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Decay times in turnover statistics of single enzymes
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
2008 (English)In: Physical review E, ISSN 1539-3755, Vol. 78, no 1, 010901-1-010901-4 p.Article in journal (Refereed) Published
Abstract [en]

The first passage times for enzymatic turnovers in nonequilibrium steady state display a statistical symmetry property related to nonequilibrium fluctuation theorems, which makes it possible to extract the chemical driving force from single molecule trajectories in nonequilibrium steady state. Below, we show that the number of decay constants needed to describe the first passage time distribution of this system is not equal to the number of states in the first passage problem, as one would generally expect. Instead, the structure of the kinetic mechanism makes half of the decay times vanish identically from the turnover time distribution. The terms that cancel out correspond to the eigenvalues of a certain submatrix of the master equation matrix for the first exit time problem. We discuss how these results make modeling and data analysis easier for such systems, and how the turnovers can be measured.

Place, publisher, year, edition, pages
2008. Vol. 78, no 1, 010901-1-010901-4 p.
Keyword [en]
Electron transitions; Data analysis; Decay constants; Decay times; Driving forces; Eigenvalues (of graphs); Exit time; First passage problem; First passage time distribution (FPT); First passage times (FPT); Kinetic mechanisms; Master equations; Non equilibrium fluctuations; Nonequilibrium steady state (NESS); Number of states; Single molecule (SM); Sub matrices; Symmetry properties; Turnover time
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-8085DOI: 10.1103/PhysRevE.78.010901ISI: 000258178600005Scopus ID: 2-s2.0-47249154762OAI: oai:DiVA.org:kth-8085DiVA: diva2:13312
Note
QC 20100820. Uppdaterad från manuskript till artikel (20100820).Available from: 2008-03-07 Created: 2008-03-07 Last updated: 2010-08-20Bibliographically approved
In thesis
1. Stochastic modeling of motor proteins
Open this publication in new window or tab >>Stochastic modeling of motor proteins
2008 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

Motor proteins are microscopic biological machines that convert chemical energy into mechanical motion and work. They power a diverse range of biological processes, for example the swimming and crawling motion of bacteria, intracellular transport, and muscle contraction. Understanding the physical basis of these processes is interesting in its own right, but also has an interesting potential for applications in medicine and nanotechnology.

The ongoing rapid developments in single molecule experimental techniques make it possible to probe these systems on the single molecule level, with increasing temporal and spatial resolution. The work presented in this thesis is concerned with physical modeling of motor proteins on the molecular scale, and with theoretical challenges in the interpretation of single molecule experiments.

First, we have investigated how a small groups of elastically coupled motors collaborate, or fail to do so, when producing strong forces. Using a simple model inspired by the motor protein PilT, we find that the motors counteract each other if the density becomes higher than a certain threshold, which depends on the asymmetry of the system.

Second, we have contributed to the interpretation of experiments in which the stepwise motion of a motor protein is followed in real time. Such data is naturally interpreted in terms of first passage processes. Our main conclusions are (1) Contrary to some earlier suggestions, the stepping events do not correspond to the cycle completion events associated with the work of Hill and co-workers. We have given a correct formulation. (2) Simple kinetic models predict a generic mechanism that gives rise to correlations in step directions and waiting times. Analysis of stepping data from a chimaeric flagellar motor was consistent with this prediction. (3) In the special case of a reversible motor, the chemical driving force can be extracted from statistical analysis of stepping trajectories.

Place, publisher, year, edition, pages
Stockholm: KTH, 2008. vii, 71 p.
Series
Trita-FYS, ISSN 0280-316X ; 2008:9
Keyword
molecular motor, motor protein, Markov process, fluctuations, statistical mechanics, microscopic reversibility
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-4664 (URN)978-91-7178-897-9 (ISBN)
Public defence
2008-03-28, FA32, AlbaNova Universitetscentrum, Roslagstullsbacken 21, Stockholm, 10:00
Opponent
Supervisors
Note
QC 20100820Available from: 2008-03-07 Created: 2008-03-07 Last updated: 2010-08-20Bibliographically approved

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