In this figure, a pca plot is shown for different protein , protein complex systems depicting the essential subspace for these systems. I want to know how can I interpret these plots ? What information I can gain from it ?
Dear Sherif Arafa:
I have no context on what kind of coordinates were used to perform this analysis, but assuming that the PCA was done on cartesian coordinates and not internal coordinates, then you can say that the PCA gives you a new coordinate system that is orthogonal to each other, and corresponds to the displacement of your original coordinates (e.g. the XYZ coordinates of the protein) with the largest mean square fluctuation (i.e. with the largest variance).
If we assume that the displacements with the highest variance in a protein are linked to its essential conformational space (i.e. if they are the ones that vary the most, it is because they are the ones that are mostly allowed, for whatever reason...), then you expect that these fluctuations are linked to the function of the protein, since the protein would not move by random thermal fluctuations, but by concerted motions, although this is not necessarily always true in the PCA analysis!!!!
The fact that you observe clusters in this analysis means that there are certain conformations of your protein that are visited more regularly, and these are the ones that contribute most to fluctuations in the cartesian coordinates of your protein.
In this example you show, the PCA can tell you similar conformations in terms of fluctuations, but they may be still not linked to relevant conformations of the protein, since the clusters do not align on any axis, and never/ rarely pass through the origin (i.e. the conformations do not or rarely visit the average structure, and are not parallel to any of the vectors with the highest fluctuations).
I hope I helped you!
Good luck.
Edward Francisco Méndez Otálvaro Thanks so much.
I understand your point but this drives me to another question..
What does passing through the origin means ? and what is the average structure ?
The origin corresponds to the point where the X and Y coordinate axes are zero. The average structure is just that: The structure that results from averaging the XYZ Cartesian positions of your protein. The variance that explains the PCA analysis is based on how close or far the Cartesian positions of the protein are from the average structure.
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