Orientation and rotational motions of single molecules by polarized total internal reflection fluorescence microscopy (polTIRFM)

Cold Spring Harbor Protocols

Volumn 7, Issue 5, 2012, Pages 535-545

  Beausang, John F ^a   Sun, Yujie ^a   Quinlan, Margot E ^a   Forkey, Joseph N ^a   Goldman, Yale E ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; CALMODULIN; FLUORESCENT DYE; MYOSIN; RHODAMINE;

ARTICLE; ASSAY; CROSS LINKING; FLUORESCENCE MICROSCOPY; MACROMOLECULE; MOLECULAR MECHANICS; MOTILITY ASSAY; POLARIZED TOTAL INTERNAL REFLECTION FLUORESCENCE MICROSCOPY; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN PURIFICATION; ROTATION; ANIMAL; CHEMISTRY; METABOLISM; METHODOLOGY; MOTION; PROTEIN BINDING; RABBIT; STAINING;

ACTINS; ANIMALS; CALMODULIN; FLUORESCENT DYES; MICROSCOPY, FLUORESCENCE; MOTION; MYOSINS; PROTEIN BINDING; RABBITS; RHODAMINES; STAINING AND LABELING;

EID: 84860576662     PISSN: 19403402     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.top069344     Document Type: Article

References (68)

1. Adams SR, Campbell RE, Gross LA, Martin BR, Walkup GK, Yao Y, Llopis J, Tsien RY. 2002. New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: Synthesis and biological applications. J Am Chem Soc 124: 6063-6076.
2. Ali MY, Uemura S, Adachi K, Itoh H, Kinosita K Jr, Ishiwata S. 2002. Myosin V is a left-handed spiral motor on the right-handed actin helix. Nat Struct Biol 9: 464-467.
3. Asenjo AB, Weinberg Y, Sosa H. 2006. Nucleotide binding and hydrolysis induces a disorder-order transition in the kinesin neck-linker region. Nat Struct Mol Biol 13: 648-654.
4. Axelrod D. 1989. Fluorescence polarization microscopy. Methods Cell Biol 30: 333-352.
5. Bartko AP, Xu K, Dickson RM. 2002. Three-dimensional single molecule rotational diffusion in glassy state polymer films. Phys Rev Lett 89: 026101.1-026101.4.
6. Beausang JF, Sun Y, Quinlan ME, Forkey JN, Goldman YE. 2012a. Fluorescent labeling of calmodulin with bifunctional rhodamine. Cold Spring Harb Protoc doi: 10.1101/pdb.prot069351.
7. Beausang JF, Sun Y, Quinlan ME, Forkey JN, Goldman YE. 2012b. Fluorescent labeling of myosin V for polarized total internal reflection fluorescence microscopy (polTIRFM) motility assays. Cold Spring Harb Protoc doi: 10.1101/pdb.prot069369.
8. Beausang JF, Sun Y, Quinlan ME, Forkey JN, Goldman YE. 2012c. Preparation of filamentous actin for polarized total internal reflection fluorescence microscopy (polTIRFM) motility assays. Cold Spring Harb Protoc doi: 10.1101/pdb.prot069377.
9. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz J, Hess HF. 2006. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313: 1642-1645.
10. Brack AS, Brandmeier BD, Ferguson RE, Criddle S, Dale RE, Irving M. 2004. Bifunctional rhodamine probes of myosin regulatory light chain orientation in relaxed skeletal muscle fibers. Biophys J 86: 2329-2341.
11. Burgess WH, Jemiolo DK, Kretsinger RH. 1980. Interaction of calcium and calmodulin in the presence of sodium dodecyl sulfate. Biochim Biophys Acta 623: 257-270.
12. Chen RF, Bowman RL. 1965. Fluorescence polarization: Measurement with ultraviolet-polarizing filters in a spectrophotofluorometer. Science 147: 729-732.
13. Chiu W, Baker ML, Almo SC. 2006. Structural biology of cellular machines. Trends Cell Biol 16: 144-150.
14. Corrie JET, Craik JS, Munasinghe VRN. 1998. A homo-bifunctional rhodamine for labeling proteins with defined orientations of a fluorophore. Bioconjug Chem 9: 160-167.
15. Corrie JET, Brandmeier BD, Ferguson RE, Trentham DR, Kendrick-Jones J, Hopkins SC, van der Heide UA, Goldman YE, Sabido-David C, Dale RE, et al. 1999. Dynamic measurement of myosin light-chain-domain tilt and twist in muscle contraction. Nature 400: 425-430.
16. Costello MJ. 2006. Cryo-electron microscopy of biological samples. Ultrastruct Pathol 30: 361-371.
17. Enderlein J, Toprak E, Selvin PR. 2005. Polarization effect on position accuracy of fluorophore localization. Opt Express 14: 8111-8120.
18. Ferguson RE, Sun YB, Mercier P, Brack AS, Sykes BD, Corrie JET, Trentham DR, Irving M. 2003. In situ orientations of protein domains: Troponin C in skeletal muscle fibers. Mol Cell 11: 865-874.
19. Forkey JN, Quinlan ME, Goldman YE. 2000. Protein structural dynamics by single-molecule fluorescence polarization. Prog Biophys Mol Biol 74: 1-35.
20. Forkey JN, Quinlan ME, Shaw MA, Corrie JET, Goldman YE. 2003. Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization. Nature 422: 399-404.
21. Forkey JN, Quinlan ME, Goldman YE. 2005. Measurement of single macromolecule orientation by total internal reflection fluorescence polarization microscopy. Biophys J 89: 1261-1271.
22. Geeves MA, Holmes KC. 2005. The molecular mechanism of muscle contraction. Adv Protein Chem 71: 161-193.
23. Goldman YE. 1998. Wag the tail: Structural dynamics of actomyosin. Cell 93: 1-4.
24. Gore J, Bryant Z, Stone MD, Nöllmann M, Cozzarelli NR, Bustamante C. 2006. Mechanochemical analysis of DNA gyrase using rotor bead tracking. Nature 439: 100-104.
25. Gutfreund H. 1995. Kinetics for the life sciences: Receptors, transmitters and catalysts Cambridge University Press, Cambridge.
26. Ha T, Glass J, Enderle T, Chemla DS, Weiss S. 1998. Hindered rotational diffusion and rotational jumps of single molecules. Phys Rev Lett 80: 2093-2096.
27. Hell SW, Dyba M, Jakobs S. 2004. Concepts for nanoscale resolution in fluorescence microscopy. Curr Opin Neurobiol 14: 599-609.
28. Hopkins SC, Sabido-David C, van der Heide UA, Ferguson RE, Brandmeier BD, Dale RE, Kendrick-Jones J, Corrie JET, Trentham DR, Irving M, et al. 2002. Orientation changes of the myosin light chain domain during filament sliding in active and rigor muscle. J Mol Biol 318: 1275-1291.
29. 2+-free calmodulin binding to unconventional myosins reveals how calmodulin acts as a regulatory switch. Structure 4: 1475-1490.
30. Hua W, Chung J, Gelles J. 2002. Distinguishing inchworm and hand-overhand processive kinesin movement by neck rotation measurements. Science 295: 844-848.
31. Igumenova TI, Frederick KK, Wand AJ. 2006. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev 106: 1672-1699.
32. Irving M, St Claire Allen T, Sabido-David C, Craik JS, Brandmeier B, Kendrick-Jones J, Corrie JET, Trentham DR, Goldman YE. 1995. Tilting of the light-chain region of myosin during step length changes and active force generation in skeletal muscle. Nature 375: 688-691.
33. Kinosita K Jr. 1999. Real time imaging of rotating molecular machines. FASEB J 2: S201-S208.
34. Kinosita K Jr, Adachi K, Itoh H. 2004. Rotation of F1-ATPase: How an ATP-driven molecular machine may work. Annu Rev Biophys Biomol Struct 33: 245-268.
35. + channel T1 recognition domain. J Biol Chem 278: 4305-4313.
36. Kreiter M, Prummer M, Hecht B, Wild UP. 2002. Orientation dependence of fluorescence lifetimes near an interface. J Chem Phys 117: 9430-9433.
37. La Porta A, Wang MD. 2004. Optical torque wrench: Angular trapping, rotation, and torque detection of quartz microparticles. Phys Rev Lett 92: 190801.
38. Lakowicz J.R. 2006. Principles of fluorescence spectroscopy, 3rd ed. Springer, New York.
39. Lieb MA, Zavislan JM, Novotny L. 2004. Single-molecule orientations determined by direct emission pattern imaging. J Opt Soc Am B 21: 1210-1215.
40. Marks KM, Nolan GP. 2006. Chemical labeling strategies for cell biology. Nat Methods 3: 591-596.
41. Mercier P, Ferguson RE, Irving M, Corrie JET, Trentham DR, Sykes BD. 2003. NMR structure of a bifunctional rhodamine labeled N-domain of troponin C complexed with the regulatory "switch" peptide from troponin I: Implications for in situ fluorescence studies in muscle fibers. Biochemistry 42: 4333-4348.
42. Min W, English BP, Luo G, Cherayil BJ, Kou SC, Xie XS. 2005. Fluctuating enzymes: Lessons from single-molecule studies. Acc Chem Res 38: 923-931.
43. Otterbein LR, Graceffa P, Dominguez R. 2001. The crystal structure of uncomplexed actin in the ADP state. Science 293: 708-711.
44. Penzkofer A, Wiedmann J. 1980. Orientation of transition dipole moments of rhodamine 6G determined by excited state absorption. Optics Commun 35: 81-86.
45. Pollard TD, Earnshaw WC. 2002. Cell biology. Saunders, Philadelphia.
46. Press WH, Teukosky SA, Vetterling WT, Flannery BP. 1992. Numerical recipes in C, 2nd ed. Cambridge University Press, Cambridge.
47. Quinlan ME, Forkey JN, Goldman YE. 2005. Orientation of the myosin light chain region by single molecule total internal reflection fluorescence polarization microscopy. Biophys J 89: 1132-1142.
48. Rasnik I, McKinney SA, Ha T. 2006. Nonblinking and long-lasting single-molecule fluorescence imaging. Nat Methods 3: 891-893.
49. Rosenberg SA, Quinlan ME, Forkey JN, Goldman YE. 2005. Rotational motions of macro-molecules by single-molecule fluorescence micros-copy. Acc Chem Res 38: 583-593.
50. Robinson JM, Kosolapov A, Deutsch C. 2006. Tertiary and quaternary structure formation of voltage-gated potassium channels. Methods Mol Biol 337: 41-52.
51. Rust MJ, Bates M, Zhuang X. 2006. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3: 793-795.
52. Sale K, Sár C, Sharp KA, Hideg K, Fajer PG. 2002. Structural determination of spin label immobilization and orientation: A Monte Carlo minimization approach. J Magn Reson 156: 104-112.
53. Seidel R, Dekker C. 2007. Single-molecule studies of nucleic acid motors. Curr Opin Struct Biol 17: 80-86.
54. Senior AE, Nadanaciva S, Weber J. 2002. The molecular mechanism of ATP synthesis by F1F0-ATP synthase. Biochim Biophys Acta 1553: 188-211.
55. Shaevitz JW, Block SM, Schnitzer MJ. 2005. Statistical kinetics of macromolecular dynamics. Biophys J 89: 2277-2285.
56. Shiroguchi K, Kinosita K Jr. 2007. Myosin V walks by lever action and Brownian motion. Science 316: 1208-1212.
57. Sick B, Hecht B, Novotny L. 2000. Orientational imaging of single molecules by annular illumination. Phys Rev Lett 85: 4482-4485.
58. Sosa H, Peterman EJG, Moerner WE, Goldstein LSB. 2001. ADP-induced rocking of the kinesin motor domain revealed by single-molecule fluorescence polarization microscopy. Nat Struct Biol 8: 540-544.
59. Strick T, Allemand JF, Croquette V, Bensimon D. 2000. Twisting and stretching single DNA molecules. Prog Biophys Mol Biol 74: 115-140.
60. 2+ and myosin binding to thin filaments during activation of skeletal muscle. Proc Natl Acad Sci 103: 17771-17776.
61. Syed S, Snyder GE, Franzini-Armstrong C, Selvin PR, Goldman YE. 2006. Adaptability of myosin V studied by simultaneous detection of position and orientation. EMBO J 25: 1795-1803.
62. Toprak E, Enderlein J, Syed S, McKinney SA, Petschek RG, Ha T, Goldman YE, Selvin PR. 2006. Defocused orientation and position imaging (DOPI) of myosin V. Proc Natl Acad Sci 103: 6495-6499.
63. 2+-ATPase of the sarcoplasmic reticulum. Annu Rev Biochem 73: 269-292.
64. van der Heide UA, Orbons B, Gerrtsen HC, Levine YK. 1992. The orientation of transition moments of dye molecules used in fluorescence studies of muscle systems. Eur Biophys J 21: 263-272.
65. Veigel C, Wang F, Bartoo ML, Sellers JR, Molloy JE. 2002. The gated gait of the processive molecular motor, myosin V. Nat Cell Biol 4: 59-65.
66. Waggoner A. 2006. Fluorescent labels for proteomics and genomics. Curr Opin Chem Biol 10: 62-66.
67. Wilson T, Massoumian F, Jusvskaitas R. 2003. Generation and focusing of radially polarized electric fields. Opt Engr 42: 3088-3089.
68. Yildiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR. 2003. Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5-nm localization. Science 300: 2061-2065.