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

[Carlos Navarro Retamal]

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).
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?
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.
Best regards,
Carlos
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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>