ArticlePloS one2013
Molecular dynamics simulations of DNA-free and DNA-bound TAL effectors.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 39 citations in OpenAlex.
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- Structural study to analyze the DNA-binding properties of DsrC protein from the dsr operon of sulfur-oxidizing bacterium Allochromatium vinosum.Journal of molecular modeling · 2019Article
- Molecular Dynamics Simulations of Wild Type and Mutants of SAPAP in Complexed with Shank3.International journal of molecular sciences · 2019Article
- Overcoming conservation in TALE-DNA interactions: a minimal repeat scaffold enables selective recognition of an oxidized 5-methylcytosine.Chemical science · 2018Article
- PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.Biophysical journal · 2018Article
- Investigating DNA supercoiling in eukaryotic genomes.Briefings in functional genomics · 2017Review
- Conformational rearrangement of 1,2-d(GG) intrastrand cis-diammineplatinum crosslinked DNA is driven by counter-ion penetration within the minor groove of the modified site.Journal of molecular modeling · 2017Article
- Non-RVD mutations that enhance the dynamics of the TAL repeat array along the superhelical axis improve TALEN genome editing efficacy.Scientific reports · 2016Article
- Metal binding mediated conformational change of XPA protein:a potential cytotoxic mechanism of nickel in the nucleotide excision repair.Journal of molecular modeling · 2016Article
- Locked and proteolysis-based transcription activator-like effector (TALE) regulation.Nucleic acids research · 2016Article
- Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study.BioMed research international · 2016Article
- DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats.Nucleic acids research · 2015Article
- Direct observation of TALE protein dynamics reveals a two-state search mechanism.Nature communications · 2015Article
- Molecular dynamics simulations of acylpeptide hydrolase bound to chlorpyrifosmethyl oxon and dichlorvos.International journal of molecular sciences · 2015Article
- Understanding the recognition mechanisms of Zα domain of human editing enzyme ADAR1 (hZα(ADAR1)) and various Z-DNAs from molecular dynamics simulation.Journal of molecular modeling · 2014Article
- Repeat 1 of TAL effectors affects target specificity for the base at position zero.Nucleic acids research · 2014Article
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- Cross dimerization of amyloid-β and αsynuclein proteins in aqueous environment: a molecular dynamics simulations study.PloS one · 2014Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
TAL (transcriptional activator-like) effectors (TALEs) are DNA-binding proteins, containing a modular central domain that recognizes specific DNA sequences. Recently, the crystallographic studies of TALEs revealed the structure of DNA-recognition domain. In this article, molecular dynamics (MD) simulations are employed to study two crystal structures of an 11.5-repeat TALE, in the presence and absence of DNA, respectively. The simulated results indicate that the specific binding of RVDs (repeat-variable diresidues) with DNA leads to the markedly reduced fluctuations of tandem repeats, especially at the two ends. In the DNA-bound TALE system, the base-specific interaction is formed mainly by the residue at position 13 within a TAL repeat. Tandem repeats with weak RVDs are unfavorable for the TALE-DNA binding. These observations are consistent with experimental studies. By using principal component analysis (PCA), the dominant motions are open-close movements between the two ends of the superhelical structure in both DNA-free and DNA-bound TALE systems. The open-close movements are found to be critical for the recognition and binding of TALE-DNA based on the analysis of free energy landscape (FEL). The conformational analysis of DNA indicates that the 5' end of DNA target sequence has more remarkable structural deformability than the other sites. Meanwhile, the conformational change of DNA is likely associated with the specific interaction of TALE-DNA. We further suggest that the arrangement of N-terminal repeats with strong RVDs may help in the design of efficient TALEs. This study provides some new insights into the understanding of the TALE-DNA recognition mechanism.
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