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Hi, I have a protein in which two domains (that can be homology modeled with a reasonably high degree of confidence though obviously not beyond question) are connected by a 120 amino acid linker, the whole protein is around 600 amino acids. I have observed by CD that when a ligand binds there is a decrease in alpha helix and an increase in beta sheet of a magnitude that would correspond to around 60 amino acids moving from helix to sheet. Small angle x-ray scattering shows a compaction of the structure on ligand binding. My question is, does anyone know of a way of analysing the primary sequence to identify where these structural changes are most likely to occur? I think that low probability scores in the secondary structure prediction might indicate an element that could exist in two secondary structure states but this seems a little unsatisfying. Thanks for your suggestions. Regards, Nathan _________________________________ Nathan Cowieson Monash Center for Synchrotron Science Monash University Clayton VIC 3800 Tel: +61 3 9902 0117 Mob: 0418 226406 [log in to unmask] _________________________________