ArticleJournal of chemical theory and computation2021
Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- Examining Genetic Variants Associated with FOXP1 Syndrome through Molecular Dynamics of Its DNA-Binding Domain and Self-Organizing Maps.Journal of chemical information and modeling · 2026Article
- SOMMD: an R package for the analysis of molecular dynamics simulations using self-organizing map.Bioinformatics (Oxford, England) · 2025Article
- Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics.Journal of computer-aided molecular design · 2025Article
- Structural assembly of the PAS domain drives the catalytic activation of metazoan PASK.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Nutrient Signaling-Dependent Quaternary Structure Remodeling Drives the Catalytic Activation of metazoan PASK.bioRxiv : the preprint server for biology · 2024Article
- Insights into the Dissociation Process and Binding Pattern of the BRCT7/8-PHF8 Complex.ACS omega · 2024Article
- Molecular Dynamics for the Optimal Design of Functionalized Nanodevices to Target Folate Receptors on Tumor Cells.ACS biomaterials science & engineering · 2023Article
- TCDD-Induced Allosteric Perturbation of the AhR:ARNT Binding to DNA.International journal of molecular sciences · 2023Article
- Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules.Biophysical reviews · 2022Review
- Recognizing the Binding Pattern and Dissociation Pathways of the p300 Taz2-p53 TAD2 Complex.JACS Au · 2022Article
- PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations.Journal of chemical theory and computation · 2022Article
- Design and Implementation of a Multidimensional Visualization Reconstruction System for Old Urban Spaces Based on Neural Networks.Computational intelligence and neuroscience · 2022Article
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Authors and funding
4 authors.
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Abstract
Several experimental studies indicated that large conformational changes, including partial domain unfolding, have a role in the functional mechanisms of the basic helix loop helix Per/ARNT/SIM (bHLH-PAS) transcription factors. Recently, single-molecule atomic force microscopy (AFM) revealed two distinct pathways for the mechanical unfolding of the ARNT PAS-B. In this work we used steered molecular dynamics simulations to gain new insights into this process at an atomistic level. To reconstruct and classify pathways sampled in multiple simulations, we designed an original approach based on the use of self-organizing maps (SOMs). This led us to identify two types of unfolding pathways for the ARNT PAS-B, which are in good agreement with the AFM findings. Analysis of average forces mapped on the SOM revealed a stable conformation of the PAS-B along one pathway, which represents a possible structural model for the intermediate state detected by AFM. The approach here proposed will facilitate the study of other signal transmission mechanisms involving the folding/unfolding of PAS domains.
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