I have tested two proteins, they are showing same elipticity pattern in far UV range? at 222nm negative elipticity changes only by 2 degrees, does this indicate something?
If not, how one can tell that there is no change in structure of both the proteins? or vice versa.
Hi Rakesh,
You didn't provide enough information for evaluating if a difference of 2 degrees indicates something.
Do you mean 2 degree after normalization to MRE ? If yes, 2 MRE is noisy and do not mean anything to me.
Do you mean 2 degrees in row measurements ? I guess you are talking about 2mdeg and not 2deg. However, impossible to know if this variation means something without information on experimental protein molar concentration, sequence length and path length.
Since two proteins have the same CD spectra, it suggests the secondary structure content are quite the same (but can be different tertiary structure). Thus, So far I know, there isn't any method to distinguish between structure of two protein since they both give the same CD spectra.
Good question. When it comes to CD and how much change in mdeg is meaningful to attribute it to structural change has been an age-old question. Look at percentage change in your values across the entire spectrum - if possible all the way down to ~190 nm. If overall percentage change is "low", it may not be meaningful to assign it to structural change. Finally it depends on which instrument and what method variability you established in the lab (baseline, S/N, operator variability etc). In other words, if the change in your measured value is above the LOQ (limit of quantitation) of the used method, then you have a real change. I know it sounds boring! But to establish a real change, we need to dig deeper. Good luck.
Hi it good question but there is not more information about your proteins because we used NMR to get the information about the structure in the solution. Good luck
Dear Rakesh Kumar ,
As said by Tapan K Das and Antoine Schramm it is presumably not significant and most likely caused by the fact that the two proteins have because of their pretty much similar CD spectrum a close to similar secondary structure. Did you check a secondary prediction? Is this what you expected? You could try a prediction by using one or more of the following examples:
http://bioinf.cs.ucl.ac.uk/psipred/
https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html
http://www.compbio.dundee.ac.uk/jpred/
Back to your question you could try to look for differences in terms of ionic strength, temperature (simply change the temperature or include complete melting curve measurements), depending on your protein you could look for differences as a result of possible protein-lipid interactions etc.
See for examples:
Article Anionic phospholipids are essential for α-helix formation of...
Chapter Characterization of helical junction zones in gelatin networ...
Chapter Characterization of helical structures in gelatin networks a...
Best regards.
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