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PBP4 Inhibitor Design

By vmulligan
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A designed inhibitor of penicillin binding protein 4 (PBP4), in blue, bound to its target.  This is currently just a model on a computer screen, though our lab is synthesizing this molecule to test its ability to inhibit the enzyme in real life.  Model created with PyMol, and rendered with Blender 2.79b (Cycles renderer).  The background was rendered with Apophysis 2.09 and composited in Photoshop.  Original design was created with Rosetta 3.8 (www.rosettacommons.org/), using algorithms developed by the artist.

This image is not in the public domain.  You may not use it for any purpose without the consent of the copyright holder.  Image copyright © 2018 Vikram K. Mulligan.
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© 2018 - 2021 vmulligan
Comments6
anonymous's avatar
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Mistress-Shade's avatar
It's almost... sexual.

Anyway, maybe I'm a bit out of the loop on your research group, but why synthesize an inhibitor for penicillin? What's the application goal?
vmulligan's avatar
Sorry -- the description was unclear.  Penicillin binding proteins (the pinkish mass in the illustration) are the proteins that antibiotics like penicillin bind to.  The binding of an antibiotic molecule inhibits the normal function of the protein (which is enzymatic -- the protein catalyzes chemical reactions involved in building the bacterial cell wall, and when it can't do its job, the bacterium can't grow and divide).  If we can make new molecules that don't look like penicillin, but which also bind in the same way to penicillin binding proteins, these could potentially be new antibiotics.  (That's the hope, anyways.  I don't want to make any extravagant claims, mind you: we have not yet proven that any of our molecules could be used as an antibiotic.)  But the purple blob is a synthetic peptide designed to bind to one of the PBPs.
vidgamer123's avatar
Yeah that uh... that sure is a purple blob in the middle of a tan blob.
vmulligan's avatar
It's what molecules look like -- see David Goodsell's work at the Protein Data Bank: pdb101.rcsb.org/motm/motm-abou… .
vidgamer123's avatar
Heh, thanks for the link but I was mostly being facetious.
vmulligan's avatar
Fair enough!  It's a fair comment that you made, though.  Proteins don't look like macroscale objects (except maybe blobs of chewing gum), so it's not unusual to squint at a picture of one and to go, "Huh?"
anonymous's avatar
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