[gmx-users] Re: How to exert different lateral pressure profile of a membrane to study its influence on a protein inserted in the double layer membrane?

[Justin A. Lemkul]

KONG Xian wrote:
> Dear Justin A. Lemkul:
> 
>          Thanks for your rapid reply.
> 
>          Just as you said, the result of my simulation with different xy 
> p_ref values didn’t vary, they are almost the same.
> 
>          I think I need consider some other ways to do what I was mean 
> to do.
> 
>         
> 
> I have read a paper that study the different lateral pressure profiles 
> of lipid membrane with respect to sterol type, I think I may chose this 
> as a way to produce different pressure profiles.
> 
>  

Membranes themselves are far more responsive to changes in pressure than are 
proteins, so unless there is a considerable difference in the lipid properties 
and also considerable interplay between the lipid dynamics and those of the 
protein, you still won't see any difference.  Again, I'd be skeptical that you'd 
ever find anything meaningful by changing the pressure in increments of 0.1 bar.

> 
> /Ollila, O. H. S., T. Rog, et al. (2007). "Role of sterol type on 
> lateral pressure profiles of lipid membranes affecting membrane protein 
> functionality: Comparison between cholesterol, desmosterol, 
> 7-dehydrocholesterol and ketosterol." _Journal of Structural Biology_ 
> *159*(2): 311-323./
> 
>  
> 
> And, what’s more, Do you think steered MD is a choice?
> 
>  

What would you steer?  Doesn't sound applicable here.

-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

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