[gmx-users] DPPC temperatur setting

[Justin A. Lemkul]

Please don't ignore requests about proper email etiquette.

>     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.
> 

Maybe I do have to repeat myself then.  Replying to a mess of unrelated content 
is inefficient and has distinct consequences on the clarity of the mailing list 
archive (which is already pretty bad, but please don't make it any worse).  Cut 
and paste the relevant text, reply, and delete the rest.

<snip>

>  
> I'm interested to analyze conformational change of receptor protein
> embedded in membrane. I already performed a dynamic whit only DPPC
> I utilized this lipid to see as it influence the conformation of 
> protein, but I want to realyze a experiment that simulate the membrane 
> as realistic as possible.
> In my first MD with DPPC/protein I found that my protein receptor tends 
> to increase the helices sizte, someone of the 7 helix tend pass from 
> alfa helix in p-helix and so on. I performed MD at 323 K  1 amt, my 
> protocoll is like your tutorial on KALP-15.
> 

Note that if you're using the same force field as the tutorial (53A6 + Berger 
lipids), the 53A6 force field has a tendency to produce pi-helical and 3-helical 
species that are not necessarily real.  Be careful in interpreting these 
observations if this is the case.

> "A DPPC/cholesterol mixture does not represent human cell membranes very 
> well, but this information is specific to different cell types.
> 
> But now I have some doubts on the use of lipid DPPC is not suitable to 
> build my realistic model, what you tink if I substitute it with DOPC.
> 

I've already told you that membrane composition is very specific to e.g. 
different cell types or even subcellular localization.  You need to do some work 
figuring out what an appropriate model would be in your case.

> Cholesterol will augment this effect, so it is hard to say what 
> temperature you should use.
> 
> I work on 323K in this way I obtain the transition face for DPPC. I want 
> just to see as the cholesterol influece the the "solvent" DPPC for my 
> proteins ( sorry for my english. I hope that you understand wath I mean)
> 
> 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.
> 
> I want to know if I add  cholesterol in DPPC membrane wath happen at 
> protein receptor and if the chol tend to clustering with the protein 
> receptor, I want to performing different MD with different % of CHOL.
> 

All that sounds reasonable, but you need to decide on what model to use, as I've 
said.  If you want to use DPPC, you have to operate under different, 
non-physiological conditions.  If you want to model physiological reality, you 
likely shouldn't be using DPPC as your primary lipid.

-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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