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Dwell Time Symmetry in Random Walks and Molecular Motors
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.ORCID iD: 0000-0003-1164-0831
2007 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 92, no 11, 3804-3816 p.Article in journal (Refereed) Published
Abstract [en]

The statistics of steps and dwell times in reversible molecular motors differ from those of cycle completion in enzyme kinetics. The reason is that a step is only one of several transitions in the mechanochemical cycle. As a result, theoretical results for cycle completion in enzyme kinetics do not apply to stepping data. To allow correct parameter estimation, and to guide data analysis and experiment design, a theoretical treatment is needed that takes this observation into account. In this article, we model the distribution of dwell times and number of forward and backward steps using first passage processes, based on the assumption that forward and backward steps correspond to different directions of the same transition. We extend recent results for systems with a single cycle and consider the full dwell time distributions as well as models with multiple pathways, detectable substeps, and detachments. Our main results are a symmetry relation for the dwell time distributions in reversible motors, and a relation between certain relative step frequencies and the free energy per cycle. We demonstrate our results by analyzing recent stepping data for a bacterial flagellar motor, and discuss the implications for the efficiency and reversibility of the force-generating subunits.

Place, publisher, year, edition, pages
2007. Vol. 92, no 11, 3804-3816 p.
Keyword [en]
MYOSIN-V PROCESSIVITY; FLUCTUATION ANALYSIS; KINESIN MOLECULES; FLAGELLAR MOTOR; KINETIC-MODELS; ROTARY MOTOR; F-1-ATPASE; ROTATION; ATP; STEPS
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-8084DOI: 10.1529/biophysj.106.103044ISI: 000246401800006Scopus ID: 2-s2.0-34250334739OAI: oai:DiVA.org:kth-8084DiVA: diva2:13311
Note
QC 20100820Available from: 2008-03-07 Created: 2008-03-07 Last updated: 2017-12-14Bibliographically 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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