[gmx-users] Protein-membrane system

[Justin A. Lemkul]

Jianguo Li wrote:
> Hi,
> 
> "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?
> 

Sounds like a job for a proper control.  If you see the same translocation in a 
pure bilayer under the same conditions, then it's not likely to be related to 
the presence of your protein, but rather an intrinsic feature of the model membrane.

-Justin

> Any comment is highly appreciated, thank you!
> 
> best regards,
> Jianguo
> 
> 
> ------------------------------------------------------------------------
> *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.
> 
> Cheers,
> Itamar.
> 
> 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> 
> <mailto:asegurac at ipn.mx <mailto:asegurac at ipn.mx>>; aldosegura at gmail.com 
> <mailto:aldosegura at gmail.com> <mailto: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 <mailto:Itamar.Kass at monash.edu>
> ============================================
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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

========================================