ArticlePloS one2016
Dynamics of Open DNA Sliding Clamps.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Responses to Ligand Binding in the Bacterial DNA Sliding Clamp "β-Clamp" Manifest in Dynamic Allosteric Effects.Proteins · 2025Article
- Functional asymmetry in processivity clamp proteins.Biophysical journal · 2025Review
- Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli.Nature communications · 2024Article
- The bacterial DNA sliding clamp, β-clamp: structure, interactions, dynamics and drug discovery.Cellular and molecular life sciences : CMLS · 2024Review
- Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication.The Journal of biological chemistry · 2024Article
- Differences in clamp loader mechanism between bacteria and eukaryotes.bioRxiv : the preprint server for biology · 2023Article
- Force-Extension Curve of a Polymer Chain Entangled with a Static Ring-Shaped Obstacle.Polymers · 2022Article
- Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts.Viruses · 2021Article
- Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.Biophysical journal · 2020Article
- Dynamics of the E. coli β-Clamp Dimer Interface and Its Influence on DNA Loading.Biophysical journal · 2019Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Steered molecular dynamic simulations of conformational lock of Cu, Zn-superoxide dismutase.Scientific reports · 2019Article
- Diffusion of ring-shaped proteins along DNA: case study of sliding clamps.Nucleic acids research · 2018Article
- Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling.Nucleic acids research · 2018Article
- Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly.Nucleic acids research · 2017Article
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Abstract
A range of enzymes in DNA replication and repair bind to DNA-clamps: torus-shaped proteins that encircle double-stranded DNA and act as mobile tethers. Clamps from viruses (such as gp45 from the T4 bacteriophage) and eukaryotes (PCNAs) are homotrimers, each protomer containing two repeats of the DNA-clamp motif, while bacterial clamps (pol III β) are homodimers, each protomer containing three DNA-clamp motifs. Clamps need to be flexible enough to allow opening and loading onto primed DNA by clamp loader complexes. Equilibrium and steered molecular dynamics simulations have been used to study DNA-clamp conformation in open and closed forms. The E. coli and PCNA clamps appear to prefer closed, planar conformations. Remarkably, gp45 appears to prefer an open right-handed spiral conformation in solution, in agreement with previously reported biophysical data. The structural preferences of DNA clamps in solution have implications for understanding the duty cycle of clamp-loaders.
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