ArticleNucleic acids research2010
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- BioSpring: An elastic network framework for interactive exploration of macromolecular mechanics.Protein science : a publication of the Protein Society · 2025Article
- Modeling the Homologous Recombination Process: Methods, Successes and Challenges.International journal of molecular sciences · 2023Review
- UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape.Membranes · 2023Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Cooperative RecA clustering: the key to efficient homology searching.Nucleic acids research · 2017Article
- Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure.Nucleic acids research · 2015Article
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.Chemical Society reviews · 2014Review
- Model of a DNA-protein complex of the architectural monomeric protein MC1 from Euryarchaea.PloS one · 2014Article
- Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites.Physical review. E, Statistical, nonlinear, and soft matter physics · 2013Article
- Ca2+ improves organization of single-stranded DNA bases in human Rad51 filament, explaining stimulatory effect on gene recombination.Nucleic acids research · 2012Article
- Accounting for large amplitude protein deformation during in silico macromolecular docking.International journal of molecular sciences · 2011Article
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson-Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.
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