Mapping the structural dynamics of the DNA gyrase N-gate
Abstract/Contents
- Abstract
- DNA gyrase is an essential bacterial molecular motor that uses ATP hydrolysis to drive the directional introduction of DNA supercoils. The enzyme employs a duplex strand passage mechanism that requires coordinating the opening and closing of three protein "gates": the N-gate, DNA-gate, and Exit-gate. The N-gate is formed by the dimerization of ATPase domains and acts as a nucleotide-dependent clamp that captures DNA for subsequent strand passage. Dynamic measurements of N-gate conformational changes are necessary to understand how gyrase harnesses chemical energy to direct changes in DNA topology. Here, we report real-time single molecule measurements of E. coli gyrase N-gate conformational dynamics under varying DNA and nucleotide conditions. We identify a landscape of distinct conformational intermediates whose populations can be shifted upon DNA and nucleotide binding. The N-gate is primarily open in the absence of DNA and nucleotide, but transiently samples closed conformations. The non-hydrolyzable ATP analog AMPPNP, but not ADP, induces stable N-gate dimerization, where FRET values are consistent with a closed conformation seen in crystal structures based on in silico modeling of dye positions. In the presence of DNA, the enzyme samples a distinct high FRET conformation of the N-gate that is consistent with an intermediate conformation previously described in studies of B. subtilis gyrase. Our measurements support a loose-coupling model in which N-gate conformations are highly dynamic and depend on both DNA and nucleotide binding. Substrate-induced N-gate conformational changes appear to be conserved across divergent bacterial species and could extend to other enzymes in the Gyrase-Hsp90-MutL (GHL) ATPase family. This work sets the stage for detailed structural modeling and for multimodal measurements that directly correlate protein and DNA dynamics in this complex molecular machine.
Description
Type of resource | text |
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Form | electronic resource; remote; computer; online resource |
Extent | 1 online resource. |
Place | California |
Place | [Stanford, California] |
Publisher | [Stanford University] |
Copyright date | 2018; ©2018 |
Publication date | 2018; 2018 |
Issuance | monographic |
Language | English |
Creators/Contributors
Author | Parente, Angelica Coco |
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Degree supervisor | Bryant, Zev David |
Degree supervisor | Pande, Vijay |
Thesis advisor | Bryant, Zev David |
Thesis advisor | Pande, Vijay |
Thesis advisor | Huang, Possu |
Degree committee member | Huang, Possu |
Associated with | Stanford University, Biophysics Program. |
Subjects
Genre | Theses |
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Genre | Text |
Bibliographic information
Statement of responsibility | Angelica Coco Parente. |
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Note | Submitted to the Biophysics Program. |
Thesis | Thesis Ph.D. Stanford University 2018. |
Location | electronic resource |
Access conditions
- Copyright
- © 2018 by Angelica Coco Parente
- License
- This work is licensed under a Creative Commons Attribution Non Commercial No Derivatives 3.0 Unported license (CC BY-NC-ND).
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