Peptide antibiotics as glue

Neurologists and neurosurgeons are well acquainted with the Gibbs Donnan effect even if they don’t know it by name.  Damage the neuronal or astrocytic cell membrane, and positive ions and water rush inside to neutralize the negative charge on the many large impermeant molecules residing inside (e.g. all RNA and all DNA because of the negatively charged phosphate backbone, and many negatively charged proteins).  Neurons and glia swell, and because the brain is enclosed in the rigid skull intracranial pressure rises.

All nonMicrobes have antiMicrobial peptides.  They are usually positively charged and are thought to work by attacking the negatively charged bacterial membrane.

The following paper [  Proc. Natl. Acad. Sci. vol. 116 p. 1017 – 1026 ’19 ] shows that LL37, a 37 amino acid antimicrobial peptide with 10 of its 37 amino acids positively charged (lysine or arginine) has another trick up its sleeve.  It enters the bacterium (E. coli in the paper) and gums things up, by binding to negatively charged bacterial DNA and proteins.   The authors were actually able to show that  motion of the DNA genome and one protein was cut in half.  The organism lived (surprising me) but not too well.

This effect should make you realize (me for the first time) the reason why so many of the big molecules in a cell  (DNA, RNA, protein) are negatively charged.  They don’t stick to each other because of electrostatic repulsion.  The cell uses this to determine which proteins can bind to DNA — there are enzymes which acetylate lysine on histone (histone acetylases) and remove it (histone deacetylases <HDACs > ).  Acetylating the amino group of lysine removes its positive charge (histones are positively charged precisely to enable them to bind DNA).

Now to finish with a chem 101 question.  The paper notes that 10^8 molecules of LL37 enter the organism resulting in a concentration of 90 milliMolar.  This is all you need to figure out the cell volume of E. Coli.  What is it.

Short and Sweet

Yamanaka strikes again. Citrulline is deiminated arginine, replacing a C=N-H (the imine) by a carbonyl C=O. An enzyme called PAD4 does the job. Why is it important? Because one of its targets is the H1 histone which links nucleosomes together. Recall that the total length of DNA in each and every one of our cells is 3 METERS. By wrapping the double helix around nucleosomes, the DNA is shortened by one order of magnitude.

So what? Well, at physiologic pH the imine probably binds another proton making it positively charged, making it bind to the negatively charged DNA phosphate backbone. Removing the imine makes this less likely to happen, so the linker doesn’t bind the double helix as tightly.

Duck soup for the chemist, but apparently no one had thought to look at this before.

This opens up the DNA (aka chromatin decondensation) for protein transcription. Why is Yamanaka involved? Because PAD4 is induced during cellular reprogramming to induced pluripotent stem cells (iPSCs), activating the expression of key stem cell genes. Inhibition of PAD4 lowers the percentage of pluripotent stem cells, reducing reprogramming efficiency. The paper is Nature vol. 507 pp. 104 – 108 ’14.

Will this may be nice for forming iPSCs, it should be noted that PAD4 is unregulated in a variety of tumors.