What we know is that the proteins get acetylated at lysine moiety. But looking into the structure, we got around more than one lysine moiety. Then how it can be possible to find out which lysine moiety has the most possibility to get acetylated.
Do we have any bioinformatic tool to search out the lysine moiety?
Hi!
I'm really not an expert in this field, but you can explore PTMs by mass spectrometry. For acetylated lysine maybe database supported analysis of MS/MS-Fragmentation patterns works?
cheers
Mass spectrometry would be the easiest. In some cases you might be able to use radioactive metabolic labelling. For example if you had a purified system with an acetylase enzyme and a protein of interest you could acetylate with 3H-acetyl-CoA, perform some sort of separation step, proteolyse the protein, and then look for radioactivity associated with band patterns to determine likely modification sites.
If you have a particular protein that you wish to determine then MS/MS fragmentation is a good tool.
If you are asking if there are any predictive methods for determining post translational modifications then I think the answer is no. However selectivity is probably structurally dependent, you could look at the local surface microenvironment around each lysine to determine accessibility and relative nucleophilicity.
You could also run an analysis on this database to determine any predictable structural motifs and potentially develop your own bioinformatic tool.
http://cplm.biocuckoo.org/
Hi check out these papers published by our group where we did acetylation using mass spectrometry and also westerns using an antilysine antibody
Article The Fasted/Fed Mouse Metabolic Acetylome: N6-Acetylation Dif...
Article Peripheral Effects of FAAH Deficiency on Fuel and Energy Hom...
Actually I am interested to know about the use of Computational Studies to find out that lysine moiety
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