[gmx-users] Applying restraints into 'secondary structure' of a Protein

Mark Abraham mark.j.abraham at gmail.com
Tue Jan 13 07:43:50 CET 2015

On Tue, Jan 13, 2015 at 3:45 AM, Carlos Navarro Retamal <cnavarro at utalca.cl>

> Dear gromacs users,
> In order to analyse the adsorption process of a Protein (amphipatic
> protein) into a POPC membrane i’m placing several conformations at
> different distances of respective membrane (on different simulations) and
> performed regular MD simulations.
> My problem is that during the production phase the protein start to move
> randomly, loosing its amphipatic nature (and in that way, moving far from
> the POPC hydrophobic interface).

Does it do that in just-water also? If the structure is not rock-stable in
water, then your required minimum amount of sampling goes up immensely,
because you will have to sample many such transitions to observe adsorption
(when/if it happens).

So, my question is: Is there a way to maintain the tertiary structure
> ('overall’) of the protein (in my particular case, two alpha helices joined
> by a loop) allowing it to maintain its amphipatic nature during the
> simulation, helping it to interact peripherally to the hydrophobic
> interface of the membrane?

The traditional hacks for doing this include distance and orientation
restraints between parts of your protein. Whether those mask relevant
motion is difficult to say, since you're not going to be able to afford the
calculation that shows what you'd observe if the restraints were absent (or
you'd just do it that way).

In any case, maybe this is not the ideal strategy to analyse the
> interaction between this two macromolecules (protein interacting
> peripherally with respect to a bilayer membrane), so if you think in
> something else please feel free to make any suggestions.

The brute-force sampling required for such a study seems to require an
amount of current resources that is impossibly large. But I don't know of
an alternative.


> Best regards,
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 71 2 201<tel://T:%20(+56)%2071%202%20201> 798
> E: c<mailto:francisco.adasme at gmail.com>arlos.navarro87 at gmail.com or
> cnavarro at utalca.cl<mailto:fadasmec at utalca.cl>
> --
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