Single-Molecule Fluorescence Studies of Protein Folding
10.1007/978-1-59745-367-7_13
Crossref book-chapter
Humana Press
Methods in Molecular Biology (297)
Bibliography

Nienhaus, G. U. (2008). Single-Molecule Fluorescence Studies of Protein Folding. Protein Structure, Stability, and Interactions, 311–337.

Authors 1
  1. G. Ulrich Nienhaus (first)
References 72 Referenced 15
  1. Levinthal, C. (1968) Are there pathways for protein folding?, J Chim Phys 65, 44–45. (10.1051/jcp/1968650044) / J Chim Phys by C. Levinthal (1968)
  2. Baldwin, R. L. (1995) The nature of protein folding pathways: The classical versus the new view, J Biomol NMR 5, 103–109. (10.1007/BF00208801) / J Biomol NMR by R. L. Baldwin (1995)
  3. Onuchic, J. N., Wolynes, P. G. (2004) Theory of protein folding, Curr Opin Struct Biol 14, 70–75. (10.1016/j.sbi.2004.01.009) / Curr Opin Struct Biol by J. N. Onuchic (2004)
  4. Wolynes, P. G., Onuchic, J. N., Thirumalai, D. (1995) Navigating the folding routes, Science 267, 1619–1620. (10.1126/science.7886447) / Science by P. G. Wolynes (1995)
  5. Onuchic, J. N., Nymeyer, H., Garcia, A. E., et al. (2000) The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios, Adv Protein Chem 53, 87–152. (10.1016/S0065-3233(00)53003-4) / Adv Protein Chem by J. N. Onuchic (2000)
  6. Dill, K. A., Chan, H. S. (1997) From Levinthal to pathways to funnels, Nat Struct Biol 4, 10–19. (10.1038/nsb0197-10) / Nat Struct Biol by K. A. Dill (1997)
  7. Callender, R. H., Dyer, R. B., Gilmanshin, R., et al. (1998) Fast events in protein folding: The time evolution of primary processes, Annu Rev Phys Chem 49, 173–202. (10.1146/annurev.physchem.49.1.173) / Annu Rev Phys Chem by R. H. Callender (1998)
  8. Eaton, W. A., Munoz, V., Hagen, S. J., et al. (2000) Fast kinetics and mechanisms in protein folding, Annu Rev Biophys Biomol Struct 29, 327–359. (10.1146/annurev.biophys.29.1.327) / Annu Rev Biophys Biomol Struct by W. A. Eaton (2000)
  9. Gruebele, M. (1999) The fast protein folding problem, Annu Rev Phys Chem 50, 485–516. (10.1146/annurev.physchem.50.1.485) / Annu Rev Phys Chem by M. Gruebele (1999)
  10. Neher, E., Sakmann, B. (1976) Single-channel currents recorded from membrane of denervated frog muscle fibres, Nature 260, 799–802. (10.1038/260799a0) / Nature by E. Neher (1976)
  11. Rief, M., Gautel, M., Oesterhelt, F., et al. (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM, Science 276, 1109–1112. (10.1126/science.276.5315.1109) / Science by M. Rief (1997)
  12. Cecconi, C., Shank, E. A., Bustamante, C., et al. (2005) Direct observation of the three-state folding of a single protein molecule, Science 23, 2057–2060. (10.1126/science.1116702) / Science by C. Cecconi (2005)
  13. Kellermayer, M. S., Smith, S. B., Granzier, H. L., et al. (1997) Folding–unfolding transitions in single titin molecules characterized with laser tweezers, Science 276, 1112–1116. (10.1126/science.276.5315.1112) / Science by M. S. Kellermayer (1997)
  14. Michalet, X., Kapanidis, A. N., Laurence, T., et al. (2003) The power and prospects of fluorescence microscopies and spectroscopies, Annu Rev Biophys Biomol Struct 32, 161–182. (10.1146/annurev.biophys.32.110601.142525) / Annu Rev Biophys Biomol Struct by X. Michalet (2003)
  15. Böhmer, M., Enderlein, J. (2003) Fluorescence spectroscopy of single molecules under ambient conditions: Methodology and technology, ChemPhysChem 4, 793–808. (10.1002/cphc.200200565) / Chemphyschem by M. Böhmer (2003)
  16. Haran, G. (2003) Single-molecule fluorescence spectroscopy of biomolecular folding, J. Phys Condens Matter 15, R1219–R1317. (10.1088/0953-8984/15/32/201) / J. Phys Condens Matter by G. Haran (2003)
  17. Schuler, B. (2005) Single-molecule fluorescence spectroscopy of protein folding, ChemPhysChem 6, 1206–1220. (10.1002/cphc.200400609) / Chemphyschem by B. Schuler (2005)
  18. Nienhaus, G. U. (2006) Exploring protein structure and dynamics under denaturing conditions by single-molecule FRET analysis, Macromol Biosci 6, 907–922. (10.1002/mabi.200600158) / Macromol Biosci by G. U. Nienhaus (2006)
  19. Förster, T. (1948) Zwischenmolekulare Energiewanderung und Fluoreszenz, Ann Physik (Leipzig) 437, 55–75 (Translated in: Biological Physics, edited by Mielczarek, E.V., Greenbaum, E., Knox, R.S., American Institute of Physics, New York, 1993, pp. 1148–1160). (10.1002/andp.19484370105)
  20. Ha, T., Enderle, T., Ogletree, D. F., et al. (1996) Probing the interaction between two single molecules: Fluorescence resonance energy transfer between a single donor and a single acceptor, Proc Natl Acad Sci USA 93, 6264–6268. (10.1073/pnas.93.13.6264) / Proc Natl Acad Sci USA by T. Ha (1996)
  21. Selvin, P. R. (2000) The renaissance of fluorescence energy transfer, Nat Struct Biol 7, 730–734. (10.1038/78948) / Nat Struct Biol by P. R. Selvin (2000)
  22. Kuzmenkina, E. V., Heyes, C. D., Nienhaus, G. U. (2006) Single-molecule FRET study of denaturant induced unfolding of RNase H, J Mol Biol 327, 313–324. (10.1016/j.jmb.2005.12.061) / J Mol Biol by E. V. Kuzmenkina (2006)
  23. Schuler, B., Lipman, E. A., Eaton, W. A. (2002) Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy, Nature 419, 743–747. (10.1038/nature01060) / Nature by B. Schuler (2002)
  24. McCarney, E. R., Werner, J. H., Bernstein, S. L., et al. (2005) Site-specific dimensions across a highly denatured protein: a single molecule study, J Mol Biol 352, 672–682. (10.1016/j.jmb.2005.07.015) / J Mol Biol by E. R. McCarney (2005)
  25. Kuzmenkina, E. V., Heyes, C. D., Nienhaus, G. U. (2005) Single molecule Förster resonance energy transfer study of protein dynamics under denaturing conditions, Proc Natl Acad Sci USA 102, 15471–15476. (10.1073/pnas.0507728102) / Proc Natl Acad Sci USA by E. V. Kuzmenkina (2005)
  26. Rhoades, E., Cohen, M., Schuler, B., et al. (2004) Two-state folding observed in individual protein molecules, J Am Chem Soc 126, 14686–14687. (10.1021/ja046209k) / J Am Chem Soc by E. Rhoades (2004)
  27. Lipman, E. A., Schuler, B., Bakajin, O., et al. (2003) Single-molecule measurement of protein folding kinetics, Science 301, 1233–1235. (10.1126/science.1085399) / Science by E. A. Lipman (2003)
  28. Wahl, M., Koberling, F., Patting, M., et al. (2004) Time-resolved confocal fluorescence imaging and spectroscopy system with single molecule sensitivity and sub-micrometer resolution, Curr Pharm Biotechnol 5, 299–308. (10.2174/1389201043376841) / Curr Pharm Biotechnol by M. Wahl (2004)
  29. Ha, T. (2001) Single molecule flourescence resonance transfer, Methods 25, 78–86. (10.1006/meth.2001.1217) / Methods by T. Ha (2001)
  30. Widengren, J., Kudryavtsev, V., Antonik, M., et al. (2006) Single-molecule detection and identification of multiple species by multiparameter fluorescence detection, Anal Chem 78, 2039–2050. (10.1021/ac0522759) / Anal Chem by J. Widengren (2006)
  31. Flomenbom, O., Klafter, J., Szabo, A. (2005) What can one learn from two-state single-molecule trajectories?, Biophys J 88, 3780–3783. (10.1529/biophysj.104.055905) / Biophys J by O. Flomenbom (2005)
  32. Zemanová, L., Schenk, A., Valler, M. J., et al. (2005) High-throughput screening of interactions between G protein-coupled receptors and ligands using confocal optics microscopy, Methods Mol Biol 305, 365–384. (10.1385/1-59259-912-5:365) / Methods Mol Biol by L. Zemanová (2005)
  33. Hazlett, T. L., Ruan, Q., Tetin, S. Y. (2005) Application of fluorescence correlation spectroscopy to hapten–antibody binding, Methods Mol Biol 305, 415–438. (10.1385/1-59259-912-5:415) / Methods Mol Biol by T. L. Hazlett (2005)
  34. Haustein, E., Schwille, P. (2003) Ultrasensitive investigations of biological systems by fluorescence correlation spectroscopy, Methods 29, 153–166. (10.1016/S1046-2023(02)00306-7) / Methods by E. Haustein (2003)
  35. Lamb, D. C., Schenk, A., Röcker, C., et al. (2000) Sensitivity enhancement in fluorescence correlation spectroscopy of multiple species using time-gated detection, Biophys J 79, 1129–1138. (10.1016/S0006-3495(00)76366-1) / Biophys J by D. C. Lamb (2000)
  36. Dertinger, T., Pacheco, V., von der Hocht, I., et al. (2007) Two-focus fluorescence correlation spectroscopy: A new tool for accurate and absolute diffusion measurements, ChemPhysChem 8, 433–443. (10.1002/cphc.200600638) / ChemPhysChem by T. Dertinger (2007)
  37. Clegg, R. M. (1996) in (Wang, X. F., and Herman, B., eds.) Fluorescence imaging spectroscopy and microscopy, pp 180–252. John Wiley & Sons.
  38. Van der Meer, B. W., Coker III, G., Chen, S.-Y. S. (1994) Resonance energy transfer: Theory and data, VCH Publishers, Inc., New York, Weinheim, Cambridge. / Resonance energy transfer: Theory and data by B. W. Meer Van der (1994)
  39. Stryer, L., Haugland, R. P. (1967) Energy transfer: A spectroscopic ruler, Proc Natl Acad Sci USA 58, 719–726. (10.1073/pnas.58.2.719) / Proc Natl Acad Sci USA by L. Stryer (1967)
  40. Rasnik, I., McKinney, S. A., Ha, T. (2005) Surfaces and orientations: Much to fret about?, Acc Chem Res 38, 542–548. (10.1021/ar040138c) / Acc Chem Res by I. Rasnik (2005)
  41. Coban, O., Lamb, D. C., Zaychikov, E., et al. (2006) Conformational heterogeneity in RNA polymerase observed by single-pair FRET microscopy, Biophys J 90, 4605–4617. (10.1529/biophysj.105.078840) / Biophys J by O. Coban (2006)
  42. Majumdar, Z. K., Hickerson, R., Noller, H. F., et al. (2005) Measurements of internal distance changes of the 30S ribosome using FRET with multiple donor–acceptor pairs: Quantitative spectroscopic methods, J Mol Biol 351, 1123–1145. (10.1016/j.jmb.2005.06.027) / J Mol Biol by Z. K. Majumdar (2005)
  43. Vörös, J. (2004) The density and refractive index of adsorbing protein layers, Biophys J 87, 553–561. (10.1529/biophysj.103.030072) / Biophys J by J. Vörös (2004)
  44. Schuler, B., Lipman, E. A., Steinbach, P. J., et al. (2005) Polyproline and the “spectroscopic ruler” revisited with single-molecule fluorescence, Proc Natl Acad Sci USA 102, 2754–2759. (10.1073/pnas.0408164102) / Proc Natl Acad Sci USA by B. Schuler (2005)
  45. Kapanidis, A. N., Lee, N. K., Laurence, T. A., et al. (2004) Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules, Proc Natl Acad Sci USA 101, 8936–8941. (10.1073/pnas.0401690101) / Proc Natl Acad Sci USA by A. N. Kapanidis (2004)
  46. Müller, B. K., Zaychikov, E., Bräuchle, C., et al. (2005) Pulsed interleaved excitation, Biophys J 89, 3508–3522. (10.1529/biophysj.105.064766) / Biophys J by B. K. Müller (2005)
  47. Panchuk-Voloshina, N., Haugland, R. P., Bishop-Stewart, J., et al. (1999) Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates, J Histochem Cytochem 47, 1179–1188. (10.1177/002215549904700910) / J Histochem Cytochem by N. Panchuk-Voloshina (1999)
  48. Mujumdar, R. B., Ernst, L. A., Mujumdar, S. R., et al. (1993) Cyanine dye labeling reagents: Sulfoindocyanine succinimidyl esters, Bioconjug Chem 4, 105–111. (10.1021/bc00020a001) / Bioconjug Chem by R. B. Mujumdar (1993)
  49. Schuler, B., Pannell, L. K. (2002) Specific labeling of polypeptides at amino-terminal cysteine residues using Cy5-benzyl thioester, Bioconjug Chem 13, 1039–1043. (10.1021/bc025509t) / Bioconjug Chem by B. Schuler (2002)
  50. Yamaguchi, J., Nemoto, N., Sasaki, T., et al. (2001) Rapid functional analysis of protein–protein interactions by fluorescent C-terminal labeling and single-molecule imaging, FEBS Lett 502, 79–83. (10.1016/S0014-5793(01)02581-9) / FEBS Lett by J. Yamaguchi (2001)
  51. Cropp, T. A., Schultz, P. G. (2004) An expanding genetic code, Trends Genet 20, 625–630. (10.1016/j.tig.2004.09.013) / Trends Genet by T. A. Cropp (2004)
  52. David, R., Richter, M. P., Beck-Sickinger, A. G. (2004) Expressed protein ligation. Method and applications, Eur J Biochem 271, 663–677. (10.1111/j.1432-1033.2004.03978.x) / Eur J Biochem by R. David (2004)
  53. Kapanidis, A. N., Weiss, S. (2002) Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules, J Chem Phys 117, 10953–10964. (10.1063/1.1521158) / J Chem Phys by A. N. Kapanidis (2002)
  54. Rhoades, E., Gussakovsky, E., Haran, G. (2003) Watching proteins fold one molecule at a time, Proc Natl Acad Sci USA 100, 3197–3202. (10.1073/pnas.2628068100) / Proc Natl Acad Sci USA by E. Rhoades (2003)
  55. Amirgoulova, E. V., Groll, J., Heyes, C. D., et al. (2004) Biofunctionalized polymer surfaces exhibit minimal interaction towards immobilized proteins, ChemPhysChem 5, 552–555. (10.1002/cphc.200400024) / ChemPhysChem by E. V. Amirgoulova (2004)
  56. Talaga, D. S., Lau, W. L., Roder, H., et al. (2000) Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy, Proc Natl Acad Sci USA 97, 13021–13026. (10.1073/pnas.97.24.13021) / Proc Natl Acad Sci USA by D. S. Talaga (2000)
  57. Rasnik, I., Myong, S., Cheng, W., et al. (2004) DNA-binding orientation and domain conformation of the E. coli rep helicase monomer bound to a partial duplex junction: Single molecule studies of fluorescently labeled enzymes, J Mol Biol 336, 395–408. (10.1016/j.jmb.2003.12.031) / J Mol Biol by I. Rasnik (2004)
  58. Wennmalm, S., Edman, L., Rigler, R. (1997) Conformational fluctuations in single DNA molecules, Proc Natl Acad Sci USA 94, 10641–10646. (10.1073/pnas.94.20.10641) / Proc Natl Acad Sci USA by S. Wennmalm (1997)
  59. Ha, T., Rasnik, I., Cheng, W., et al. (2002) Initiation and re-initiation of DNA unwinding by the Escherichia coli rep helicase, Nature 419, 638–641. / Escherichia coli rep helicase Nature by T. Ha (2002)
  60. Groll, J., Amirgoulova, E., Ameringer, T., et al. (2004) Biofunctionalized, ultrathin coatings of cross-linked star-shaped poly(ethylene oxide) allow reversible folding of immobilized proteins, J Am Chem Soc 126, 4234–4239. (10.1021/ja0318028) / J Am Chem Soc by J. Groll (2004)
  61. Dickson, R. M., Cubitt, A. B., Tsien, R. Y., et al. (1997) On/off blinking and switching behaviour of single molecules of green fluorescent protein, Nature 388, 3558–3358. / Nature by R. M. Dickson (1997)
  62. Lu, H. P., Xun, L., Xie, X. S. (1998) Single molecule enzymatic dynamics, Science 282, 1877–1882. (10.1126/science.282.5395.1877) / Science by H. P. Lu (1998)
  63. Boukobza, E., Sonnenfeld, A., Haran, G. (2001) Immobilization in surface-tethered lipid vesicles as a new tool for single biomolecule spectroscopy, J Phys Chem B 105, 12165–12170. (10.1021/jp012016x) / J Phys Chem B by E. Boukobza (2001)
  64. Harada, Y., Sakurada, K., Aoki, T., et al. (1990) Mechanochemical coupling in actomyosin energy transduction studied by in vitro movement assay, J Mol Biol 216, 49–68. (10.1016/S0022-2836(05)80060-9) / J Mol Biol by Y. Harada (1990)
  65. Englander, S. W., Calhoun, D. B., Englander, J. J. (1987) Biochemistry without oxygen, Anal Biochem 161, 300–306. (10.1016/0003-2697(87)90454-4) / Anal Biochem by S. W. Englander (1987)
  66. Schuler, B. (2007) Application of single molecule Förster resonance energy transfer to protein folding, Methods Mol Biol 350, 115–138. / Methods Mol Biol by B. Schuler (2007)
  67. Eggeling, C., Berger, S., Brand, L., et al. (2001) Data registration and selective single-molecule analysis using multi-parameter fluorescence detection, J Biotechnol 86, 163–180. (10.1016/S0168-1656(00)00412-0) / J Biotechnol by C. Eggeling (2001)
  68. Friedel, M., Baumketner, A., Shea, J. E. (2006) Effects of surface tethering on protein folding mechanisms, Proc Natl Acad Sci USA 103, 8396–8401. (10.1073/pnas.0601210103) / Proc Natl Acad Sci USA by M. Friedel (2006)
  69. Yamasaki, K., Ogasahara, K., Yutani, K., et al. (1995) Folding pathway of Escherichia coli ribonuclease HI: A circular dichroism, fluorescence, and NMR study, Biochemistry 34, 16552–16562. (10.1021/bi00051a003) / Biochemistry by K. Yamasaki (1995)
  70. Parker, M. J., Marqusee, S. (1999) The cooperativity of burst phase reactions explored, J Mol Biol 293, 1195–1210. (10.1006/jmbi.1999.3204) / J Mol Biol by M. J. Parker (1999)
  71. Staniforth, R. A., Burston, S. G., Smith, C. J., et al. (1993) The energetics and cooperativity of protein folding: A simple experimental analysis based upon the solvation of internal residues, Biochemistry 32, 3842–3851. (10.1021/bi00066a003) / Biochemistry by R. A. Staniforth (1993)
  72. Parker, M. J., Spencer, J., Clarke, A. R. (1995) An integrated kinetic analysis of intermediates and transition states in protein folding reactions, J Mol Biol 253, 771–786. (10.1006/jmbi.1995.0590) / J Mol Biol by M. J. Parker (1995)
Dates
Type When
Created 16 years, 8 months ago (Dec. 8, 2008, 9:56 p.m.)
Deposited 2 years, 3 months ago (May 22, 2023, 3:11 p.m.)
Indexed 1 year ago (Sept. 5, 2024, 3:39 a.m.)
Issued 16 years, 11 months ago (Sept. 30, 2008)
Published 16 years, 11 months ago (Sept. 30, 2008)
Published Online 16 years, 11 months ago (Sept. 30, 2008)
Published Print 16 years, 8 months ago (Jan. 1, 2009)
Funders 0

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@inbook{Nienhaus_2008, title={Single-Molecule Fluorescence Studies of Protein Folding}, ISBN={9781597453677}, ISSN={1940-6029}, url={http://dx.doi.org/10.1007/978-1-59745-367-7_13}, DOI={10.1007/978-1-59745-367-7_13}, booktitle={Protein Structure, Stability, and Interactions}, publisher={Humana Press}, author={Nienhaus, G. Ulrich}, year={2008}, month=sep, pages={311–337} }