From: Philip Blood (philb_at_hec.utah.edu)
Date: Wed Nov 02 2005 - 18:16:19 CST
It depends on what type of membrane (and what side of the membrane) you
want to model. PC lipids are generally pretty abundant on both sides of
the plasma membrane, whereas PE lipids are pretty much exclusively found
on the cytoplasmic side of the membrane. So you would want to look at
where this protein is found and decide how complex you want your
membrane model to be. The cytoplasmic side of the membrane also has
charged lipid species such as phosphatidylserine (PS) and
phsophatidylinositol (PI) which are important for interactions with
proteins in the cytoplasm. The exact details vary depending on the
given cell type and the type of membrane that you are modeling.
Charles Danko wrote:
> I know the chemical differences between POPC and POPE lipids provided
> with the VMD membrane plugin, and Ive seen both used in simulations of
> membrane proteins. My question is whether or not there is a prefered
> species for MD simulations? Why? What is thought to be more
> accurate? Does it depend on the protein you are modeling?
> I am curious about any thoughts/ suggested reading along this line.
> Charles Danko
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