LibME-automatic extraction of 3D ligand-binding motifs for mechanistic analysis of protein-ligand recognition.

Identifying conserved binding motifs is an efficient way to study protein-ligand recognition. Most 3D binding motifs only contain information from the protein side, and so motifs that combine information from both protein and ligand sides are desired. Here, we propose an algorithm called LibME (Ligand-binding Motif Extractor), which automatically extracts 3D binding motifs composed of the target ligand and surrounding conserved residues.

Strict Major Histocompatibility Complex Molecule Class-Specific Binding by Co-Receptors Enforces MHC-Restricted αβ TCR Recognition during T Lineage Subset Commitment.

Since the discovery of co-receptor dependent αβTCR recognition, considerable effort has been spent on elucidating the basis of CD4 and CD8 lineage commitment in the thymus. The latter is responsible for generating mature CD4 helper and CD8αβ cytotoxic T cell subsets. Although CD4(+) and CD8(+) T cell recognition of peptide antigens is known to be MHC class II- and MHC class I-restricted, respectively, the mechanism of single positive (SP) thymocyte lineage commitment from bipotential double-positive (DP) progenitors is not fully elucidated.

Structural insights into cofactor recognition of yeast mitochondria 3-oxoacyl-ACP reductase OAR1.

3-Oxoacyl-(acyl-carrier-protein) reductase (OAR1 or FabG, EC.1.1.

Hepatitis B virus and hepatocellular carcinoma at the miRNA level.

Aim: To study Hepatitis B virus (HBV) infection and its association with hepatocellular carcinoma (HCC) at the miRNA level.

Methods: Three cellular models were used to investigate miRNA expression changes during HBV infection: human HepG2 hepatoblastoma cell line as a model without HBV infection; HepG2 cell line transfected with a 1.3-fold full-length HBV genome as an acute infection model; and HepG2.

Crystal structure of Natratoxin, a novel snake secreted phospholipaseA2 neurotoxin from Naja atra venom inhibiting A-type K+ currents.

Snake secreted phospholipasesA2 (sPLA2s) are widely used as pharmacological tools to investigate their role in diverse pathophysiological processes. Some members of snake venom sPLA2s have been found to block voltage-activated K(+) channels (K(v) channels). However, most studies involved in their effects on ion channels were indirectly performed on motor nerve terminals while few studies were directly done on native neurons.

Purification, partial characterization, crystallization and preliminary X-ray diffraction of a novel cardiotoxin-like basic protein from Naja naja atra (South Anhui) venom.

A novel cardiotoxin-like basic protein was isolated from the venom of the Chinese cobra (Naja naja atra) from the south of Anhui in China. The protein inhibits the expression of vascular endothelial growth factor and basic fibroblast growth factor in human lung cancer cell line H1299 and induces the haemolysis of rabbit erythrocytes under low-lecithin conditions. After a two-step chromatographic purification, the resultant 7 kDa protein was crystallized by the hanging-drop vapour-diffusion method at room temperature.

Purification, crystallization and preliminary X-ray analysis of Hsp33 from Saccharomyces cerevisiae.

The heat-shock protein Hsp33 from the yeast Saccharomyces cerevisiae has been overexpressed, purified and crystallized. A crystal was obtained using the hanging-drop vapour-diffusion method and a data set was collected to 2.7 A resolution.

Developmental expression of FXPRLamide neuropeptides in peptidergic neurosecretory cells of diapause- and nondiapause-destined individuals of the cotton bollworm, Helicoverpa armigera.

The diapause hormone (DH)-pheromone biosynthesis activating neuropeptide (PBAN) gene encodes five neuropeptides, DH, PBAN, alpha-SGNP, beta-SGNP, and gamma-SGNP (subesophageal ganglion neuropeptide). All share the C-terminal pentapeptide FXPRLamide sequence and are produced in the subesophageal ganglion (SG). Expression of the DH-PBAN gene in the central nervous system of embryonic, larval, pupal, and adult Helicoverpa armigera (Har) was studied using in situ hybridization, whole-mount immunocytochemistry, and competitive ELISA.

Mutation of G138P Enhanced the Thermostability of D-glucose Isomerase.

In order to enhance the thermostability of D-glucose isomerase (GI), Gly 138 was decided to be the target to be replaced by molecular design. The mutant G138P was obtained by in vitro site-directed mutagenesis of GI gene. The recombinant plasmid pTKD-GI containing mutant site was expressed in E.

Studies on the Relationship Between the Biological Activities and the Circular Dichroism of South Anhui Dienagkistrodon Acutus Hemorrhagins.

The solution conformations of three hemorrhagic toxins, designated as AaH I, AaH III and AaH IV, from South Anhui Dienagkistrodon acutus have been studied by CD spectra. The secondary structure of AaH I consisted of 25.8% alpha-helix, 12.

Effects of Site-specific Mutagenesis of K253 and N184V on the Thermostability of D-Glucose Isomerase.

In order to enhance the thermostability of D-Glucose isomerase (GI), its mutants, GIK253R and GIN184V, were obtained with the double primer method of site-directed mutagenesis. Then their biochemical properties were assayed and compared with wild-type GI. The results showed that: (1) The mutant K253R was less stable than the wild-type GI at 70 degrees and 80 degrees.