Journal: Molecular genetics and metabolism

Article Title: Outcomes and genotype-phenotype correlations in 52 individuals with VLCAD deficiency diagnosed by NBS and enrolled in the IBEM-IS database

doi: 10.1016/j.ymgme.2016.05.007

Figure Lengend Snippet: Ribbon representation of VLCAD crystal structure, modeled using the published atomic coordinates of the VLCAD monomer, PDB code: 3B96. Modeled is the dimer form, lacking the C-termini disordered regions, and palmitoyl-CoA at the active sites. Depicting mutation positions are in CPK using the InsightII Modeling software (Dassault Systèmes, BIOVIA Corp – formerly Accelrys Technologies, San Diego, CA). Subunits A and B are colored light jade and gray, respectively. The novel mutations described in this manuscript are represented in different colored CPK and are described in the text and Table 2. The stick structures of FAD and palmitoyl-CoA are colored yellow and green, respectively. The stick structure of Glu462 (precursor numbering, Glu422 in mature numbering; GenBank accession number P49748.1), the catalytic base, is colored red. The view in panel A emphasizes the homology to other ACADs while in panel B shows the monomer interface. Note the mutations at the monomer interface, predicting a destabilizing effect on the dimer assembly.

Article Snippet: Depicting mutation positions are in CPK using the InsightII Modeling software (Dassault Systèmes, BIOVIA Corp – formerly Accelrys Technologies, San Diego, CA).

Techniques: Mutagenesis, Software

Journal: PLoS ONE

Article Title: Structural Basis for Certain Naturally Occurring Bioflavonoids to Function as Reducing Co-Substrates of Cyclooxygenase I and II

doi: 10.1371/journal.pone.0012316

Figure Lengend Snippet: A . The superimposed structures of COX I and II in complex with hematin and AA. The white labels indicate the two potential binding sites for quercetin as identified by the Active-Site-Search function in InsightII . B . Docking results for quercetin in S ite -2 of COX I. C . Docking results for quercetin in S ite -2 of COX II. D . Enlarged view of the interaction of quercetin with hematin and key amino acid residues in the peroxidase active sites of COX I. E . Enlarged view of the interaction of quercetin with hematin and key amino acid residues in the peroxidase active site of COX II. The protein structure was shown in the ribbon format in A , B and C . COX I was colored in pink and COX II in purple. AA was colored in light green for COX I and dark green for COX II. Quercetin was colored in light red for COX I and magenta for COX II. Carbon atoms in hematin were colored in yellow for COX I and orange for COX II whereas nitrogen atoms were colored in blue, oxygen atoms in red, and magnesium in silver. The green dashes represent the hydrogen bonds. Hematin, AA, key amino acid residues, and quercetin are shown in the ball and stick format. For amino acid residues, oxygen atoms are shown in red, carbon atoms in gray, and nitrogen atoms in blue. Hydrogens are omitted in these molecules.

Article Snippet: Energy minimization and molecular docking were performed on a Dell Precision 690 workstation using the InsightII modeling software (Version 2005, Accelrys Inc. San Diego, CA) installed in a Red Hat Enterprise Linux WS4.0 operating system.

Techniques: Binding Assay