Pipeline publication

[…] b' family [] (probability to be a true positive more than to 99%, E-value equal to 1.2 x10-42). The third scoring hit was the ubiquitin E2 variant (UEV) family (Pfam ID: PF05743) that includes UBC homologs such as Tsg101, Mms2 and UEV1 (probability to be a true positive equal to 96.44%, E-value equal to 1.3 x10-4). Peo belongs to the UEV family because it contains an aspartic acid residue (at position 106, according to SwissProt numbering) in place of the E2 active site cysteine, and it is unable to catalyze ubiquitin transfer as it lacks the cysteine that forms a transient thioester bond with the C-terminus of ubiquitin (Ub)., Prediction of potentially disordered regions using the GeneSilico MetaDisorder server (http://iimcb.genesilico.pl/metadisorder/) revealed that at the C-terminus of Peo there is a stretch of ~ 70 aa (from residue 177 to 244, according SwissProt numbering) that has the tendency to be intrinsically disordered (i.e. lack a unique three dimensional structure at least in the absence of a binding partner), while the region including residues 16\xe2\x80\x93176 shows propensity to form a folded globular domain with a well-defined pattern of secondary structures as revealed by the Quick2d web server analysis []., Because no homologous structure with sufficiently high sequence identity with Peo is available, we performed the Peo modeling using the composite approach implemented in I-TASSER server (Iterative Threading ASSEmbly Refinement) [].The Peo sequence from residue 16 to 176 (predicted to fold in a globular domain) was submitted to the server and the model with the best confidence score (C-score = 0.5) returned by I-TASSER was selected. We added hydrogen atoms in this model using HAAD software [] and refined it close to the native structure using FG-MD molecular dynamics based algorithm []., Our final refined model of Peo was evaluated as a potentially extremely good model (with a predicted LGscore of 2.50) by the PRO-Q model quality assessment program []. The QMEAN score [] was 0.6 (the variability range is 0\xe2\x80\x931, with 1 being a perfect model). Collectively these parameters indicate that the Peo three-dimensional model is sufficiently accurate for making functional inferences., We thank P. Dimitri for providing us with the lethal mutant collection from which we isolated peo 1, Carlo Santolamazza and Giorgio Belloni for their assistance during the early stages of this work. We also thank Claudia Berdini for help in the construction and expression of the GST-HOAP truncations. Further thanks are due to Dan L. Lindsley for the late lethal collection used to isolate the peo h allele, to Paul Taghert for the peo mutant alleles, and to Gianni Prosseda for' […]

Pipeline specifications

Software tools Metadisorder, I-TASSER, HAAD, FG-MD, QMEAN
Organisms Drosophila melanogaster