Baudelaire comes to Chemistry

Could an evil molecule be beautiful? In Les Fleurs du Mal, a collection of poems, Baudelaire argued that there was a certain beauty in evil. Well, if there ever was an evil molecule, it’s the Abeta42 peptide, the main component of the senile plaque of Alzheimer’s disease, a molecule whose effects I spent my entire professional career as a neurologist ineffectually fighting. And yet, in a recent paper on the way it forms the fibrils constituting the plaque I found the structure compellingly beautiful.

The papers are Proc. Natl. Acad. Sci. vol. 113 pp. 9398 – 9400, E4976 – E4984 ’16. People have been working on the structure of the amyloid fibril of Alzheimer’s for decades, consistently stymied by its insolubility. The authors solved it not by Xray crystallography, not by cryoEM, but by solid state NMR. They basically looked at the distance constraints between pairs of isotopically labeled atoms, and built their model that way. Actually they built a bouquet of models using computer aided energy minimization of the peptide backbone. Another independent study produced nearly the same set.

The root mean square deviation of backbone atoms of the 10 lowest energy models of the bouquets in the two studies was small (.89 and .71 Angstroms). Even better the model bouquets of the two papers resemble each other.

There are two chains of Abeta42, EACH shaped like a double horseshoe (similar to the letter S). The two S’s meet around a twofold axis. The interface between the two S’s is form by two noncontiguous areas on each monomer (#15 – #17) and (#34 – #37).

The hydrophilic amino terminal residues (#1 – #14) are poorly ordered, but amino acids #15 – #42 are arranged into 4 short beta strands (I only see 3 obvious ones) that stack up and down the fibril into parallel in register beta-sheets. Each stack of double horseshoes forms a thread and the two threads twist around each other to form a two stranded protofilament.

Glycines allow sharp turns at the corners of the horseshoes. Hydrogen bonds between amides link the two layers of the fibrils. Asparagine side chains form ladders of hydrogen bonds up and down the fibrils. Water isn’t present between the layers because the beta sheets are so close together (counterintuitively this decreases the entropy, because water molecules don’t have to align themselves just so to solvate the side chains).

Each of the horseshoes is stabilized by hydrophobic interactions among the hydrophobic side chains buried in the core. Charged residues are solvent exposed. The interface between the two horsehoes is a hydrophobic interface.

Many of the famlial mutations are on the outer edges of double S structure — they are K16N, A21G, D23N, E22A, E22K, E22G, E22Q.

The surface hydrophobic patch formed by V40 and A42 may explain the greater rate of secondary nucleation by Abeta42 vs. Abeta40.

The cryoEM structures we have of Abeta42 are different showing the phenomenon of amyloid polymorphism.

The PNAS paper used reombinant Abeta and prepared homogenous fibrils by repeated seeding of dissolved Abeta42 with preformed fibrils. The other study used chemically synthesized Abeta and got fibrils without seeding. Details of pH, peptide concentration, salt concentration differed, and yet the results are the same, making both structures more secure.

The new structure doesn’t immediately suggest the toxic mechanism of Abeta.

To indulge in a bit of teleology — the structure is so beautiful and so intricately designed, that the aBeta42 peptide has probably been evolutionarily optimized to perform an (as yet unknown) function in our bodies. Animals lacking Abeta42’s parent (the amyloid precursor protein) don’t form neuromuscular synapses correctly, but they are viable.

Les fleurs du PTEN

Les fleurs du Mal is a volume of poetry by Baudelaire about the beauty of evil and depravity. I have the same esthetic appreciation for the horrible things a mutant of PTEN does. It’s awful, but incredibly elegant chemically.

Back in the day med students used to be told ‘know syphylis and you’ll know medicine’ because of its varied clinical manifestations. PTEN is like that for cellular and molecular biology.

PTEN (Phosphatase and TENsin homolog) is a gene mutated in many forms of cancer. So it was regarded as a tumor suppressor, keeping our cells on the straight and narrow. Naturally cancer cells ‘try’ (note the anthropomorphism) to neutralize it. PI3K is a universal tumor driver, integrating growth factor signaling with downstream circuitries of cell proliferation, metabolism and survival.

Inositol is a 6 membered ring (all carbons) with one OH group attached to each carbon, which are numbered 1 through 6. PI3K puts phosphate on the 3 position, PTEN takes it off. Since this is how PI3K signaling begins, cells lacking PTEN grow faster and migrate aberrantly (e.g. spread).

Enter Proc. Natl. Acad. Sci. vol. 112 pp. 13976 – 13981 ’15 which carefully studied a PTEN mutant found in an unfortunate man with aggressive prostate cancer. It just changed one of the 403 amino acids (#126) from alanine to glycine. Not a big deal you say,it’s just a change of CH3 (alanine) to H (glycine). #126 is near the active site of the enzyme. One might expect that the mutation inhibits PTEN’s phosphatase activity (e.g. its enzymatic activity). Not so — the mutations shifts the activity so the enzyme. Instead of removing phosphate from the 3 position of inositol, the phosphate at the 5 position is removed (leaving the 3 position alone). This shifts inositol phosphate levels in the cell with hyperactivation of PI3K signaling (which requires inositol phospholipids containing phosphate at the 3 position).

What happens is that inositol phosphates fit into the mutant active site with the 5 position near the catalytic amino acid (cysteine). Essentially the 6 membered ring rotates the 3 position away from cysteine and puts the 5 position there instead. This changes PTEN from a tumor suppressor (anti-oncogene) to an oncogene.

To a chemist this is elegant and beautiful (apologies Baudelaire).

PTEN has taught us a huge amount about the control of protein levels, pseudogenes, competitive endogenous RNA (ceRNA). You can read all about this in https://luysii.wordpress.com/2014/01/20/why-drug-discovery-is-so-hard-reason-24-is-the-3-untranslated-region-of-every-protein-a-cerna/

That’s fairly grim, so here’s a link to one of the great comedians of years past — Jonathan Winters

http://biggeekdad.com/2013/04/jonathan-winters-stick/

It’s politically incorrect and sure to offend the humorless pompous prigs. Enjoy ! ! !