Post Translational Modifications Puns

https://www.ncbi.nlm.nih.gov/pubmed/31577934

Softic S1, Meyer JG2, Wang GX3, Gupta MK4, Batista TM3, Lauritzen HPMM3, Fujisaka S5, Serra D6, Herrero L6, Willoughby J7, Fitzgerald K7, Ilkayeva O8, Newgard CB8, Gibson BW2, Schilling B2, Cohen DE9, Kahn CR10.

Abstract

Dietary sugars, fructose and glucose, promote hepatic de novo lipogenesis and modify the effects of a high-fat diet (HFD) on the development of insulin resistance. Here, we show that fructose and glucose supplementation of an HFD exert divergent effects on hepatic mitochondrial fun

I've been trying to reconcile PTM and DNA, PTMs are so much more complex than just coding for the amino acid in general but yet there is no information media like DNA -> RNA for PTMS but then looking at the triplet code i see some redundancy i.e different triplets coding for the same amino acids , it got me thinking this is strange perhaps its not coding for the same amino acid but the same amino acid with some sort of label ( i have no idea what this is but just from the math i feel like if this existed it would explain a lot) , some of these amino acids have 4 combinations that result in it being coded into the protein at large.

i just wondered if this is something being thought about, also if its stupid why?

thanks for your time

Just a bit confused with terminology - are they the same?

I'm searching for one really interesting, what do you guys think?

Where is the cell does post translational modification such as phosphorylation, glycosylation, lipidation, methylation, etc occur? In house proteins are made by free floating ribosomes in the cytoplasm. Extracellular proteins are made in the RER. So can the answer be the cytoplasm, ER (rough, smooth and lumen?) and the Golgi Apparatus? Am I missing something here?

So I was doing a Western blot and I've tried almost EVERYTHING to detect the protein of a gene that I've transfected into my lymphocyte cell line. Nothing works. I eventually figure out that the epitope that my antibody is supposed to bind to is heavily phosphorelated. I read somewhere that people add EDTA to their RIPA buffer to inhibit kinases. "But it's a pre-made RIPA buffer from Sigma, so it should already have EDTA. Right?"

Wrong. I add EDTA and do everything over. Boom, I see my protein.

Now I'm having the same issue with a different, but very similar protein. In this case though, I suspect it could be ubiquitenated residues. Anyone ever encounter anything like this before? Is this even feasible?

My antibody is hitting two splice forms of its target (although the manufacturer only shows one)...I'll take that but for some reason both bands seem to be almost 20-25kD too high. I expect glycosylation and phosphorylation could push them up a bit but that's a lot more than I'd expect.

For clarity: this is an SDS-PAGE western with NaF/Na3VO4. I'm targeting BTK(y223).

Hi biologists and enthusiasts...

I'm writing a doctoral thesis that is nitty gritty biochemistry and protein protein interactions.... so it came as a shock to me when my boss asked for a photogenic tree of species with conservation within my protein of interest. It turns out that for a lot of Phylum Chordata, but not species like C. elegans which also has this protein, the modified region is very conserved.

Ok cool - that probably means that negative selection of this region highlights that it is important and this modification probably serves function in these animals... but I'd really like a reference to appropriately cite this.

Considering myself a complete outsider to this area of biology - could any of you make a suggestion please?

http://www.ncbi.nlm.nih.gov/pubmed/23772978

Greetings!

I am new to the field of proteomics, and in my first set of data to analyse, I studied a pure culture of Methanobacterium formicicum in the absence and presence of activated carbon. I only identified 500 of the 2400 proteins that compose M. formicicum's proteome. I also used the cRAP database to identify the contaminants. I know that PTMs play a major role in identification, and as I have already specified the usual Carbamidomethilation of Cytosine and Oxidation of Methionie - the usual PTMs, used in Compomics tools and MaxQuant - I wanted to know what more PTMs I should be searching for.

Using UniProt's ID mapping I found very little PTMs in the columns of " PTM / Processsing". What other resources do I have to find PTMs? Only literature?

Thank you for your attention!

EDIT: In this article, new searches on unidentified spectra in PRIDE database confidently identified many modified peptides

Can't seem to get a straight answer out of google. Smh

Journal of the American Chemical SocietyDOI: 10.1021/jacs.0c01576

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