Globularity, secondary structure predictions and PDB scan

Globularity was predicted using GlobPlot [18]. The program identifies regions of globularity (order) and disorder within protein sequences. Its approach is based on a running sum of the propensity for amino acids to be in an ordered or disordered state. In order to avoid “edge” effects, a GlobPlot score was calculated for a concatemer of six tandem repeats (using the default parameters for the batch version). Secondary structure predictions were made using PSIPRED [19]. PSIPRED identifies homologous sequences and predicts secondary structure based on the position specific scoring matrices generated by PSI-BLAST [20]. The Protein Data Bank (PDB) was searched for candidate repeat regions using PDB-BLAST [http://blast.ncbi.nlm.nih.gov/Blast.cgi] and RCSB PDB (http://www.rcsb.org/pdb/home/home.do#Subcategory-search_sequences]) [21]. For the NCBI BLAST PDB search we used the quadruple of repeat motifs.