[gmx-users] re: How to exert different lateral pressure profile of a lipid membrane

[KONG Xian]

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.

I just find a relevant paper. They control the target pressure in the xy
plane to 10 bar while keep the z target pressure 1 bar, thus producing a
surface tension. They intend to study the mechanosensitivity of a protein. I
think it's a nice implication for me. 

FISCHER, G., KOSINSKA-ERIKSSON, U., APONTE-SANTAMARIA, C., PALMGREN, M.,
GEIJER, C., HEDFALK, K., HOHMANN, S., DE GROOT, B. L., NEUTZE, R. &
LINDKVIST-PETERSSON, K. 2009. Crystal Structure of a Yeast Aquaporin at 1.15
angstrom Reveals a Novel Gating Mechanism. Plos Biology, 7


> 
> /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.
 I haven't think too much on this method. 
I thought I could exert some force on the atoms that are close with lipids,
namely those atoms that are on the surface of the protein， thus mimicking
the effects of the membrane lipids on the protein. 
It's not a mature thoughts, I think I should think it for a little longer
time. 
Thanks for your kindly discussion which is inspirational.

KONG Xian
THU, Beijing

 

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