[gmx-users] Protein-membrane system

Jianguo Li ljggmx at yahoo.com.sg
Thu Feb 17 03:53:37 CET 2011


"3000 water molecule per lipids per second" corresponds to 0.000384 water 
molecules transferred across the membrane per nano second (assume the system 
contains 128 lipids). It seems water translocation should not be observed in a 
simulation of 10 ns, but I am not sure. And I only find one reference 
paper(Biophysical Journal, Volume 96, 2009, pg4493–4501) about the water 
translocation across the membrane, in which a asymmetric membrane is used.  

I also have similar observations for my protein-membrane system. I observed 
10~15 times water translocation arosss the membrane during 100 ns simulation 
when my protein adsorbed on the membrane. I am wondering these water 
translocation is normal in all-atom simulations or they are due to the 
protein-induced membrane deformation?

Any comment is highly appreciated, thank you!

best regards,

From: Itamar Kass <itamar.kass at monash.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, 17 February 2011 07:20:19
Subject: Re: [gmx-users] Protein-membrane system

Dear Aldo,

It is totally OK to see water molecules within the bilayer, both in simulations 
and real life. If I am not totally wrong, 3000 water molecule per lipids per 
second are being transferred across the bilayer without any protein involvement.

If your system is stable, the lipids density profile seems OK as well as its the 
thickness, you are fine.


On 17/02/11 5:48 AM, Justin A. Lemkul wrote:
> Aldo Segura wrote:
>> Dear gmx-users,
>> I completed a MD (10 ns) of my protein-membrane system. When I perform a visual 
>>inspection (VMD) of md_0_1.gro file I observed a few water molecules within the 
>>bilayer. In previous steps (e.g. equilibration) this was not observed. Could be 
>>expected such behavior?
> Membrane protein systems take a long time (tens of ns or maybe more) to 
>equilibrate, so some water may drift in and out during the initial few ns as 
>voids in the lipids open and close.  Nothing to worry about, unless for some 
>reason they persist out past the expected equilibration time.
> -Justin
>> Best regards,
>> *//*
>> */============================== =========
>> Aldo Segura-Cabrera
>> Laboratorio de Bioinformática
>> Centro de Biotecnología Genómica
>> Instituto Politécnico Nacional
>> Blvd. Del Maestro esquina Elías Piña, 88710
>> Reynosa, Tamaulipas, México.
>> (899)9243627 ext. 87747
>> e-mail: asegurac at ipn.mx <mailto:asegurac at ipn.mx>; aldosegura at gmail.com 
>><mailto:aldosegura at gmail.com>
>> ============================== ===========/*


"In theory, there is no difference between theory and practice. But, in 
practice, there is." - Jan L.A. van de Snepscheut

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu

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