I have a polymer with a single amino acid sidechain and some linear linker groups. CD studies indicate presence of peptide like beta structures. The structure is very compact in solution as seen from MD simulations and is dominated by presence of salt bridges.
How can analyse presence of ordered structure such as beta strands/sheet in this polymer? Or is there a way to visualise ribbon or CA trace in some molecular modelling software?
Have you considered X-ray scattering or FTIR? For ordered beta sheet structures, you may be able to detect by simple fluorometric dye binding assays using Congo Red or Thioflavin T.
CD is actually a great method for this. Since it is sensitive to peptide backbone, you already have one meaningful suggestion of beta sheet. You might want to look at the old Curtis Johnson papers about CD and protein structure, such as http://www.sciencedirect.com/science/article/pii/0003269786902411
To test for 'order', you might consider doing a classical denaturation curve in the CD, using either guanidine or urea. 'Proof' of structure can come from your native CD spectra, as you mentioned, and then the ability to remove that structure by chemical denaturation.
If your single amino acid happens to be an aromatic, you might have a chance at doing one of several fluorescence measurements to get some sort of physical measurement of structure: quenching, polarization, or possibly energy transfer.
This reference may be useful:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092812/pdf/nihms270730.pdf
but actual experimental measurements by CD (as stated above) are often preferable in my experience.
Hi Neha,
As said before, CD is a great experiment to study your protein. To analyze the secondary structure behavior in you MD simulation you can use the DSSP algorithm, which compute intra-backbone hydrogen bonds and the data can be easily plotted with GNUplot to visualize changes of secondary structure elements over time.
The CD signal in the near UV region used in for secondary structure analysis is dominated by the backbone signal with only a minor contribution from the side-chains.
You can use the standard analysis then if the backbone of your polymer is the same as a peptide. If it is not, you will have to form a basis set by getting the polymer in different secondary structures. This will probably be difficult. Trifluoroethanol will induce helices in most peptides. I dont know of a beta-sheet forming solvent.
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