PMAP: databases for analyzing proteolytic events and pathways

Igarashi, Yoshinobu; Heureux, Emily; Doctor, Kutbuddin S.; Talwar, Priti; Gramatikova, Svetlana; Gramatikoff, Kosi; Zhang, Ying; Blinov, Michael L.; Ibragimova, S. S.; Boyd, Sarah; Ratnikov, Boris I.; Cieplak, Piotr; Godzik, Adam; Smith, Jeffrey W.; Osterman, Andrei L.; Eroshkin, Alexey

doi:10.1093/nar/gkn683

Cited by 56 publications

(33 citation statements)

References 29 publications

(26 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In general, less than 3% of aspartic acid cleavage sites are detected in the absence of exogenous caspase, suggesting little caspase activation. Several small-scale studies have previously identified a total of 37 and 68 substrates for caspase-2 and caspase-6, respectively (11,22,23). More than half of the previously reported caspase-2 substrates were found in our dataset (19 of the 37), and we identified 13 of 61 caspase-6 substrates reported in the CutDB database (cutdb.burnham.org/).…”

Section: Resultsmentioning

confidence: 58%

Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles

Julien

Zhuang

Wiita

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

111

106

View full text Add to dashboard Cite

Proteases constitute the largest enzyme family, yet their biological roles are obscured by our rudimentary understanding of their cellular substrates. There are 12 human caspases that play crucial roles in inflammation and cell differentiation and drive the terminal stages of cell death. Recent N-terminomics technologies have begun to enumerate the diverse substrates individual caspases can cleave in complex cell lysates. It is clear that many caspases have shared substrates; however, few data exist about the catalytic efficiencies (k cat /K M ) of these substrates, which is critical to understanding their true substrate preferences. In this study, we use quantitative MS to determine the catalytic efficiencies for hundreds of natural protease substrates in cellular lysate for two understudied members: caspase-2 and caspase-6. Most substrates are new, and the cleavage rates vary up to 500-fold. We compare the cleavage rates for common substrates with those found for caspase-3, caspase-7, and caspase-8, involved in apoptosis. There is little correlation in catalytic efficiencies among the five caspases, suggesting each has a unique set of preferred substrates, and thus more specialized roles than previously understood. We synthesized peptide substrates on the basis of protein cleavage sites and found similar catalytic efficiencies between the protein and peptide substrates. These data suggest the rates of proteolysis are dominated more by local primary sequence, and less by the tertiary protein fold. Our studies highlight that global quantitative rate analysis for posttranslational modification enzymes in complex milieus for native substrates is critical to better define their functions and relative sequence of events.N-terminomics | caspase | proteolysis | proteomics | apoptosis C aspases are cysteine-class proteases that typically cleave after aspartic acid and play critical roles in cellular remodeling during development, cell differentiation, inflammation, and cell death (reviewed in refs. 1-3). There are 12 caspases in humans alone, which have been classically grouped on the basis of sequence homology, domain architecture, and cell biology as inflammatory (caspase-1, caspase-4, caspase-5, and caspase-11), apoptotic initiators (caspase-2, caspase-8, caspase-9, and caspase-10), or executioners (caspase-3, caspase-6, and caspase-7) (4, 5). Identifying the natural protein substrates for caspases can provide important insights into their cellular roles. A series of large-scale proteomic studies from several laboratories has collectively identified nearly 2,000 native proteins cleaved after an aspartic acid during apoptosis of human cells (recently reviewed in refs. 6-8). By adding individual caspases to extracts, it has been possible to begin to identify caspasespecific substrates, ranging from just a few, in the case of caspase-4, caspase-5, and caspase-9 (9), to several hundred for caspase-1, caspase-3, caspase-7, and caspase-8 (10, 11). Some of these substrates overlap, but others are unique to specific caspase...

show abstract

Section: Resultsmentioning

confidence: 58%

Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles

Julien

Zhuang

Wiita

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

111

106

View full text Add to dashboard Cite

show abstract

“…Consensus Disorder Prediction [34] discriminated ordered and disordered regions in the sequence (Fig. 5 and Fig.…”

Section: Resultsmentioning

confidence: 97%

Protective Epitopes of the Plasmodium falciparum SERA5 Malaria Vaccine Reside in Intrinsically Unstructured N-Terminal Repetitive Sequences

et al. 2014

View full text Add to dashboard Cite

The malaria vaccine candidate antigen, SE36, is based on the N-terminal 47 kDa domain of Plasmodium falciparum serine repeat antigen 5 (SERA5). In epidemiological studies, we have previously shown the inhibitory effects of SE36 specific antibodies on in vitro parasite growth and the negative correlation between antibody level and malaria symptoms. A phase 1 b trial of the BK-SE36 vaccine in Uganda elicited 72% protective efficacy against symptomatic malaria in children aged 6–20 years during the follow-up period 130–365 days post–second vaccination. Here, we performed epitope mapping with synthetic peptides covering the whole sequence of SE36 to identify and map dominant epitopes in Ugandan adult serum presumed to have clinical immunity to P. falciparum malaria. High titer sera from the Ugandan adults predominantly reacted with peptides corresponding to two successive N-terminal regions of SERA5 containing octamer repeats and serine rich sequences, regions of SERA5 that were previously reported to have limited polymorphism. Affinity purified antibodies specifically recognizing the octamer repeats and serine rich sequences exhibited a high antibody-dependent cellular inhibition (ADCI) activity that inhibited parasite growth. Furthermore, protein structure predictions and structural analysis of SE36 using spectroscopic methods indicated that N-terminal regions possessing inhibitory epitopes are intrinsically unstructured. Collectively, these results suggest that strict tertiary structure of SE36 epitopes is not required to elicit protective antibodies in naturally immune Ugandan adults.

show abstract

“…Each entry contains a proteolytic event relating a protease, a substrate, and a cleavage site and a description of the biological context. CutDB is part of the larger PMAP website, which also contains protease and substrate databases and tools for determining protease specificities and mapping signaling pathways (73). The termini-oriented protein function inferred database (TopFIND) is also open to user contributions (74).…”

Section: Methods For Enriching Protein N Termini-n-terminalmentioning

confidence: 99%

Proteolytic Post-translational Modification of Proteins: Proteomic Tools and Methodology

Rogers

Overall²

2013

Molecular & Cellular Proteomics

141

View full text Add to dashboard Cite

Proteolytic processing is a ubiquitous and irreversible post-translational modification involving limited and highly specific hydrolysis of peptide and isopeptide bonds of a protein by a protease. Cleavage generates shorter protein chains displaying neo-N and -C termini, often with new or modified biological activities. Within the past decade, degradomics and terminomics have emerged as significant proteomics subfields dedicated to characterizing proteolysis products as well as natural protein N and C termini. Here we provide an overview of contemporary proteomics-based methods, including specific quantitation, data analysis, and curation considerations, and highlight exciting new and emerging applications within these fields enabling in vivo analysis of proteolytic events. Proteolysis involves the breakdown of proteins into smaller polypeptides or amino acids through the hydrolysis of peptide bonds by a protease. This represents a remarkably significant, but often underappreciated, post-translational modification (PTM) 1 in that is it irreversible yet also ubiquitous. Consequently, the functional sequence of a protein can very rarely be predicted from its transcript, as proteolysis products form new (neo-) N and C termini. These cleavage events, or proteolytic processing events, can result in activation, inactivation, completely altered protein function, and even excision of "neo-proteins" with growth factor activity from an extracellular matrix parent molecule, and they regulate a vast array of biological processes (1). These include DNA replication, cell cycle progression, cell proliferation, and cell death, as well as pathological processes such as inflammation, cancer, arthritis, and cardiovascular disease. For example, in protein synthesis and maturation, precise selective removal of the N-terminal methionine and the signal peptide is essential for correct protein maturation and secretion. In some proteins, scission of the chain forms a molecule with four termini when linked by disulfide bridges. Through the removal of signal, nuclear, and mitochondrial localization sequences and ectodomain shedding, proteases regulate protein localization, and in viral infection, via cleavage of pre-and pro-domains and polyprotein processing, inactive proteins are converted into their active form(s), are inactivated, or change receptor-binding affinity. Thus, proteolysis is involved in much more than the mere degradation and turnover of proteins, important though these processes are in homeostasis.Proteases exist in all orders of life and constitute one of the largest enzyme families in humans (2), and more than 30 drugs targeting these enzymes are currently approved for clinical use (3). However, in order to fully comprehend the cellular function(s) of a given protease, one must have knowledge of the proteins processed by that protease, as well as the functions of these substrates and specific processing events. This is currently far from the case, as half of all human proteases have no known substrates (4). Degradomic...

show abstract

PMAP: databases for analyzing proteolytic events and pathways

Cited by 56 publications

References 29 publications

Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles

Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles

Protective Epitopes of the Plasmodium falciparum SERA5 Malaria Vaccine Reside in Intrinsically Unstructured N-Terminal Repetitive Sequences

Proteolytic Post-translational Modification of Proteins: Proteomic Tools and Methodology

Contact Info

Product

Resources

About