Subject: Helix dipoles continued

From: [email-masked] (Trevor Creamer)
Date: Wed, 27 Apr 94 11:29:54 -0600

Continuing the recent discussion on helix dipoles......

People interested in this may want to have a look at a paper
that's just come out :

	P.Chakrabarti, Protein Engineering v.7(4), p.471-474(1994)

The author analyses the distributions of ions bound to the ends of
helices in proteins and comes to the conclusion that the helix 
dipole has little, if any, effect on the ion positions.
So, just how important is the dipole ?

Cheers,
       Trevor
________________________________________________________________________

Trevor P. Creamer                             Dept. of Biochemistry
Email  - [email-masked]              & Molecular Biophysics
Phone  - (314) 362 4123                       Washington University
Fax    - (314) 362 4115                       St. Louis, Missouri 63110
                                              U.S.A.
________________________________________________________________________

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From: [email-masked] (Malcolm Davis)
Date: 27 Apr 1994 15:23:01 -0400

The "helix dipole" with 1/2 a charge unit at one end of the alpha
helix and -1/2 at the other, yielding a dipole moment of L/2, looks
like a dipole only at distances much larger than L.  Since, most of
the interesting stuff happens at distances much shorter than this the
dipole part of the helix dipole is probably not significant.

At nearer distances, it still might be useful to view the helix as
producing a charge separation, so that near each end you see the field
of a net charge, but even this can be led to incorrect conclusions by
ignoring the local variation in the fields very near the helix.

Consider how such an approximation can lead to an incorrect conclusion
in a simple model system.  At large separations, a linear chain of
dipoles

 		+:-   +:-   +:-   +:-

will look like a "macrodipole"

                +                   -

If one then asks about the interaction with a similar parallel strand,
the macrodipole view

                +                   -
                   +                   -

would lead one to conclude that the interaction is very unfavorable,
but the detailed view

		+:-   +:-   +:-   +:-
		   +:-   +:-   +:-   +:-

shows that the interactions are not so bad after all.

--
Malcolm E. Davis

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