three-dimensional structure analysis  (National Research Council Canada)

Journal: Nucleic Acids Research

Article Title: Mechanistic studies of small molecule ligands selective to RNA single G bulges

doi: 10.1093/nar/gkaf559

Figure Lengend Snippet: Coumarin derivatives can selectively bind to RNA G 1 × 0 bulges: ( A ) RNA structures of the 1 × 0 RNA bulges used for in vitro binding profiling using the FP assay. N = G , A , U , or C (RNA1-4). ( B ) Heatmap profile of the ΔmP = (FP RNA-ligand – FP ligand ) × 1000 for RNA binders in the presence of [RNA] = 5 or 1 μM (red = high polarization, blue = low polarization). ( C ) ΔmP of RNA-ligand complex for RNA ligands at 5 μM. Each data point represents a measurement of a ligand in the 69-compound collection. **** indicates P < .0001. ( D ) Dose-response curves for compounds (SMSM6, C30) selectively binding to the bulged G RNA (RNA1) compared to an 11-nucleotide GA-rich sequence that would form a double loop-like RNA structure measured by the FP assay.

Article Snippet: 3-Dimensional (3D) structures of three coumarin derivatives (C30, C30-Me, and SMSM64) were prepared using ChemBio Tool.

Techniques: In Vitro, Binding Assay, FP Assay, Sequencing

Journal: Nucleic Acids Research

Article Title: Mechanistic studies of small molecule ligands selective to RNA single G bulges

doi: 10.1093/nar/gkaf559

Figure Lengend Snippet: Protonation state of the ligands contributes to the RNA binding. ( A ) Equilibria for the protonation reactions of four coumarin derivatives. ( B ) Protonation energy (relative to C29) was calculated using DFT with B3LYP 6–31G(d) basis set. ( C ) Observed binding affinity of the four compounds.

Article Snippet: 3-Dimensional (3D) structures of three coumarin derivatives (C30, C30-Me, and SMSM64) were prepared using ChemBio Tool.

Techniques: RNA Binding Assay, Binding Assay

Journal: International Journal of Molecular Sciences

Article Title: A Novel Homozygous Missense Variant of PIGT Related to Multiple Congenital Anomalies-Hypotonia Seizures Syndrome 3 with Elevated of Serum ALP Level in a Thai Newborn Patient

doi: 10.3390/ijms26062790

Figure Lengend Snippet: Prediction of protein stability at the alteration site through interaction formation. ( a ) Visualization performed using BIOVIA Discovery Studio Visualizer (Version 21.1.0.20298). ( b ) Conservation of amino acids around position 86 in PIGT across different species. An asterisk ( * ) indicates p.86 of the PIGT protein in each species. ( c , d ) Comparison of intramolecular bonds at the alteration site in wild-type (wt) and mutant (mt) proteins, computed and visualized via DDMut.

Article Snippet: The three-dimensional structures of both the wild-type and mutant PIGT (PDB: 7wld) were visualized using BIOVIA software [ ].

Techniques: Comparison, Mutagenesis