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Back-stepping, hidden substeps, and conditional dwell times in molecular motors
Institute for Physical Science and Technology, University of Maryland.
Institute for Physical Science and Technology, University of Maryland.
Institute for Physical Science and Technology, University of Maryland.
2007 (English)In: Physical Review E, ISSN 1539-3755, Vol. 75, no 2, p. 021909-1-021909-16Article in journal (Refereed) Published
Abstract [en]

Processive molecular motors take more-or-less uniformly sized steps, along spatially periodic tracks, mostly forwards but increasingly backwards under loads. Experimentally, the major steps can be resolved clearly within the noise but one knows biochemically that one or more mechanochemical substeps remain hidden in each enzymatic cycle. In order to properly interpret experimental data for back-to-forward step ratios, mean conditional step-to-step dwell times, etc., a first-passage analysis has been developed that takes account of hidden substeps in N-state sequential models. The explicit, general results differ significantly from previous treatments that identify the observed steps with complete mechanochemical cycles; e.g., the mean dwell times tau(+) and tau(-) prior to forward and back steps, respectively, are normally unequal although the dwell times tau(++) and tau(- -) between successive forward and back steps are equal. Illustrative (N=2)-state examples display a wide range of behavior. The formulation extends to the case of two or more detectable transitions in a multistate cycle with hidden substeps.

Place, publisher, year, edition, pages
2007. Vol. 75, no 2, p. 021909-1-021909-16
Keywords [en]
Biochemistry; Enzymes; Mathematical models; Molecular structure; Back-to-forward step ratios; Conditional dwell times; First-passage analysis; Molecular motors
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-8083DOI: 10.1103/PhysRevE.75.021909ISI: 000244531900070OAI: oai:DiVA.org:kth-8083DiVA, id: diva2:13310
Note
QC 20100820Available 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. p. vii, 71
Series
Trita-FYS, ISSN 0280-316X ; 2008:9
Keywords
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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