Nonkinetic modeling of the mechanical unfolding of multimodular proteins: Theory and experiments

Biophysical Journal

Volumn 101, Issue 6, 2011, Pages 1504-1512

  Benedetti, F ^a   Micheletti, C ^b,c   Bussi, G ^c   Sekatskii, S K ^a   Dietler, G ^a  

^a EPFL   (Switzerland)

^b SISSA   (Italy)

^c ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ATOMIC FORCE MICROSCOPY; CHEMICAL STRUCTURE; KINETICS; MONTE CARLO METHOD; PROTEIN UNFOLDING; STATISTICS;

KINETICS; MICROSCOPY, ATOMIC FORCE; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN UNFOLDING; STOCHASTIC PROCESSES;

EID: 80053128757     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.07.047     Document Type: Article

References (34)

1. Y. Cao, and H.B. Li Polyprotein of GB1 is an ideal artificial elastomeric protein Nat. Mater. 6 2007 109 114 (Pubitemid 46197646)
2. Y. Cao, and C. Lam H.B. Li Nonmechanical protein can have significant mechanical stability Angew. Chem. Int. Ed. 45 2006 642 645 (Pubitemid 43121465)
3. M. Carrion-Vazquez, and A.F. Oberhauser J.M. Fernandez Mechanical and chemical unfolding of a single protein: a comparison Proc. Natl. Acad. Sci. USA 96 1999 3694 3699 (Pubitemid 29168972)
4. M. Sandal, and F. Valle B. Samor Conformational equilibria in monomeric α-synuclein at the single-molecule level PLoS Biol. 6 2008 e6
5. D.J. Brockwell, and G.S. Beddard S.E. Radford Mechanically unfolding the small, topologically simple protein L Biophys. J. 89 2005 506 519 (Pubitemid 41098304)
6. P.E. Marszalek, and H. Lu J.M. Fernandez Mechanical unfolding intermediates in titin modules Nature 402 1999 100 103
7. H. Li, and W.A. Linke J.M. Fernandez Reverse engineering of the giant muscle protein titin Nature 418 2002 998 1002 (Pubitemid 34976037)
8. M. Carrion-Vazquez, and H.B. Li J. Fernandez The mechanical stability of ubiquitin is linkage dependent Nat. Struct. Mol. Biol. 10 2003 738 743 (Pubitemid 37052413)
9. H. Li, and M. Carrion-Vazquez J. Fernandez Point mutations alter the mechanical stability of immunoglobulin modules Nat. Struct. Mol. Biol. 7 2000 1117 1120
10. G. Lee, and K. Abdi P.E. Marszalek Nanospring behaviour of ankyrin repeats Nature 440 2006 246 249 (Pubitemid 43372106)
11. A.F. Oberhauser, and P.K. Hansma J.M. Fernandez Stepwise unfolding of titin under force-clamp atomic force microscopy Proc. Natl. Acad. Sci. USA 98 2001 468 472 (Pubitemid 32105065)
12. B. Sorce, and S. Sabella P.P. Pompa Single-molecule mechanical unfolding of amyloidogenic β2-microglobulin: the force-spectroscopy approach ChemPhysChem 10 2009 1471 1477
13. E. Evans, and K. Ritchie Dynamic strength of molecular adhesion bonds Biophys. J. 72 1997 1541 1555 (Pubitemid 27133095)
14. A. Garg Escape-field distribution for escape from a metastable potential well subject to a steadily increasing bias field Phys. Rev. B 51 1995 15592 15595
15. A. Imparato, F. Sbrana, and M. Vassalli Reconstructing the free energy landscape of a polyprotein by single-molecule experiments Europhys. Lett. 82 2008 58006
16. A.F. Oberhauser, and M. Carrión-Vázquez Mechanical biochemistry of proteins one molecule at a time J. Biol. Chem. 283 2008 6617 6621
17. R. Best, and D.J. Brockwell J. Clarke Force mode AFM as a tool for protein folding studies Anal. Chim. Acta 479 2003 87 105 (Pubitemid 36173937)
18. D.J. Brockwell, and G.S. Beddard S.E. Radford The effect of core destabilization on the mechanical resistance of I27 Biophys. J. 83 2002 458 472 (Pubitemid 34694749)
19. D. Aioanei, B. Samor, and M. Brucale Maximum likelihood estimation of protein kinetic parameters under weak assumptions from unfolding force spectroscopy experiments Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 80 2009 61916
20. F. Benedetti, S.K. Sekatskii, and G. Dietler Single-molecule force spectroscopy of multimodular proteins: a new method to extract kinetic unfolding parameters J. Adv. Microsc. Res. 6 2011 1 6
21. W.T. King, M.H. Su, and G.L. Yang Monte Carlo simulation of mechanical unfolding of proteins based on a simple two-state model Int. J. Biol. Macromol. 46 2010 159 166
22. H. Dietz, and F. Berkemeier M. Rief Anisotropic deformation response of single protein molecules Proc. Natl. Acad. Sci. USA 103 2006 12724 12728 (Pubitemid 44298628)
23. G. Hummer, and A. Szabo Thermodynamics and kinetics of single-molecule force spectroscopy E. Barkai, F.L.H. Brown, M. Orrit, H. Yang, Theory and Evaluation of Single-Molecule Signals 2008 World Scientific Singapore 139 175
24. H. Li Engineering proteins with tailored nanomechanical properties: a single molecule approach Org. Biomol. Chem. 5 2007 3399 3406 (Pubitemid 47587690)
25. E. Florin, and M. Rief H. Gaub Sensing specific molecular interactions with the atomic force microscope Biosens. Bioelectron. 10 1995 895 901
26. M. Sandal, and F. Benedetti B. Samor Hooke: an open software platform for force spectroscopy Bioinformatics 25 2009 1428 1430
27. M. Schlierf, and M. Rief Single-molecule unfolding force distributions reveal a funnel-shaped energy landscape Biophys. J. 90 2006 L33 L35
28. M. Rief, and M. Gautel H.E. Gaub Reversible unfolding of individual titin immunoglobulin domains by AFM Science 276 1997 1109 1112 (Pubitemid 27218118)
29. M. Rief, J.M. Fernandez, and H.E. Gaub Elastically coupled two-level systems as a model for biopolymer extensibility Phys. Rev. Lett. 81 1998 4764 4767 (Pubitemid 128626983)
30. R.C. Zinober, and D.J. Brockwell D.A. Smith Mechanically unfolding proteins: the effect of unfolding history and the supramolecular scaffold Protein Sci. 11 2002 2759 2765 (Pubitemid 35365243)
31. R. Berkovich, and S. Garcia-Manyes J.M. Fernandez Collapse dynamics of single proteins extended by force Biophys. J. 98 2010 2692 2701
32. E. Gumbel Statistics of Extremes 2004 Dover Mineola, NY
33. W. Press, and S. Teukolsky B. Flannery Numerical Recipes, 3rd ed.: The Art of Scientific Computing 2007 Cambridge University Press Cambridge, United Kingdom
34. B.W. Silverman Density Estimation for Statistics and Data Analysis 1986 Chapman & Hall/CRC Boca Raton, FL