title: Novel Bioinformatics-Based Approach for Proteomic Biomarkers Prediction of Calpain-2 &Caspase-3 Protease Fragmentation: Application to βII-Spectrin Protein.
abstract: The crucial biological role of proteases has been visible with the development of degradomics discipline involved in the determination of the proteases/substrates resulting in breakdown-products (BDPs) that can be utilized as putative biomarkers associated with different biological-clinical significance. In the field of cancer biology, matrix metalloproteinases (MMPs) have shown to result in MMPs-generated protein BDPs that are indicative of malignant growth in cancer, while in the field of neural injury, calpain-2 and caspase-3 proteases generate BDPs fragments that are indicative of different neural cell death mechanisms in different injury scenarios. Advanced proteomic techniques have shown a remarkable progress in identifying these BDPs experimentally. In this work, we present a bioinformatics-based prediction method that identifies protease-associated BDPs with high precision and efficiency. The method utilizes state-of-the-art sequence matching and alignment algorithms. It starts by locating consensus sequence occurrences and their variants in any set of protein substrates, generating all fragments resulting from cleavage. The complexity exists in space O(mn) as well as in O(Nmn) time, where N, m, and n are the number of protein sequences, length of the consensus sequence, and length per protein sequence, respectively. Finally, the proposed methodology is validated against βII-spectrin protein, a brain injury validated biomarker.
authors.affiliation: Department of Electrical and Computer Engineering, American University of Beirut, Riad El Solh, Beirut, Lebanon.
authors.forename: Atlal
authors.initials: A
authors.lastname: El-Assaad
authors.affiliation: Department of Electrical and Computer Engineering, American University of Beirut, Riad El Solh, Beirut, Lebanon.
authors.forename: Zaher
authors.initials: Z
authors.lastname: Dawy
authors.affiliation: Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Riad El Solh, Beirut, Lebanon.
authors.forename: Georges
authors.initials: G
authors.lastname: Nemer
authors.affiliation: Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Riad El Solh, Beirut, Lebanon.
authors.forename: Firas
authors.initials: F
authors.lastname: Kobeissy
mesh_terms: D000465:Algorithms; D000818:Animals; D002154:Calpain / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics*; D053148:Caspase 3 / Q000235:genetics*; D016923:Cell Death / Q000235:genetics; D019295:Computational Biology; D006801:Humans; D020782:Matrix Metalloproteinases / Q000235:genetics; D008840:Microfilament Proteins / Q000235:genetics*; D009474:Neurons / Q000378:metabolism / Q000473:pathology; D010447:Peptide Hydrolases; D040901:Proteomics; D013049:Spectrin
chemical_list: D002154:Calpain; D002352:Carrier Proteins; D053148:Caspase 3; D020782:Matrix Metalloproteinases; D008840:Microfilament Proteins; D010447:Peptide Hydrolases; D013049:Spectrin; C569870:CAPN2 protein, human