ArticleProceedings of the National Academy of Sciences of the United States of America2015
Molecular determinants of the interactions between proteins and ssDNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Spatiotemporal characterization of single-stranded DNA Intermediates after UV Irradiation: I: Post-replication gaps formed during slow growth.PLoS genetics · 2026Article
- Excessive Existence of Positively Charged Amino Acids Caused Off-Target Recognition in the Seed Region ofInternational journal of molecular sciences · 2025Article
- Impact of ions, pH and the nature of substrate on the structure and activity of a robust single-stranded DNA binding (SSB)-like protein from Phi11.Archives of microbiology · 2025Article
- Sodium Ion-Induced Structural Transition on the Surface of a DNA-Interacting Protein.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs.Life science alliance · 2024Article
- Rapid Long-distance Migration of RPA on Single Stranded DNA Occurs Through Intersegmental Transfer Utilizing Multivalent Interactions.Journal of molecular biology · 2024Article
- Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability.RSC advances · 2024Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA.PloS one · 2023Article
- Replication Protein A Utilizes Differential Engagement of Its DNA-Binding Domains to Bind Biologically Relevant ssDNAs in Diverse Binding Modes.Biochemistry · 2022Article
- Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches.Biomolecules · 2022Review
- Single-molecule biophysics experimentsiScience · 2022Article
- A comparative study of protein-ssDNA interactions.NAR genomics and bioinformatics · 2021Article
- The Essential, Ubiquitous Single-Stranded DNA-Binding Proteins.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Protein Diffusion on Charged Biopolymers: DNA versus Microtubule.Biophysical journal · 2020Article
- Tubulin tails and their modifications regulate protein diffusion on microtubules.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- ssDNA diffuses along replication protein A via a reptation mechanism.Nucleic acids research · 2020Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Sliding Mechanism at a Coiled-Coil Interface.Biophysical journal · 2019Article
- Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.PLoS computational biology · 2019Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ssDNA binding proteins (SSBs) protect ssDNA from chemical and enzymatic assault that can derail DNA processing machinery. Complexes between SSBs and ssDNA are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssDNA and the geometric and energetic complexity of the interfaces that it forms. Here, we report a newly developed coarse-grained model to predict the structure of SSB-ssDNA complexes. The model is successfully applied to predict the binding modes of six SSBs with ssDNA strands of lengths of 6-65 nt. In addition to charge-charge interactions (which are often central to governing protein interactions with nucleic acids by means of electrostatic complementarity), an essential energetic term to predict SSB-ssDNA complexes is the interactions between aromatic residues and DNA bases. For some systems, flexibility is required from not only the ssDNA but also, the SSB to allow it to undergo conformational changes and the penetration of the ssDNA into its binding pocket. The association mechanisms can be quite varied, and in several cases, they involve the ssDNA sliding along the protein surface. The binding mechanism suggests that coarse-grained models are appropriate to study the motion of SSBs along ssDNA, which is expected to be central to the function carried out by the SSBs.
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