Statistical properties of the dichotomous noise generated in biochemical processes

• Autorzy: Kurzynski M
• Języki publikacji: EN

Abstrakty

EN

Dichotomous noise detected with the help of various single-molecule techniques convincingly reveals the actual occurrence of a multitude of conformational substates composing the native state of proteins. The nature of the stochastic dynamics of transitions between these substates is determined by the particular statistical properties of the noise observed. These involve nonexponential and possibly oscillatory time decay of the second order autocorrelation function, its relation to the third order autocorrelation function, and a relationship to dwell-time distribution densities and their correlations. Processes gated by specific conformational substates are distinguished from those with fluctuating barriers. This study throws light on the intriguing matter of the possibility of multiple stepping of the myosin motor along the actin filament per ATP molecule hydrolyzed.

Słowa kluczowe

EN

single-molecule technique; biochemical process; noise; statistical property; protein molecule; dwell-time distribution density; molecular gear; time autocorrelation function

• Wydawca: -
• Czasopismo: Cellular and Molecular Biology Letters
• Rocznik: 2008
• Tom: 13
• Numer: 4
• Opis fizyczny: p.502-513,fig.,ref.

Twórcy

autor

Kurzynski M

• Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland

Bibliografia

• 1.Kurzyński, M. A synthetic picture of intramolecular dynamics of proteins. Towards a contemporary statistical theory of biochemical processes. Progr. Biophys. Molec. Biol. 69 (1998) 23-82.
• 2. Caflish, A. Network and graph analyses of folding free energy surfaces. Curr. Opin. Struct. Biol. 16 (2006) 71-79.
• 3. Sansom, M.P.S., Ball, F.G., Kerry, C.J., McGee, R., Ramsey, R.J. and Usherwood, P.N.R. Markov, fractal, diffusion, and related models of ion channel gating. A comparison with experimental data from two ion channels. Biophys. J. 56 (1989) 1229-1243.
• 4. Fuliński, A., Grzywna, Z., Mellor, I., Siwy, Z. and Usherwood, P.N.R. Non-Markovian character of ionic current fluctuations in membrane channels. Phys. Rev. E 58 (1998) 919-924.
• 5. Lu, H.P., Xun, L. and Xie, S. Single-molecule enzymatic dynamics. Science 282 (1998) 1877-1882.
• 6. Edman, L., Foeldes-Papp, Z., Wennmalm, S. and Rigler, R. The fluctuating enzyme: a single molecule approach. Chem. Phys. 247 (1999) 11-22.
• 7. Flomenbom, O., Velonia, K., Loos, D., Masuo, S., Cotlet, M., Engelborghs, Y., Hofkens, J., Rowan, A.E., Nolte, R.J.M., Van der Auweraer, M., de Schryver, F.C. and Klafter, J. Stretched exponential decay and correlations in the catalytic activity of fluctuating single lipase molecules. Proc. Natl. Acad. Sci. USA 102 (2005) 2368-2372.
• 8. Knight, A.E., Veigel, C., Chambers, C. and Molloy, J.E. Analysis of singlemolecule mechanical recordings: application to acto-myosin interactions. Progr. Biophys. Molec. Biol. 77 (2001) 45-72.
• 9. Kurzyński, M. The Thermodynamic Machinery of Life, Springer, Berlin, 2006, Appendixes B and D.
• 10. Frauenfelder, H., Sligar, S.G. and Wolynes, P.G. The energy landscapes and motions in proteins. Science 254 (1991) 1598-1602.
• 11. Lerch, H.P., Mikhailov, A.S. and Hess, B. Conformational-relaxation models of single-enzyme kinetics. Proc. Natl. Acad. Sci. USA 99 (2002) 15410-15415.
• 12. Keyes, T. Principles of mode-mode coupling theory, in: Statistical Mechanics, Part B: Time-Dependent Processes (Berne, B.J., Ed.), Plenum, New York, 1977, 259-309.
• 13. Edman, L. and Riegler, R. Memory landscapes of single-enzyme molecules. Proc. Natl. Acad. Sci. USA 97 (2000) 8266-8271.
• 14. Quian, H. and Elson, E.L. Single-molecule enzymology: stochastic Michaelis-Menten kinetics. Biophys. Chem. 101 (2002) 565-576.
• 15. Boguna, M., Berezhkovskii, A.M. and Weiss, G.H. Residence time densities for non-Markovian systems. The two-state system. Physica A 282 (2000) 474-485.
• 16. Flomenbom, O. and Silbey, R.J. Utilizing the information content in twostate trajectories. Proc. Natl. Acad. Sci. USA 103 (2006) 10907-10910.
• 17. Bruno, W.J., Yang, J. and Pearson, J.E. Using independent open-to- closed transitions to simplify aggregated Markov models of ion gating kinetics. Proc. Natl. Acad. Sci. USA 102 (2006) 6326-6331.
• 18. Kurzyński, M. and Chełminiak, P. Mean first-passage time in the stochastic theory of biochemical processes. Application to actomyosin molecular motor. J. Statist. Phys. 110 (2003) 137-181.
• 19. Kurzyński, M. The Thermodynamic Machinery of Life, Springer, Berlin, 2006, Chapter 9, see also errata.
• 20. Howard, J. Mechanics of Motor Proteins and the Cytoskeleton, Sinauer, Sunderland, 2001.
• 21. Kitamura, K., Tokunaga, M., Iwane, A.H. and Yanagida, T. A single Mosin head moves along an actin filament with regular steps of 5.3 nanometers. Nature 397 (1999) 129-134.
• 22. Kitamura, K., Tokunaga, M., Esaki, S., Iwane, A.H. and Yanagida, T. Mechanism of muscle contraction based on stochastic properties of single actomyosin motors observed in vitro. Biophysics 1 (2005) 1-19.
• 23. Liu, X. and Pollack, G.H. Stepwise sliding of single actin and myosin filaments. Biophys. J. 86 (2004) 353-358.
• 24. Kojima, H., Kikumoto, M., Sakakibara, H. and Oiwa, K. Mechanical properties of a single-headed processive motor, inner-arm dynein subspecies-c of Chlamydomonas studied at the single molecule level. J. Biol. Phys. 28 (2002) 335-345.
• 25. Mallik, R., Carter, B.C., Lex, S.A., King, S.J. and Gross, S.P. Cytoplasmic dynein functions as a gear in response to load. Nature 427 (2004) 649-652.
• 26. Shao, Q. and Gao, Y.Q. On the hand-over-hand mechanism of kinesin. Proc. Natl. Acad. Sci. USA 103 (2006) 8072-8077.