Single molecule enzymology: Watching the reaction

Current Opinion in Chemical Biology

Volumn 13, Issue 4, 2009, Pages 436-442

  Gershenson, Anne ^a  

^a BRANDEIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; ENZYME INHIBITOR;

BIOCATALYSIS; CHEMISTRY; METABOLISM; MICROSCOPY; MOVEMENT (PHYSIOLOGY); PROCEDURES; SOLUBILITY;

BIOCATALYSIS; ENZYME INHIBITORS; ENZYMES; MICROSCOPY; MOVEMENT; SOLUBILITY;

EID: 84861854858     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2009.06.011     Document Type: Review

References (51)

1. Joo C, Balci H, Ishitsuka Y, Buranachai C, Ha T. Advances in single-molecule fluorescence methods for molecular biology. Annu Rev Biochem 2008, 77:51-76.
2. Neuman KC, Nagy A. Single-molecule force spectroscopy, optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 2008, 5:491-505.
3. van Mameren J, Peterman EJG, Wuite GJL. See me, feel me, methods to concurrently visualize and manipulate single DNA molecules and associated proteins. Nucl Acids Res 2008, 36:4381-4389.
4. Walter NG, Huang C-Y, Manzo AJ, Sobhy MA. Do-it-yourself guide, how to use the modern single-molecule toolkit. Nat Methods 2008, 5:475-489.
5. Herbert KM, Greenleaf WJ, Block SM. Single-molecule studies of RNA polymerase: motoring along. Annu Rev Biochem 2008, 77:149-176.
6. Blanchard SC. Single-molecule observations of ribosome function. Curr Opin Struct Biol 2009, 19:103-109.
7. Pyle AM. Translocation and unwinding mechanisms of RNA and DNA helicases. Annu Rev Biophys 2008, 37:317-336.
8. Gennerich A, Vale RD. Walking the walk, how kinesin and dynein coordinate their steps. Curr Opin Cell Biol 2009, 21:59-67.
9. English BP, Min W, van Oijen AM, Lee KT, Luo G, Sun H, Cherayil BJ, Kou SC, Xie XS. Ever-fluctuating single enzyme molecules. Michaelis-Menten equation revisited. Nat Chem Biol 2006, 2:87-94.
10. Gorris HH, Rissin DM, Walt DR. Stochastic inhibitor release and binding from single-enzyme molecules. Proc Natl Acad Sci U S A 2007, 104:17680-17685.
11. Matthews BW. The structure of E. coli beta-galactosidase. C R Biologies 2005, 328:549-556.
12. Rissin DM, Gorris HH, Walt DR. Distinct and long-lived activity states of single enzyme molecules. J Am Chem Soc 2008, 130:5349-5353.
13. Roy R, Hohng S, Ha T. A practical guide to single-molecule FRET. Nat Methods 2008, 5:507-516.
14. Hanson JA, Duderstadt K, Watkins LP, Bhattacharyya S, Brokaw J, Chu J-W, Yang H. Illuminating the mechanistic roles of enzyme conformational dynamics. Proc Natl Acad Sci U S A 2007, 104:18055-18060.
15. Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M et al. Intrinsic motions along an enzymatic reaction trajectory. Nature 2007, 450:838-844.
16. Adachi K, Oiwa K, Nishizaka T, Furuike S, Noji H, Itoh H, Yoshida M, Kinosita K Jr. Coupling of rotation and catalysis in F1-ATPase revealed by single-molecule imaging and manipulation. Cell 2007, 130:309-321.
17. Furuike S, Adachi K, Sakaki N, Shimo-Kon R, Itoh H, Muneyuki E, Yoshida M, Kinosita S K. Jr. Temperature dependence of the rotation and hydrolysis activities of F1-ATPase. Biophys J 2008, 95:761-770.
18. Furuike S, Hossain MD, Maki Y, Adachi K, Suzuki T, Kohori A, Itoh H, Yoshida M, Kinosita K Jr. Axle-less F1-ATPase rotates in the correct direction. Science 2008, 319:955-958.
19. Hossain MD, Furuike S, Maki Y, Adachi K, Suzuki T, Kohori A, Itoh H, Yoshida M, Kinosita K Jr. Neither helix in the coiled coil region of the axle of F1-ATPase plays a significant role in torque production. Biophys J 2008, 95:4837-4844.
20. Masaike T, Koyama-Horibe F, Oiwa K, Yoshida M, Nishizaka T. Cooperative three-step motions in catalytic subunits of F1-ATPase correlate with 80- and 40- substep rotations. Nat Struct Mol Biol 2008, 15:1326-1333
21. Nakamoto RK, Baylis Scanlon JA, Al-Shawi MK. The rotary mechanism of the ATP synthase. Arch Biochem Biophys 2008, 476:43-50.
22. Watanabe R, Iino R, Shimabukuro K, Yoshida M, Noji H. Temperature-sensitive reaction intermediate of F1-ATPase. EMBO Rep 2008, 9:84-90.
23. Finkelstein IJ, Greene EC. Single molecule studies of homologous recombination. Molecular BioSystems 2008, 4:1094-1104.
24. Cisse I, Okumus B, Joo C, Ha T Fueling protein-DNA interactions inside porous nanocontainers. Proc Natl Acad Sci U S A 2007, 104:12646-12650.
25. van der Heijden T, Modesti M, Hage S, Kanaar R, Wyman C, Dekker C. Homologous recombination in real time. DNA strand exchange by RecA. Mol Cell 2008, 30:530-538.
26. Robertson RB, Moses DN, Kwon Y, Chan P, Zhao W, Chi P, Klein H, Sung P, Greene EC. Visualizing the disassembly of S. cerevisiae Rad51 nucleoprotein filaments. J Mol Biol 2009, 388:703-720.
27. Farbman ME, Gershenson A, Licht S. Single-molecule analysis of nucleotide-dependent substrate binding by the protein unfoldase ClpA. J Am Chem Soc 2007, 129:12378-12379.
28. Farbman ME, Gershenson A, Licht S. Role of a conserved pore residue in the formation of a prehydrolytic high substrate affinity state in the AAA+ chaperone ClpA. Biochemistry 2008, 47:13497-13505.
29. Kinosita K, Adachi K, Itoh H. Rotation of F1-ATPase. How an ATP-driven molecular machine may work. Annu Rev Biophys Biomol Struct 2004, 33:245-268.
30. von Ballmoos C, Cook GM, Dimroth P. Unique rotary ATP synthase and its biological diversity. Annu Rev Biophys 2008, 37:43-64.
31. Noji H, Yasuda R, Yoshida M, Kinosita K Jr. Direct observation of the rotation of F1-ATPase. Nature 1997, 386:299-302.
32. Nishizaka T, Oiwa K, Noji H, Kimura S, Muneyuki E, Yoshida M, Kinosita K. Chemomechanical coupling in F1-ATPase revealed by simultaneous observation of nucleotide kinetics and rotation. Nat Struct Mol Biol 2004, 11:142-148.
33. o resolution of F1-ATPase from bovine heart mitochondria. Nature 1994, 370:621-628.
34. Bowler MW, Montgomery MG, Leslie AGW, Walker JE. Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 A resolution. J Biol Chem 2007, 282:14238-14242.
35. Wang H, Oster G. Energy transduction in the F1 motor of ATP synthase. Nature 1998, 396:279-282.
36. Greenleaf WJ, Woodside MT, Block SM. High-resolution, singlemolecule measurements of biomolecular motion. Annu Rev Biophys Biomol Struct 2007, 36:171-190.
37. Abbondanzieri EA, Bokinsky G, Rausch JW, Zhang JX, Le Grice SFJ, Zhuang X Dynamic binding orientations direct activity of HIV reverse transcriptase. Nature 2008, 453:184-189.
38. Liu S, Abbondanzieri EA, Rausch JW, Grice SFJL, Zhuang X. Slide into action. Dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates. Science 2008, 322:1092-1097.
39. Sarafianos SG, Marchand B, Das K, Himmel DM, Parniak MA, Hughes SH, Arnold E. Structure and function of HIV-1 reverse transcriptase. Molecular mechanisms of polymerization and inhibition. J Mol Biol 2009, 385:693-713.
40. Pu M, Fang X, Redfield AG, Gershenson A, Roberts MF. Correlation of vesicle binding and phospholipid dynamics with phospholipase C activity. Insights into phosphatidylcholine activation and surface dilution inhibition. J Biol Chem 2009, 284:16099-16107.
41. Rhoades E, Ramlall TF, Webb WW, Eliezer D. Quantification of alpha-synuclein binding to lipid vesicles using fluorescence correlation spectroscopy. Biophys J 2006, 90:4692-4700.
42. Rusu L, Gambhir A, McLaughlin S, Rädler J. Fluorescence correlation spectroscopy studies of peptide and protein binding to phospholipid vesicles. Biophys J 2004, 87:1044-1053.
43. Takakuwa Y, Pack CG, An XL, Manno S, Ito E, Kinjo M. Fluorescence correlation spectroscopy analysis of the hydrophobic interactions of protein 4.1 with phosphatidyl serine liposomes. Biophys Chem 1999, 82:149-155.
44. Chiu C-R, Huang W-N, Wu W-G, Yang T-S. Fluorescence singlemolecule study of cobra phospholipase A2 action on a supported gel-phase lipid bilayer. Chemphyschem 2009, 10:549-558.
45. Rocha S, Hutchison JA, Peneva K, Hermann A, Müllen KM, Skjøt M, Jørgensen CI, Svendsen A, De Schryver FC, Hofkens J et al. Linking phospholipase mobility to activity by singlemolecule wide-field microscopy. Chemphyschem 2009, 10:151-161.
46. Sonesson AW, Elofsson UM, Callisen TH, Brismar H. Tracking single lipase molecules on a trimyristin substrate surface using quantum dots. Langmuir 2007, 23:8352-8356.
47. Sharonov A, Bandichhor R, Burgess K, Petrescu AD, Schroeder F, Kier AB, Hochstrasser RM. Lipid diffusion from single molecules of a labeled protein undergoing dynamic association with giant unilamellar vesicles and supported bilayers. Langmuir 2008, 24:844-850.
48. Knight JD, Falke JJ. Single-molecule fluorescence studies of a PH domain. Newinsights into the membrane docking reaction. Biophys J 2009, 96:566-582.
49. Fazio T, Visnapuu M-L, Wind S, Greene EC. DNA curtains and nanoscale curtain rods. High-throughput tools for single molecule imaging. Langmuir 2008, 24:10524-10531.
50. Comellas-Aragones M, Engelkamp H, Claessen VI, Sommerdijk NAJM, Rowan AE, Christianen PCM, Maan JC, Verduin BJM, Cornelissen JJLM, Nolte RJM. A virus-based single-enzyme nanoreactor. Nat Nanotechnol 2007, 2:635-639.
51. Reiner JE, Crawford AM, Kishore RB, Goldner LS, Helmerson K, Gilson MK. Optically trapped aqueous droplets for single molecule studies. Appl Phys Lett 2006, 89: 013904.