A transformation for the mechanical fingerprints of complex biomolecular interactions

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

Volumn 110, Issue 41, 2013, Pages 16432-16437

  Zhang, Yaojun ^a   Dudko, Olga K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Complex interactions; Force spectroscopy; Kinetic rate; Single molecule

Indexed keywords

NUCLEIC ACID; PROTEIN;

ARTICLE; CONFORMATIONAL TRANSITION; DISSOCIATION; ENERGY; KINETICS; MACROMOLECULE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; SINGLE MOLECULE FORCE SPECTROSCOPY; SPECTROSCOPY;

COMPLEX INTERACTIONS; FORCE SPECTROSCOPY; KINETIC RATE; SINGLE MOLECULE;

BIOMECHANICAL PHENOMENA; KINETICS; MACROMOLECULAR SUBSTANCES; MODELS, CHEMICAL; MOLECULAR CONFORMATION; SPECTRUM ANALYSIS;

EID: 84885361696     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1309101110     Document Type: Article

References (24)

1. Alberts B, et al., eds (2008) Molecular Biology of the Cell (Garland Science, New York).
2. Onuchic JN, Luthey-Schulten Z, Wolynes PG (1997) Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem 48:545-600.
3. Dill KA, Chan HS (1997) From Levinthal to pathways to funnels. Nat Struct Biol 4(1): 10-19.
4. Evans E (2001) Probing the relation between force-lifetime-and chemistry in single molecular bonds. Annu Rev Biophys Biomol Struct 30:105-128.
5. Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276(5315):1109-1112.
6. Marszalek PE, Li H, Fernandez JM (2001) Fingerprinting polysaccharides with singlemolecule atomic force microscopy. Nat Biotechnol 19(3):258-262.
7. Dudko OK, Hummer G, Szabo A (2006) Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys Rev Lett 96(10):108101.
8. Dudko OK, Hummer G, Szabo A (2008) Theory, analysis, and interpretation of singlemolecule force spectroscopy experiments. Proc Natl Acad Sci USA 105(41):15755-15760.
9. Greenleaf WJ, Frieda KL, Foster DAN, Woodside MT, Block SM (2008) Direct observation of hierarchical folding in single riboswitch aptamers. Science 319(5863):630-633.
10. Kim J, Zhang CZ, Zhang X, Springer TA (2010) A mechanically stabilized receptor-ligand flex-bond important in the vasculature. Nature 466(7309):992-995.
11. Zhou R, et al. (2011) SSB functions as a sliding platform that migrates on DNA via reptation. Cell 146(2):222-232.
12. Neupane K, Yu H, Foster DAN, Wang F, Woodside MT (2011) Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism. Nucleic Acids Res 39(17):7677-7687.
13. Kaiser CM, Goldman DH, Chodera JD, Tinoco I, Jr., Bustamante C (2011) The ribosome modulates nascent protein folding. Science 334(6063):1723-1727.
14. Stigler J, Ziegler F, Gieseke A, Gebhardt JCM, Rief M (2011) The complex folding network of single calmodulin molecules. Science 334(6055):512-516.
15. Anthony PC, Perez CF, García-García C, Block SM (2012) Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer. Proc Natl Acad Sci USA 109(5): 1485-1489.
16. Strunz T, Oroszlan K, Schumakovitch I, Güntherodt HJ, Hegner M (2000) Model energy landscapes and the force-induced dissociation of ligand-receptor bonds. Biophys J 79(3):1206-1212.
17. Derényi I, Bartolo D, Ajdari A (2004) Effects of intermediate bound states in dynamic force spectroscopy. Biophys J 86(3):1263-1269.
18. Li L, Huang HHL, Badilla CL, Fernandez JM (2005) Mechanical unfolding intermediates observed by single-molecule force spectroscopy in a fibronectin type III module. J Mol Biol 345(4):817-826.
19. Cecconi C, Shank EA, Bustamante C, Marqusee S (2005) Direct observation of the three-state folding of a single protein molecule. Science 309(5743):2057-2060.
20. Zwanzig R (1988) Diffusion in a rough potential. Proc Natl Acad Sci USA 85(7):2029-2030.
21. Best RB, Hummer G (2010) Coordinate-dependent diffusion in protein folding. Proc Natl Acad Sci USA 107(3):1088-1093.
22. Schlierf M, Berkemeier F, Rief M (2007) Direct observation of active protein folding using lock-in force spectroscopy. Biophys J 93(11):3989-3998.
23. Hoffmann A, Woodside MT (2011) Signal-pair correlation analysis of single-molecule trajectories. Angew Chem Int Ed Engl 50(52):12643-12646.
24. Suzuki Y, Dudko OK (2010) Single-molecule rupture dynamics on multidimensional landscapes. Phys Rev Lett 104(4):048101.