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Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models
DNA glycosylase is responsible for repairing DNA damage to maintain the genome stability and integrity. However, how glycosylase can efficiently and accurately recognize DNA lesions across the enormous DNA genome remains elusive. It has been hypothesized that glycosylase translocates along the DNA b...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
National Academy of Sciences
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7486748/ https://www.ncbi.nlm.nih.gov/pubmed/32820079 http://dx.doi.org/10.1073/pnas.2002971117 |
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author | Peng, Sijia Wang, Xiaowei Zhang, Lu He, Shanshan Zhao, Xin Sheng Huang, Xuhui Chen, Chunlai |
author_facet | Peng, Sijia Wang, Xiaowei Zhang, Lu He, Shanshan Zhao, Xin Sheng Huang, Xuhui Chen, Chunlai |
author_sort | Peng, Sijia |
collection | PubMed |
description | DNA glycosylase is responsible for repairing DNA damage to maintain the genome stability and integrity. However, how glycosylase can efficiently and accurately recognize DNA lesions across the enormous DNA genome remains elusive. It has been hypothesized that glycosylase translocates along the DNA by alternating between a fast but low-accuracy diffusion mode and a slow but high-accuracy mode when searching for DNA lesions. However, the slow mode has not been successfully characterized due to the limitation in the spatial and temporal resolutions of current experimental techniques. Using a newly developed scanning fluorescence resonance energy transfer (FRET)–fluorescence correlation spectroscopy (FCS) platform, we were able to observe both slow and fast modes of glycosylase AlkD translocating on double-stranded DNA (dsDNA), reaching the temporal resolution of microsecond and spatial resolution of subnanometer. The underlying molecular mechanism of the slow mode was further elucidated by Markov state model built from extensive all-atom molecular dynamics simulations. We found that in the slow mode, AlkD follows an asymmetric diffusion pathway, i.e., rotation followed by translation. Furthermore, the essential role of Y27 in AlkD diffusion dynamics was identified both experimentally and computationally. Our results provided mechanistic insights on how conformational dynamics of AlkD–dsDNA complex coordinate different diffusion modes to accomplish the search for DNA lesions with high efficiency and accuracy. We anticipate that the mechanism adopted by AlkD to search for DNA lesions could be a general one utilized by other glycosylases and DNA binding proteins. |
format | Online Article Text |
id | pubmed-7486748 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | National Academy of Sciences |
record_format | MEDLINE/PubMed |
spelling | pubmed-74867482020-09-23 Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models Peng, Sijia Wang, Xiaowei Zhang, Lu He, Shanshan Zhao, Xin Sheng Huang, Xuhui Chen, Chunlai Proc Natl Acad Sci U S A Physical Sciences DNA glycosylase is responsible for repairing DNA damage to maintain the genome stability and integrity. However, how glycosylase can efficiently and accurately recognize DNA lesions across the enormous DNA genome remains elusive. It has been hypothesized that glycosylase translocates along the DNA by alternating between a fast but low-accuracy diffusion mode and a slow but high-accuracy mode when searching for DNA lesions. However, the slow mode has not been successfully characterized due to the limitation in the spatial and temporal resolutions of current experimental techniques. Using a newly developed scanning fluorescence resonance energy transfer (FRET)–fluorescence correlation spectroscopy (FCS) platform, we were able to observe both slow and fast modes of glycosylase AlkD translocating on double-stranded DNA (dsDNA), reaching the temporal resolution of microsecond and spatial resolution of subnanometer. The underlying molecular mechanism of the slow mode was further elucidated by Markov state model built from extensive all-atom molecular dynamics simulations. We found that in the slow mode, AlkD follows an asymmetric diffusion pathway, i.e., rotation followed by translation. Furthermore, the essential role of Y27 in AlkD diffusion dynamics was identified both experimentally and computationally. Our results provided mechanistic insights on how conformational dynamics of AlkD–dsDNA complex coordinate different diffusion modes to accomplish the search for DNA lesions with high efficiency and accuracy. We anticipate that the mechanism adopted by AlkD to search for DNA lesions could be a general one utilized by other glycosylases and DNA binding proteins. National Academy of Sciences 2020-09-08 2020-08-20 /pmc/articles/PMC7486748/ /pubmed/32820079 http://dx.doi.org/10.1073/pnas.2002971117 Text en Copyright © 2020 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/ https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) . |
spellingShingle | Physical Sciences Peng, Sijia Wang, Xiaowei Zhang, Lu He, Shanshan Zhao, Xin Sheng Huang, Xuhui Chen, Chunlai Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models |
title | Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models |
title_full | Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models |
title_fullStr | Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models |
title_full_unstemmed | Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models |
title_short | Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models |
title_sort | target search and recognition mechanisms of glycosylase alkd revealed by scanning fret-fcs and markov state models |
topic | Physical Sciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7486748/ https://www.ncbi.nlm.nih.gov/pubmed/32820079 http://dx.doi.org/10.1073/pnas.2002971117 |
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