[gmx-users] Translation motion during MD

[Justin A. Lemkul]

nahren manuel wrote:
> Dear Gromacs Users,
> 
> Yes Justin I totally agree with you and your point is well taken.  But 
> given the fact that if i dont restrain the protein, they rotate and I 
> dont get the formation of clusters.
> 

If you know the manner in which the clusters should form, then isn't this just a 
problem of poor initial orientation?

> Yes, i do want to protein to rotate in the plane of the membrane, but 
> not the rotation that membrane-proximal become membrane -distal (this 
> flipping rotation, if I may call like that)
> 

This sounds like a problem.  If you have an ectodomain with a known structure, 
then the transmembrane portion shouldn't be too complex, right?  If there's an 
anchoring transmembrane helix, it is trivial to construct and add onto the 
structure.

> Another alternate I was thinking was to do a steered MD, but since there 
> is no clue which part (which domain in the protein) form cluster, this 
> method doesn't help either.
> 

I guess this rebuts my comment above...

> Is  applying semiisotropic pressure a good idea ? similar to what one 
> would do in membrane simulation.
> 

I don't see why not.  Membranes should deform independently in x/y and z, so 
semiisotropic is fine.

-Justin

> Best,
> nahren
> 
> --- On *Thu, 11/11/10, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
> 
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] Translation motion during MD
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Thursday, November 11, 2010, 4:14 PM
> 
> 
> 
>     nahren manuel wrote:
>      > Dear Gromacs Users,
>      >
>      > I am simulating a Membrane protein, the extracellular domain
>     alone (since the structure of only extracellular domain is solved).
>     So I will have to simulate the protein in such a way that only the
>     translational motion is allowed but the rotational motions are
>     prevented (which would mimic the behavior of the protein attached to
>     the membrane).
>      >
> 
>     I don't understand how you conclude that your protein shouldn't
>     rotate.  Even if the transmembrane portion was there, the protein
>     could certainly rotate in the plane of the membrane.
> 
>      > The protein is expected to former dimer and multimers on the cell
>     surface, so I want to restrict motion only to 2D. This would give an
>     idea as to how the protein clusters on the membrane surface
>     (studying this multimerization looks too ambitious, but want to make
>     an attempt).
>      >
> 
>     I suppose you could place a weak position restraint on all atoms in
>     the z-dimension only.  I would seriously question the validity of
>     doing so, though.  If you force a system into a preconceived
>     behavior that masks other missing information, I'd say you're just
>     causing the events to happen, not allowing them to occur naturally. 
>     You're also causing unnatural forces between the membrane and the
>     protein.  If the membrane deforms or undulates, the protein cannot
>     accommodate this change.  This is true no matter how you restrict
>     this 2-D motion, and I think it would be a serious problem.
> 
>     -Justin
> 
>      > Best,
>      > nahren
>      >
>      >
>      >
>      >
>      >
>      >
>      >
> 
>     -- ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     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
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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