I have 5 proteins and a single ligand. Only two has experimental data to support my study, however other 3 don't have any report. All 5 proteins containing a single ligand binding motif.
I docked the ligand conserved binding region of all proteins and performed a long range MD simulation in Gromacs. I did all the primary analysis like RMSD, Rg, H-bond, RMSF and even PCA. After PCA I found a different kind of global motions two proteins. Now how Can I say ... whats really going on during dynamics? And What will be the other analyses to distinguish and depicts the results ?? Kindly help in this regard.
How long are your simulations? Domain motions like opening and closing may take several hundred ns to observe, so anything shorter is simply insufficient to draw any conclusions.
Hi Jitendra,
Now that you are done with validating RMSD , RMSF etc. you can can get a better insight if you could analyse the MD frames. so that you can come to know what exactly is the conformational changes of ligand and protein during the simulation time. If you couldn't find any valid observation you can also try performing MD for another 10ns more.
Thank you !
The real questions are: (1) what "experimental data" (this is a very ambiguous term) do you have and (2) what do those data tell you about dynamics? Your two known systems should guide the analysis of the three unknown systems. Without establishing what you should analyze (which really should be largely decided before doing any actual simulations), you're just shooting in the dark on the three systems without experimental data. If you can provide more information about the available data and your objective, you'll stand a better chance of getting more useful replies. There is no boilerplate answer to what analysis you should do for any MD analysis.
Justin,
1. Experimental Data: mutational data on ligand binding. They stated some 5-6 amino acids are responsible for ligand binding.
and (2) in another experiment, two crystallographic structures show open and close conformation upon ligand binding.
In this context, (a) I am trying to observe the opening or, closing mechanism of five different proteins from MD trajectories.
(b) Wish to explore the ligand binding mechanism and the supposed critical amino acids involved in the interaction.
For this I already analyzed the PCA, RMSD, RG and H-bonds. I am thinking these analysis might not be sufficient what I am trying to explore. So I am thinking to do more analysis. However Don't know what type of analysis will give support to my study.
How long are your simulations? Domain motions like opening and closing may take several hundred ns to observe, so anything shorter is simply insufficient to draw any conclusions.
- Badges
- Science topic