Towards the Improved Discovery and Design of Functional Peptides: Common Features of Diverse Classes Permit Generalized Prediction of Bioactivity

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Title: Towards the Improved Discovery and Design of Functional Peptides: Common Features of Diverse Classes Permit Generalized Prediction of Bioactivity
Authors: Mooney, Catherine
Haslam, Niall J.
Pollastri, Gianluca
Shields, Denis C.
Permanent link: http://hdl.handle.net/10197/3891
Date: Oct-2012
Abstract: The conventional wisdom is that certain classes of bioactive peptides have specific structural features that endow their particular functions. Accordingly, predictions of bioactivity have focused on particular subgroups, such as antimicrobial peptides. We hypothesized that bioactive peptides may share more general features, and assessed this by contrasting the predictive power of existing antimicrobial predictors as well as a novel general predictor, PeptideRanker, across different classes of peptides.We observed that existing antimicrobial predictors had reasonable predictive power to identify peptides of certain other classes i.e. toxin and venom peptides. We trained two general predictors of peptide bioactivity, one focused on short peptides (4-20 amino acids) and one focused on long peptides (>20 amino acids). These general predictors had performance that was typically as good as, or better than, that of specific predictors. We noted some striking differences in the features of short peptide and long peptide predictions, in particular, high scoring short peptides favour phenylalanine. This is consistent with the hypothesis that short and long peptides have different functional constraints, perhaps reflecting the difficulty for typical short peptides in supporting independent tertiary structure.We conclude that there are general shared features of bioactive peptides across different functional classes, indicating that computational prediction may accelerate the discovery of novel bioactive peptides and aid in the improved design of existing peptides, across many functional classes. An implementation of the predictive method, PeptideRanker, may be used to identify among a set of peptides those that may be more likely to be bioactive.
Funding Details: Science Foundation Ireland
Type of material: Journal Article
Publisher: PLOS
Copyright (published version): 2012 Mooney et al
Keywords: PeptidesBioactivity
Subject LCSH: Bioactive compounds
Peptides
DOI: 10.1371/journal.pone.0045012
Language: en
Status of Item: Peer reviewed
Appears in Collections:Conway Institute Research Collection
Computer Science Research Collection
CASL Research Collection
Medicine Research Collection

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