I wish to calculate the extent of twisting that my protein undergoes. Is there a tool/script/software that will enable this calculation? It is a beta barrel domain of the protein that is undergoing this twist. Any help/ insights on how to go about such analysis would be immensely helpful. Thank you.
I have calculated twisting in protein. This protein has 12 sub-units and twist angle is average bending of all sub-units with respect to an axis, which passes through center of mass of upper and lower part. Details are given in Fig. 1C and D of following publication.
http://www.sciencedirect.com/science/article/pii/S000634951400126X
@Rajendra Kumar: Thank you so much for immediate response and link. Now I do get an understanding of how I could possibly go about with the calculation. But in my case the twist happens within a single domain and the protein is not a dimer or tetramer. The beta sheets undergo a right handed twist and my objective s to quantify the extent of this twisting. May I request you to kindly provide your valuable suggestions on these lines?
Thank you in advance.
As you wrote, I assume that beta-sheet is like a barrel. A principal axis can be constructed, which would be form be two center of mass of the atoms present at both end of the barrel. Then, by taking two atoms (C-alpha) present at both end of each strand, dihedral angle can be calculated. This angle will be tilt of each strand with respect to principal axis. Average of these angles will be twist angle of the barrel.
It is very similar to Fig. 1C and D, only difference is that you have to consider each strand separately as a sub-unit.
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