Calpain Cleavage Prediction Using Multiple Kernel Learning

Calpain, an intracellular C alpha(2+)-dependent cysteine protease, is known to play a role in a wide range of e metabolic path through limited proteolysis of its substrate However, only a limited number of he e substrates are currently known, e exact mechanism of substrate recognition and cleavage by calpain still largely unknown While previous research has successfully applied standard machine-learning algorithms to accurately predict substrate cleavage by other similar types of proteases, their approach does not extend well to calpain, possibly due to its particular mode of proteolytic action and limited amount of experimental data. Through the use of Multiple Kernel Learning, a recent extension to the classic Support Vector Machine framework, we were able to train complex models based on rich, heterogeneous feature sets, leading to significantly improved prediction quality (6% over highest AUC score produced by state-of-the-art methods). In addition producing a stronger machine-learning model for the prediction of calpain cleavage, we were able to highlight importance and role of each feature of substrate sequences in defining specificity: primary sequence, secondary structure and solvent accessibility. Most notably, we showed there existed significant specificity differences across calpain sub-types despite previous assumption to the contrary. Prediction accuracy further successfully validated using, as an unbiased mutated sequences of calpastatin endogenous inhibitor of calpain) modified to no longer block calpain's proteolytic action. An online implementation of our prediction tool is available at http.//calpain.org.