Tag Archives: things in heaven and earth

Amyloid structure at last !

As a neurologist, I’ve been extremely interested in amyloid  since I started in the late 60s.  The senile plaque of Alzheimers disease is made of amyloid.  The stuff was insoluble gunk. All we had back in the day was Xray diffraction patterns showing two prominent reflections at 4 and 9 Angstroms, so we knew there was some sort of repetitive structure.

My notes on papers on the subject over the past 20 years contain  about 100,000 characters (but relatively little enlightenment until recently).

A while ago I posted some more homework problems — https://luysii.wordpress.com/2021/09/30/another-homework-assignment/

Homework assignment #1:  design a sequence of 10 amino acids which binds to the same sequence in the reverse order forming a plane 4.8 Angstroms thick.

Homework assignment #2 design a sequence of 60 amino acids which forms a similar plane 4.8 Angstroms thick, such that two 60 amino acid monomers bind to each other.

Feel free to use any computational or theoretical devices currently at our disposal, density functional theory, force fields, rosetta etc. etc.

Answers to follow shortly

Hint:  hundreds to thousands of planes can stack on top of each other.

 

If you have a subscription to Cell take a look at a marvelous review full of great pictures and diagrams [ Cell vol. 184 pp. 4857 – 4873 ’21 ].

 

Despite all that reading I never heard anyone predict that a significantly long polypeptide chain could flatten out into a 4.8 Angstrom thick sheet, essentially living in 2 dimensions.  All the structures we had  (alpha helix, beta pleated sheet < they were curved >, beta barrel, solenoid, Greek key) live in 3 dimensions.

 

 

So amyloid is not a particular protein, but a type of conformation a protein can assume (like the structures mentioned above).

 

 

So start with NH – CO – CHR.  NH  CO and C in the structure all lie in the same plane (the H and the side chain of the amino acid < R >  project out of the plane).

 

Here’s a bit of elaboration for those of you whose organic chemistry is a distant memory.  The carbon in the carbonyl bond (CO) has 3 bonding orbitals in one plane 120 degrees apart, with the 4th orbital perpendicular to the plane — this is called sp2 hybridization.  The nitrogen can also be hybridized to sp2.  This lets the pair of electrons above the plane roam around moving toward the carbon.  Why is this good?  Because any time you let electrons roam around you increase their entropy (S) and anything increasing entropy lowers their free energy (F)which is given by the formula F = H – TS where H is enthalpy (a measure of bond strength, and T is the absolute temperature in Kelvin.

 

 

So N and CO are in one plane, and so are the bonds from  N and C to the adacent atoms (C in both cases).

 

You can fit the plane atoms into a  rectangle 4.8 Angstroms high.  Well that’s one 2 dimensional rectangle, but the peptide bond between NH and CO in adjacent rectangles allows you to tack NH – CO – C s together while keeping them in a 3 dimensional parallelopiped 4.8 Angstroms high.

 

 

Notice that in the rectangle the NH and CO bonds are projecting toward the top and bottom of the rectangle, which means that in each plane  NH – CO – CHR s, the NH and CO are pointing out of the 2 dimensional plane (and in opposite directions to boot). This is unlike protein structure in which the backbone NHs and COs hydrogen bond to each other.  There is nothing in this structure for them to bond to.

 

 

What they do is hydrogen bond to another 3 dimensional parallelopiped (call it a sheet, but keep in mind that this is NOT the beta sheet you know about from the 3 dimensional structures of proteins we’ve had for years).

 

 

So thousands of sheets stacked together form the amyloid fibril.

 

Where does the 9 Angstrom reflection of cross beta come from?  Consider the  [ NH – CHR – CO ]  backbone as it lies in the 4.8  thick plane (I never thought such a thing would be even possible ! ).  It curves around like a snake lying flat.  Where are the side chains?  They are in the 4.8 thick plane, separating parts of the meandering backbone from each other — by an average of 9 Angstroms

 

Here is an excellent picture of the Alzheimer culprit — the aBeta42 peptide as it forms the amyloid of the senile plaque

 

 

You can see the meandering backbone and the side chains keeping the backbone apart.

 

 

That’s just the beginning of the paper, and I’ll have lots more to say about amyloid as I read further.   Once again, biology instructs chemistry and biochemistry giving it more “things in heaven and earth, Horatio, than are dreamt of in your philosophy.”