For publication of results, please cite the following article:
Calpains constitute an important family of the
Ca2+-dependent cysteine proteases, which contain a nucleophilic cysteine
in the catalytically active site (Goll et al
, 2003
; Franco et al
, 2005
;
Zatz et al
, 2005
; Liu et al
, 2008
). Calpains are widely expressed in mammalians and conserved across eukaryotes (Futai et al
, 2001
; Croall et al
, 2007
).
For instance, in budding yeast, at least one calpain-like protease,
Rim13/Cpl1, has been identified, although its functions are still
elusive (Hayashi et al
, 2001
).
In humans, there are over 14 distinct members of the calpain
superfamily, some of which are tissue specific. Calpain 1 (μ-calpain,
micromolar Ca2+-requiring) and Calpain 2 (m-calpain, millimolar
Ca2+-requiring) are ubiquitously expressed and well characterized
isoforms (Huang et al
, 2005
). Through spatial and temporal cleavage of a variety of substrates to change their conformation, function and stability (Glading et al
, 2002
),
Ca2+-activated calpains play an important role in numerous biological
processes, including the regulation of gene expression, signal
transduction, cell death/apoptosis, remodeling cytoskeletal attachments
during cell fusion/motility and cell cycle progression (Squier et al
, 1999
; Tan et al
, 2006
; Yousefi et al
, 2006
). Moreover, calpain aberrancies are frequently implicated in a variety of diseases and cancers (Arrington et al
, 2006
; Williams et al
, 2008
).
Although many studies have tried to dissect the regulatory roles and
molecular mechanisms of calpain-dependent cleavage, in fact our
understanding of calpain is still fragmentary.
In this work, we collected 368
experimentally verified calpain cleavage sites in 130
proteins. With a previously developed algorithm of GPS
(Group-based Prediction System)(Xue et al
, 2008
),
we developed a novel software package of GPS-CCD (Calpain Cleavage
Detector) for the prediction of calpain cleavage sites. The
leave-one-out validation and 4-, 6-, 8-, 10-fold cross-validations were
performed to evaluate the performance of the prediction system. By
comparison, the GPS 2.0
algorithm was employed for its outstanding prediction performance, with an accuracy 89.98%
, sensitivity 60.87%
and specificity 90.07%
.
Furthermore, there are many proteins experimentally identified as
calpain substrates for which the exact cleavage sites have not been
verified, and we collected 196 such proteins from PubMed. As an
application, we predicted potential calpain cleavage sites for these
targets. These prediction results might be a useful resource for
further experimental investigation. Finally, the online service and
local packages of GPS-CCD
1.0 were implemented in JAVA 1.5 (J2SE 5.0) and are freely available for academic researchers at: http://ccd.biocuckoo.org/
.
GPS-CCD
1.0 User Interface
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