Coiled coil structures deviations

Table 2. Energies (in kcal/mol) of the 10 lowest energy decoys of the final population with backbone RMS deviation to the NMR structure and secondary structure content. The first row designates the secondary structure content of the NMR structure.. The letters H and c indicate amino acids in Helix and coil structure respectively. Green letters indicate correct, red incorrect secondary structure.

Chemical shifts are very sensitive probes of the molecular environment of a spin. However, in many cases their dependence on the structure is complicated and either not fully understood or too intricate to allow the derivation of reliable conformational constraints [37, 38]. An exception in this respect are the deviations of 13C (and, to some extent, 1 xf) chemical shifts from their random coil values that are correlated with the local... 

Furthermore, in flexible linear peptides the chemical shifts are typical of random structures similar to nonfolded proteins. Deviation from these random shifts sometimes identifies specific conformational preferences. NH-proton chemical shifts depend strongly on external influences (solvent, temperature, concentration, specific sequence). Random coil shifts for these protons correlate less well than chemical shifts of the a-protons or a-carbonsJ19-261 Not only are the shift differences of different heterotopic protons similar, but also those of diastereotopic P-protons. A preferred side-chain conformation is normally only found when there is also a preferred backbone conformation. 

The first structure of a dimeric DmNcd construct (PDB code 2NCD amino acids 281-700 Sablin et al., 1998) turned out to be perfectly symmetric (by contrast to dimers of rat kinesin-1) the two molecules of a dimer are related by a crystallographic twofold axis. The symmetry axis coincides with the axis of the coiled-coil (Fig. 3C). A similar construct (PDB code 1CZ7 amino acids 295-700 Kozielski et al., 1999) crystallized in a different space group with two dimers per asymmetric unit. Although none of the dimers has a proper twofold symmetry, their conformation is not far from that. The deviation from perfect symmetry can be described by 2- and 10-degree torsions, respectively. 

After the assignment process is complete, various types of NMR data can be used to build up a picture of the secondary structure of the peptide (based on coupling constants, chemical shifts, and NOEs) and then, if required, a full 3D structure can be determined. Figure 6 shows some of this information for Vcl.l. As noted earlier, deviations from random coil chemical shifts provide an indication of secondary structure, and in the case of Vcl.l. a region of negative aH secondary shifts provides a first indication that the helix typically present in a-conotoxins is indeed present in Vcl.l (Fig. 6A). This conclusion is supported by the CSI, coupling, and NOE data in Fig. 6B. Finally, the 3D structure is shown in various representations in the lower panels of the figure (58). 

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