ArticleBiochemistry2011
Escherichia coli processivity clamp β from DNA polymerase III is dynamic in solution.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 49 citations in OpenAlex.
- Responses to Ligand Binding in the Bacterial DNA Sliding Clamp "β-Clamp" Manifest in Dynamic Allosteric Effects.Proteins · 2025Article
- Long-Range Destabilizing Effects of Mutations at theBiochemistry · 2025Article
- Functional asymmetry in processivity clamp proteins.Biophysical journal · 2025Review
- 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
- Molecular mechanism of muscarinic acetylcholine receptor M3 interaction with Gq.Communications biology · 2024Article
- Differences in clamp loader mechanism between bacteria and eukaryotes.bioRxiv : the preprint server for biology · 2023Article
- Distal Mutations in the β-Clamp of DNA Polymerase III* Disrupt DNA Orientation and Affect Exonuclease Activity.Journal of the American Chemical Society · 2023Article
- Biochemical and structural basis for differential inhibitor sensitivity of EGFR with distinct exon 19 mutations.Nature communications · 2022Article
- Review
- A loosened gating mechanism of RIG-I leads to autoimmune disorders.Nucleic acids research · 2022Article
- Trapped Ion Mobility Spectrometry of Native Macromolecular Assemblies.Analytical chemistry · 2021Article
- Dynamics of the E. coli β-Clamp Dimer Interface and Its Influence on DNA Loading.Biophysical journal · 2019Article
- HDX-MS reveals dysregulated checkpoints that compromise discrimination against self RNA during RIG-I mediated autoimmunity.Nature communications · 2018Article
- The Macromolecular Machines that Duplicate the Escherichia coli Chromosome as Targets for Drug Discovery.Antibiotics (Basel, Switzerland) · 2018Review
- HDX reveals the conformational dynamics of DNA sequence specific VDR co-activator interactions.Nature communications · 2017Article
- Mechanism of opening a sliding clamp.Nucleic acids research · 2017Article
- Electrostatic Interactions at the Dimer Interface Stabilize the E. coli β Sliding Clamp.Biophysical journal · 2017Article
- Cloning, recombinant production and crystallographic structure of Proliferating Cell Nuclear Antigen from radioresistant archaeonBiochemistry and biophysics reports · 2016Review
- DnaC traps DnaB as an open ring and remodels the domain that binds primase.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Escherichia coli DNA polymerase III is a highly processive replicase because of the presence of the β clamp protein that tethers DNA polymerases to DNA. The β clamp is a head-to-tail ring-shaped homodimer, in which each protomer contains three structurally similar domains. Although multiple studies have probed the functions of the β clamp, a detailed understanding of the conformational dynamics of the β clamp in solution is lacking. Here we used hydrogen exchange mass spectrometry to characterize the conformation and dynamics of the intact dimer β clamp and a variant form (I272A/L273A) with a weakened ability to dimerize in solution. Our data indicate that the β clamp is not a static closed ring but rather is dynamic in solution. The three domains exhibited different dynamics, though they share a highly similar tertiary structure. Domain I, which controls the opening of the clamp by dissociating from domain III, contained several highly flexible peptides that underwent partial cooperative unfolding (EX1 kinetics) with a half-life of ~4 h. The comparison between the β monomer variant and the wild-type β clamp showed that the β monomer was more dynamic. In the monomer, partial unfolding was much faster and additional regions of domain III also underwent partial unfolding with a half-life of ~1 h. Our results suggest that the δ subunit of the clamp loader may function as a "ring holder" to stabilize the transient opening of the β clamp, rather than as a "ring opener".
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.