Computational protocol: Structure-Activity Relationship of Chlorotoxin-Like Peptides

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Protocol publication

[…] The known three-dimensional structural coordinates of the chlorotoxin and chlorotoxin-like peptides for the search of the best template, superimposition and structural evaluation were retrieved from the Brookhaven Protein Data Bank [], except the toxin Lqh8/6 [], whose structural coordinates were kindly provided by Dr. Constantin T. Craescu (Orsay, France). All known toxin sequences were obtained from Swiss Protein Data Bank []. Similarities between different sequences were analysed using the program FASTA [] and/or BLAST []. Multiple sequence alignment was carried out using the program CLUSTAL X [] with default parameters and manually adjusted where necessary. The phylogenetic lineage was calculated using the phylogeny inference program Phylip [].Three-dimensional structural models of Bs-Tx7 and GaTx1 were constructed using the known crystal/NMR structural templates. Homology models were generated automatically using the software MODELLER 8.0 [,] and/or the online Swiss-Modeling Server []. The predicted models have been evaluated for geometry, stereochemistry and energy distributions. The ENERGY command of the MODELLER and/or PROSA has been used for determining reliability. The models have been further evaluated by the programs “PROCHECK” and “WHATCHECK” [,]. Variability among the models has been compared by superposition of Cα traces and the backbones onto the template structure and calculated as RMSD. WEBLAB Viewer Pro (v4.0) (MSI, San Diego, CA, USA)was used for visualization of the structures. […]

Pipeline specifications

Software tools Clustal W, PHYLIP, MODELLER, PROCHECK, WHAT_CHECK
Applications Phylogenetics, Protein structure analysis
Organisms Homo sapiens
Diseases Neoplasms
Chemicals Amino Acids, Calcium, Potassium, Sodium