Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data.

Biology Direct
Regev Schweiger, Michal Linial

Abstract

Phosphorylation is the most prevalent post-translational modification on eukaryotic proteins. Multisite phosphorylation enables a specific combination of phosphosites to determine the speed, specificity and duration of biological response. Until recent years, the lack of high quality data limited the possibility for analyzing the properties of phosphorylation at the proteome scale and in the context of a wide range of conditions. Thanks to advances of mass spectrometry technologies, thousands of phosphosites from in-vivo experiments were identified and archived in the public domain. Such resource is appropriate to derive an unbiased view on the phosphosites properties in eukaryotes and on their functional relevance. We present statistically rigorous tests on the spatial and functional properties of a collection of approximately 70,000 reported phosphosites. We show that the distribution of phosphosites positioning along the protein tends to occur as dense clusters of Serine/Threonines (pS/pT) and between Serine/Threonines and Tyrosines, but generally not as much between Tyrosines (pY) only. This phenomenon is more ubiquitous than anticipated and is pertinent for most eukaryotic proteins: for proteins with > or = 2 phosphosites,...Continue Reading

References

Jan 1, 1987·Annual Review of Biochemistry·A M EdelmanE G Krebs
Jan 1, 1985·Annual Review of Biochemistry·T Hunter, J A Cooper
Jan 1, 1987·Annual Review of Neuroscience·J H Schwartz, S M Greenberg
Jan 1, 1974·Biochimie·K GibsonJ Kruh
Nov 13, 1998·Science·M H CardoneJ C Reed
Jun 27, 2000·Bioinformatics·L J McGuffinD T Jones
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
May 15, 2002·Trends in Biotechnology·Matthias MannAkhilesh Pandey
Aug 31, 2002·Nucleic Acids Research·Vasily RamenskyShamil Sunyaev
Dec 10, 2002·Science·G ManningS Sudarsanam
Mar 1, 2003·Nature Biotechnology·Matthias Mann, Ole N Jensen
Mar 27, 2004·Bioinformatics·Jonathan J WardDavid T Jones
Dec 21, 2004·Nucleic Acids Research·Amos BairochLai-Su L Yeh
Dec 21, 2004·Nucleic Acids Research·U GüldenerH W Mewes
Dec 21, 2004·Nucleic Acids Research·Rachel A DrysdaleUNKNOWN FlyBase Consortium
Oct 1, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jeremy Gunawardena
Dec 31, 2005·Nucleic Acids Research·Cathy H WuBaris Suzek
Aug 16, 2006·Trends in Genetics : TIG·Jason Ptacek, Michael Snyder
Nov 10, 2006·Methods in Molecular Biology·Maria V Turkina, Alexander V Vener
Jan 24, 2007·Proceedings of the National Academy of Sciences of the United States of America·Judit VillénSteven P Gygi
Jun 16, 2007·Cell·Rune LindingTony Pawson
Jun 23, 2007·Nature Reviews. Molecular Cell Biology·Jeffrey A Ubersax, James E Ferrell
Jul 24, 2007·Cellular Signalling·Parag Patwardhan, W Todd Miller
Aug 2, 2007·PloS One·Emmanuel J ChangTerry Gaasterland
Aug 19, 2007·Proteomics·Mark O CollinsJyoti S Choudhary
Oct 27, 2007·Nucleic Acids Research·Francesca DiellaToby J Gibson
Nov 6, 2007·Proceedings of the National Academy of Sciences of the United States of America·Alan M MosesRichard Durbin
Nov 28, 2007·Nucleic Acids Research·Robert D FinnAlex Bateman
Mar 18, 2008·Molecular Cell·Daniel Y L MaoFrank Sicheri
Aug 2, 2008·Proceedings of the National Academy of Sciences of the United States of America·Noah DephoureSteven P Gygi
Sep 27, 2008·Bioinformatics·L HolmA Schenkel

❮ Previous
Next ❯

Citations

Jan 31, 2012·Molecular & Cellular Proteomics : MCP·Grigoris D AmoutziasStephen G Oliver
May 31, 2012·Molecular & Cellular Proteomics : MCP·Jonathan C TrinidadAlma L Burlingame
Jun 28, 2011·Science·Jamie M KeckMark Winey
Feb 11, 2011·Biology Direct·Yerbol Z KurmangaliyevMikhail S Gelfand
Jan 18, 2013·PLoS Computational Biology·Stefka TyanovaDmitrij Frishman
Mar 19, 2013·PLoS Computational Biology·Jonathan WoodsmithUlrich Stelzl
Feb 25, 2014·Journal of Proteomics·Alistair V G EdwardsMartin R Larsen
Apr 8, 2014·Database : the Journal of Biological Databases and Curation·Jing LiLu Xie
Dec 3, 2014·Journal of Molecular Biology·Hafumi NishiAnna R Panchenko
Dec 3, 2014·Journal of Proteomics·Nicole St-DenisDavid W Litchfield
Jun 6, 2014·Chemical Reviews·Francois-Xavier TheilletPhilipp Selenko
Nov 10, 2015·Nature Structural & Molecular Biology·Michael J BegleyLewis C Cantley
Dec 25, 2013·Molecular Systems Biology·Pedro BeltraoVera van Noort
Oct 28, 2011·Cell Cycle·Michele H JonesMark Winey
Dec 14, 2011·Structure·Hafumi NishiAnna R Panchenko
Aug 8, 2014·Frontiers in Genetics·Christian R LandryAlan M Moses
Aug 26, 2014·Frontiers in Genetics·Hafumi NishiAnna R Panchenko
Nov 26, 2015·BioMed Research International·Heming YaoMinghui Wang
Oct 4, 2013·Journal of Proteome Research·Mao PengBas van Breukelen
Jan 4, 2017·Nature Communications·Veronika CsizmokJulie D Forman-Kay
Mar 23, 2017·GigaScience·Panayotis VlastaridisGrigoris D Amoutzias
May 2, 2017·PLoS Computational Biology·Ying LiTingting Li
May 17, 2014·Molecular & Cellular Proteomics : MCP·Antonio PalmeriPier Federico Gherardini
Feb 17, 2018·Molecular & Cellular Proteomics : MCP·Clement M PotelSimone Lemeer
Nov 3, 2017·The Analyst·Justine V ArringtonW Andy Tao
Jun 25, 2019·PLoS Biology·David Bradley, Pedro Beltrao
Nov 15, 2019·Protein Science : a Publication of the Protein Society·Ryotaro KoikeMotonori Ota
Feb 28, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Alain Robichon
Aug 15, 2019·Bioinformatics·Hongyang Li, Yuanfang Guan
Aug 1, 2019·Nature Methods·Brian C SearleJudit Villén
Aug 28, 2019·International Journal of Molecular Sciences·Lorea VelascoArturo Muga
Jan 5, 2017·The Biochemical Journal·Ricardo Soares-Dos-ReisCarlos Reguenga

❮ Previous
Next ❯

Software Mentioned

ELM
. ELM
PSIPRED
SysPTM
Phospho
DISOPRED
DisEMBL

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.