It is quite common to assume that CD spectra of a peptide with maximum ~200 nm and minimum at ~ 218 nm represents beta-sheet structure. what does they mean? if I get only one of them (in my case only minimum at 218 nm) what can I say about the structure?
Deer Elad,
Without a graph hard to be sure. Note that disordered proteins are caracterized by a minimum at 200nm that overlap with the beta sheet maximum. Thus, if your protein contain enough disordered segments (like loops), your result could be interpreted as mixed beta/loopy protein.
best
Antoine
That's true, Antoine. I've seen CD spectra of random-coiled peptides even with a slight maximum around 220 nm, which might reduce the intensity of the beta sheet minimum at 218 nm observed by Elad.
Elad, maybe your CD software package has an algorithm to estimate the secondary structural contributions from your spectrum? And if not, there are possibilities to do this online, for example here:
https://sites.bmb.colostate.edu/sreeram/CDPro/
Best regards,
Joscha
Dear Antoine and Joscha - I attach the spectrum. It looks to me like some weird variation of beta-sheet structure, but I wonder whether I can milk more structural information from this spectrum (parallel/anti-parallel, sheet twisting direction etc.)? moreover - I haven't experienced beta-sheet with no significant maximum at low wavelengths
Possibly a combination of some beta structure with disordered regions. The disordered region having a negative CD at 200 so counteracting the positive CD of the beta.
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