Multiscale complex network of protein conformational fluctuations in single-molecule time series

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

Volumn 105, Issue 2, 2008, Pages 536-541

  Li, Chun Biu ^a,b,e   Yang, Haw ^c,d   Komatsuzaki, Tamiki ^a,b,e  

^a KOBE UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Anomalous diffusion; Single molecule experiment; Time series analysis

Indexed keywords

FLUORESCENT DYE;

ARTICLE; DIFFUSION; ELECTRON TRANSPORT; PRIORITY JOURNAL; PROBABILITY; PROTEIN CONFORMATION; PROTEIN STRUCTURE; TIME SERIES ANALYSIS; TOPOGRAPHY;

BIOPHYSICS; COMPUTER SIMULATION; DIFFUSION; ELECTRONS; FLUORESCENCE RESONANCE ENERGY TRANSFER; MARKOV CHAINS; MODELS, MOLECULAR; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR CONFORMATION; PHOTONS; PROTEIN CONFORMATION; PROTEIN FOLDING; SPECTROPHOTOMETRY; TIME; TIME FACTORS;

EID: 38649113858     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0707378105     Document Type: Article

References (37)

1. Xie XS, Trautman JK (1998) Annu Rev Phys Chem 49:441-480.
2. Moerner WE, Fromm DP (2003) Rev Sci Inst 74:3597-3619.
3. Barkai E, Jung Y, Silbey R (2004) Annu Rev Phys Chem 55:457-507.
4. Lippitz M, Kulzer F, Orrit M (2005) ChemPhysChem 6:770-789.
5. Michalet X, Weiss S, Jager M (2006) Chem Rev 106:1785-1813.
6. Frauenfelder H, Sligar SG, Wolynes PG (1991) Science 254:1598-1603.
7. Stillinger FH (1995) Science 267:1935-1939.
8. Wales DJ (2003) Energy Landscapes. (Cambridge Univ Press, Cambridge, UK).
9. Krivov SV, Karplus M (2004) Proc Natl Acad Sci USA 101:14766-14770.
10. Rao F, Caflisch A (2004) J Mol Biol 342:299-306.
11. Gfeller D, Rios PDL, Caflisch A, Rao F (2007) Proc Natl Acad Sci USA 104:1817-1822.
12. Ball KD, Berry RS, Kunz RE, Li F-Y, Proykova A, Wales DJ (1996) Science 271:963.
13. Albert R, Barabási A-L (2002) Rev Mod Phys 74:47-97.
14. Gallos LK, Song C, Havlin S, Makse HA (2007) Proc Natl Acad Sci USA 104:7746-7751.
15. Yang H, Luo G, Karnchanaphanurach P, Louie TM, Rech I, Cova S, Xun L, Xie XS (2003) Science 302:262-266.
16. Talaga DS, Lau WL, Roder H, Tang JY, Jia YW, DeGrado WF, Hochstrasser RM (2000) Proc Natl Acad Sci USA 97:13021-13026.
17. Schuler B, Lipman EA, Eaton EA (2002) Nature 419:743-747.
18. Rhoades E, Gussakovsky E, Haran G (2003) Proc Natl Acad Sci USA 100:3197-3202.
19. Kinoshita M, Kamagata K, Maeda M, Goto Y, Komatsuzaki T, Takahashi S (2007) Proc Natl Acad Sci USA 104:10453-10458.
20. Min W, Luo G, Cherayil BJ, Kou SC, Xie XS (2005) Phys Rev Lett 94:198302.
21. Tang J, Marcus RA (2006) Phys Rev E 73:022102.
22. Debnath P, Min W, Xie XS, Cherayil BJ (2005) J Chem Phys 123:204903.
23. Luo G, Andricioaei I, Xie XS, Karplus M (2006) J Phys Chem B 110:9363-9367.
24. Watkins LP, Yang H (2004) Biophys J 86:4015-4029.
25. Watkins LP, Yang H (2005) J Phys Chem B 109:617-628.
26. Edman L, Rigler R (2000) Proc Natl Acad Sci USA 97:8266-8271.
27. Witkoskie JB, Cao J (2004) J Chem Phys 121:6361-6372.
28. Flomenbom O, Klafter J, Szabo A (2005) Biophys J 88:3780-3783.
29. Zwanzig R (2001) Nonequilibrium Statistical Mechanics (Oxford Univ Press, New York).
30. Crutchfield JP, Young K (1989) Phys Rev Lett 63:105.
31. Shalizi CR, Crutchfield JP (2001) J Stat Phys 104:819-881.
32. Brandes U, Kenis P, Raab J, Schneider V, Wagner D (1999) J Theor Politics 11:75-106.
33. Daubechies I (1992) Ten Lectures on Wavelets (Soc Indust Appl Math, New York).
34. Moser CC, Keske JM, Warncke K, Farid RS, Dutton PL (1992) Nature 355:796-802.
35. Yang H, Xie XS (2002) J Chem Phys 117:10965-10979.
36. Krzanowski WJ (2003) J App Stat 30:743-750.
37. Nerukh D, Karvounis G, Glen RC (2002) J Chem Phys 117:9611-9617.