a question of protein subunit symmetry and normal coordinate analysis

[evidenso]

Hey
Im doing vibrational spectroscopy (Raman, nir, vis/uv) of a protein called C-reactive Protein. Its a symmetric molecule regarding the subunits http://en.wikipedia.org/wiki/C-reactive_protein

Then i wondered if one can apply normal coordinate analysis (using symmetry and group theory) to the molecule? does this make sense? will it give any information about forces between the subunits? or am I wrong? ;)

[Mike H]

Interesting question. Not entirely sure myself.

I know normal mode analysis has been used quite extensively in vibrational/Raman studies of metal centers in proteins, as well as in protein dynamics studies, looking within the protein and not among interacting monomers, leastways. I'm not familiar enough with the literature beyond that, although I do recall some work being done on using various scattering methods to study subunit motions within a larger protein (David Calloway, a biophysicist at NYU, was involved in this work). I dimly recall that there were some approximations made in the analysis of the scattering data, so you might not get as much detailed site-specific information as you'd like.

I would say try it and see what happens. Let us know how it works out!