Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database

Khoury, George; Baliban, Richard C.; Floudas, Christodoulos A.

doi:10.1038/srep00090

Cited by 784 publications

(669 citation statements)

References 18 publications

Supporting

Mentioning

663

Contrasting

Unclassified

Order By: Relevance

“…Furthermore, the diversity in substrates is substantially increased by posttranslational modifications. Indeed, upwards of 50% of proteins are thought to be posttranslationally modified with glycosylation being one of the most abundant alterations (5). Typically, protein glycosylation constitutes glycans attached to asparagine side chains (N linked) or serine/threonine side chains (O linked).…”

mentioning

confidence: 99%

Recognition of protein-linked glycans as a determinant of peptidase activity

Noach

Ficko-Blean

Pluvinage

et al. 2017

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

137

View full text Add to dashboard Cite

The vast majority of proteins are posttranslationally altered, with the addition of covalently linked sugars (glycosylation) being one of the most abundant modifications. However, despite the hydrolysis of protein peptide bonds by peptidases being a process essential to all life on Earth, the fundamental details of how peptidases accommodate posttranslational modifications, including glycosylation, has not been addressed. Through biochemical analyses and X-ray crystallographic structures we show that to hydrolyze their substrates, three structurally related metallopeptidases require the specific recognition of O-linked glycan modifications via carbohydrate-specific subsites immediately adjacent to their peptidase catalytic machinery. The three peptidases showed selectivity for different glycans, revealing protein-specific adaptations to particular glycan modifications, yet always cleaved the peptide bond immediately preceding the glycosylated residue. This insight builds upon the paradigm of how peptidases recognize substrates and provides a molecular understanding of glycoprotein degradation.

show abstract

mentioning

confidence: 99%

Recognition of protein-linked glycans as a determinant of peptidase activity

Noach

Ficko-Blean

Pluvinage

et al. 2017

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

137

View full text Add to dashboard Cite

show abstract

“…In addition, Lys-24 of hAhR was shown to be lysine acetylated (Lundby et al, 2012). Moreover, both N-glycosylation sites and O-glycosylation sites are predicted to be present in hAhR sequence (GenBank: AAH69390.1), by using NetOGlyc 4.0 server (http://www.cbs.dtu.dk/services/ NetOGlyc/) (our unpublished work) (Khoury, et al, 2011;Chen et al, 2015). Thus, the relative high molecular weight of the AhR in HEK293T, MCF-7 or SK-N-SH at around 130 kDa may partly be explained by the possible posttranslational modifications.…”

Section: Discussionmentioning

confidence: 99%

Development and characterization of monoclonal antibodies against human aryl hydrocarbon receptor

Tian

Pei

Xie

et al. 2016

Journal of Environmental Sciences

View full text Add to dashboard Cite

Aryl hydrocarbon receptor (AhR), a ligand-dependent nuclear receptor, is involved in a diverse spectrum of biological and toxicological effects. Due to the lack of three dimensional (3D) crystal or nuclear magnetic resonance structure, the mechanisms of these complex effects of AhR remain to be unclear. Also, commercial monoclonal antibodies (mAbs) against human AhR protein (hAhR), as alternative immunological tools, are very limited. Thus, in order to provide more tools for further studies on hAhR, we prepared two mAbs (1D6 and 4A6) against hAhR. The two newly generated mAbs specifically bound to amino acids 484-508 (located in transcription activation domain) and amino acids 201-215 (located in Per-ARNT-Sim domain) of hAhR, respectively. These epitopes were new as compared with those of commercial mAbs.The mAbs were also characterized by enzyme-linked immunosorbent assay, western blot, immunoprecipitation and indirect immunofluorescence assay in different cell lines. The results showed that the two mAbs could recognize the linearized AhRs in six different human cell lines and a rat hepatoma cell line, as well as the hAhR with native conformations. We concluded that the newly generated mAbs could be employed in AhR-based bioassays for analysis of environmental contaminants, and held great potential for further revealing the spatial structure of AhR and its biological functions in future studies.

show abstract

“…Until now, there have been 72320 post-translational modifications reported experimentally in the UniProt Knowledgebase (UniProtKB), of which 49062 were phosphorylations, 5736 N-linked glycosylations and 5164 acetylations (252,260). Oxidative PTMs are included within, but do not exclusively comprise, the remaining 12,358 modifications, so it can be seen that there has been comparitively less focus on them in the proteomics field.…”

Section: Report On 10 Years Of Ptm Research (2003-2012)mentioning

confidence: 99%

Post-translational Modifications and Mass Spectrometry Detection

Silva

Vitorino

Domingues

et al. 2013

Free Radical Biology and Medicine

114

View full text Add to dashboard Cite

In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being posttranslationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry.

show abstract

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database

Cited by 784 publications

References 18 publications

Recognition of protein-linked glycans as a determinant of peptidase activity

Recognition of protein-linked glycans as a determinant of peptidase activity

Development and characterization of monoclonal antibodies against human aryl hydrocarbon receptor

Post-translational Modifications and Mass Spectrometry Detection

Contact Info

Product

Resources

About