Skip to main content
SpringerLink
Log in

Statistical Mechanics of Force-Induced Transitions of Biopolymers

  • Reference work entry
  • First Online:
Handbook of Computational Chemistry

  • 4453 Accesses

Abstract

Single molecule force spectroscopy constitutes a robust method for probing the unfolding of biomolecules. Knowledge gained from statistical mechanics is helping to build our understanding about more complex structure and function of biopolymers. Here, we have review some of the models and techniques that have been employed to study force-induced transitions in biopolymers. We briefly describe the merit and limitation of these models and techniques. In this context, we discuss statistical models of polymer along with numerical techniques, which may provide enhanced insight in understanding the unfolding of biomolecules.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 749.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adcock, S. A., & McCammon, J. A. (2006). Molecular Dynamics: Survey of methods for simulating the activity of proteins. Chemical Reviews, 106, 1589–1615.

    Article  CAS  Google Scholar 

  • Allen, M. P., & Tildesley, D. J. (1987). Computer simulations of liquids. Oxford: Oxford Science.

    Google Scholar 

  • Bhattacharjee, S. M. (2000). Unzipping DNAs: Towards the first step of replication. Journal of Physics A, 33, L423–L428.

    Article  CAS  Google Scholar 

  • Binder, K. (1995). Monte Carlo and molecular dynamics simulations in polymer science. New York: Oxford University Press.

    Google Scholar 

  • Binder, K. (1997). Applications of Monte Carlo methods to statistical physics. Reports on Progress in Physics, 60, 487–559.

    Article  CAS  Google Scholar 

  • Bustamante, C., Smith, S. B., Liphardt, J., & Smith, D. (2000). Single-molecule studies of DNA mechanics. Current Opinion in Structural Biology, 10, 279–285.

    Article  CAS  Google Scholar 

  • Bustamante, C., Chemla, Y. R., Forde, N. R., & Izhaky, D. (2004). Mechanical processes in biochemistry. The Annual Review of Biochemistry, 73, 705–748.

    Article  CAS  Google Scholar 

  • Cecconi, C., Shank, E. A., Bustamante, C., & Marqusee, S. (2005). Direct observation of the three-state folding of a single protein molecule. Science, 309, 2057–2060.

    Article  CAS  Google Scholar 

  • Chatney, D., Cocco, S., Monasson, R., & Thieffry, D. (2004). Multiple aspects of DNA and RNA: From biophysics to bioinformatics: Lecture notes of the Les Houches Summer School. The Netherlands: Elsevier.

    Google Scholar 

  • Cloizeaux, J. D. (1974). Langrangian theory for a self-avoiding random chain. Physical Review A, 10, 1665–1669.

    Article  Google Scholar 

  • Dai, L., Liu, F., & Ou-Yang, Z-C. (2003). Maximum-entropy calculation of the end-to-end distance distribution of force-stretched chains. Journal of Chemical Physics, 119, 8124.

    Article  CAS  Google Scholar 

  • de Gennes, P. G. (1979). Scaling concepts in polymer physics. Ithaca/London: Cornell University Press.

    Google Scholar 

  • des Cloizeaux, J., & Jannink, G. (1990). Polymers in solution. Oxford: Clarendon.

    Google Scholar 

  • Doi, M., & Edwards, S. F. (1986). The theory of polymer dynamics. Oxford: Clardenden.

    Google Scholar 

  • Domb, C., & Lebowitz, J. L. (1989). Phase transition and critical phenomena(Vol. 13). New York: Academic.

    Google Scholar 

  • Forgacs, G., Lipowsky, R., & Nieuwenhuizen, T. M. (1995). The behaviour of interfaces in ordered and disordered systems(Vol. 14). Oxford: Clarendon.

    Google Scholar 

  • Frenkel, D., & Smit, B. (2002). Understanding molecular simulation. London: Academic.

    Google Scholar 

  • Giri, D., & Kumar, S. (2006). Effects of the eye phase in DNA unzipping. Physical Review E, 73, 050903(R).

    Google Scholar 

  • Grassberger, P., Nadler, W., & Barkema, G. T. (1999). The Monte Carlo approach to biopolymers and protein folding. Singapore: World Scientific.

    Google Scholar 

  • Grosberg, A. Y., & Khokhlov, A. R. (1994). Statistical physics of macromolecules. New York: American Institute of Physics.

    Google Scholar 

  • Huenenberger, P. (2005). Thermostat algorithms for molecular dynamics simulations. Advances in Polymer Science, 173, 105–149.

    Article  CAS  Google Scholar 

  • Kleinert, H. (1990). Path integrals in quantum mechanics, satistics, and polymer physics. Singapore: World Scientific.

    Book  Google Scholar 

  • Kumar, S. (2009). Can reentrance be observed in force induced transitions? Europhysics Letters, 85, 38003.

    Article  Google Scholar 

  • Kumar, S., & Giri, D. (2005). Force-induced conformational transition in a system of interacting stiff polymers: Application to unfolding. Physical Review E, 72, 052901.

    Article  Google Scholar 

  • Kumar, S., & Giri, D. (2007). Does changing the pulling direction give better insight into biomolecules? Physical Review Letters, 98, 048101.

    Article  Google Scholar 

  • Kumar, S., Giri, D., & Bhattacharjee, S. M. (2005). Force induced tripple point for interacting polymers. Physical Review E, 71, 051804.

    Article  Google Scholar 

  • Kumar, S., Jensen, I., Jaconsen, J. L., & Guttmann, A. J. (2007). Role of conformational entropy in force induced biopolymer unfolding. Physical Review Letters, 98, 128101–128104.

    Article  Google Scholar 

  • Kumar, S., & Li, M. (2010). Biomolecules under mechanical force. Physics Reports, 486, 1–74.

    Article  CAS  Google Scholar 

  • Kumar, S., & Mishra, G. (2008). Force-induced stretched state: Effects of temperature. Physical Review E, 78, 011907.

    Article  Google Scholar 

  • Landau, D. P., & Binder, K. (2005). A guide to Monte Carlo simulations in statistical physics. New York: Cambridge University Press.

    Book  Google Scholar 

  • Leckband, D., & Israelachvili, J. (2001). Intermolecular forces in biology. Quarterly Review of Biophysics, 34, 105–267.

    Article  CAS  Google Scholar 

  • Lubensky, D. K., & Nelson, D. R. (2000). Pulling pinned polymers and unzipping DNA. Physical Review Letters, 85, 1572–1575.

    Article  CAS  Google Scholar 

  • Marenduzzo, D., Bhattacharjee, S. M., Maritan, A., Orlandini, E., & Seno, F. (2001 a). Dynamical scaling of the DNA unzipping transition. Physical Review Letters, 88, 028102.

    Google Scholar 

  • Marenduzzo, D., Trovato, A., & Maritan, A. (2001 b). Phase diagram of force-induced DNA unzipping in exactly solvable models. Physical Review E, 64, 031901.

    Google Scholar 

  • Marko, J., & Siggia, E. (1995). Stretching DNA. Macromolecules, 28, 8759–8770.

    Article  CAS  Google Scholar 

  • Mishra, G., Giri, D., & Kumar, S. (2009). Stretching of a single stranded DNA: Evidence for structural transition. Physical Review E, 79, 031930.

    Article  Google Scholar 

  • Mishra, P. K., Kumar, S., & Singh, Y. (2003). A simple and exactly solvable model for a semi flexible polymer chain interacting with a surface. Physica A, 323, 453–465.

    Article  CAS  Google Scholar 

  • Mishra, P. K., Kumar, S., & Singh, Y. (2005). Force-induced desorption of a linear polymer chain adsorbed on an attractive surface. Europhysics Letters, 69, 102–108.

    Article  CAS  Google Scholar 

  • Muller, M., Katsov, K., & Schick, M. (2006). Biological and synthetic membranes: What can be learned from a coarse-grained description? Physics Reports, 434, 113–176.

    Article  Google Scholar 

  • Muller-Plathe, F. (1997). Coarse-graining in polymer simulation: From the atomistictothemesoscopicscaleandback.ChemPhysChem,3,754–769.

    Google Scholar 

  • Privman, V., & Svrakic, N. M. (1989). Directed models of polymers, interfaces, and clusters. Berlin: Springer.

    Google Scholar 

  • Rief, M., Clausen-Schaumann, H., & Gaub, H. E. (1999). Sequence-dependent mechanics of single DNA molecules. Nature Structural Biology, 6, 346–349.

    Article  CAS  Google Scholar 

  • Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J. M., & Gaub, H. E. (1997). Reversible unfolding of individual titin immunoglobulin domains by AFM. Science, 276, 1109–1112.

    Article  CAS  Google Scholar 

  • Rosa, A., Hoang, T. X., Marenduzzo, D., & Maritan, A. (2003 a). Elasticity of semiflexible polymers with and without self-interactions. Macromolecules, 36, 10095–10102.

    Google Scholar 

  • Rosa, A., Marenduzzo, D., Maritan, A., & Seno, F. (2003 b). Mechanical unfolding of directed polymers in a poor solvent: Critical exponents. Physical Review E, 67, 041802.

    Google Scholar 

  • Singh, A. R., Giri, D., & Kumar, S. (2009 a). Force induced unfolding of bio-polymers in a cellular environment: A model study. Journal of Chemical Physics, 131, 065103.

    Google Scholar 

  • Singh, A. R., Giri, D., & Kumar, S. (2009 b). Effects of molecular crowding on stretching of polymers in poor solvent. Physical Review E, 79, 051801.

    Google Scholar 

  • Smith, S. B., Finzi, L., & Bustamante, C. (1992). Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science, 258, 1122–1126.

    Article  CAS  Google Scholar 

  • Smith, S. B., Cui, Y., & Bustamante, C. (1996). Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules. Science, 271, 795–799.

    Article  CAS  Google Scholar 

  • Thijssen, J. M. (1999). Computational physics. Cambridge: Cambridge University.

    Google Scholar 

  • Tskhovrebova, L., Trinick, K., Sleep, J. A., & Simons, R. M. (1997). Elasticity and unfolding of single molecules of the giant muscle protein titin. Nature, 387, 308–312.

    Article  CAS  Google Scholar 

  • Vanderzande, C. (1998). Lattice models of polymers. Cambridge: Cambridge University Press.

    Book  Google Scholar 

  • Zhou, H. J., Zhou, J., Ou-Yang, Z. C., & Kumar, S. (2006). Collapse transition of two-dimensional flexible and semiflexible polymers. Physical Review Letters, 97, 158302.

    Article  Google Scholar 

Download references

Acknowledgments

We would like to thank D. Giri, A. R. Singh, and G. Mishra for many helpful discussions. Financial assistance from the Department of Science and Technology, New Delhi is gratefully acknowledged.

Author information

Authors and Affiliations

  1. Department of Physics, Banaras Hindu University, 221 005, Varanasi, India

    Sanjay Kumar

Authors
  1. Sanjay Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA

    Jerzy Leszczynski

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media B.V.

About this entry

Cite this entry

Kumar, S. (2012). Statistical Mechanics of Force-Induced Transitions of Biopolymers. In: Leszczynski, J. (eds) Handbook of Computational Chemistry. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0711-5_8

Download citation

Publish with us

Policies and ethics

Search

Navigation