Learning rates and states from biophysical time series: A Bayesian approach to model selection and single-molecule FRET data

Biophysical Journal

Volumn 97, Issue 12, 2009, Pages 3196-3205

  Bronson, Jonathan E ^a   Fei, Jingyi ^a   Hofman, Jake M ^b,c   Gonzalez Jr , Ruben L ^a   Wiggins, Chris H ^b  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b Yahoo Research ^*  (United States)

^c YAHOO RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 73449090455     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.09.031     Document Type: Article

References (34)

1. Koster, D., C. Wiggins, and N. Dekker. 2006. Multiple events on single molecules: Unbiased estimation in single-molecule biophysics. Proc. Natl. Acad. Sci. USA. 103:1750-1755.
2. Moffitt, J. R., Y. R. Chemla, K. Aathavan, S. Grimes, P. J. Jardine, et al. 2009. Intersubunit coordination in a homomeric ring ATPase. Nature. 457:446-450.
3. Munro, J. B., R. B. Altman, N. O'Connor, and S. C. Blanchard. 2007. Identification of two distinct hybrid state intermediates on the ribosome. Mol. Cell. 25:505-517.
4. Zhuang, X. W., L. E. Bartley, H. P. Babcock, R. Russell, T. J. Ha, et al. 2000. A single-molecule study of RNA catalysis and folding. Science. 288:2048-2051.
5. Zhuang, X. W., H. Kim, M. J. B. Pereira, H. P. Babcock, N. G. Walter, et al. 2002. Correlating structural dynamics and function in single ribozyme molecules. Science. 296:1473-1476.
6. Fei, J., P. Kosuri, D. D. MacDougall, and R. L. Gonzalez. 2008. Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol. Cell. 30:348-359.
7. Yildiz, A., M. Tomishige, R. D. Vale, and P. R. Selvin. 2004. Kinesin walks hand-over-hand. Science. 303:676-678.
8. Wiita, A. P., R. Perez-Jimenez, K. A. Walther, F. Grater, B. J. Berne, et al. 2007. Probing the chemistry of thioredoxin catalysis with force. Nature. 450:124-127.
9. Myong, S., I. Rasnik, C. Joo, T. M. Lohman, and T. Ha. 2005. Repetitive shuttling of a motor protein on DNA. Nature. 437:1321-1325.
10. Jares-Erijman, E. A., and T. M. Jovin. 2003. FRET imaging. Nat. Biotechnol. 21:1387-1395.
11. Joo, C., H. Balci, Y. Ishitsuka, C. Buranachai, and T. Ha. 2008. Advances in single-molecule fluorescence methods for molecular biology. Annu. Rev. Biochem. 77:51-76.
12. Roy, R., S. Hohng, and T. Ha. 2008. A practical guide to single-molecule FRET. Nat. Methods. 5:507-516.
13. Schuler, B., and W. A. Eaton. 2008. Protein folding studied by singlemolecule FRET. Curr. Opin. Struct. Biol. 18:16-26.
14. Rabiner, L. R. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE. 77:257-286.
15. Qin, F., A. Auerbach, and F. Sachs. 1997. Maximum likelihood estimation of aggregated Markov processes. Proc. R. Soc. Lond. B. Biol. Sci. 264:375-383.
16. Qin, F., A. Auerbach, and F. Sachs. 2000. A direct optimization approach to hidden Markov modeling for single channel kinetics. Biophys. J. 79:1915-1927.
17. Andrec, M., R. M. Levy, and D. S. Talaga. 2003. Direct determination of kinetic rates from single-molecule photon arrival trajectories using hidden Markov models. J. Phys. Chem. A. 107:7454-7464.
18. McKinney, S. A., C. Joo, and T. Ha. 2006. Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophys. J. 91:1941-1951.
19. Bishop, C. M. 2006. Pattern Recognition and Machine Learning. Springer, New York.
20. MacKay, D. J. 2003. Information Theory, Inference, and Learning Algorithms. Cambridge University Press, Cambridge, United Kingdom.
21. Neal, R. 1993. Probabilistic Inference Using Markov Chain Monte Carlo Methods. Technical Report CRG-TR-93-1, Department of Computer Science, University of Toronto.
22. Dahan, M., A. A. Deniz, T. J. Ha, D. S. Chemla, P. G. Schultz, et al. 1999. Ratiometric measurement and identification of single diffusing molecules. Chem. Phys. 247:85-106.
23. Ji, S., B. Krishnapuram, and L. Carin. 2006. Variational Bayes for continuous hidden Markov models and its application to active learning. IEEE Trans. Pattern Anal. Mach. Intell. 28:522-532.
24. Viterbi, A. J. 1967. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Inform. Theory. 13:260-269.
25. Cornish, P. V., D. N. Ermolenko, H. F. Noller, and T. Ha. 2008. Spontaneous intersubunit rotation in single ribosomes. Mol. Cell. 30:578-588.
26. Moazed, D., and H. F. Noller. 1989. Intermediate states in the movement of transfer RNA in the ribosome. Nature. 342:142-148.
27. Blanchard, S. C., H. D. Kim, R. L. Gonzalez, Jr., J. D. Puglisi, and S. Chu. 2004. tRNA dynamics on the ribosome during translation. Proc Natl. Acad. Sci, USA. 101:12893-12898.
28. Kim, H. D., J. D. Puglisi, and S. Chu. 2007. Fluctuations of transfer RNAs between classical and hybrid states. Biophys. J. 93:3575-3582.
29. Agirrezabala, X., J. Lei, J. L. Brunelle, R. F. Ortiz-Meoz, R. Green, et al. 2008. Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol. Cell. 32:190-197.
30. Julian, P., A. L. Konevega, S. H. Scheres, M. Lazaro, D. Gil, et al. 2008. Structure of ratcheted ribosomes with tRNAs in hybrid states. Proc. Natl. Acad. Sci. USA. 105:16924-16927.
31. Cornish, P. V., D. N. Ermolenko, D.W.Staple, L.Hoang, R. P. Hickerson, et al. 2009. Following movement of the L1 stalk between three functional states in single ribosomes. Proc. Natl. Acad. Sci. USA. 106:2571-2576.
32. Fei, J., J. E. Bronson, J. M. Hofman, R. L. Srinivas, C. H. Wiggins, et al. 2009. Allosteric collaboration between elongation factor G and the ribosomal L1 stalk direct tRNA movements during translation. Proc. Natl. Acad. Sci. USA. (published ahead of print, doi: 10.1073/ pnas.0908077106).
33. Sternberg, S. H., J. Fei, N. Prywes, K. A. McGrath, and R. L. Gonzalez, Jr. 2009. Translation factors direct intrinsic ribosome dynamics during termination and ribosome recycling. Nat. Struct. Mol. Biol. 16:861-868.
34. Schwarz, G. 1978. Estimating the dimension of a model. Ann. Stat. 6:461-464.