Statistical Properties of the Dichotomous Noise Generated in Biochemical Processes

Overview

Journal Cell Mol Biol Lett

Publisher Biomed Central

Specialties Biochemistry
Cell Biology
Molecular Biology

Date 2008 May 7

PMID 18458826

Authors

Michal Kurzynski

Affiliations

Soon will be listed here.

Abstract

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.

References

Kojima H, Kikumoto M, Sakakibara H, Oiwa K . Mechanical Properties of a Single-Headed Processive Motor, Inner-Arm Dynein Subspecies-c of ChlamydomonasStudied at the Single Molecule Level. J Biol Phys. 2013; 28(3):335-45. PMC: 3456751. DOI: 10.1023/A:1020300319224. View

Shao Q, Gao Y . On the hand-over-hand mechanism of kinesin. Proc Natl Acad Sci U S A. 2006; 103(21):8072-7. PMC: 1472431. DOI: 10.1073/pnas.0602828103. View

Lu H, Xun L, Xie X . Single-molecule enzymatic dynamics. Science. 1998; 282(5395):1877-82. DOI: 10.1126/science.282.5395.1877. View

Bruno W, Yang J, Pearson J . Using independent open-to-closed transitions to simplify aggregated Markov models of ion channel gating kinetics. Proc Natl Acad Sci U S A. 2005; 102(18):6326-31. PMC: 1088360. DOI: 10.1073/pnas.0409110102. View

Liu X, Pollack G . Stepwise sliding of single actin and Myosin filaments. Biophys J. 2003; 86(1 Pt 1):353-8. PMC: 1303800. DOI: 10.1016/S0006-3495(04)74111-9. View

Kitamura K, Tokunaga M, Iwane A, Yanagida T . A single myosin head moves along an actin filament with regular steps of 5.3 nanometres. Nature. 1999; 397(6715):129-34. DOI: 10.1038/16403. View

Kitamura K, Tokunaga M, Esaki S, Iwane A, Yanagida T . Mechanism of muscle contraction based on stochastic properties of single actomyosin motors observed . Biophysics (Nagoya-shi). 2016; 1:1-19. PMC: 5036627. DOI: 10.2142/biophysics.1.1. View

Caflisch A . Network and graph analyses of folding free energy surfaces. Curr Opin Struct Biol. 2006; 16(1):71-8. DOI: 10.1016/j.sbi.2006.01.002. View

Frauenfelder H, Sligar S, Wolynes P . The energy landscapes and motions of proteins. Science. 1991; 254(5038):1598-603. DOI: 10.1126/science.1749933. View

10.

Flomenbom O, Velonia K, Loos D, Masuo S, Cotlet M, Engelborghs Y . Stretched exponential decay and correlations in the catalytic activity of fluctuating single lipase molecules. Proc Natl Acad Sci U S A. 2005; 102(7):2368-72. PMC: 548972. DOI: 10.1073/pnas.0409039102. View

11.

Qian H, Elson E . Single-molecule enzymology: stochastic Michaelis-Menten kinetics. Biophys Chem. 2002; 101-102:565-76. DOI: 10.1016/s0301-4622(02)00145-x. View

12.

Flomenbom O, Silbey R . Utilizing the information content in two-state trajectories. Proc Natl Acad Sci U S A. 2006; 103(29):10907-10. PMC: 1544147. DOI: 10.1073/pnas.0604546103. View

13.

Kurzynski M . A synthetic picture of intramolecular dynamics of proteins. Towards a contemporary statistical theory of biochemical processes. Prog Biophys Mol Biol. 1998; 69(1):23-82. DOI: 10.1016/s0079-6107(97)00033-3. View

14.

Sansom M, Ball F, Kerry C, McGee R, Ramsey R, Usherwood P . Markov, fractal, diffusion, and related models of ion channel gating. A comparison with experimental data from two ion channels. Biophys J. 1989; 56(6):1229-43. PMC: 1280626. DOI: 10.1016/S0006-3495(89)82770-5. View

15.

Edman L, Rigler R . Memory landscapes of single-enzyme molecules. Proc Natl Acad Sci U S A. 2000; 97(15):8266-71. PMC: 26936. DOI: 10.1073/pnas.130589397. View

16.

Lerch H, Mikhailov A, Hess B . Conformational-relaxation models of single-enzyme kinetics. Proc Natl Acad Sci U S A. 2002; 99(24):15410-5. PMC: 137730. DOI: 10.1073/pnas.232376799. View

17.

Knight A, Veigel C, Chambers C, Molloy J . Analysis of single-molecule mechanical recordings: application to acto-myosin interactions. Prog Biophys Mol Biol. 2001; 77(1):45-72. DOI: 10.1016/s0079-6107(01)00010-4. View

18.

Mallik R, Carter B, Lex S, King S, Gross S . Cytoplasmic dynein functions as a gear in response to load. Nature. 2004; 427(6975):649-52. DOI: 10.1038/nature02293. View