Proteome-wide analysis of protein carboxy termini: C terminomics

Schilling, Oliver; Barré, Olivier; Huesgen, Pitter F.; Overall, Christopher M.

doi:10.1038/nmeth.1467

Cited by 140 publications

(181 citation statements)

References 24 publications

Supporting

Mentioning

175

Contrasting

Order By: Relevance

“…Two methods currently exist for proteomic analysis of protein C termini: C-terminal amine-based isotope labeling of substrates (C-TAILS), and COFRADIC combined with strong cation exchange chromatography (54,55) (Table I). During C-TAILS, proteins are dimethylated at ␣-and -amines (Fig.…”

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

140

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

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

140

View full text Add to dashboard Cite

show abstract

“…Owing to the continuous propagation of MS-based proteomics throughout life sciences, there has been a tremendous development of approaches to analyze proteins, 35 their abundances, 36,37 their interaction partners, 38,39 their mature N and C termini, 40,41 as well as their PTM patterns. 10 Although several of these MS-based techniques have been used to deepen our understanding of human platelets (Figure 1), we are only beginning to exploit the range of possibilities, which is far beyond the mere identification of the most abundant proteins.…”

Section: Current State Of Platelet Proteomicsmentioning

confidence: 99%

What Can Proteomics Tell Us About Platelets?

Burkhart

Gambaryan

Watson

et al. 2014

Circulation Research

105

View full text Add to dashboard Cite

More than 130 years ago, it was recognized that platelets are key mediators of hemostasis. Nowadays, it is established that platelets participate in additional physiological processes and contribute to the genesis and progression of cardiovascular diseases. Recent data indicate that the platelet proteome, defined as the complete set of expressed proteins, comprises >5000 proteins and is highly similar between different healthy individuals. Owing to their anucleate nature, platelets have limited protein synthesis. By implication, in patients experiencing platelet disorders, platelet (dys)function is almost completely attributable to alterations in protein expression and dynamic differences in post-translational modifications. Modern platelet proteomics approaches can reveal (1) quantitative changes in the abundance of thousands of proteins, (2) post-translational modifications, (3) protein–protein interactions, and (4) protein localization, while requiring only small blood donations in the range of a few milliliters. Consequently, platelet proteomics will represent an invaluable tool for characterizing the fundamental processes that affect platelet homeostasis and thus determine the roles of platelets in health and disease. In this article we provide a critical overview on the achievements, the current possibilities, and the future perspectives of platelet proteomics to study patients experiencing cardiovascular, inflammatory, and bleeding disorders.

show abstract

“…6A), in the LR11 cytoplasmic tail, were not observed. Notably, C-terminal peptides are under-represented in complex proteomic samples and only recently have C terminus-centric techniques been reported (33). To circumvent these issues, the Group-based Prediction System (GPS) version 2.1 software, with a modified version of Group-based Phosphorylation Scoring algorithm, was used to predict potential Rho kinase phosphorylation sites in the LR11 cytoplasmic tail (34,35).…”

Section: Mutagenesis Of Lr11 Ser-2206 Reduces Lr11 Ectodomainmentioning

confidence: 99%

Rho Kinase II Phosphorylation of the Lipoprotein Receptor LR11/SORLA Alters Amyloid-β Production

Herskowitz

Seyfried

Gearing³

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

LR11, also known as SorLA, is a mosaic low-density lipoprotein receptor that exerts multiple influences on Alzheimer disease susceptibility. LR11 interacts with the amyloid-␤ precursor protein (APP) and regulates APP traffic and processing to amyloid-␤ peptide (A␤). The functional domains of LR11 suggest that it can act as a cell surface receptor and as an intracellular sorting receptor for trans-Golgi network to endosome traffic. We show that LR11 over-expressed in HEK293 cells is radiolabeled following incubation of cells with [ 32 P i ]orthophosphate. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used to discover putative LR11 interacting kinases. Rho-associated coiled-coil containing protein kinase (ROCK) 2 was identified as a binding partner and a candidate kinase acting on LR11. LR11 and ROCK2 co-immunoprecipitate from post-mortem human brain tissue and drug inhibition of ROCK activity reduces LR11 phosphorylation in vivo. Targeted knockdown of ROCK2 with siRNA decreased LR11 ectodomain shedding while simultaneously increasing intracellular LR11 protein level. Site-directed mutagenesis of serine 2206 in the LR11 cytoplasmic tail reduced LR11 shedding, decreased LR11 phosphorylation in vitro, and abrogated LR11 mediated A␤ reduction. These findings provide direct evidence that LR11 is phosphorylated in vivo and indicate that ROCK2 phosphorylation of LR11 may enhance LR11 mediated processing of APP and amyloid production.

show abstract

Proteome-wide analysis of protein carboxy termini: C terminomics

Cited by 140 publications

References 24 publications

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

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

What Can Proteomics Tell Us About Platelets?

Rho Kinase II Phosphorylation of the Lipoprotein Receptor LR11/SORLA Alters Amyloid-β Production

Contact Info

Product

Resources

About