normal Protein conformational changes

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10 years 1 month ago #3882 by dariush
Protein conformational changes was created by dariush
Hi All,

I know it is not feasible to study protein folding/unfolding using MARTINI. However, when I use ElNeDyn force field, I can monitor conformational changes, using RMSD, in some extent.
Could you please let me know whether this RMSD results is meaningful? How much I can trust on RMSD results?
In the system containing membrane-protein, I could see that strong interactions represent higher RMSD values for protein (about 0.3nm) while weak interactions give lower RMSD (about 0.2-0.25 nm). I have to mention that it is known that my protein undergoes partial unfolding during the strong interactions.

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9 years 11 months ago #4014 by xavier
Replied by xavier on topic Protein conformational changes
In case this still applies: the RMSD is nothing else than a measure of the deformation of an object, e.g. a protein, from a reference. It does not give more information. As such you can trust the values.

Then to infer any meaningful interpretation on their values you have to convince yourself and a reader that the changes are indeed representative of a change … may be localising the deformation might help.

dariush wrote: Hi All,

I know it is not feasible to study protein folding/unfolding using MARTINI. However, when I use ElNeDyn force field, I can monitor conformational changes, using RMSD, in some extent.
Could you please let me know whether this RMSD results is meaningful? How much I can trust on RMSD results?
In the system containing membrane-protein, I could see that strong interactions represent higher RMSD values for protein (about 0.3nm) while weak interactions give lower RMSD (about 0.2-0.25 nm). I have to mention that it is known that my protein undergoes partial unfolding during the strong interactions.

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