Computational protocol: The Core Cysteines, (C909) of Islet Antigen-2 and (C945) of Islet Antigen-2β, Are Crucial to Autoantibody Binding in Type 1 Diabetes

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Protocol publication

[…] The crystal structures of the IA-2 PTP residues 709–979 (PDB ID: 2I1Y) () and the IA-2β PTP residues 750–1015 (PDB ID: 2QEP) () were used to model amino acid changes. InsightII was used to mutate/append the residues, and the structures were then minimized using Discover (Accelrys Inc., San Diego, CA). During initial stages of minimization, all atoms were restrained. Subsequently, all atoms were gradually allowed freedom to move, enabling backbone and side-chain flexibility as the system relaxed. Images were generated using a combination of Chimera (University of California San Francisco), Gimp (Gnu Image Manipulation Program, http://www.gimp.org/), and Powerpoint (Microsoft). The effects of serine or alanine mutations on the surface structure were investigated by measuring the root mean square deviation (RMSD) from the WT position of the WPAE loop in the models, following mutation and energy minimization. This method was also used to assess the effects of adding a sulfonate to C909 in IA-2 to mimic the effects of oxidation and of alkylation with NEM. Additional homology modeling was performed using HHPRED software (ftp://toolkit.lmb.uni-muenchen.de/HH-suite/) to predict the effect of alanine substitution for W799 and for C909 using lower sequence identity PTP homologs as templates. […]

Pipeline specifications

Software tools GIMP, HHPred, HHalign
Applications Miscellaneous, Protein structure analysis, Amino acid sequence alignment
Organisms Homo sapiens
Diseases Diabetes Mellitus
Chemicals Cysteine, Tyrosine, Glutamic Acid