Can the changes in radius of gyration of elongated protein also tell the compactness of the protein? If yes, is a difference in Rg of 30 A significant?
Thanks in advance.
Without context, there's no way to know. I would argue that Rg is not terribly useful for globular proteins, anyway, so using it to study intermediates of (mis)folding is a much better application.
Without context, there's no way to know. I would argue that Rg is not terribly useful for globular proteins, anyway, so using it to study intermediates of (mis)folding is a much better application.
One interesting exception, which highlight the similar view, as mentiond by Dr. Justin Lemkul:
Denatured State Ensembles with the Same Radii of Gyration Can Form Significantly Different Long-Range Contacts
http://pubs.acs.org/doi/abs/10.1021/bi4008337
In mechanical pulling simulations I found useful to describe the process in terms of time evolution of gyration radius of specific protein region. In that context, changes of 30 A were significant (see http://pubs.acs.org/doi/abs/10.1021/ct500283s).
However it is no general rule, it strongly depend on your specific question (significant for what??). I suggest also to check the relative difference between the gyration radius and not only the absolute difference and to see the single component of gyration tensor that could provide a more precise view of the elongation process.
The good thing about Rg is that it can be experimentally measured by techniques such as SAXS.
But it is a measure of compactness that reduces all shape information to a single number (as if everything was a shpere). For highly asymetric proteins, it can miss relevant shape changes. Maybe an ellipsoid can be more informative. Here you can play with the different shapes and see what Rg does capture and what it doesn't:
http://www.staff.tugraz.at/manfred.kriechbaum/xitami/java/rgcalc.html
Also be aware that Rg depends on the polypeptide chain length.
In addition, the experimental measurements depend on the technique employed. If you use DLS, for example, you get a hydrodynamic radius, whose quantitative ratio to Rg depends on the state of the protein (it is not the same for a compact globule than for something more similar to a random coil).
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