My FTIR data is in % transmittance. I wish to determine the %beta sheet content,alpha helical content, beta turn content and anti beta content from this data. I tried using the Unnscrambler software but i dont seem to get the hang of it. Can someone please guide me?
In principle, you could apply curve fitting procedures on your amide I and/or amide III bands in order to estimate the content of the different secondary structures in your protein. There is a vast bibliography about the position of the different structures in the amides bands. Be aware of some problems: if you hte protein has an important water content, this adsorbe heavily in the mid-IR in the amide I range at about 1640 cm-1, more or less where alfa-helix appears. For this reason amide III curve fitting in FTIR appears more reliable. Moreover if your protein has a lot of aromatic residues, these would absorbe heavily both in the amide I ande amide III regions rendering very difficult the estimation of the secondary structure. If you can, try Raman spectroscopy or dueturated water as solvent.
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