ArticleBiophysical journal2011
Base-flipping mechanism in postmismatch recognition by MutS.
Article in Biophysical journal, 2011. 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.
- The interplay between supercoiling and DNA modifying enzymes at the single-molecule level.Scientific reports · 2026Article
- The 'very moment' when UDG recognizes a flipped-out uracil base in dsDNA.Scientific reports · 2025Article
- Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond.Journal of chemical information and modeling · 2022Article
- Screening and testing potential inhibitors of sulphide gas production by sulphate-reducing bacteria.Journal of molecular modeling · 2021Article
- Protein Loop Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates.The journal of physical chemistry letters · 2021Article
- Single gold-bridged nanoprobes for identification of single point DNA mutations.Nature communications · 2019Article
- Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates.The journal of physical chemistry letters · 2018Article
- Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process.Nucleic acids research · 2018Article
- Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage.Scientific reports · 2017Article
- Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways.PLoS computational biology · 2016Article
- Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.The journal of physical chemistry. B · 2016Article
- The structural impact of DNA mismatches.Nucleic acids research · 2015Article
- Hamiltonian Mapping Revisited: Calibrating Minimalist Models to Capture Molecular Recognition by Intrinsically Disordered Proteins.The journal of physical chemistry letters · 2014Article
- Differential mismatch recognition specificities of eukaryotic MutS homologs, MutSα and MutSβ.Biophysical journal · 2014Article
- Recent advances in transferable coarse-grained modeling of proteins.Advances in protein chemistry and structural biology · 2014Review
- DNA bending propensity in the presence of base mismatches: implications for DNA repair.The journal of physical chemistry. B · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
DNA mismatch recognition and repair is vital for preserving the fidelity of the genome. Conserved across prokaryotes and eukaryotes, MutS is the primary protein that is responsible for recognizing a variety of DNA mismatches. From molecular dynamics simulations of the Escherichia coli MutS-DNA complex, we describe significant conformational dynamics in the DNA surrounding a G·T mismatch that involves weakening of the basepair hydrogen bonding in the basepair adjacent to the mismatch and, in one simulation, complete base opening via the major groove. The energetics of base flipping was further examined with Hamiltonian replica exchange free energy calculations revealing a stable flipped-out state with an initial barrier of ~2 kcal/mol. Furthermore, we observe changes in the local DNA structure as well as in the MutS structure that appear to be correlated with base flipping. Our results suggest a role of base flipping as part of the repair initiation mechanism most likely leading to sliding-clamp formation.
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