Inferring the diameter of a biopolymer from its stretching response
Toan, Ngo Minh, Marenduzzo, Davide and Micheletti, C. (Cristian). (2005) Inferring the diameter of a biopolymer from its stretching response. Biophysical Journal, Vol.89 (No.1). pp. 80-86. ISSN 0006-3495
WRAP_Toan_Inferring_diameter.pdf - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
Official URL: http://dx.doi.org/10.1529/biophysj.104.058081
We investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve depends on the polymer structural parameters: its thickness and granularity (spacing of the monomers). The expression is used to analyze experimental data for the stretching of various different types of biopolymers: polypeptides, polysaccharides, and nucleic acids. Besides recovering elastic parameters (such as the persistence length) that are consistent with those obtained from standard entropic models, the approach allows us to extract viable estimates for the polymers diameter and granularity. This shows that the basic structural polymer features have such a profound impact on the elastic behavior that they can be recovered with the sole input of stretching measurements.
|Item Type:||Journal Article|
|Subjects:||Q Science > QP Physiology|
|Divisions:||Faculty of Science > Mathematics|
|Library of Congress Subject Headings (LCSH):||Biopolymers, Polymers -- Surfaces, Polymers -- Mathematical models|
|Journal or Publication Title:||Biophysical Journal|
|Official Date:||July 2005|
|Page Range:||pp. 80-86|
|Access rights to Published version:||Open Access|
|Funder:||Istituto Nazionale Fisica della Materia (INFM)|
1. C. Bustamante, Z. Bryant and S.B. Smith, Ten years of tension: single-molecule DNA mechanics, Nature 421 (2003), pp. 423–427.
2. S.B. Smith, L. Finzi and C. Bustamante, Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads, Science 258 (1992), pp. 1122–1126.
3. P. Cluzel, A. Lebrun, C. Heller, R. Lavery, J.-L. Viovy, D. Chatenay and F. Caron, DNA: an extensible molecule, Science 271 (1996), pp. 792–794.
4. T.R. Strick, J.-F. Allemand, D. Bensimon, A. Bensimon and V. Croquette, The elasticity of a single supercoiled DNA molecule, Science 271 (1996), pp. 1835–1837.
5. C. Bouchiat, M.D. Wang, J.F. Allemand, T. Strick, S.M. Block and V. Croquette, Estimating the persistence length of a worm-like chain molecule from force-extension measurements, Biophys. J. 76 (1999), pp. 409–413.
6. J.R. Wenner, M.C. Williams, I. Rouzina and V.A. Bloomfield, Salt dependence of the elasticity and overstretching transition of single DNA molecules, Biophys. J. 82 (2002), pp. 3160–3169.
7. W.A. Linke, M. Kulke, H. Li, S. Fujita-Becker, C. Neagoe, D.J. Manstein, M. Gautel and J.M. Fernandez, PEVK domain of titin: an entropic spring with actin-binding properties, J. Struct. Biol. 137 (2002), pp. 194–205.
8. H. Li, W. Linke, A. Oberhauser, M. Carrion-Vazquez, J. Kerkvliet, H. Lu, P. Marszalek and J. Fernandez, Reverse engineering of the giant muscle protein titin, Nature 418 (2002), pp. 998–1002.
9. H. Li, A.F. Oberhauser, S.D. Redick, M. Carrion-Vazquez, H.P. Erickson and J.M. Fernandez, Multiple conformations of PEVK proteins detected by single-molecule techniques, Proc. Natl. Acad. Sci. USA 98 (2001), pp. 10682–10686.
10. M. Rief, J. Pascual, M. Saraste and H.E. Gaub, Single molecule force spectroscopy of spectrin repeats: low unfolding forces in helix bundles, J. Mol. Biol. 286 (1999), pp. 553–561.
11. P.E. Marszalek, A.F. Oberhauser, Y.-P. Pang and J.M. Fernandez, Polysaccharide elasticity governed by chair-boat transitions of the glucopyranose ring, Nature 396 (1998), pp. 661–664.
12. P.M. Williams, S.B. Fowler, R.B. Best, J.L. Toca-Herrera, K.A. Scott, A. Steward and J. Clarke, Hidden complexity in the mechanical properties of titin, Nature 422 (2003), pp. 446–449.
13. R.B. Best, S.B. Fowler, J.L. Toca-Herrera, A. Steward, E. Paci and J. Clarke, Mechanical unfolding of a titin Ig domain: structure of transition state revealed by combining AFM, protein engineering and molecular dynamics simulations, J. Mol. Biol. 330 (2003), pp. 867–877.
14. M.D. Wang, H. Yin, R. Landick, J. Gelles and S.M. Block, Stretching DNA with optical tweezers, Biophys. J. 72 (1997), pp. 1335–1346.
15. D. Boal, Mechanics of the Cell, Cambridge University Press, Cambridge (2002).
16. P. Pincus, Excluded volume effects and stretched polymer chains, Macromolecules 9 (1976), pp. 386–388.
17. C. Bustamante, J.F. Marko, E.D. Siggia and S. Smith, Entropic elasticity of lambda-phage DNA, Science 265 (1994), pp. 1599–1600.
18. Cieplak, M., T. X. Hoang, and M. O. Robbins. 2002. Proteins. Folding and stretching in a Go-like model of titin. 49:114–124.
19. M. Cieplak, T.X. Hoang and M.O. Robbins, Stretching of proteins in the entropic limit, Phys. Rev. E 69 (2004), p. 011912.
20. M. Gao, M. Wilmanns and K. Schulten, Steered molecular dynamics studies of titin I1 domain unfolding, Biophys. J. 83 (2002), pp. 3435–3445.
21. P.E. Marszalek, H. Lu, H.B. Li, M. Carrion-Vazquez, A.F. Oberhauser, K. Schulten and J.M. Fernandez, Mechanical unfolding intermediates in titin modules, Nature 402 (1999), pp. 100–103.
22. P. Flory, Statistical Mechanics of Chain Molecules, Hanser Publisher, Munich (1989).
23. J.F. Marko and E.D. Siggia, Stretching DNA, Macromolecules 28 (1995), pp. 8759–8770.
24. P. Hansen and R. Podgornik, Wormlike chains in the large-d limit, J. Chem. Phys. 114 (2001), pp. 8637–8648.
25. G. Buck and J. Orloff, A simple energy function for knots, Topol. Appl. 61 (1995), pp. 205–214.
26. R. Litherland, J. Simon, O. Durumeric and E. Rawdon, Thickness of knots, Topol. Appl. 91 (1999), pp. 233–244.
27. O. Gonzales and J.H. Maddocks, Global curvature, thickness and the ideal shapes of knots., Proc. Natl. Acad. Sci. USA 96 (1999), pp. 4769–4773.
28. V. Katrich, W.K. Olson, P. Pieranski, J. Dubochet and A. Stasiak, Properties of ideal composite knots, Nature 388 (1997), pp. 148–151.
29. A. Stasiak and J.H. Maddocks, Best packing in proteins and DNA, Nature 406 (2000), pp. 251–253.
30. A. Maritan, C. Micheletti, A. Trovato and J.R. Banavar, Optimal shapes of compact strings, Nature 406 (2000), pp. 287–290.
31. D. Marenduzzo and C. Micheletti, Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness, J. Mol. Biol. 330 (2003), pp. 485–492.
32. V.V. Rybenkov, N.R. Cozzarelli and A.V.S. Vologodskii, Probability of DNA knotting and the effective diameter of the DNA double helix, Proc. Natl. Acad. Sci. USA 90 (1993), pp. 5307–5311.
33. P.E. Marszalek, Y.-P. Pang, H. Li, J.E. Yazal, A.F. Oberhauser and J.M. Fernandez, Atomic levers control pyranose ring conformations, Proc. Natl. Acad. Sci. USA 96 (1999), pp. 7894–7898.
34. P.E. Marszalek, H. Li and J.M. Fernandez, Fingerprinting polysaccharides with single-molecule atomic force microscopy, Nat. Biotechnol. 19 (2001), pp. 258–262.
35. M. Rief, M. Gautel, F. Oesterhelt, J. Fernandez and H.E. Gaub, Reversible unfolding of individual titin immunoglobulin domains by AFM, Science 276 (1997), pp. 1109–1112.
36. G. Buck, Four-thirds power law for knots and links, Nature 392 (1998), pp. 238–239.
37. E. Rawdon, Approximating smooth thickness, J. Knot Theor. Ramif. 9 (2000), pp. 113–145.
38. J. Banavar, A. Maritan, C. Micheletti and A. Trovato, Geometry and physics of proteins, Proteins 47 (2002), pp. 315–322.
39. J.R. Banavar, A. Flammini, D. Marenduzzo and A. Maritan, Tubes near the edge of compactness and folded protein structures, J. Phys. Condens. Matter. 15 (2003), pp. S1787–S1796.
40. S. Premilat and J.J. Hermans, Conformational statistics of short chains of poly(L-alanine) and poly(glycine) generated by Monte Carlo method and the partition functions of chains with constrained ends, J. Chem. Phys. 59 (1973), pp. 2602–2612.
41. P.J. Flory and V.W.C. Chang, Moments and distribution function for poly(dimethylsiloxane) chains of finite length, Macromolecules 9 (1976), pp. 33–40.
42. P.-M. Lam, Excluded volume effects in gene stretching, Biopolymers 64 (2002), pp. 57–62.
44. C. Storm and P.C. Nelson, Theory of high-force DNA stretching and overstretching, Phys. Rev. E 67 (2003), p. 051906.
45. A. Rosa, T.X. Hoang, D. Marenduzzo and A. Maritan, Elasticity of semiflexible polymers with and without self-interactions, Macromolecules 36 (2003), pp. 10095–10102.
46. A. Lamura, T.W. Burkhardt and G. Gompper, Semiflexible polymer in a uniform force field in two dimensions, Phys. Rev. E 64 (2001), p. 061801.
47. G. Lee, W. Nowak, J. Jaroniec, Q. Zhang and P. Marszalek, Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides, Biophys. J. 87 (2004), pp. 1456–1465.
48. T. Odijk, Stiff chains and filaments under tension, Macromolecules 28 (1995), pp. 7016–7018.
49. T. Odijk, Hexagonally packed DNA within bacteriophage T7 stabilized by curvature stress, Biophys. J. 75 (1998), pp. 1223–1227.
50. R. Podgornik, P. Hansen and V. Parsegian, Elastic moduli renormalization in self-interacting stretchable polyelectrolytes, J. Chem. Phys. 113 (2000), pp. 9343–9350.
51. N. Lee and D. Thirumalai, Stretching DNA: role of electrostatic interactions, Eur. Phys. J. B 12 (1999), pp. 599–605.
52. D. Marenduzzo, C. Micheletti, H. Seyed-allaei, A. Trovato and A. Maritan, Continuum model for polymers with finite thickness, J. Phys. A-Math. Gen. 38 (2005), pp. L277–L283.
Actions (login required)