Dears,
I run several Coarse grained simulations of a transmembrane protein using Martini FF.
In order to do a deep analysis of my systems, I backmapped a part of the trajectory from CG to AA.
I calculated local and maximum angle per helix over time using bendix (VMD) and their RMSD. From the analysis and the visualisation of the trajectory, I can notice big conformational changes within one helix: it became kinked and from the analysis of SS evolution I can also see local unfolding of the helical structure.. This helix contains proline residues (and we know that this one is helix breaker) but also a motif for cholesterol binding.
Now, I would like to investigate the reasons of the bending of the helix and its conformational behaviour: if it's due to cholesterol binding or other reasons.... Which type of analysis I can do here, any suggestions?
Also, my protein contains multiple TM helices and I would like to investigate/quantify the global structural rearrangements of the helices, for example distance between helices over time maybe? Any ideas about tools that I can use, please?
Finally, I would also like to compute the evolution of the volume of the pocket (binding site) over time. Which software I can use?
Thank's in advance for your help.
These kind of studies can't be done by running coarse-grained simulations - if you really want to track the changes on the conformations of the system, you should study in atomic scales.
I am a novice here. But I completely agree to Ramin Ekhteiari Salmas 's comment. Also is it really meaningful to run a simulation in CG manner and then make it AA?
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