[gmx-users] coiled coil unfolding

Marzinek, Jan j.marzinek10 at imperial.ac.uk
Mon Jul 4 10:24:03 CEST 2011

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?



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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