Molecular Modelling and Fibre Diffraction

[ennui]

Hello everyone,

 

I've just found this forum today and I've been reading a few posts. It's very interesting, I'm glad I found it.

 

I'm wondering if anyone out there knows a lot about molecular modelling (i.e. with PyMol) and X-ray fibre diffraction. Alas, I don't have access to solid-state NMR so I can't get any detailed knowledge of the oligomer I'm working with.

 

As part of a research I'm investigating the structure of amyloid proteins by using X-ray fibre diffraction. I have a small de novo peptide which I've assembled into a fibre; from this, I've generated an X-ray diffraction pattern and electron micrographs.

 

From both of these I've calculated a unit cell. I've tested the unit cell by making a .pdb model of the peptide in PyMol (with the 'build' option) and measured the x, y & z dimensions.

 

I've been running simulated diffractions with the .pdb file of my guessed structure, in the calculated unit cell. I'm comparing these to the actual diffraction pattern, to see how accurate my PyMol model is.

 

The initial simulated patterns were good, they matched nearly all the X-ray reflections (or 'spots' as the crystallographers call them!), except for a very odd 6-angstrom reflection on the equatorial axis which isn't on the real pattern.

 

At the moment the model is 2 beta-sheets of my hexapeptide running parallel, associated by aromatic and hydrophobic groups in the interface. I've tried shifting them so they're staggered and not lined up perfectly - but there is still a 6 angstrom reflection.

 

Also, I've tried changing the angles of the rotamers for the R-groups between the beta-sheets (which are the 'zip' in the fibre axis of the amyloid), but to no avail.

 

I can't think of any other edit to my molecular model to get rid of this 6-angstrom reflection: I'm really not sure what's causing it.

 

Does anyone have any advice?

 

Thank you.

Edited December 17, 2008 by ennui