PMC

CusB-CusB interactions. (a) The interactions between molecules 1 and 2 of CusB. Residues E118, Y119, R186, E252 and E292 of molecule 1 of CusB participate to form hydrogen bonds with residues T139, D142, T206, N312 and N113 of molecule 2 of CusB, respectively. These hydrogen-bonded distances are 2.7, 2.7, 3.0, 3.0 and 3.0 Å, respectively. (b) The interactions between molecules 1 and 6 of CusB. Residues N113, N228, and N312 of molecule 1 of CusB pair up with R292, the backbone oxygen of A126, and E252 of molecule 6 of CusB to form three hydrogen bonds. D142 of molecule 1 of CusB also participates to form two hydrogen bonds with Y119 and R297 of molecule 6 of CusB. These hydrogen-bonded distances are 2.7, 2.8, 3.1, 2.7 and 2.8 Å, respectively.

Crystal structure of F126A-sm1. (A) Superposition of F126A-sm1(blue) onto OspA-sm1 (red). The mutated residue (F126) is shown as spheres. (B) The root-mean-squared deviations (RMSD) for the C^α atoms are plotted versus residue number. The positions of β-strands and the C-terminal helix are shown as bars. The mutation site is indicated as a red circle. (C) Rearrangements of residues surrounding the F126 site in F126A-sm1. OspA-sm1 is shown in red and F126A-sm1 in blue. The backbone atoms are shown as stick models. The side chains are displayed only for residues in the hydrophobic ladder (F102, L109, F126 (A126 in the mutant) and V132).

Delineation of the syntaxin 5/Sly1-binding mode. (A) Differences (ΔδHα) between the observed Hα chemical shifts of the syntaxin 5 N-terminal peptide bound to the Sly1 N-terminal domain and the chemical shifts expected for a random coil conformation. Negative ΔδHα values are indicative of α-helix formation. The Hα protons of residues 1–6 could not be assigned. (B) 2D ¹³C-filtered, ¹³C-edited NOESY spectrum of ¹⁵N,¹³C-labeled Sly1 N-terminal domain bound to unlabeled syntaxin 5 peptide. This spectrum reveals intermolecular NOEs between protons from the syntaxin 5 peptide (F1 dimension) and protons from the Sly1 N-terminal domain (F2 dimension). Arrows point to NOEs between F10 of syntaxin 5 and methyl-containing residues of Sly1 (I125, A126, V138, and V141). (C) Homology model of the structure of the Sly1 N-terminal domain based on the crystal structure of Munc18-1. Helices and β-strands are labeled as α1–α5 and β1–β5, respectively. The side chains of I125, A126, V138, and V141 are shown as solid blue spheres. The binding site for F10 of syntaxin 5 is indicated with a green asterisk. The orange arrow points at the site where syntaxin 1 binds to the N-terminal domain of Munc18-1 (helices α2, α3, and strand β2).

(A) Western blot analysis of SOX2 protein expression after transfection of a negative control oligonucleotide (NC), Pre-miR-126 (126), Pre-miR-522 (522), SOX2 siRNA (siR), and Anti-miR-126 (A126) in the indicated gastric cancer cell lines and mouse ES cells. The final concentrations were 50 nM for Pre-miRNAs and siRNA, and 100 nM for Anti-miR-126, respectively. α-tubulin expression was used as a protein loading control. (B) Quantitative real-time RT-PCR analysis of SOX2 mRNA expression after transfection of the negative control, Pre-miR-126 and SOX2 siRNA into HSC43 cells. The expression levels were normalized against internal GAPDH expression. The assays were performed in triplicate, and the bars indicate s.d. *P<0.05.