Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways
Escherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologi...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2015-08-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/08193 |
| _version_ | 1818019571223756800 |
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| author | Sukrit Suksombat Rustem Khafizov Alexander G Kozlov Timothy M Lohman Yann R Chemla |
| author_facet | Sukrit Suksombat Rustem Khafizov Alexander G Kozlov Timothy M Lohman Yann R Chemla |
| author_sort | Sukrit Suksombat |
| collection | DOAJ |
| description | Escherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologies remain speculative. Here, we used single-molecule force and fluorescence spectroscopy to investigate E. coli SSB binding to ssDNA. Stretching a single ssDNA-SSB complex reveals discrete states that correlate with known binding modes, the likely ssDNA conformations and diffusion dynamics in each, and the kinetic pathways by which the protein wraps ssDNA and is dissociated. The data allow us to construct an energy landscape for the ssDNA-SSB complex, revealing that unwrapping energy costs increase the more ssDNA is unraveled. Our findings provide insights into the mechanism by which proteins gain access to ssDNA bound by SSB, as demonstrated by experiments in which SSB is displaced by the E. coli recombinase RecA. |
| first_indexed | 2024-04-14T07:54:05Z |
| format | Article |
| id | doaj.art-b7448e1a7dea47899245e8ff58cfaa57 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:54:05Z |
| publishDate | 2015-08-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-b7448e1a7dea47899245e8ff58cfaa572022-12-22T02:05:06ZengeLife Sciences Publications LtdeLife2050-084X2015-08-01410.7554/eLife.08193Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathwaysSukrit Suksombat0Rustem Khafizov1Alexander G Kozlov2Timothy M Lohman3Yann R Chemla4Department of Physics, Center for the Physics of Living Cells, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United StatesDepartment of Physics, Center for the Physics of Living Cells, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United StatesDepartment of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, United StatesDepartment of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, United StatesDepartment of Physics, Center for the Physics of Living Cells, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United StatesEscherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologies remain speculative. Here, we used single-molecule force and fluorescence spectroscopy to investigate E. coli SSB binding to ssDNA. Stretching a single ssDNA-SSB complex reveals discrete states that correlate with known binding modes, the likely ssDNA conformations and diffusion dynamics in each, and the kinetic pathways by which the protein wraps ssDNA and is dissociated. The data allow us to construct an energy landscape for the ssDNA-SSB complex, revealing that unwrapping energy costs increase the more ssDNA is unraveled. Our findings provide insights into the mechanism by which proteins gain access to ssDNA bound by SSB, as demonstrated by experiments in which SSB is displaced by the E. coli recombinase RecA.https://elifesciences.org/articles/08193single stranded DNA binding proteinoptical tweezerenergy landscapeprotein-nucleic acid interactionsingle molecule |
| spellingShingle | Sukrit Suksombat Rustem Khafizov Alexander G Kozlov Timothy M Lohman Yann R Chemla Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways eLife single stranded DNA binding protein optical tweezer energy landscape protein-nucleic acid interaction single molecule |
| title | Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways |
| title_full | Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways |
| title_fullStr | Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways |
| title_full_unstemmed | Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways |
| title_short | Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways |
| title_sort | structural dynamics of e coli single stranded dna binding protein reveal dna wrapping and unwrapping pathways |
| topic | single stranded DNA binding protein optical tweezer energy landscape protein-nucleic acid interaction single molecule |
| url | https://elifesciences.org/articles/08193 |
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