Hopefully this is a quickie for someone who knows more about bio than I do. PBP2, which is a membrane-bound protein in methicillin-resistant Staphylococcus aureus (MRSA) and other bacteria catalyzes linking of peptidoglycans. Which side of the cell membrane/wall does the exposed part of the protein reside on (cytoplasm, or outside)? The diagrams don't say and my background is not in biology.

 

The paper I'm looking at is here:

http://www.sciencemag.org/cgi/content/full/315/5817/1402

 

Thanks for your help.

This is very easy. Imagine the setup of a the bacterium. Staphylococcus is Gram-positive. So you got the plasma membrane then you got a multi-layered cell wall consisting of peptidogylcans. So the function of the protein in question is involved in the cross-linking of the cell wall. So where, logically, does the active part of the protein has to be located?

It's "very easy" for someone who has background in biology. Mine is in computer science and math, so a direct answer would be helpful. Anyway, I guess you're saying it looks like this (could you confirm?):

 

OUTSIDE CELL

============ (Cell wall)

PBP2

--------------------membrane

cytoplasm

 

PBP2 is bound to the membrane but acts upon the cell wall. I didn't realize membrane and cell wall were separate entities in bacteria, I only knew that about plants.

 

So for something like penicillin to function, does it then have to be absorbed through the cell wall?

Yup, you got it right. Regardless of background, the important thing is to know which information is missing and where to get it. That's why I described the cell wall setup rather than saying "outside", which probably wouldn't have helped much in the long run.

 

Now regarding penicillin and bacterial cell walls. Unlike the plasma membrane the cell wall is basically porous. As such it is for the most part not a barrier for instance for antibiotics. Be advised, however, that many Gram-positive bacteria (those that possess a cell wall system as described above, Gram-negative bacterial cell walls are setup differently) often a additional layers on top of the cell wall (e.g. mycolic acids and surface layer proteins) that might act as barriers.

Thank you for the explanation.

 

Here's a bit of a stretch, now: What size protein might make it through the cell-wall? I ask because I'm looking at some open-source protein design software and wondering whether it might be possible to target the GT chain active site in the TF-GT complex (transferase-glycosyltransferase) with some high-affinity protein as recommended by authors (except with a protein as opposed to a typical antibiotic) .

That's a bit tricky, as it really depends on the bacterium. In B. subtilis I remember a size cut-off of around 50kDa for globular proteins. However, glycosyltransferase involved in cell wall assembly are pretty exposed anyway and especially during active growth I'd assume that they should be rather accessible.