ArticleJournal of chemical information and modeling2024
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains.
Article in Journal of chemical information and modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Discovery of High-Affinity Peptide Ligands Targeting the SPIN1 Tudor 3 Domain Via a Minimalist Pruning Strategy.ACS medicinal chemistry letters · 2026Article
- In situ characterization of amine-forming enzymes shows altered oligomeric state.Protein science : a publication of the Protein Society · 2025Article
- Predicting fragment binding modes using customized Lennard-Jones potentials in short molecular dynamics simulations.Computational and structural biotechnology journal · 2025Article
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3 authors.
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Abstract
Cosolvent molecular dynamics (MD) simulations have proven to be powerful in silico tools to predict hotspots for binding regions on protein surfaces. In the current study, the method was adapted and applied to two Tudor domain-containing proteins, namely Spindlin1 (SPIN1) and survival motor neuron protein (SMN). Tudor domains are characterized by so-called aromatic cages that recognize methylated lysine residues of protein targets. In the study, the conformational transitions from closed to open aromatic cage conformations were investigated by performing MD simulations with cosolvents using six different probe molecules. It is shown that a trajectory clustering approach in combination with volume and atomic distance tracking allows a reasonable discrimination between open and closed aromatic cage conformations and the docking of inhibitors yields very good reproducibility with crystal structures. Cosolvent MDs are suitable to capture the flexibility of aromatic cages and thus represent a promising tool for the optimization of inhibitors.
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