Mechanical response of the RecA nucleoprotein filament to increasing D-loop length
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2026
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| author | Sabei, Afra Prévost, Chantal Prentiss, Mara Danilowicz, Claudia Neukirch, Sebastien Detruit, Alexandre |
| author_facet | Sabei, Afra Prévost, Chantal Prentiss, Mara Danilowicz, Claudia Neukirch, Sebastien Detruit, Alexandre |
| contents | <p>This repository contains the files and data associated with the article: <strong>Mechanical response of the RecA nucleoprotein filament to increasing D-loop length</strong> by Afra Sabei, Chantal Prévost, Mara Prentiss, Claudia Danilowicz, Sébastien Neukirch, and Alexandre Détruit.</p> <h3>DESCRIPTION</h3> <ul> <li> <p><strong>Trajectories</strong>: Contains the structural files for the RecA nucleoprotein filaments (NPFs) with varying D-loop sizes (9bp, 12bp, 15bp, 21bp, 36bp, 45bp, and 54bp). Initial structures were derived from the CryoEM structure (PDB: 7jy9). Filament expansion was performed by replicating subunits using the <strong>Heligeom</strong> module of the <strong>PTools</strong> library. Models are named based on the number of stable heteroduplex base pairs(replicas are uploaded separately).</p> </li> <li> <p><strong>Parameters</strong>: All-atom Molecular Dynamics (MD) simulations were prepared using the <strong>VMD auto PSF builder</strong> (VMD 1.9.2). Systems were solvated in a TIP3P water model with a physiological ionic concentration of 0.15 mol/l. Simulations were performed using <strong>NAMD</strong> (versions 2.12 and 2.13) and the <strong>CHARMM36m</strong> force field including CMAP corrections. Conditions included periodic boundary conditions via PME, 2 fs time steps (SHAKE algorithm), and temperature/pressure regulation via Nosé-Hoover-Langevin piston.</p> </li> <li> <p><strong>Scripts</strong>: Contains the following Python scripts for modeling and analysis:</p> <ul> <li> <p><code>construction_bioarxiv.py</code>: Script for the construction of the NPF models.</p> </li> <li> <p><code>cmap_bioarxiv.py</code>: Post-processing script for generating contact maps.</p> </li> <li> <p><code>site_II_bioarxiv.py</code>: Post-processing script for site II distance calculations.</p> </li> </ul> </li> </ul> <h3>REFERENCES</h3> <p>[1] H. Yang, C. Zhou, A. Dhar, and N. P. Pavletich. Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures. <em>Nature</em>, 586(7831):801–806, 2020.</p> <p>[2] A. J. Conover, C. Danilowicz, R. Gunaratne, V. W. Coljee, N. Kleckner, and M. Prentiss. Changes in the tension in dsDNA alter the conformation of RecA bound to dsDNA-RecA filaments. <em>Nucleic Acids Res</em>, 39(20):8833–43, 2011.</p> <p>[3] J. C. Bell and S. C. Kowalczykowski. Mechanics and single-molecule interrogation of DNA recombination. <em>Annu Rev Biochem</em>, 85:193–226, 2016.</p> <p>[4] A. Saladin, S. Fiorucci, P. Poulain, C. Prévost, and M. Zacharias. PTools: An opensource molecular docking library. <em>BMC Struct. Biol.</em>, 9:27–37, 2009.</p> <p>[5] B. Boyer et al. An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. <em>PLoS One</em>, 10(3):e0116414, 2015.</p> <p>[6] B. Boyer, B. Laurent, C. H. Robert, and C. Prévost. Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. <em>Bio Protoc</em>, 11(14):e4097, 2021.</p> <p>[7] A. D. Mackerell Jr, M. Feig, and C. L. Brooks 3rd. Extending the treatment of backbone energetics in protein force fields... <em>J Comput Chem</em>, 25:1400–1415, 2004.</p> <p>[8] J. C. Phillips et al. Scalable molecular dynamics with NAMD. <em>J Comput Chem</em>, 26:1781–1802, 2005.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18377475 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Mechanical response of the RecA nucleoprotein filament to increasing D-loop length Sabei, Afra Prévost, Chantal Prentiss, Mara Danilowicz, Claudia Neukirch, Sebastien Detruit, Alexandre <p>This repository contains the files and data associated with the article: <strong>Mechanical response of the RecA nucleoprotein filament to increasing D-loop length</strong> by Afra Sabei, Chantal Prévost, Mara Prentiss, Claudia Danilowicz, Sébastien Neukirch, and Alexandre Détruit.</p> <h3>DESCRIPTION</h3> <ul> <li> <p><strong>Trajectories</strong>: Contains the structural files for the RecA nucleoprotein filaments (NPFs) with varying D-loop sizes (9bp, 12bp, 15bp, 21bp, 36bp, 45bp, and 54bp). Initial structures were derived from the CryoEM structure (PDB: 7jy9). Filament expansion was performed by replicating subunits using the <strong>Heligeom</strong> module of the <strong>PTools</strong> library. Models are named based on the number of stable heteroduplex base pairs(replicas are uploaded separately).</p> </li> <li> <p><strong>Parameters</strong>: All-atom Molecular Dynamics (MD) simulations were prepared using the <strong>VMD auto PSF builder</strong> (VMD 1.9.2). Systems were solvated in a TIP3P water model with a physiological ionic concentration of 0.15 mol/l. Simulations were performed using <strong>NAMD</strong> (versions 2.12 and 2.13) and the <strong>CHARMM36m</strong> force field including CMAP corrections. Conditions included periodic boundary conditions via PME, 2 fs time steps (SHAKE algorithm), and temperature/pressure regulation via Nosé-Hoover-Langevin piston.</p> </li> <li> <p><strong>Scripts</strong>: Contains the following Python scripts for modeling and analysis:</p> <ul> <li> <p><code>construction_bioarxiv.py</code>: Script for the construction of the NPF models.</p> </li> <li> <p><code>cmap_bioarxiv.py</code>: Post-processing script for generating contact maps.</p> </li> <li> <p><code>site_II_bioarxiv.py</code>: Post-processing script for site II distance calculations.</p> </li> </ul> </li> </ul> <h3>REFERENCES</h3> <p>[1] H. Yang, C. Zhou, A. Dhar, and N. P. Pavletich. Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures. <em>Nature</em>, 586(7831):801–806, 2020.</p> <p>[2] A. J. Conover, C. Danilowicz, R. Gunaratne, V. W. Coljee, N. Kleckner, and M. Prentiss. Changes in the tension in dsDNA alter the conformation of RecA bound to dsDNA-RecA filaments. <em>Nucleic Acids Res</em>, 39(20):8833–43, 2011.</p> <p>[3] J. C. Bell and S. C. Kowalczykowski. Mechanics and single-molecule interrogation of DNA recombination. <em>Annu Rev Biochem</em>, 85:193–226, 2016.</p> <p>[4] A. Saladin, S. Fiorucci, P. Poulain, C. Prévost, and M. Zacharias. PTools: An opensource molecular docking library. <em>BMC Struct. Biol.</em>, 9:27–37, 2009.</p> <p>[5] B. Boyer et al. An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. <em>PLoS One</em>, 10(3):e0116414, 2015.</p> <p>[6] B. Boyer, B. Laurent, C. H. Robert, and C. Prévost. Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. <em>Bio Protoc</em>, 11(14):e4097, 2021.</p> <p>[7] A. D. Mackerell Jr, M. Feig, and C. L. Brooks 3rd. Extending the treatment of backbone energetics in protein force fields... <em>J Comput Chem</em>, 25:1400–1415, 2004.</p> <p>[8] J. C. Phillips et al. Scalable molecular dynamics with NAMD. <em>J Comput Chem</em>, 26:1781–1802, 2005.</p> |
| title | Mechanical response of the RecA nucleoprotein filament to increasing D-loop length |
| url | https://doi.org/10.5281/zenodo.18377475 |