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A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases

Y-family DNA polymerases are characterized by low-fidelity synthesis on undamaged DNA and ability to catalyze translesion synthesis over the damaged DNA. Their translocation along the DNA template is an important event during processive DNA synthesis. In this work we present a Brownian ratchet model...

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Detalles Bibliográficos
Autor principal: Xie, Ping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138451/
https://www.ncbi.nlm.nih.gov/pubmed/21699732
http://dx.doi.org/10.1186/1742-4682-8-22
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author Xie, Ping
author_facet Xie, Ping
author_sort Xie, Ping
collection PubMed
description Y-family DNA polymerases are characterized by low-fidelity synthesis on undamaged DNA and ability to catalyze translesion synthesis over the damaged DNA. Their translocation along the DNA template is an important event during processive DNA synthesis. In this work we present a Brownian ratchet model for this translocation, where the directed translocation is rectified by the nucleotide binding to the polymerase. Using the model, different features of the available structures for Dpo4, Dbh and polymerase ι in binary and ternary forms can be easily explained. Other dynamic properties of the Y-family polymerases such as the fast translocation event upon dNTP binding for Dpo4 and the considerable variations of the processivity among the polymerases can also be well explained by using the model. In addition, some predicted results of the DNA synthesis rate versus the external force acting on Dpo4 and Dbh polymerases are presented. Moreover, we compare the effect of the external force on the DNA synthesis rate of the Y-family polymerase with that of the replicative DNA polymerase.
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spelling pubmed-31384512011-07-19 A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases Xie, Ping Theor Biol Med Model Research Y-family DNA polymerases are characterized by low-fidelity synthesis on undamaged DNA and ability to catalyze translesion synthesis over the damaged DNA. Their translocation along the DNA template is an important event during processive DNA synthesis. In this work we present a Brownian ratchet model for this translocation, where the directed translocation is rectified by the nucleotide binding to the polymerase. Using the model, different features of the available structures for Dpo4, Dbh and polymerase ι in binary and ternary forms can be easily explained. Other dynamic properties of the Y-family polymerases such as the fast translocation event upon dNTP binding for Dpo4 and the considerable variations of the processivity among the polymerases can also be well explained by using the model. In addition, some predicted results of the DNA synthesis rate versus the external force acting on Dpo4 and Dbh polymerases are presented. Moreover, we compare the effect of the external force on the DNA synthesis rate of the Y-family polymerase with that of the replicative DNA polymerase. BioMed Central 2011-06-24 /pmc/articles/PMC3138451/ /pubmed/21699732 http://dx.doi.org/10.1186/1742-4682-8-22 Text en Copyright ©2011 Xie; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Xie, Ping
A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases
title A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases
title_full A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases
title_fullStr A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases
title_full_unstemmed A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases
title_short A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases
title_sort nucleotide binding rectification brownian ratchet model for translocation of y-family dna polymerases
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138451/
https://www.ncbi.nlm.nih.gov/pubmed/21699732
http://dx.doi.org/10.1186/1742-4682-8-22
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