International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.

Primary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined<5 × 10(-8)) and used pathway analysis to identify JAK-STAT/IL12/IL27 signalling and cytokine-cytokine pathways, for which relevant therapies exist

Water data on HIV protease.

<p>The SACP water molecules predicted to bind to HIV protease. The simulation produces that key water molecule (a) experimentally known to be at the center of the binding site. All of the other water molecules from SACP obey the water exclusion principle and bind in a ring just outside of the site (b-c). Two key aspartates are at the center of the binding site (Asp25 and Asp125 colored with green carbons in panel a). The ligand indinavir is shown with yellow carbons in all three panels. Part of the protein surface is hidden to reveal the binding site. Three different protonation states were simulated, a) ASP25 and ASP125, b) ASH25 and ASP125, c) ASH25 and ASH125 with all giving comparable results.</p

RecA data.

<p>RecA hydrolyzes ATP to ADP that can be enzymatically converted to H₂O₂, which oxidizes amplex red to the fluorescent molecule resorufin. The steady state rate of creation of the fluorescence is plotted on the y-axis in relative fluorescence units (RFU). The addition of a RecA inhibitor decreases the rate of production of RFUs in a concentration dependent manner. 6-Hydroxydopamine inhibits RecA with an IC₅₀ of 23 uM. To our knowledge, this is an almost singular example of potently breaking a protein-protein interaction with such a small fragment and quite a remarkable prediction given how difficult it is to inhibit RecA (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183327#sec015" target="_blank">Discussion</a> section). The experiments were done in triplicate and all gave virtually the same binding affinity.</p

Hot spots on MDM2/X.

<p>a) p53-MDM2 protein-protein interaction displayed with overlay of computed fragments. b) p53-MDMX protein-protein interaction displayed with overlay of computed fragments. The MDM surfaces are presented in gray. The p53 peptide is colored magenta. The computed fragments are shown in green. Strikingly, the fragments predict a high affinity site at L26 for MDM2 but not MDMX, which is in accord with the experimental finding on the differential binding.</p

Hot spots on RecA.

<p>a) Sites where a diversity of fragments simultaneously binds with high affinity and where no high affinity waters appear. The sites correspond to the ATP binding site (ATP is shown in magenta), an interaction site between RecA monomers (top right site), and the DNA binding site (upper left site). Three universally conserved residues (K216, F217, and R222) from the neighboring subunit (yellow ribbons) are shown with magenta carbons and the interactions at the RecA-RecA site for these residues are shown in (b). Mutations of these three residues will result in the loss of RecA function, although F217Y results in a 250-fold increase in the interaction between RecA subunits. SACP predicts that alkylamines bind in the RecA pocket mimicking K216 interactions (b) and that phenol mimics the F217 interaction. SACP also predicts that adding extra hydroxyl groups to the benzene ring results in a higher affinity (c). When the fragment patterns are combined, SACP creates 6-Hydroxydopamine in the RecA-RecA interaction site.</p