How to convert the cd data to percent alpha helix by cdnn software?
Answers
I recently performed CD analysis for my protein of interest in 50mM sodium phosphate buffer. The curve that I got had a dip at 218 nm and 208 nm with a peak at 195 nm ( Keeping in mind that alpha helix has a dip at 222 nm and 208 and a peak at 193 nm whereas beta sheet has a dip at 218 nm and a peak at 195 nm). What can I infer from this data about the secondary structure of my protein. Is it alpha helix or beta sheet or a mixture of both of them. Also, how can I justify the presence of dips and peaks characteristic for both alpha helix and beta sheet
Answer:
Answer:Alpha-helices have 3.6 amino acid residues per turn, ie a helix 36 amino acids long would form 10 turns. The separation of residues along the helix axis is 5.4/3.6 or 1.5 Angstroms, ie the alpha-helix has a rise per residue of 1.5 Angstroms