Rate limit of protein elastic response is tether dependent

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 36, 2012, Pages 14416-14421

  Berkovich, Ronen ^a   Hermans, Rodolfo I ^a,b   Popa, Ionel ^a   Stirnemannc, Guillaume ^a   Garcia Manyes, Sergi ^a,c   Berne, Bruce J ^a   Fernandez, Julio M ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

Force spectroscopy; Protein diffusion; Single molecule; Viscoelasticity

Indexed keywords

POLYPEPTIDE; PROTEIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; DIFFUSION; FAST FORCE SPECTROMETRY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ISOLATION; SPECTROMETRY; VISCOELASTICITY;

ANIMALS; BIOPHYSICS; DIFFUSION; ELASTICITY; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; MICROSCOPY, ATOMIC FORCE; MOLECULAR DYNAMICS SIMULATION; MUSCLES; PROTEINS;

ANIMALIA;

EID: 84865975569     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1212167109     Document Type: Article

References (34)

1. Linke WA (2008) Sense and stretchability: The role of titin and titin-associated proteins in myocardial stress-sensing and mechanical dysfunction. Cardiovasc Res 77:637-648.
2. Li HB, et al. (2002) Reverse engineering of the giant muscle protein titin. Nature 418:998-1002.
3. Greenewalt CH (1960) The wings of insects and birds as mechanical oscillators. Proc Am Philos Soc 104:605-611.
4. Deban SM, Richardson JC (2011) Cold-blooded snipers: Thermal independence of ballistic tongue projection in the salamander hydromantes platycephalus. J Exp Zool A 315A:618-630.
5. Roberts TJ, Marsh RL, Weyand PG, Taylor CR (1997) Muscular force in running turkeys: The economy of minimizing work. Science 275:1113-1115. (Pubitemid 27097307)
6. Bustamante C, Marko JF, Siggia ED, Smith S (1994) Entropic elasticity of Lambda-Phage DNA. Science 265:1599-1600.
7. Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276:1109-1112. (Pubitemid 27218118)
8. Haas E, Katchalskikatzir E, Steinberg IZ (1978) Brownian-motion of ends of oligopeptide chains in solution as estimated by energy-transfer between chain ends. Biopolymers 17:11-31. (Pubitemid 8275354)
9. Hagen SJ, Hofrichter J, Szabo A, Eaton WA (1996) Diffusion-limited contact formation in unfolded cytochrome c: Estimating the maximum rate of protein folding. Proc Natl Acad Sci USA 93:11615-11617. (Pubitemid 26347170)
10. Lapidus LJ, Steinbach PJ, Eaton WA, Szabo A, Hofrichter J (2002) Effects of chain stiffness on the dynamics of loop formation in polypeptides. Appendix: Testing a 1-dimensional diffusion model for peptide dynamics. J Phys Chem B 106:11628-11640. (Pubitemid 35361136)
11. Moglich A, Joder K, Kiefhaber T (2006) End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation. Proc Natl Acad Sci USA 103:12394-12399. (Pubitemid 44267270)
12. Hummer G, Szabo A (2001) Free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proc Natl Acad Sci USA 98:3658-3661. (Pubitemid 32249826)
13. Dudko OK, Graham TGW, Best RB (2011) Locating the barrier for folding of single molecules under an external force. Phys Rev Lett 107:208301.
14. Kawakami M, Byrne K, Brockwell DJ, Radford SE, Smith DA (2006) Viscoelastic study of the mechanical unfolding of a protein by AFM. Biophys J 91:L16-L18.
15. Khatri BS, et al. (2008) Internal friction of single polypeptide chains at high stretch. Faraday Discuss 139:35-51.
16. Calderon CR, Harris NC, Kiang CH, Cox DD (2009) Analyzing single-molecule manipulation experiments. J Mol Recognit 22:356-362.
17. Calderon CP, Harris NC, Kiang CH, Cox DD (2009) Quantifying multiscale noise sources in single-molecule time series. J Phys Chem B 113:138-148.
18. Guo SL, Li N, Lad N, Desai S, Akhremitchev BB (2010) Distributions of parameters and features of multiple bond ruptures in force spectroscopy by atomic force microscopy. J Phys Chem C 114:8755-8765.
19. Minh DDL (2006) Free-energy reconstruction from experiments performed under different biasing programs. Phys Rev E 74:061120.
20. Minh DDL (2007) Multidimensional potentials of mean force from biased experiments along a single coordinate. J Phys Chem B 111:4137-4140.
21. Lin JC, Thirumalai D (2008) Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J Am Chem Soc 130:14080-14081.
22. Sotomayor M, Schulten K (2007) Single-molecule experiments in vitro and in silico. Science 316:1144-1148. (Pubitemid 46877468)
23. Schlierf M, Li HB, Fernandez JM (2004) The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques. Proc Natl Acad Sci USA 101:7299-7304. (Pubitemid 38638027)
24. Li PTX, Collin D, Smith SB, Bustamante C, Tinoco I (2006) Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys J 90:250-260.
25. Berkovich R, Garcia-Manyes S, Urbakh M, Klafter J, Fernandez JM (2010) Collapse dynamics of single proteins extended by force. Biophys J 98:2692-2701.
26. Hyeon CB, Morrison G, Pincus DL, Thirumalai D (2009) Refolding dynamics of stretched biopolymers upon force quench. Proc Natl Acad Sci USA 106:20288-20293.
27. Corless RM, Gonnet GH, Hare DEG, Jeffrey DJ, Knuth DE (1996) Onthe Lambert W function. Adv Comput Math 5:329-359.
28. Li HB, et al. (2001) Multiple conformations of PEVK proteins detected by single-molecule techniques. Proc Natl Acad Sci USA 98:10682-10686.
29. Walther KA, et al. (2007) Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy. Proc Natl Acad Sci USA 104:7916-7921. (Pubitemid 47185851)
30. Berkovich R, Garcia-Manyes S, Klafter J, Urbakh M, Fernandez JM (2010) Hopping around an entropic barrier created by force. Biochem Biophys Res Commun 403:133-137.
31. Fernandez JM, Li HB (2004) Force-clamp spectroscopy monitors the folding trajectory of a single protein. Science 303:1674-1678. (Pubitemid 38338326)
32. Kramers HA (1940) Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7:284-304.
33. Popa I, Fernandez JM, Garcia-Manyes S (2011) Direct quantification of the attempt frequency determining the mechanical unfolding of ubiquitin protein. J Biol Chem 286:31072-31079.
34. Ptitsyn OB (1995) Molten globule and protein folding. Adv Protein Chem 47:83-229.