[gmx-users] How to choose lipid molecules?

[Jochen Hub]

liang wrote:
> Dear Jochen,
>
> Thanks for your information. Can you provide me some references about
> lipid types and properties,
> and the combimation of the recent "popular" membrance proteins (KcsA,
> OmpA, M2, Gramacidin A and Aquaporin) ?
> I have searched several publications, but still didn't get very useful
> information.
http://scholar.google.com/
I don't really know what to suggest. I think you should carefully read a
number of reviews and built upon the experience of your supervisor, if
possible. A nice start for Membranes can, e.g., be found in
"Bioelectrochemistry of Membranes", edited by Walz, Teissie, Milazzo.
And there are dozens of reviews on membrane channels. Check google scholar.

Cheers, Jochen


>
> Really thanks for your help, and i hope i would not be bothering you.
>
> Best regards,
>
> Liang
>
>
> ----- Original Message ----- From: "Jochen Hub" <jhub at gwdg.de>
> To: "liang" <petrucci123 at vip.sina.com>; "Discussion list for GROMACS
> users" <gmx-users at gromacs.org>
> Sent: Thursday, December 13, 2007 11:16 PM
> Subject: Re: [gmx-users] How to choose lipid molecules?
>
>
>> liang wrote:
>>> Dear all,
>>> I am a freshman to membrane protein simulation, and i was wondering
>>> how to choose lipid molecules for my system.
>>> As we know, there are lots of lipid molecules: DMPC, DPPC, POPE.....
>>> but how do people decide that which type of lipid to use? and what
>>> kinds of criteria should we follow?
>> Lipids differ in their chain length, chain saturation, head groups size.
>> There are, e.g., phospholipids, glycolipids. Some are ionic,
>> zwitter-ionic, or neutral. They differ in the phases they adopt at
>> whatever temperature, there are wedge-like and cone-like shapted lipids,
>> etc. There are parameters for some lipids available (including those you
>> mentioned), and for many there is no topology availabe (yet). Membranes
>> may include glycerin, ...
>>
>> I guess you need to think abount the quetion you want to address and
>> then choose the lipid you want to simulate. An important issue is, or
>> course, to simulate a lipid membrane which you may compare to
>> experiments.
>>
>> Cheers,
>> Jochen
>>
>>
>>> Thanks so much!
>>> Liang
>>> ------------------------------------------------------------------------
>>>
>>>
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>>
>> -- 
>> ************************************************
>> Jochen Hub
>> Max Planck Institute for Biophysical Chemistry
>> Computational biomolecular dynamics group
>> Am Fassberg 11
>> D-37077 Goettingen, Germany
>> Email: jhub[at]gwdg.de
>> ************************************************
>>
>>
>
>
> .
>


-- 
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************