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Exercises Proteomics III

Exercises Proteomics III. Exercise 1 T he Phosphosite Plus datatabase contains a large amount of data from various modification-proteomics studies . Start with some simple operations :

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Exercises Proteomics III

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  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?

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