[gmx-users] coiled coil unfolding

[Marzinek, Jan]

Dear Gromacs Users,



I am running the simualtions between ligands (10-30) and protein - coiled coil segment. My ligand is strongly hydrophobic and the hydrohpohobic strand between two monomers is obviously hidden. I found that my proetin is unfloding from terminals, two strands open allowing ligands to come into hydrophobic residues - the helical structure is partly destroyed as well as coiled coil.

That sounds ok in terms of hydrophobicity.



However, maybe I should run simulation with constrained backbone and coiled coil? What do you think?



Regards,



Jan






===========================================================
Jan Marzinek
PhD Candidate
Centre for Process Systems Engineering
Department of Chemical Engineering
Imperial College London
South Kensington Campus
London SW7 2AZ
E: j.marzinek10 at imperial.ac.uk<mailto:j.marzinek10 at imperial.ac.uk>
M: +44(0)7411 640 552
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