Computational protocol: Biochemical characterization and comparison of aspartylglucosaminidases secreted in venom of the parasitoid wasps Asobara tabida and Leptopilina heterotoma

Similar protocols

Protocol publication

[…] The cDNA sequence of A. tabida venom AGA (ACX94224) was previously reported [,]. L. heterotoma venom AGA (KP888635) was identified from venom apparatus transcriptomics data []. The A. tabida (AtAGA), L. heterotoma (LhAGA), and Homo sapiens (hAGA, P20933) predicted AGA protein sequences were aligned with MAFFT []. Signal peptide and N-glycosylation sites prediction were performed with SignalP (http://www.cbs.dtu.dk/services/) and NetNGlyc (http://www.cbs.dtu.dk/services/NetNGlyc/), respectively. Pfam (http://pfam.janelia.org/) was used to search for protein domains. Protein disulfide bonds were predicted using DIpro (http://scratch.proteomics.ics.uci.edu/).Molecular modeling of mature AtAGA and LhAGA was done with the Phyre server using default parameters (http://www.sbg.bio.ic.ac.uk/phyre2/) []. For both proteins, the model with highest confidence (100%) and coverage (76% and 75% for AtAGA and LhAGA, respectively) was obtained using the crystal structure with PDB code 1P4V as template. Model quality was assessed by the QMEAN server (http://swissmodel.expasy.org/qmean/) []. Briefly, QMEAN score is a global reliability score with values ranging between 0 (lower accuracy) and 1 (greater accuracy). The associated Z-score relates this QMEAN score to the scores of a non-redundant set of high-resolution X-ray structures of similar size with ideal values being close to 0. Visualization of AtAGA and LhAGA model structures, superposition with the hAGA crystal structure (PDB code: 1APY) [], and root mean square deviations were obtained using PyMOL v0.99 (http://www.pymol.org). […]

Pipeline specifications

Software tools MAFFT, SignalP, NetNGlyc, DIpro, Phyre, QMEAN, PyMOL
Databases Pfam ExPASy
Application Protein structure analysis
Organisms Homo sapiens, Drosophila melanogaster
Diseases Lysosomal Storage Diseases, Aspartylglucosaminuria