Subject: Re: CCL:helix dipole

From: Rafael N Szeinfeld <[email-masked]>
Date: Tue, 19 Apr 1994 09:14:41 -0300 (BDT)

On Tue, 19 Apr 1994, Margaret Wong wrote:

> 
> Dear Networkers
> 
> Is there any way to calculate the dipole on a helix
> in a protein.  Several papers I have read recently talk
> about the importance of the helix-dipole but none quantify
> this value.
> 
> 
> THANKS
> 
> 
> Margaret Wong
> 
>   _    Dr Margaret Wong     V    [email-masked]  _--_|\    
>  (_)o  Chemistry Dept      | |   [email-masked]     /      \    
>  /\  \ Swinburne Uni      /___\   Ph.  03 819 8542          \_.--.x/
>        Hawthorn,OZ,3122  /_____\  Fax  03 819 0834                v 
> 
	For each pair of opposite charges in the helix you have a dipole
momentum vector that points from the positive to the negative charge so I
suppose the total dipole momenta vector of that helix will be the
vectorial sum of all these vectors. How to calculate it in practice (that 
is, if there are approximation methods or computer algorhitms) I don't know.
	Hope this help.

			Rafael Najmanovich

---

From: Gustavo Mercier <[email-masked]>
Date: Tue, 19 Apr 1994 17:31:27 -0400 (EDT)

> about the importance of the helix-dipole but none quantify

Hi!

The initial suggestion of a helix dipole moment was by Hol et. al.
Nature v. 273, p. 443-446, 1978. If I remember correctly in this
paper the dipole was approximated by 0.5xL where L is the length
of the alpha helix. This is crude but occassionally useful.

How to compute the helix - dipole, or for that matter the moment
associated with a given element of a protein structure is not a
trivial matter. For example,

1) Excluding solvent effects, you can simply use SUM(i) qixRi for the
segment you are interested. You may or may not include the sidechains.
Other variations in this theme are also possible, like vectorial
sums of the the C=O bond moment that contributes to the helix macrodipole

2) If you want to include solvent effects using state of the art
techniques, things are a bit more complex. You may consider a finite
element solution to the Poisson equation as done
by M K. Gilson and coworkers. You may also like to look at R. Zauhar's
work who uses boundary elements methods for the same purpose.
Programs that implement the finite element method include UHBD and
Delphi. I have not seen Zauhar's boundary element method in a program
available for distribution.

Good Luck,

gus mercier
[email-masked]