Following a molecular dynamics simulations, one of the results obtained was related to radius of gyration. What is the importance of RoG with regards to protein structure and how to interpret the RoG data?
"The radius of gyration of a protein is a measure of its compactness. If a protein is stably folded, it will likely maintain a relatively steady value of Rg. If a protein unfolds, its Rg will change over time." - http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/10_analysis2.html
I'd love to hear an answer from someone who knew more than me.
Would this imply that in case of disordered regions, the RoG would fluctuate significantly?
From what I understand, and I don't have a complete understanding, it's not so much about how ordered or disordered the protein (I'm assuming that's what this is for) is, but more about how folded, or compact it is.
Radius of gyration is simply a measure of the distance between the centre of mass of the protein to both of it's termini, it has very little directly to do with order.
http://www.gromacs.org/Documentation/Terminology/Radius_of_Gyration
Dear Manas,
Radius of gyration as an indicator of protein structure compactness. It is concern with how can regular secondary structures are compactly packed in to 3D structure of protein.α proteins have the highest radius of gyration throughout the protein size range considered, suggesting a less tight packing as compared with β-and (α + β)-proteins. The lowest radius of gyration and, accordingly, the tightest packing are characteristic of α/β-proteins.
http://link.springer.com/article/10.1134/S0026893308040195
DISORDERED PROTEIN REGIONS AND RADIUS OF GYRATION
The radius of gyration of proteins unfolded by low pH, methanol, urea or guanidinium chloride are typically 1.5 to 2.5 times larger than the radius of gyration of the same proteins in their native globular states. Note however, that denaturation does not always result in complete conversion to extended coil formation,some structure may persist.
The time point where IDP adopts lowest energy, i.e more compactness can be observed from RoG(Radius of Gyration). Mostly during simulation time period IDPs adopts most compact structure.
read this paper:
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0112456&type=printable
Rg is a parameter to show the change in the protein structure compactness during a simulation.
in general, Rg value indicate the compactness of proteins....which in turn reflects its stability. the more it fluctuates the less it is stable at that point of time. hence, it plays a significant role during comparative studies.
please let me know if i have missed something.
An increase in RoG values implies a decrease in protein structure compactness, thereby suggesting increased flexibility and less stability.
RoG is used to determine the compactness of a protein. When a protein is very compact, it tends not to fold easily. RoG is usually ploted after MD for a protein-ligand complex. This elucidate the stability of the complex in addition to the RMSD.
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