Re: Software for Viewing the Effect of Amino Acid Modifications (or Substitutions) on Secondary Stru

peter Murray-rust (
Sun, 9 Jun 1996 19:17:50 +0100 (BST)

On Sat, 8 Jun 1996, Catherine O'Malley wrote:

> Here's kind of a wild question. I wonder if anyone knows of software

> that could do the following: Suppose you had a protein with a PDB file
> entry. Naturally, you could visualize the structure using Rasmol. But
> say you wanted to find out how chemical aging of amino acid residues

Just to check - you mean things like de-amidation and sulfoxidation? And,
of course, crosslinking.

> might affect secondary structure. Is there a program that would allow
> you to do this? Also, is there any software that permits you to examine
> the effect of amino acid substitutions on secondary structure? I know

This is the way to start, I assume. let's say you have an ASN->ASP
through de-amidation. This is conceptually the same as a mutation. The
ways you might attack it are to:
- search existing databases
- use a modelling program (which represents interatomic forces by
a forcefield)
- visualise it and come up with ideas.

All three could be tried. However, modeling very rarely results in
anything other that minor changes in local structure. It would be
unlikely that a radical change (e.g. helix->sheet would be modelled).

> this is a longshot, but I thought I'd ask anyway.

You will - presumably - have microheterogeneity of the proteins. So some
might have more than one change. If you have proteins where
oligomerisation is important, this could affect the oligomerisation.

So - in essence - this is an area where you need as much
experimental data as possible :-)


Peter Murray-Rust, Glaxo Research & Dev. (; (BioMOO: PeterMR)
Birkbeck College,, CBMT/Daresbury,