I am trying to find the permeation pathway of a Zinc+2 ion on a TM transporter, the Zinc is found in the crystal, but the SMD does not work properly, it does not move the ion, or it destroy the membrane protein system if I pull too hard. I have also done 500 ns of normal MD, the Zinc is so charged that I guess the force field electrostatic parameters don’t allow it to move from its initial stable position.
QUESTION:
Is there an alternative technique to learn about the permeatin pathway of a zinc+2 ion moves through the membrane in AMBER???
The initial position of the ion is known…
THanks!!!
Fabian
Fabian Glaser PhD
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
> On 4 Jan 2017, at 13:39, Fabian Glaser <fabian.glaser.gmail.com> wrote:
>
> Sorry I didn't explain it properly, the starting position is inside the tunnel... I want to discover the path the ion takes going out from the tunnel, without pulling.... Nothing happens....
>
> But i don't know how to do it properly....
>
> Thanks again!!!
>
> Fabian
>
> On Jan 4, 2017 13:34, "Huang Jing" <jing.huang8911.gmail.com <mailto:jing.huang8911.gmail.com>> wrote:
> In my opinion, it is not necessary to pull the Zn atoms inside the tunnel
> artifically; Zn atoms would go inside automatically in the long-time
> molecular dynamics procedure, if the transformation is turely happened;
> Jing
>
> On Wed, Jan 4, 2017 at 12:24 PM, Fabian gmail <fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com>>
> wrote:
>
> > Hi Jing,
> >
> > Thanks for your answer, my system is the Yiip transporter, PDB 3h90, which
> > has crystallographic Zincs, the one I am trying to pull it is indeed inside
> > the tunnel, I really don’t have much experience with SMD, I do have with
> > MD, I am trying to pull only the ion inside the channel to the
> > extracellular side, but I don’t know really what is the correct way to do
> > it, it looks like it is so strongly attached electrostatically to its
> > surroundings, that I need to apply to much force, and the vector in amber
> > is problematic also…
> >
> > I constructed the system with CHARMM GUI for membrane builders, it worked
> > fine, and a simple simulation of 500 ns also worked fine, but the ion does
> > not move from its initial position. The Zn+2 I am trying to pull is Zn4 on
> > chain A using a dimer. Any suggestion or examples will be more than
> > welcomed.
> >
> > Best regards,
> >
> > Fabian
> >
> >
> > Fabian Glaser PhD
> > Head of the Structural Bioinformatics section
> > Bioinformatics Knowledge Unit - BKU
> > The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
> > Engineering
> > Technion - Israel Institute of Technology, Haifa, Israel
> >
> >
> >
> > > On 4 Jan 2017, at 12:07, Huang Jing <jing.huang8911.gmail.com <mailto:jing.huang8911.gmail.com>> wrote:
> > >
> > > It is diffcult to answer, as it is uncertain what your system/model looks
> > > like;
> > > your system is (Zn2+ + transporter tunnel) and then the SMD is applied to
> > > the whole system ?
> > >
> > > jing
> > >
> > > On Wed, Jan 4, 2017 at 11:33 AM, Fabian gmail <fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com>>
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> I am trying to perform SMD with a Zinc +2 ion inside a transporter
> > tunnel,
> > >> but either the Zn does not move at all, or if apply too much force the
> > >> system is destroyed, or I am doing something wrong….
> > >>
> > >> Can anyone please direct me to some good paper using amber for this
> > >> specific purpose?
> > >> Meaning trying to pull an ion from its initial X-ray position out of the
> > >> transmembrane region of a transporter?
> > >>
> > >> I am starting to think that amber is not well suited for treating this
> > >> specific question or that the forcefield parameters for Zn+2 are not
> > good
> > >> enough. Another thing that is probably making the work more difficult is
> > >> that the vector I am using to pull is centered in a water molecule on
> > the
> > >> approximate direction of the channel exit, but obviously the channel is
> > not
> > >> a vector…
> > >>
> > >> Anyway any paper or review or information that could help me to make
> > this
> > >> experiment more correct will greatly help me.
> > >>
> > >> Thanks!!
> > >>
> > >> Fabian
> > >>
> > >> Fabian Glaser PhD
> > >> Head of the Structural Bioinformatics section
> > >> Bioinformatics Knowledge Unit - BKU
> > >> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
> > >> Engineering
> > >> Technion - Israel Institute of Technology, Haifa, Israel
> > >>
> > >>
> > >>
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Received on Wed Jan 04 2017 - 05:30:04 PST
