[gmx-users] unfolding a protein

[Justin A. Lemkul]

Quoting Siavoush Dastmalchi <Dastmalchi.s at tbzmed.ac.ir>:

> Hi Justi,
>
> Thanks for the comments. Yes, I am showing MD ~.mdp file and I know that my
> system is not neutral. I am not following the unfolding path and my intention
> by unfolding the protein is to get a conformation which I could regard it as
> one of the feasible unfolded conformations.
> Do you think, not neutralizing the system will somehow prevent unfolding?

I don't think the ions are the cause.  I think your simulation time is way too
short to be seeing unfolding.  I mentioned the ions because simulating a
charged system is not necessarily a real approximation of a physiological (or
in vitro) system.  The world does not bear a net charge!

I would suggest adding counterions to neutralize the charge, and use PME instead
of cut-off.  I think it is more reliable, based on my experience.  The cut-off
method for calculating electrostatics is quicker, but I believe PME is more
accurate.

-Justin

>
> Cheers, Siavoush
>
> ________________________________
>
> From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
> Sent: Wed 2008/02/20 06:35 È.Ù
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] unfolding a protein
>
>
>
> Quoting Siavoush Dastmalchi <Dastmalchi.s at tbzmed.ac.ir>:
>
> > Hi there,
> >
> >
> >
> > I want to unfold a protein (hen egg white lysozyme) which has got 4
> disulfide
> > bounds. I have tried 1 ns of MD at 400 K either in vacuum or hydrated form
> > and it didn't unfold. I know it may need longer time, but it doesn't show
> any
> > sign of even starting to unfold. I think I am restraining the protein in
> some
> > way. Please see below the content of ~.mdp file that I use.
>
> My guess is that 1 ns is far too short to see any signs of unfolding.
> Typically, we think of protein folding on the microsecond - second timescale,
> so even if you speed things along by running your simulation at higher
> temperature, you should be running tens of nanoseconds, if not 100 or more.
> Check the literature to see what other people consider a reasonable time
> scale.
>
> Also, what have you done in terms of minimization and equilibration?  Are you
> showing the production MD .mdp file?
>
> As far as "thinking" you are restraining your protein, these are things you
> need
> to be very sure of :-)  Your topology likely specifies #include "posre.itp"
> if
> you include a "define" statement within your .mdp file (which I don't see),
> so
> I doubt you are restraining your protein in any way.
>
> >
> >
> >
> > Would you please let me know how I could unfold a protein using an MD
> > simulation?
> >
> > Do you think unfolding a water soluble protein in vacuum would be faster?
>
> Maybe, but what would it prove?
>
> As a side note, are you including counterions in your simulation?  I don't
> see
> them incorporated into your tc-grps, so I'm wondering if you have an
> electroneutral system.
>
> -Justin
>
> >
> >
> >
> > Cheers, Siavoush
> >
> >
> >
> > cpp                      = /lib/cpp
> > include                  = -I../top
> > integrator               = md
> > dt                       = 0.002
> > nsteps                   = 500000
> > nstxout                  = 1000
> > nstvout                  = 1000
> > nstlog                   = 100
> > nstenergy                = 100
> > nstxtcout                = 100
> > xtc_grps                 = protein sol
> > energygrps               = protein sol
> > nstlist                  = 10
> > ns_type                  = grid
> > rlist                    = 0.8
> > coulombtype              = cut-off
> > rcoulomb                 = 1.4
> > rvdw                     = 1.4
> > pbc                      = xyz
> > tcoupl                   = berendsen
> > tc-grps                  = protein sol
> > tau_t                    = 0.1 0.1
> > ref_t                    = 400 400
> > Pcoupl                   = berendsen
> > Pcoupltype               = isotropic
> > tau_p                    = 1.0
> > compressibility          = 4.5e-5
> > ref_p                    = 1.0
> > gen_vel                  = yes
> > gen_temp                 = 400
> > gen_seed                 = 173529
> > constraints              = all-bonds
> >
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>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
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>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================