GPS-CCD: A Novel Computational Program for the Prediction of Calpain Cleavage Sites

As one of the most essential post-translational modifications (PTMs) of proteins, proteolysis, especially calpain-mediated cleavage, plays an important role in many biological processes, including cell death/apoptosis, cytoskeletal remodeling, and the cell cycle. Experimental identification of calpain targets with bona fide cleavage sites is fundamental for dissecting the molecular mechanisms and biological roles of calpain cleavage. In contrast to time-consuming and labor-intensive experimental approaches, computational prediction of calpain cleavage sites might more cheaply and readily provide useful information for further experimental investigation. In this work, we constructed a novel software package of GPS-CCD (Calpain Cleavage Detector) for the prediction of calpain cleavage sites, with an accuracy of 89.98%, sensitivity of 60.87% and specificity of 90.07%. With this software, we annotated potential calpain cleavage sites for hundreds of calpain substrates, for which the exact cleavage sites had not been previously determined. In this regard, GPS-CCD 1.0 is considered to be a useful tool for experimentalists. The online service and local packages of GPS-CCD 1.0 were implemented in JAVA and are freely available at: http://ccd.biocuckoo.org/.

[1]  Ichigaku Takigawa,et al.  CaMPDB: a resource for calpain and modulatory proteolysis. , 2010, Genome informatics. International Conference on Genome Informatics.

[2]  E. Hall,et al.  Identification and characterization of PEBP as a calpain substrate , 2006, Journal of neurochemistry.

[3]  Yu Xue,et al.  GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy *S , 2008, Molecular & Cellular Proteomics.

[4]  Alan Wells,et al.  Cutting to the chase: calpain proteases in cell motility. , 2002, Trends in cell biology.

[5]  Peter Tompa,et al.  On the Sequential Determinants of Calpain Cleavage* , 2004, Journal of Biological Chemistry.

[6]  T. Holak,et al.  Identification of calpain cleavage sites in the G1 cyclin-dependent kinase inhibitor p19INK4d , 2006, Biological chemistry.

[7]  Anna Huttenlocher,et al.  Regulating cell migration: calpains make the cut , 2005, Journal of Cell Science.

[8]  Neil D. Rawlings,et al.  MEROPS: the peptidase database , 2009, Nucleic Acids Res..

[9]  Yu Xue,et al.  GPS: a comprehensive www server for phosphorylation sites prediction , 2005, Nucleic Acids Res..

[10]  Klaus Ersfeld,et al.  The calpains: modular designs and functional diversity , 2007, Genome Biology.

[11]  Guoliang Chen,et al.  A genome‐wide analysis of sumoylation‐related biological processes and functions in human nucleus , 2005, FEBS letters.

[12]  T. Maeda,et al.  Constitutive Activation of the pH-Responsive Rim101 Pathway in Yeast Mutants Defective in Late Steps of the MVB/ESCRT Pathway , 2005, Molecular and Cellular Biology.

[13]  Nancy D Denslow,et al.  Proteolysis of multiple myelin basic protein isoforms after neurotrauma: characterization by mass spectrometry , 2008, Journal of neurochemistry.

[14]  Neil D. Rawlings,et al.  A large and accurate collection of peptidase cleavages in the MEROPS database , 2009, Database J. Biol. Databases Curation.

[15]  Yu Xue,et al.  DOG 1.0: illustrator of protein domain structures , 2009, Cell Research.

[16]  James C. Whisstock,et al.  PoPS: a computational tool for modeling and predicting protease specificity , 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

[17]  A. Malkinson,et al.  Calpain and calpastatin regulate neutrophil apoptosis , 1999, Journal of cellular physiology.

[18]  N. Hooper,et al.  A broad‐spectrum fluorescence‐based peptide library for the rapid identification of protease substrates , 2006, Proteomics.

[19]  K. Wang,et al.  The calpain family and human disease. , 2001, Trends in molecular medicine.

[20]  Rachael P. Huntley,et al.  The GOA database in 2009—an integrated Gene Ontology Annotation resource , 2008, Nucleic Acids Res..

[21]  P. Davies,et al.  Determination of peptide substrate specificity for mu-calpain by a peptide library-based approach: the importance of primed side interactions. , 2005, The Journal of biological chemistry.

[22]  Kris Gevaert,et al.  SitePredicting the cleavage of proteinase substrates. , 2009, Trends in biochemical sciences.

[23]  D. Rubinsztein,et al.  Novel targets for Huntington's disease in an mTOR-independent autophagy pathway. , 2008, Nature chemical biology.

[24]  S. Jordt,et al.  Chronic exposure to paclitaxel diminishes phosphoinositide signaling by calpain-mediated neuronal calcium sensor-1 degradation , 2007, Proceedings of the National Academy of Sciences.

[25]  R. Schnellmann,et al.  Calpain 10: a mitochondrial calpain and its role in calcium-induced mitochondrial dysfunction. , 2006, American journal of physiology. Cell physiology.

[26]  J. Bibb,et al.  Extrasynaptic NMDA Receptors Couple Preferentially to Excitotoxicity via Calpain-Mediated Cleavage of STEP , 2009, The Journal of Neuroscience.

[27]  Jeffrey W. Smith,et al.  CutDB: a proteolytic event database , 2006, Nucleic Acids Res..

[28]  Ming Liu,et al.  Calpain in the CNS: From Synaptic Function to Neurotoxicity , 2008, Science Signaling.

[29]  P. Greer,et al.  Ubiquitous Calpains Promote Both Apoptosis and Survival Signals in Response to Different Cell Death Stimuli* , 2006, Journal of Biological Chemistry.

[30]  M. Zatz,et al.  Calpains and disease. , 2005, The New England journal of medicine.

[31]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[32]  K. Suzuki,et al.  The protease activity of a calpain-like cysteine protease in Saccharomyces cerevisiae is required for alkaline adaptation and sporulation , 1999, Molecular and General Genetics MGG.

[33]  W. Sossin,et al.  The atypical protein kinase C in Aplysia can form a protein kinase M by cleavage , 2009, Journal of neurochemistry.

[34]  D. E. Goll,et al.  The calpain system. , 2003, Physiological reviews.

[35]  Thomas Schaffner,et al.  Calpain-mediated cleavage of Atg5 switches autophagy to apoptosis , 2006, Nature Cell Biology.