PXD002532

PXD002532 is an original dataset announced via ProteomeXchange.

Title	Proteomic QSAR analysis of calpain substrate specificity
Description	Calpains are intracellular Ca2+-regulated cysteine proteases that are essential for various cellular functions. Mammalian conventional calpains (calpain-1 and calpain-2) modulate the structure and function of their substrates by limited proteolysis; however, their substrate specificity remains unclear because the amino acid (aa) sequences around their cleavage sites are very diverse. To clarify calpains’ substrate specificities, 84 20-mer oligopeptides, corresponding to P10-P10’ of reported cleavage site sequences, were proteolyzed by calpains, and the catalytic efficiencies (kcat/Km) were globally determined by LC/MS. This analysis revealed 483 cleavage site sequences, including 360 novel ones. The kcat/Kms for 119 sites ranged from 12.5~1,710 M-1s-1. Most sites were cleaved by both calpain-1 and -2 with a similar kcat/Km. The aa compositions of the novel sites were not significantly different from the 420 previously reported sites, suggesting calpains have a strict implicit rule for sequence specificity, and that the limited proteolysis of intact substrates is due to the substrates’ higher-order structures. Cleavage position frequencies indicated that longer sequences N-terminal to the cleavage site (P-sites) than C-terminal (P’-sites) were preferred for proteolysis. Quantitative structure-activity relationship (QSAR) analyses using partial least-squares regression and >1,300 aa descriptors achieved kcat/Km prediction with r=0.834, and binary-QSAR modeling attained 64.8% prediction accuracy for 132 reported calpain cleavage sites independent of our model construction. These results outperformed previous calpain cleavage predictors, and revealed the importance of the P2, P3’, P4’, and P1-P2 contexts. This study increases our understanding of calpain substrate specificities, and opens calpains to “next-generation,” i.e., activity-related quantitative and context-dependent analyses.
HostingRepository	PRIDE
AnnounceDate	2016-07-19
AnnouncementXML	Submission_2016-07-19_04:17:58.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hiroyuki Sorimachi
SpeciesList	scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Oryctolagus cuniculus algirus; NCBI TaxID: 230741; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Ovis aries (Sheep); NCBI TaxID: 9940; scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031;
ModificationList	iTRAQ8plex-116 reporter+balance reagent acylated residue; acetylated residue
Instrument	4800 Proteomics Analyzer; QSTAR

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-13 07:40:04	ID requested
⏵ 1	2016-07-19 04:17:59	announced

Shinkai-Ouchi F, Koyama S, Ono Y, Hata S, Ojima K, Shindo M, duVerle D, Ueno M, Kitamura F, Doi N, Takigawa I, Mamitsuka H, Sorimachi H, Predictions of Cleavability of Calpain Proteolysis by Quantitative Structure-Activity Relationship Analysis Using Newly Determined Cleavage Sites and Catalytic Efficiencies of an Oligopeptide Array. Mol Cell Proteomics, 15(4):1262-80(2016) [pubmed]

curator keyword: Biological

submitter keyword: calpain, substrate specificity, QSAR, PLS

Hiroyuki Sorimachi
contact affiliation	Calpain Project Department of Advanced Science for Biomolecules Igakuken (Tokyo Metropolitan Institute of Medical Science) 2-1-6 Kamikitazawa, Setagaya-ku Tokyo 156-8506, Japan
contact email	sorimachi-hr@igakuken.or.jp
lab head
Hiroyuki Sorimachi
contact affiliation	Tokyo Metropolitan Institute of Medical Science (Igakuken)
contact email	sorimachi-hr@igakuken.or.jp
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002532
     1. Label: PRIDE project
     2. Name: Proteomic QSAR analysis of calpain substrate specificity