Prediction and Analysis of Quorum Sensing Peptides Based on Sequence Features

Akanksha Rajput, Amit Kumar Gupta, Manoj Kumar, Lukasz Kurgan
2015 PLoS ONE  
Quorum sensing peptides (QSPs) are the signaling molecules used by the Gram-positive bacteria in orchestrating cell-to-cell communication. In spite of their enormous importance in signaling process, their detailed bioinformatics analysis is lacking. In this study, QSPs and non-QSPs were examined according to their amino acid composition, residues position, motifs and physicochemical properties. Compositional analysis concludes that QSPs are enriched with aromatic residues like Trp, Tyr and Phe.
more » ... At the N-terminal, Ser was a dominant residue at maximum positions, namely, first, second, third and fifth while Phe was a preferred residue at first, third and fifth positions from the C-terminal. A few motifs from QSPs were also extracted. Physicochemical properties like aromaticity, molecular weight and secondary structure were found to be distinguishing features of QSPs. Exploiting above properties, we have developed a Support Vector Machine (SVM) based predictive model. During 10-fold cross-validation, SVM achieves maximum accuracy of 93.00%, Mathew's correlation coefficient (MCC) of 0.86 and Receiver operating characteristic (ROC) of 0.98 on the training/testing dataset (T 200p+200n ). Developed models performed equally well on the validation dataset (V 20p+20n ). The server also integrates several useful analysis tools like "QSMotifScan", "ProtFrag", "MutGen"and "PhysicoProp". Our analysis reveals important characteristics of QSPs and on the basis of these unique features, we have developed a prediction algorithm "QSPpred" (freely available at: http://crdd.osdd.net/servers/qsppred).
doi:10.1371/journal.pone.0120066 pmid:25781990 pmcid:PMC4363368 fatcat:73rakkelcfgq7k2nlcxvyfx6vu