Tropomyosin structure prediction

A second widely used sequence-based approach relies on matrices of residue frequencies, pioneered by Parry (1982). He showed that the residue distribution at the seven heptad positions of the putative coiled-coil segments of myosin, tropomyosin, o-keratin, and hemaglutinin are asymmetric, and proposed a method by which the residue frequencies could be used to predict whether a sequence of unknown structure would form a coiled coil. This approach was implemented with modifications in... 

A recent study by Marti et al. (2007) used an in silico motif-based allergenicity prediction protocol to generate a recombinant peptide which showed the same IgE-reactivity as shrimp full-length tropomyosin. This motif-generating algorithm may be used in the future to identify major IgE-binding structures of other coiled-coil proteins. 

Fig. 12. Predicted approximate quaternary structure of troponin-tropomyosin. Tj and Ta, Ti and Tj regions of troponin T C, troponin C TM, tropomyosin O, position of N terminus O, position of C terminus. Symbols (l), ( ), and (3) indicate four calcium...

The ability to predict a band intensity profile opens up an important additional dimension in vibrational analysis. It means that we will be able to relate subtle spectral differences to small structural changes with a greater degree of confidence. Thus, it has been possible to confirm that an observed three-component contour of the amide I band of tropomyosin is indeed expected for a coiled-coil a-helix [142]. Extensions to understanding the normal modes of proteins become possible [143]. The systematic incorporation in an SDFF of dipoles and dipole fluxes to calculate IR intensities [144] will finally bring to the vibrational analysis of polymeric molecules the completeness and flexibility needed to make it a much more powerful structural tool. 

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