I am trying to simulate alpha synuclein (1xq8.pdb) in GROMACS using GROMOS53a6 ff. I have run it for 200 ns. At the end of simulation alpha helix protein losses its helical structure. I am not able to understand the cause behind this. I have uploaded the pymol image of both initial and final structure. Any type of suggestions are welcome.
The longest axis of the initial structure is about 158 Angstroms. And the unstructured tail may be very mobile, as indicated by crystallographic B-factors . . .
What was the solvent, water? What was the shape (and size) of the simulated system, box (x, y, z) or sphere (radius)? What boundary conditions were applied, periodic or nonperiodic? What was the cutoff for Coulombic interactions? How were electrostatic interactions beyond the cutoff treated?
Can you share the simulation setup (input files)?
SOlvent is water.
The SHape of the box - 17.68454 X 17.68454 X17.68454
Boundary condition periodic
Input files (.mdp) are attached.
Martin Klvana
Dear Abhik,
the structure you used for your simulation was determined in the presence of detergent micelles. The "horse-shoe" structure of a-syn appears bound to such micelles or to a lipid bilayer - to be more precise, to liposomes, as the curvature of the surface appears to play a role. See e.g. Article Alpha-Synuclein: Horseshoe Conformation on Intact Large Unil...
for more about this.If you simulated the protein in water it takes its unstructured form - a-syn in solution is an IDP, an intrinsically disordered protein.
Also this article is quite informative: Article Membrane interactions of intrinsically disordered proteins: ...
I hope that answers your question.
Best regards
Johann
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