From: Karol Kaszuba (karol.kaszuba_at_moskit.uwm.edu.pl)
Date: Fri Oct 26 2007 - 04:57:35 CDT
Hello,
I am preparing 30ns simulation of big membrane x=130, y=130.
In properly equilibrated membrane I will insert a model of GPCR.
However I am not sure if a membrane of this size is still enough big for
my receptor. The problem is that my model has a long cytoplasmatic loop
and I am not sure about the mobility of this loop - does the loop will
escape outside the membrane.
The simulation of the bilayer will take a lot of time so I want to be sure
that membrane will be big enough.
I can solve this problem in two ways:
- increase the membrane size - I do not want to do it,
- move the receptor much more to the corner of bilayer.
1) And here is my question - does the stability of a simulation will be
influenced by the position of a protein. A picture with protein
positioned in bilayer can be found at
http://www.uwm.edu.pl/kfib/badania/bilayer130x130.jpg
2) Does the time of 30ns is sufficient to equilibrate a membrane of this
size ?
3) In the work of Kandt et al, 2007 (full title below) I found that the
protein cavities should be solvated however in the "Building Gramicidin
tutorial" the HOH molecules that overlaped protein were removed - if I
understand well overlap is not equal "to water which is inside but do not
overlap with protein" - in conclusion - HOH molecules should fill the
protein cavities - correct?
Christian Kandt , Walter L Ash , D Peter Tieleman
Methods. 2007 Apr ;41 (4):475-88 17367719
Setting up and running molecular dynamics simulations of membrane proteins.
Thank you in advance,
Regards,
Karol
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