Q: Helix dipoles

Simon Brocklehurst (smb@bioch.ox.ac.uk)
Mon, 4 Mar 1996 15:16:03 +0000 (GMT)

Hi everyone!
Now that people are starting to get used to thinking about
3-D protein structures, I thought now might be a good time to try to
start up another discussion.

Here's the question I'd like to pose...

Imagine that you have two "ideal" (i.e. no distortions from regular
geometry) helices in similar environments in a protein: one an
alpha-helix; the other a 3-10- helix. And imagine further that
these two helices are of the same length.

Which (if either) of the two helices would you predict has the greater
dipole moment, and why?

In arguing the case for which ever you choose, it would be helpful
if you could say a little about what you consider the structural
basis of the helix dipole to be.

This question may seem a little abstract to some of you. I
hope it will encourage you to think about the differences between
these two types of helix in terms of what they actually "look like"
as opposed to simply thinking in terms of definitions like: "it consists
of i, i+x hydrogen bonds and y residues per turn" etc...
That is, to answer the question, you will probably have to look at an
example of both types of structural motif using Rasmol.

As always, please don't be afraid to post your answers to the list.
I look forward to seeing what you have to say... if anything!

-- Simon
| ,_ o Simon M. Brocklehurst,
| / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry,
| \>> | University of Oxford, Oxford, UK.
| \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/