AMBER Archive (2009)

Subject: Re: [AMBER] Gly -> Ala mutation

From: Jason Swails (jason.swails_at_gmail.com)
Date: Sun Nov 08 2009 - 11:53:29 CST

Hello,

You can write your own script/program to do the transformation. Soon there
will be a release of a new MM-PB(GB)SA script for amber that should be
faster and more user-friendly (and should handle alanine-scanning more
easily). However, even this new script does not handle Gly-Ala mutations
since this is more complex than every other mutation. For every other
residue, all that is needed to handle an alanine mutation is to remove
extraneous atoms and readjust some bond lengths to match those in alanine.
Glycine is the only amino acid that has fewer atoms than alanine, so in
order to perform that mutation, atoms would need to be added to the system.
This is non-trivial, because the question becomes "where do we add those
extra atoms?" (Ala has more degrees of freedom than Gly)

It may even be the case that in a specific conformation, an alanine would
not even fit where there's a glycine, so you would get an unphysically high
penalty for mutating that residue. Thus, the short version, there is no
clear-cut, systematic way to handle a Gly->Ala mutation, so it's not done.

Furthermore, alanine scanning is designed more to measure the electrostatic
(and perhaps VDW) effects that a particular sidechain has on the activity of
a protein. Glycine (and proline, though Pro->Ala is an allowed mutation in
the upcoming version if not this one) more often serves a role in modulating
the structure of a protein, so alanine scanning is often ill-suited to
probing the importance of a Glycine in the first place.

Hope this helps,
Jason

On Sun, Nov 8, 2009 at 12:25 PM, manoj singh <mks.amber_at_gmail.com> wrote:

> Hi all!
>
> The mm_pbsa.pl can't do Gly->Ala mutation. Is there any way to do this
> mutation in trajectory.
>
> Sincerely,
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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