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Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments

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Morin, José A. and Ibarra, Borja and Cao García, Francisco Javier (2016) Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments. Journal of statistical mechanics: theory and experiment . ISSN 1742-5468

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Official URL: http://dx.doi.org/10.1088/1742-5468/2016/05/054031


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http://iopscience.iop.org/Publisher


Abstract

Single-molecule manipulation experiments of molecular motors provide essential information about the rate and conformational changes of the steps of the reaction located along the manipulation coordinate. This information is not always sufficient to define a particular kinetic cycle. Recent single-molecule experiments with optical tweezers showed that the DNA unwinding activity of a Phi29 DNA polymerase mutant presents a complex pause behavior, which includes short and long pauses. Here we show that different kinetic models, considering different connections between the active and the pause states, can explain the experimental pause behavior. Both the two independent pause model and the two connected pause model are able to describe the pause behavior of a mutated Phi29 DNA polymerase observed in an optical tweezers single-molecule experiment. For the two independent pause model all parameters are fixed by the observed data, while for the more general two connected pause model there is a range of values of the parameters compatible with the observed data (which can be expressed in terms of two of the rates and their force dependencies). This general model includes models with indirect entry and exit to the long-pause state, and also models with cycling in both directions. Additionally, assuming that detailed balance is verified, which forbids cycling, this reduces the ranges of the values of the parameters (which can then be expressed in terms of one rate and its force dependency). The resulting model interpolates between the independent pause model and the indirect entry and exit to the long-pause state model


Item Type:Article
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© 2016 IOP Publishing.
This work was supported by grants FIS2010-17440 (to FJC) and BFU2012-31825 (to BI) from the Ministerio de Ciencia e Innovacion (Spain) and GR35/14-920911 (to FJC) from the Universidad Complutense de Madrid and Banco Santander (Spain).

Uncontrolled Keywords:DNA Replication; Polymerase.
Subjects:Sciences > Physics > Nuclear physics
ID Code:38635
Deposited On:02 Sep 2016 15:57
Last Modified:10 Dec 2018 14:57

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