I have an alpha-helix embedded in a bilayer. I'm using gromacs 5+ and plumed 2.2. I want to encourage the protein to sample a 'rotation', so I can then put it up against another helix to find the best packing interface.
I have two sets of collective variable in mind so far
1) The COM distance between the helices (so the rotation is monitored over a range).
2) The helicity content in each helix.
But how do I monitor the rotation?
Thanks
Anthony
Hi Alejandro,
Thanks for the comment. My concern would be how to keep the reference points (for the angle) fixed during the simulation? Earlier I tried using two dihedral angles, where points A,B and C,D were two alpha-carbon atoms on the respective two helical proteins of the dimer. Unfortunately, as more potentials were applied, the alpha-carbons moved, rather than the whole protein. This gave the impression that the two proteins were rotating but in fact only a couple of their side chains were.
However, I see that the paper your linked has a mention of helical 'spin', I'll give that a good read. Many thanks.
Hi, I'm not sure, never have worked with such systems, but I think that ifs the helicity is also biased and the proteins are "deformed", then any geometric definition, pseudo-dihedral or inertia axis, etc, will be affected, ad they assume the system is semi-rigid, one option is to restrain the peptides rmsd and just spin them around..maybe
Hi Anthony,
I have the same question that you ask. I have studied and found to use "spinangle" for rotation of each helix and "distanceXY" for the distance in XY plane of two proteins, but I didnt know how to write a plumed.dat file base on these options. Can you help me? I searched for the template in plumed website but i couldnt find ant thing.
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