PubMed

Identification of phosphorylation sites in glycine N-met  
2006 Apr - Protein science : a publication of the Protein Society
Luka Z, Ham AJ, Norris JL, Yeo EJ, Yermalitsky V, Glenn B, Caprioli RM, Liebler DC, Wagner C
Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
Previous studies have shown that rat glycine N-methyltransferase (GNMT) is phosphorylated in vivo, and could be phosphorylated in vitro on serine residues with a significant increase of enzyme activity, but no phosphorylation sites were identified. In this work the identification of the...

Glycine reductase mechanism.  
2004 Oct - Current opinion in chemical biology
Andreesen JR
Institut für Mikrobiologie der Universität Halle, Kurt-Mothes-Str. 3, 06120 Halle, Germany. j.andreesen@mikrobiologie.uni-halle.de
The ability of some anaerobic bacteria to conserve energy via a soluble substrate level phosphorylation system by reducing glycine to acetyl-phosphate has been an intriguing mechanism for about half a century. The genes implicated in this system have been sequenced and form an operon structure...

Prediction of phosphorylation sites using SVMs.  
2004 Nov 22 - Bioinformatics (Oxford, England)
Kim JH, Lee J, Oh B, Kimm K, Koh I
National Genome Research Institute, 5 Nokbun-Dong, Eunpyung-Gu, Seoul, 122-701 Korea. jh7521@ngri.re.kr
MOTIVATION: Phosphorylation is involved in diverse signal transduction pathways. By predicting phosphorylation sites and their kinases from primary protein sequences, we can obtain much valuable information that can form the basis for further research. Using support vector machines, we...

GPS: a comprehensive www server for phosphorylatio  
2005 Jul 1 - Nucleic acids research
Xue Y, Zhou F, Zhu M, Ahmed K, Chen G, Yao X
School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, PR China.
... the data set; here, we present a comprehensive PK-specific prediction server GPS, which could predict kinase-specific phosphorylation sites from protein primary sequences for 71 different PK groups. GPS has been implemented in PHP and is available on a www server at http://973-proteinweb.ustc.edu.cn/gps/gps_web/.

Highly specific prediction of phosphorylation sites in pr  
2004 Dec 12 - Bioinformatics (Oxford, England)
Koenig M, Grabe N
CeVis, University of Bremen, Universitaetsallee 29, 28359 Bremen, Germany. koenig@cevis.uni-bremen.de
... functional protein sequences has inherent problems. In predicting phosphorylation sites, problems came from the shortness of phosphorylation sites, the difficulties in maintaining many different predefined models of binding sites, and the difficulties of obtaining highly sensitive predictions...

Phosphopeptide mapping and identification of phosph  
2001 May - Current protocols in protein science / editorial board, John E. Coligan ... [et al.]
Meisenhelder J, Hunter T, van der Geer P
The Salk Institute for Biological Studies, La Jolla, California, USA.
... analyzed by HPLC and mass spectrometry or peptide microsequencing. Such mapping gives information about the number of phosphorylation sites present in the protein, and can also be used to find out if sites of phosphorylation on a protein change upon treatment of cells with specific agents.

A support vector machine approach to the identificatio  
- Cellular & molecular biology letters
Plewczyński D, Tkacz A, Godzik A, Rychlewski L
BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznań, Poland. darman@bioinfo.pl
We describe a bioinformatics tool that can be used to predict the position of phosphorylation sites in proteins based only on sequence information. The method uses the support vector machine (SVM) statistical learning theory. The statistical models for phosphorylation by various types...

GPS: a comprehensive www server for phosphorylatio  
2005 Jul 1 - Nucleic acids research
Xue Y, Zhou F, Zhu M, Ahmed K, Chen G, Yao X
School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, PR China.
... fundamental role in most of the cellular regulatory pathways. Experimental identification of protein kinases' (PKs) substrates with their phosphorylation sites is labor-intensive and often limited by the availability and optimization of enzymatic reactions. Recently, large-scale analysis...

Scoring of predicted GRK2 phosphorylation sites in N  
2006 Sep 15 - Bioinformatics (Oxford, England)
Arthur JW, Sanchez-Perez A, Cook DI
Department of Medicine, University of Sydney Sydney, Australia. jarthur@med.usyd.edu.au
... Pharmacol., 61, 707-709]. Additional findings in our lab pointed towards a possible role for GRK2 in the phosphorylation and inactivation of Nedd4-2. RESULTS: We have predicted GRK2 phosphorylation sites on Nedd4-2 by combining sequence analysis, homology modeling and surface accessibility calculations....

Identification of a novel phosphorylation site in ataxin-  
2005 May 15 - Biochimica et biophysica acta
Vierra-Green CA, Orr HT, Zoghbi HY, Ferrington DA
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St. Minneapolis, MN 55455, USA.
However, mutation of the site serine 776 to an alanine did not abolish all phosphorylation of the protein ataxin-1, suggesting the presence of additional phosphorylation sites [E.S. Emiamian, M.D. Kaytor, L.A. Duvick, T. Zu, S.K. Tousey, H.Y. Zoghbi, H.B. Clark, H.T. Orr, Serine 776 of...

NetPhosYeast: prediction of protein phosphorylation s  
2007 Apr 1 - Bioinformatics (Oxford, England)
Ingrell CR, Miller ML, Jensen ON, Blom N
University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
We here present a neural network-based method for the prediction of protein phosphorylation sites in yeast--an important model organism for basic research. Existing protein phosphorylation site predictors are primarily based on mammalian data and show reduced sensitivity on yeast phosphorylation...

Gain and loss of phosphorylation sites in human canc  
2008 Aug 15 - Bioinformatics (Oxford, England)
Radivojac P, Baenziger PH, Kann MG, Mort ME, Hahn MW, Mooney SD
School of Informatics, Indiana University, 901 East Tenth Street, Bloomington, IN 47408, USA.
... mutations, those in kinase genes represent the most enriched set of mutations that disrupt phosphorylation sites, suggesting phosphorylation target site mutation is an active cause of phosphorylation deregulation. Overall, this evidence suggests both gain and loss of a phosphorylation site...

Multiple reaction monitoring to identify sites of protein  
2005 Aug - Molecular & cellular proteomics : MCP
Unwin RD, Griffiths JR, Leverentz MK, Grallert A, Hagan IM, Whetton AD
Faculty of Medical and Human Sciences, University of Manchester, United Kingdom.
Phosphorylation sites on these proteins were located. The technique, which we have called multiple reaction monitoring-initiated detection and sequencing (MIDAS), is shown to be a highly sensitive approach to the determination of protein phosphorylation.

The importance of intrinsic disorder for protein phosph  
2004 Feb 11 - Nucleic acids research
Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK
School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA.
... the high variability of amino acid residues flanking a relatively limited number of experimentally identified phosphorylation sites, reliable prediction of such sites still remains an important issue. Here we report the development of a new web-based tool for the prediction of protein...

Regulation of human methylenetetrahydrofolate reduc  
2005 Jul 26 - Proceedings of the National Academy of Sciences of the United States of America
Yamada K, Strahler JR, Andrews PC, Matthews RG
Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA. yamadak@umich.edu
... alkaline phosphatase removes seven phosphoryl groups from the enzyme. Thr-34 was identified as one of the seven phosphorylation sites by using a monoclonal antibody directed toward pThr-Pro. Mutation of Thr-34 to Ala completely blocks modification as judged by mass spectrometric analysis,...

Analysis of protein phosphorylation by mass spectrom  
2005 Mar - Methods (San Diego, Calif.)
Garcia BA, Shabanowitz J, Hunt DF
Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
... regulating cell signaling and ultimately function of biological systems. Detection of phosphopeptides and localization of phosphorylation sites remains quite a challenge, even if the protein is purified to near homogeneity. Mass spectrometry has become a vital technique that is routinely...

PERspective on PER phosphorylation.  
2008 Jul 1 - Genes & development
Blau J
Department of Biology, New York University, New York, New York 10003, USA. justin.blau@nyu.edu
... relevant sites have been difficult to identify in spite of knowing the relevant kinase. In this issue of Genes & Development, Chiu and colleagues (1758-1772) identify a key phosphorylation site on PER that recruits the F-box protein Slimb to trigger PER degradation and set clock speed.

MSK1 activity is controlled by multiple phosphorylatio  
2005 Apr 15 - The Biochemical journal
McCoy CE, Campbell DG, Deak M, Bloomberg GB, Arthur JS
MRC Protein Phosphorylation Unit, Faculty of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
... these sites, the N-terminal T-loop residue Ser-212 and the 'hydrophobic motif' Ser-376 are phosphorylated by the C-terminal kinase domain of MSK1, and their phosphorylation is essential for the catalytic activity of the N-terminal kinase domain of MSK1 and therefore for the phosphorylation...

Gain and loss of phosphorylation sites in human canc  
2008 Aug 15 - Bioinformatics (Oxford, England)
Radivojac P, Baenziger PH, Kann MG, Mort ME, Hahn MW, Mooney SD
School of Informatics, Indiana University, 901 East Tenth Street, Bloomington, IN 47408, USA.
... and contribution these variants make to a clinical phenotype is a formidable problem. RESULTS: In this study, we investigate the role of phosphorylation in somatic cancer mutations and inherited diseases. Somatic cancer mutation datasets were shown to have a significant enrichment for mutations...

Charge environments around phosphorylation sites in  
2008 Mar 25 - BMC structural biology
Kitchen J, Saunders RE, Warwicker J
Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK. j.kitchen@student.manchester.ac.uk
BACKGROUND: Phosphorylation is a central feature in many biological processes. Structural analyses have identified the importance of charge-charge interactions, for example mediating phosphorylation-driven allosteric change and protein binding to phosphopeptides. Here, we examine computationally...