[gmx-users] DPPC temperatur setting

[Justin A. Lemkul]

marco miele wrote:

Please heed this:

>     When replying, please edit your Subject line so it is more specific
>     than "Re: Contents of gmx-users digest..."
> 

...and don't reply to the entire digest.  I just stated the reasons a few 
minutes ago and won't bother to repeat myself again here.

<snip>

>     marco miele wrote:
>      > Hi everybody
>      > I am starting to analyze the membrane system composed with DPPC
>     lipids,
>      > I saw  both MD membrane paper and KALP-15 tutorial to setting a 323K.
>      > My question is That
>      > in this way we working around 50 C, which is not body temperature
>     37 C,
>      > this is not realistic approach,
>      > If my interest is to obtain data that respects the human body
>     condition
>      > can I to setting the temperature at 310 = 37 C or a make mistake and
>      > obtain artefacts data.
>      >
> 
>     The reason for using 323 K in the case of DPPC is that (1) it is a
>     common
>     experimental temperature and (2) it is above the phase-transition
>     temperature
>     for this lipid.  Anywhere below 315 K or so and your membrane will
>     enter a gel
>     phase, which is not representative of the membrane properties in
>     vivo.  Working
>     with DPPC thus involves a tradeoff - you can either produce a liquid
>     phase (like
>     in vivo) or physiological temperature (while losing the physical
>     properties
>     associated with cellular membranes).  The latter is often
>     disfavored, but the
>     end result is that DPPC is simply a poor choice to represent cell
>     membranes, but
>     is often a useful in vitro model, depending on your aims and
>     available data.
> 
>     -Justin
> 
> 
>  
> My aim is to obtain a good model for analyzing a receptor protein (not 
> channel).
> I prepared a system with DPPC CHOL and Protein, but  I am not sure fore 
> only temperature.
> 
> "The latter is often disfavored, but the end result is that DPPC is 
> simply a poor choice to represent cell membranes,
> but is often a useful in vitro model, depending on your aims and 
> available data."
> 
> What kind of lipid you suggest me, in vision of system indicated before 
> DPPC CHOL PROTEIN.
> I am interesting to understand if the conformation of protein is 
> mantained in diff % of CHOL.
> 

Well, if you're convinced you want to model DPPC/cholesterol membranes, then I'm 
not going to try to suggest you do anything else.  Only you know what your goals 
are and what experimental observables you're trying to reproduce or expand upon. 
  A DPPC/cholesterol mixture does not represent human cell membranes very well, 
but this information is specific to different cell types.

If you just want to measure the effects of cholesterol on some arbitrary lipid 
model, then it doesn't much matter what you use, but you'll have to deal with 
the assumption that pure DPPC would inherently be in the gel phase in vivo. 
Cholesterol will augment this effect, so it is hard to say what temperature you 
should use.  If you state the assumption that pure DPPC should be simulated at 
roughly 323 K and everything is relative to that, it's part of the 
interpretation of your results.

-Justin

-- 
========================================

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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