Cell Physiology Source Book. A Molecular Approach by Nicholas Sperelakis

By Nicholas Sperelakis

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To determine ~, one merely has to look down the N-C`" axis using the C'-N bond as a reference and determine the angle made between the C'-N bond and the C`'-C' bond as shown in Fig. 7. To determine xtr, one uses the N-C`" bond as a reference and measures its angle with the C'-N bond. The dihedral angle co is the interpeptide dihedral angle, which is determined by rotation around the C'-N bond shown in Fig. 7. It can be measured by determining the angle made between the C`'-C' bond and the N-C" bond when sighting down the C'-N bond.

This detergent interacts with denatured proteins to form a strongly negatively charged complex (the negative charge arising from the SO24- groups of SDS). The proteins are first denatured by heat, then the SDS is added in large excess. The SDS-protein complexes all contain about the same negative charge because the SDS swamps out all of the protein charges. Since the charges are all the same, the proteins all separate from one another strictly on the basis of their sizes. From Eq. 36, the larger polypeptide chains of higher molecular weight migrate the most slowly while the lower molecular weight proteins migrate more rapidly towards the anode.

Using conformational energy calculations based on ECEPP, all of the low-energy minimum conformations for the 20 naturally occurring amino acids have been computed as a function of the dihedral angles 9 and ~ . In Fig. 8, these energies are plotted as isoenergetic contours in the same way that different elevations are plotted on contour maps. All of the amino acids have at least seven basic low-energy minima as indicated by the dots in Fig. 8. Note in this figure that large regions of the map are energetically forbidden and that the allowed (low-energy) regions of the map are relatively restricted (Fig.

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