Re: [AMBER] GPI-anchor protein cleavage

From: Jason Swails <>
Date: Tue, 16 Jun 2015 18:06:20 -0600

On Tue, Jun 16, 2015 at 12:49 PM, Aditya Padhi <> wrote:

> Dear Amber Users,
> I am working on a protein, which is known to cleave few GPI-anchor proteins
> (Glycosylphosphatidylinisotol). Also, I know that there are several other
> candidate GPI-anchor proteins which may or may not be cleaved by my protein
> of interest. I was wondering, if there is any tool/method in Amber using
> which I can atleast get some preliminary information on these.

You really need a more specific question. QM/MM can be used to probe
chemical reactions in enzymes. You can combine that with PMF methods like
umbrella sampling to get free energies along a reaction coordinate. You
can also run classical MD on your system and look at particular
interactions that may be occurring near the active site (and see if there
are differences between those that *do* cleave and those that *don't*).
Again, the types of simulations you would run would depend very heavily on
what you ultimately hope to learn through your simulations.

The QM studies are probably not "preliminary" studies, since they will
require a lot of time to set up, run, and learn how to perform effectively
if you've never done it before.

> The 3D structure of my protein of interest and most of the GPI-anchor
> proteins is not available. I was therefore wondering if there is any such
> tools/methods available that I am missing.

​This makes it a very challenging problem. You may be able to use homology
modeling to develop a starting conformation, but that is certainly not
guaranteed to work and it would take a fair amount of time to learn how to
do it.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 16 2015 - 17:30:03 PDT
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