1 / 1

Exercises Proteomics III

This exercise involves the analysis of protein modifications using the Phosphosite Plus database. Start with RNF216, examining observed PTMs, their frequency, and their relation to homology domains via InterPro. Then, compare human and murine RNF216, focusing on targets of kinases CDK2, PKA, CK2A1, and CK2A2. Additionally, dig into MS-Proteomics projects studying endothelial cell phosphorylation, identifying common stimuli and comparing datasets. Finally, investigate conserved linear motifs ITAM and ITIM, exploring their phosphorylation status and kinase specificity.

faunia
Télécharger la présentation

Exercises Proteomics III

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. ExercisesProteomicsIII Exercise 1 The Phosphosite Plus datatabasecontains a large amountofdatafromvariousmodification-proteomicsstudies. Start withsome simple operations: I am currentlyworking on a proteincalled RNF216. Which PTMs of RNF216 havebeenobserved, andwhichoneshavebeenseen multiple times? Consideronlythe PTMs seenat least 5 times: howdoesthemodifiedposition in thesequencerelatetohomologydomains (askInterpro). Comparethesituationof human andmurine RNF216. Have a lookatthetargetsofprotein kinases CDK2, PKA, CK2A1 and CK2A2. Comparethesequencelogos. Exercise 2 UsePhosphosite Plus tosearchfor MS-Proteomicsprojectsthatstudy phosphorylation in endothelialcelllines. What was themostfrequentlyusedstimulus in thesestudies? Select two different studiesandcomparethelistofidentified phosphorylation targets. Create a VENN diagramofthetwoprojects (on theproteinlevel - duplicatesremoved). Howbigistheoverlapofthetwodatasets? Whatoverlapwouldhavebeenexpected in a randomizedsituation, assuming 20.000 detectableproteins? Exercise3 Therearetwoeukarotic linear motifswith a conserved Tyr-phosphorylation sitecalled 'ITAM' and 'ITIM'. Searchtheinternet, theliterature, or a suitable linear motifdatabasefor a definitionofthesetwomotifs, includingtheconservationpatternandsomeexampleproteinsthatcontainthesemotifs. Whatdoestheabbreviationofthemotifnamesmean? Usetheseexampleproteinstoquerythephosphosite plus database. Is theconserved Tyr residuereportedasbeing phosphorylated? Itisreportedwhichprotein kinase(s) is/areresponsible? SearchPhosphositeforthetargetspecificityofthese kinases. Look atthesequencelogos. Doesone (ormore) ofthe kinase preferencesexplainthe ITAM and ITIM conservationpattern? If so, whichone? If not, couldyouspeculateabout alternative reasonsfor ITAM/ITIM conservation?

More Related