ArticlePLoS computational biology2014
Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 41 citations in OpenAlex.
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- Computational Insights into the Dynamic Structural Features and Binding Characteristics of Recombinase UvsX Compared with RecA.Molecules (Basel, Switzerland) · 2023Article
- Structure and DNA binding analysis of AT-rich interaction domain present in human BAF-B specific subunit BAF250b.Protein science : a publication of the Protein Society · 2022Article
- Lipid Rafts Interaction of the ARID3A Transcription Factor with EZRIN and G-Actin Regulates B-Cell Receptor Signaling.Diseases (Basel, Switzerland) · 2021Article
- The PyInteraph Workflow for the Study of Interaction Networks From Protein Structural Ensembles.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations.Methods in molecular biology (Clifton, N.J.) · 2021Article
- A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy.Scientific reports · 2020Article
- Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.PLoS computational biology · 2019Review
- Effects of Distal Mutations on the Structure, Dynamics and Catalysis of Human Monoacylglycerol Lipase.Scientific reports · 2018Article
- An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass.Scientific reports · 2017Article
- DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.Nucleic acids research · 2016Article
- The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B.Scientific reports · 2016Article
- Dissecting protein architecture with communication blocks and communicating segment pairs.BMC bioinformatics · 2016Article
- The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer.Frontiers in molecular biosciences · 2016Article
- E2 superfamily of ubiquitin-conjugating enzymes: constitutively active or activated through phosphorylation in the catalytic cleft.Scientific reports · 2015Article
- Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.Frontiers in molecular biosciences · 2015Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ARID is a DNA-binding domain involved in several transcriptional regulatory processes, including cell-cycle regulation and embryonic development. ARID domains are also targets of the Human Cancer Protein Interaction Network. Little is known about the molecular mechanisms related to conformational changes in the family of ARID domains. Thus, we have examined their structural dynamics to enrich the knowledge on this important family of regulatory proteins. In particular, we used an approach that integrates atomistic simulations and methods inspired by graph theory. To relate these properties to protein function we studied both the free and DNA-bound forms. The interaction with DNA not only stabilizes the conformations of the DNA-binding loops, but also strengthens pre-existing paths in the native ARID ensemble for long-range communication to those loops. Residues in helix 5 are identified as critical mediators for intramolecular communication to the DNA-binding regions. In particular, we identified a distal tyrosine that plays a key role in long-range communication to the DNA-binding loops and that is experimentally known to impair DNA-binding. Mutations at this tyrosine and in other residues of helix 5 are also demonstrated, by our approach, to affect the paths of communication to the DNA-binding loops and alter their native dynamics. Overall, our results are in agreement with a scenario in which ARID domains exist as an ensemble of substates, which are shifted by external perturbation, such as the interaction with DNA. Conformational changes at the DNA-binding loops are transmitted long-range by intramolecular paths, which have their heart in helix 5.
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