Re: Peptide insertion into a membrane

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Oct 17 2013 - 15:08:10 CDT

In real life, I wouldn't expect the insertion of a peptide into a membrane
to take place in low nanosecond time scales; I speculate it would go a few
orders of magnitudes slower. If standard simulation techniques would make
it happen that much faster, then these techniques would not be an
acceptable representation of reality.

Trying to study phenomena that are beyond accessible simulation time
scales is an extremely common occurrence in the field, and there exists an
enormous body of literature on the subject, with many different tricks and
techniques available to obtain specific kinds of information
(thermodynamics, kinetics, mechanism...)

Increasing the temperature doesn't sound like a good idea because doing so
in a significant matter is likely to fatally distort the observables you
want to study in the first place. Instead, one thing that could be
considered is starting from an educated guess of how the peptide is
inserted, equilibrate for a long time, then slowly pull the peptide out of
the membrane with an external force. This is not entirely trivial to do,
but neither are the other options. Again, please refer to the literature.

On 10/17/2013 08:44 AM, Villalain Boullon, Jose wrote:
> Dear All,
>
> I have been looking for a similar problem in the forum, but I have been
> unable to find an answer for the problem I have.
>
> I am using the NAMD membrane tutorial to guide me in the simulation of a
> system composed of a relatively hydrophobic peptide and a membrane (POPC).
> We know, as observed experimentally, that the peptide inserts into the
> membrane, probably located at the membrane interface (observed through IR,
> DSC and fluorescence). I would like to study the insertion of the peptide
> into the membrane as well as its location; however, until now and after
> several nanoseconds the peptide remains always in the water phase. The
> peptide is unconstrained, I have used either constant pressure or constant
> pressure and area, PME and a temperature of 310K.
>
> Perhaps I should increase the temperature to a higher one as I have read
> in some works or I should increase steadily the temperature, but I do not
> know which is the next step I have to do in order to observe the
> penetration of the peptide into the membrane.
>
> Could you give me some suggestion about the steps I should do?. Thanks a
> lot in advance.
>
> Regards,
>
> Josť.
>

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