMD simulations. Good agreement with experimental data, such as for the trends in changes in average force and the maximum force with respect to the temperature, was obtained. This study identifies two competing pathways for the mechanical unfolding of I27, and illustrates the significance of combining various techniques to examine protein folding.

Keywords

Protein folding Steered molecular dynamics Denaturation Mechanical stability Titin I27 Folding pathways 

Notes

Acknowledgments

UDP thanks the Department of Biotechnology (DBT), Govt. of India, for the Innovative Young Biotechnologist Award. We acknowledge DBT for financial assistance (BT/03/IYBA/2010).

Supplementary material

894_2011_1298_MOESM1_ESM.doc (2.1 mb)
ESM 1 Figures of force–extension profiles at different temperatures, probability distributions of the unfolding forces, extensions at peak force, changes in the hydrogen-bond distances during the rupture of BE, FG, and FC strands, and extension vs. time profiles from constant force SMD simulations. (DOC 2102 kb)

References

  1. 1.
    Forman JR, Clarke J (2007) Mechanical unfolding of proteins: insights into biology, structure and folding. Curr Opin Struct Biol 17:58–66CrossRefGoogle Scholar
  2. 2.
    Kumar S, Li MS (2010) Biomolecules under mechanical force. Phys Rep 486:1–74Google Scholar
  3. 3.
    Best RB, Clarke J (2002) What can atomic force microscopy tell us about protein folding? Chem Commun 183–193Google Scholar
  4. 4.
    Bustamante C, Chemla YR, Forde NR, Izhaky D (2004) Mechanical processes in biochemistry. Annu Rev Biochem 73:705–748CrossRefGoogle Scholar
  5. 5.
    Greenleaf WJ, Frieda KL, Foster DAN, Woodside MT, Block SM (2008) Direct observation of hierarchical folding in single riboswitch aptamers. Science 319:630–633CrossRefGoogle Scholar
  6. 6.
    Li PTX, Vieregg J, Tinoco I Jr (2008) How RNA unfolds and refolds. Annu Rev Biochem 77:77–100CrossRefGoogle Scholar
  7. 7.
    Hyeon C, Morrison G, Thirumalai D (2008) Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. Proc Natl Acad Sci USA 105:9604–9609Google Scholar
  8. 8.
    Colizzi F, Perozzo R, Scapozza L, Recanatini M, Cavalli A (2010) Single-molecule pulling simulations can discern active from inactive enzyme inhibitors. J Am Chem Soc 132:7361–7371Google Scholar
  9. 9.
    Dobson CM, Šali A, Karplus M (1998) Protein folding: a perspective from theory and experiment. Angew Chem Int Ed 37:868–893CrossRefGoogle Scholar
  10. 10.
    Carrion-Vazquez M, Oberhauser AF, Fowler SB, Marszalek PE, Broedel SE, Clarke J, Fernandez JM (1999) Mechanical and chemical unfolding of a single protein: a comparison. Proc Natl Acad Sci USA 96:3694–3699Google Scholar
  11. 11.
    Botello E, Harris NC, Sargent J, Chen WH, Lin KJ, Kiang CH (2009) Temperature and chemical denaturant dependence of forced unfolding of titin i27. J Phys Chem B 113:10845–10848CrossRefGoogle Scholar
  12. 12.
    Cao Y, Li H (2008) How do chemical denaturants affect the mechanical folding and unfolding of proteins? J Mol Biol 375:316–324CrossRefGoogle Scholar
  13. 13.
    Taniguchi Y, Brockwell DJ, Kawakami M (2008) The effect of temperature on mechanical resistance of the native and intermediate states of I27. Biophys J 95:5296–5305CrossRefGoogle Scholar
  14. 14.
    Schlierf M, Rief M (2005) Temperature softening of a protein in single-molecule experiments. J Mol Biol 354:497–503CrossRefGoogle Scholar
  15. 15.
    Hyeon C, Thirumalai D (2003) Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? Proc Natl Acad Sci USA 100:10249–10253CrossRefGoogle Scholar
  16. 16.
    Klimov D, Thirumalai D (1999) Stretching single-domain proteins: phase diagram and kinetics of force-induced unfolding. Proc Natl Acad Sci USA 96:6166–6170CrossRefGoogle Scholar
  17. 17.
    Isralewitz B, Gao M, Schulten K (2001) Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol 11:224–230CrossRefGoogle Scholar
  18. 18.
    Improta S, Politou AS, Pastore A (1996) Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity. Structure 4:323–337CrossRefGoogle Scholar
  19. 19.
    Humphrey W, Dalke A, Schulten K (1996) VMD: Visual Molecular Dynamics. J Mol Graph 14:33–38CrossRefGoogle Scholar
  20. 20.
    Labeit S, Kolmerer B, Linke WA (1997) The giant protein titin: emerging roles in physiology and pathophysiology. Circul Res 80:290–294Google Scholar
  21. 21.
    Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276:1109–1112CrossRefGoogle Scholar
  22. 22.
    Kellermayer MSZ, Smith SB, Granzier HL, Bustamante C (1997) Folding–unfolding transitions in single titin molecules characterized with laser tweezers. Science 276:1112–1116Google Scholar
  23. 23.
    Tskhovrebova L, Trinick J, Sleep J, Simmons R (1997) Elasticity and unfolding of single molecules of the giant muscle protein titin. Nature 387:308–312CrossRefGoogle Scholar
  24. 24.
    Lu H, Schulten K (2000) The key event in force-induced unfolding of titin’s immunoglobulin domains. Biophys J 79:51–65Google Scholar
  25. 25.
    Lu H, Schulten K (1999) Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interpret atomic force microscopy observations. Chem Phys 247:141–153Google Scholar
  26. 26.
    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
  27. 27.
    Fowler SB, Best RB, Toca Herrera JL, Rutherford TJ, Steward A, Paci E, Karplus M, Clarke J (2002) Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J Mol Biol 322:841–849CrossRefGoogle Scholar
  28. 28.
    Cieplak M, Hoang TX, Robbins MO (2002) Folding and stretching in a Go like model of titin. Proteins Struct Funct Bioinf 49:114–124CrossRefGoogle Scholar
  29. 29.
    Ho BK, Agard DA (2010) An improved strategy for generating forces in steered molecular dynamics: the mechanical unfolding of titin, e2lip3 and ubiquitin. PloS one 5:e13068Google Scholar
  30. 30.
    Li PC, Makarov DE (2003) Theoretical studies of the mechanical unfolding of the muscle protein titin: bridging the time-scale gap between simulation and experiment. J Chem Phys 119:9260–9268CrossRefGoogle Scholar
  31. 31.
    Li MS, Gabovich A, Voitenko A (2008) New method for deciphering free energy landscape of three-state proteins. J Chem Phys 129:105102CrossRefGoogle Scholar
  32. 32.
    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 Comput Chem 26:1781–1802CrossRefGoogle Scholar
  33. 33.
    Mackerell AD, Feig M, Brooks CL (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25:1400–1415CrossRefGoogle Scholar
  34. 34.
    MacKerell AD, Bashford D, Bellott DRL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, 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
  35. 35.
    Izrailev S, Stepaniants S, Isralewitz B, Kosztin D, Lu H, Molnar F, Wriggers W, Schulten K (1999) Steered molecular dynamics. In: Deuflhard P, Hermans J, Leimkuhler B, Mark A, Skeel RD, Reich S (eds) Computational molecular dynamics: challenges, methods, ideas. Springer, Berlin, 4:39–65Google Scholar
  36. 36.
    Balsera M, Stepaniants S, Izrailev S, Oono Y, Schulten K (1997) Reconstructing potential energy functions from simulated force-induced unbinding processes. Biophys J 73:1281–1287CrossRefGoogle Scholar
  37. 37.
    Rueda M, Ferrer-Costa C, Meyer T, Pèrez A, Camps J (2007) A consensus view of protein dynamics. Proc Natl Acad Sci USA 104:796–801Google Scholar
  38. 38.
    Mackerell A (2004) Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 25:1584–1604CrossRefGoogle Scholar
  39. 39.
    Faver JC, Benson ML, He X, Roberts BP, Wang B, Marshall MS, Sherrill CD, Merz Jr KM (2011) The energy computation paradox and ab initio protein folding. PloS one 6:e18868Google Scholar
  40. 40.
    Law R, Liao G, Harper S, Yang G, Speicher DW, Discher DE (2003) Pathway shifts and thermal softening in temperature-coupled forced unfolding of spectrin domains. Biophys J 85:3286–3293CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  1. 1.Center for Computational Natural Sciences and BioinformaticsInternational Institute of Information TechnologyHyderabadIndia

Personalised recommendations