Circular Dichroism (CD) Spectroscopy for determine secondary structure of enzyme.
Dear Navdeep Raghuwanshi ,
It is not entirely sure what your question is. If you mean that the percentages alpha helix and beta sheet does not add up to 100% then this is indeed possible. CD is pretty good (and accurate) when it comes to these secondary structural elements, the remaining roughly 50% is ‘something else’ (depending on the definition, deconvolution program used etc. it can be defined as unstructured, random coil, other structural elements like extended helix etc.).
I presume that the (3D-)structure is not known (yet), otherwise you can use/check for example UniProt (https://www.uniprot.org ).
Personally, I would suggest the following steps:
-Perform secondary structure predictions. See for example for a selection of the various programs available: Article The role and significance of potential lipid-binding regions...
-Use at least two different deconvolution programs (Google “circular dichroism deconvolution software” for some good suggestions)
So, you get a good idea what to expect and whether your experimental finding make sense. Do realize that performing one experiment (under one circumstance) might not be the most ‘accurate’ one. A technique like circular dichroism is perhaps not the most accurate one for ‘absolute’ values of alpha helix percentages etc. but is extremely useful to monitor changes while changing parameters like temperature, pH, ion strength etc.
Hopefully this answers your question somewhat.
Best regards.
Thank you very much sir for your valuable suggestions.
Best Regards
Navdeep
Dear Navdeep Raghuwanshi
I definitely agree with what Rob Keller wrote.
I would also add it's important to pay attention to the deconvolution you've done, not trusting the figures right away, since two different data sets might lead to two distinct results with sometimes large discrepancies in between.
An other point concerns the experiment itself. Larger the wavelength range, better it is. For accurate secondary structure estimate, it's good to be able to record data at least below 190 nm.
Last but not least, the new AI program AlphaFold might be interresting to run in order to see whether your deconvolution is consistent or not with the struture prediction. Of course, this is only a prediction program but it can be used as the programs for secondary structure predictions are.
Best regards
Yves
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Enzymology
- Enzymes