Computational protocol: A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3

Similar protocols

Protocol publication

[…] Models of the kinase domains of RHWT, RHL503S, ME49WT, and ME49S503L were constructed from ffas03 profile-profile alignments (http://ffas.burnham.org/ffas-cgi/cgi/ffas.pl) using the PDB0709 and SCOP175 profile databases. The top PDB0709 and SCOP175 alignments (corresponding to templates 3cokA and d1s9ja, respectively) were selected for each of the three sequences, resulting in a total of six structural models. Structural models were built using Spanner (http://sysimm.ifrec.osaka-u.ac.jp/cgi-bin/spanner), which employs a fragment assembly algorithm to produce a gapless alignment to the template. The structural models were then submitted to the SeSAW functional annotation server (http://sysimm.ifrec.osaka-u.ac.jp/SeSAW/). SeSAW uses a combined structure and sequence profile–profile similarity score () to rank their similarity to known structures. The model built on SCOP domain d1s9ja (dual-specificity mitogen-activated protein kinase kinase 1) resulted in significantly higher SeSAW scores than that built on PDB entry 3cokA (323.0 and 253.0, respectively) so the d1s9ja model was ultimately retained for further analysis. Residues 387–452 could not be modeled with as high a confidence as the rest of the structure as a result of a large insertion and were omitted from and Fig. S7. The predicted active site cavity location was based on that of d1s9ja dual-specificity MAP kinase kinase 1. Electrostatic surfaces were prepared using the eF-surf server (http://ef-site.hgc.jp/eF-surf/) and eF-site (). […]

Pipeline specifications

Software tools FFAS, SeSaw
Databases eF-site
Application Protein structure analysis
Organisms Toxoplasma gondii, Homo sapiens
Diseases Sprains and Strains, Spinocerebellar Ataxias