Similar protocols

Pipeline publication

[…] analyzed by peak integration using ORIGIN 7.0 software. All histo-blood group antigens (purity >90%) were obtained from Elicityl SA, except Leb, which was obtained from IsoSep AB., For identification of proteins with structural similarity to BabA, the apo-BabA PDB file (accession code: 4ZH0) was uploaded onto the Dali server () for an atomic coordinates similarity search within the PDB. For analysis of strain conservation of the Leb binding site, available babA gene sequences corresponding to the crown (amino acids 183 to 253 in mature BabA J99) from Leb binding strains identified in (–) were obtained from the European Nucleotide Archive and GenBank. After removal of duplicate sequences, CLC Main WorkBench 7.6 (CLC bio) was used for the multiple sequence alignment (protein) of BabA J99 with 21 H. pylori strains., To search for DNA sequences with similarity to the BabA crown, the BabA gene fragment corresponding to the crown [that is, complement(914203–914421) in GenBank accession no. AE001439.1] was submitted to Nucleotide-BLAST. The nucleotide collection (nr/nt) database was searched using megablast, discontiguous, and blastn algorithms. To search for protein sequences with similarity to the BabA crown, the BabA protein fragment corresponding to the crown [that is, residues 203 to 273 in GenBank accession no. AAD06409.1] was submitted to Protein-BLAST. The nonredundant protein sequences (nr) database was searched using BLAST algorithms optimized for protein-protein, position-specific iterated, pattern hit initiated, and domain enhanced lookup time accelerated BLAST., For crystallographic experiments, apo-BabA and BabA:Leb structural models were built from diffraction data sets collected from single crystals after multiple rounds of iterative refinement. For biophysical analysis, binding isotherms obtained from ITC were fitted to a nonlinear least squares curve with Origin 7.0 after multiple iterations until a fixed minimal χ2 value was achieved. An unpaired two-tailed Welch’s t test was used to determine if the thermodynamic parameters associated with BabA:Leb binding from three independent experiments at pH 4.5 and 7.4 were significantly different from each other., We thank G. Davies and G. Holdgate of Ast […]

Pipeline specifications

Software tools CLC Main Workbench, CLC Genomics Workbench, BLASTN, DELTA-BLAST
Organisms Helicobacter pylori, Helicobacter pylori J99
Diseases Stomach Diseases, Gastrointestinal Neoplasms, Digestive System Neoplasms
Chemicals Amino Acids, Hydrogen