What does CD spectra at 230nm tell you about? I am working with Cu/Zn SOD which is a dimeric protein. I can see some changes in the far-UV spectra at and around 230nm. So I would like to know how an increase or decrease in ellipticity at 230nm signify?
Dear Nidhi
to interpret the CD spectras, you need to analize the general profile changes.
Which kind of experiments are you doing with Cu-Zn SOd1 --> thermal denaturation? metal depletion? unfolding using alcools or other compounds?
Which kind of changes did you observe at 230nm? increase of decrease?
Attached you can file the tipical profiles due to the different secondary structures.
The most of proteins are a mix of those structure and you can try to predict the relative % using different softwares as for example DICOPROT
https://dicroprot-prabi.ibcp.fr/
SOD1 is a strong beta barrel therefore during unfolding or fold shift you need to se a shift of the curve profile in the direction of one other.
here you can find a CD profile of SOD1 mature and aggregated that i perfomed many years ago during my pHD
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899188/figure/F2/
when i add the opportunity to face this intriguig protein.
best regards
Manuele
Dear Nidhidi,
Sometimes some tertiary interactions between aromatic residues form a minima at 230nm in CD. I got one with MPT63. Some people found it in SOD also. I'm referring some papers. Hope you'll find what you are looking for.
http://www.sciencedirect.com/science/article/pii/S0022283606011776
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010064#pone.0010064-Svensson1
I agree with Martinelli and just want to add that you should try the top two programs for deciphering percent of alpha and beta structure (one of which is mentioned above- Dichhroweb). Remember that the curves are a combination of the percentages of different structures and thus only after doing this analysis you can get the whole story.
Gustavo
Thank you Manuele. I am trying to standardize the time dependence for the reduction of the protein using TCEP, a reducing agent. Depending on the concentration and time frame it takes for the protein to reduce, I will be conducting other more relevaant experiemnts. So with the addition of TCEP with ascending concentrations, I see a decrease in ellipticity (less negative) around 218nm (the protein is largely and an increase in ellipticity around 230nm. I have been following the thesis of previous graduate students, who have plots of MRE against wavelenght at 230nm.
I will try the following links and see if it helps. Thanks a lot again!
Hey Amrita,
Thanks! I will browse through those papers and see if it helps!
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