Re: Peptide insertion into a membrane

From: Lucas (lucasbleicher_at_gmail.com)
Date: Thu Oct 17 2013 - 17:33:38 CDT

Emad Tajkhorshid's group is using an interesting approach to attack
this problem:

Accelerating membrane insertion of peripheral proteins with a novel
membrane mimetic model.
http://www.ncbi.nlm.nih.gov/pubmed/22824277

I've met him a few months ago in a workshop and he said the required
templates and scripts should be available soon - which reminds me I
should contact him again...

2013/10/17 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>:
> 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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