As Carlos suggested modelling the unfolded state is very difficult. In an
approximate way you can consider the unfolded state as a collection of
dipeptides. In our recent study (DOI: 10.1021/acs.biochem.5b00946) we
utilized such an approximation and found out the relative stability of
mutant with respect to WT.
On Sun, Feb 28, 2016 at 12:25 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> in that case, you'll need to measure the deltaG of wild type to mutant in
> the folded state, and also deltaG for wild type to mutant in the unfolded
> state. You can't just do the folded state calculation using methods that I
> know about. The unfolded state can be difficult to model due to the size of
> the water box and also sampling the huge conformational space needed for
> the averages to converge. Typically you would need to make some
> approximations for the unfolded state calculation.
>
> I suggest searching the literature to find examples of this sort of
> calculation. It's at the very edge of what I would consider feasible, and
> much will depend on the properties of your particular protein. The methods
> can be very challenging, so rather than trying lots of possibilities you
> want to look and see what has worked for others and then adapt it to your
> needs. I would not suggest taking on a project like calculating the impact
> of mutation of folding free energy without doing a literature search first.
> Once you decide on methods, then the Amber list will be a great resource
> for the technical questions you might have while implementing them.
>
> On Sat, Feb 27, 2016 at 1:48 PM, Mijiddorj Batsaikhan <
> b.mijiddorj.gmail.com
> > wrote:
>
> > Dear Carlos and Rajeswari,
> >
> > Thank you for your reply. Main point is folding difference between wt
> and a
> > mutant. Thank you again.
> >
> >
> > Batsaikhan
> >
> > On Sun, Feb 28, 2016 at 1:32 AM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > I agree, and in fact I don't think its straightforward to calculate G
> > > itself anyway, deltaG is much easier. but again, it really depends on
> the
> > > process for which you want to compare wild type and mutant. there are
> > many
> > > methods for free energy calculation, and it's hard to recommend one
> > without
> > > knowing what the actual endpoints are.
> > >
> > > On Sat, Feb 27, 2016 at 12:11 PM, Rajeswari A. <
> > > rajeswari.biotech.gmail.com>
> > > wrote:
> > >
> > > > Please have a look at the following thread. It was suggested that
> you
> > > > cannot compare the G(wt) and G(mutant) directly. But you can compare
> > the
> > > > delta G from both.
> > > >
> > > > http://archive.ambermd.org/201511/0167.html
> > > > On 27-Feb-2016 6:44 pm, "Carlos Simmerling" <
> > carlos.simmerling.gmail.com
> > > >
> > > > wrote:
> > > >
> > > > > TI is usually considered to be more accurate, but takes more time
> to
> > > run.
> > > > > MMPBSA just requires the MD simulation for each mutant. You could
> > start
> > > > by
> > > > > looking at tutorials A3 and A9.
> > > > >
> > > > > On Sat, Feb 27, 2016 at 8:02 AM, Mahdieh Hadi <
> > mahdieh.hadi.bric.ku.dk
> > > >
> > > > > wrote:
> > > > >
> > > > > > Thanks a lot. and which one is more accurate?
> > > > > >
> > > > > > ________________________________________
> > > > > > From: Carlos Simmerling [carlos.simmerling.gmail.com]
> > > > > > Sent: Saturday, February 27, 2016 1:48 PM
> > > > > > To: AMBER Mailing List
> > > > > > Subject: Re: [AMBER] How to analyze mutational free energy
> > > difference?
> > > > > >
> > > > > > this can be done either with TI or by using MD with MMPBSA,
> > depending
> > > > on
> > > > > > the level of accuracy that you need.
> > > > > >
> > > > > > On Sat, Feb 27, 2016 at 7:46 AM, Mahdieh Hadi <
> > > mahdieh.hadi.bric.ku.dk
> > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > I have almost the same problem. Which tutorial is suitable for
> > > ligand
> > > > > > > binding?
> > > > > > > ________________________________________
> > > > > > > From: Carlos Simmerling [carlos.simmerling.gmail.com]
> > > > > > > Sent: Saturday, February 27, 2016 1:39 PM
> > > > > > > To: AMBER Mailing List
> > > > > > > Subject: Re: [AMBER] How to analyze mutational free energy
> > > > difference?
> > > > > > >
> > > > > > > what is the process for which you want the free energy? ligand
> > > > binding?
> > > > > > > folding? activation? then we can suggest tutorials for that.
> > > > > > >
> > > > > > > On Sat, Feb 27, 2016 at 2:34 AM, Mijiddorj Batsaikhan <
> > > > > > > b.mijiddorj.gmail.com
> > > > > > > > wrote:
> > > > > > >
> > > > > > > > Dear users,
> > > > > > > >
> > > > > > > > I want to make mutational free energy difference of protein
> > > > structure
> > > > > > > > (delta G = G wild-type - G mutant). If you do not mind,
> please
> > > give
> > > > > me
> > > > > > > > advice, and suggestions of related tutorials.
> > > > > > > >
> > > > > > > >
> > > > > > > > Batsaikhan
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
> > > > > > > > AMBER.ambermd.org
> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >
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>
--
Rajeswari A,
PhD Research Scholar,
Computational Biophysics Lab,
Department of Biotechnology,
Indian Institute of Technology Madras,
Chennai 600 036, Tamil Nadu, India.
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Received on Mon Feb 29 2016 - 04:30:05 PST
