Proteins direct identification/localization

Another subsynaptic fraction derived directly from presynaptic specializations, the presynaptic particle fraction (PPF) can be separated from PSD by adjusting the pH of Triton X-100 extraction of isolated trans-synaptic scaffolds. As one might expect, it has been shown that the major proteins of the PPF, clathrin and dynamin, are concentrated in the presynaptic compartment (Phillips et al. 2005). These investigators used multidimensional protein identification technology (MudPIT) to compare the PPF and the PSD fraction. Of 341 proteins identified, 50 localized in the PPF, 231 in the PSD fraction, and 60 were found to be common to both fractions. The PPF was also characterized by a low proportion of actin and actin-associated proteins along with a high proportion of vesicle proteins. The authors concluded that the PPF consists of presynaptic proteins not cormected to the actin-based synaptic framework and that clathrin may be an anchorage scaffold for many presynaptic proteins. 

While the structure and force field uniquely determine the vibrational frequencies of the molecule, the structure cannot in general be obtained directly from the spectrum. However, to a useful approximation, the atomic displacements in many of the vibrational modes of a large molecule are concentrated in the motions of atoms in small chemical groups, and these localized modes are to a good approximation transferable between molecules. Therefore, in the early studies of peptides and proteins (Sutherland, 1952), efforts were directed mainly to the identification of such characteristic frequencies and the determination of their relation to the structure of the molecule. This kind of analysis depended on empirical correlations of the spectra of chemically similar molecules. 

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