Main-chain conformation

The loop region between the two a helices binds the calcium atom. Carboxyl side chains from Asp and Glu, main-chain C =0 and H2O form the ligands to the metal atom (see Figure 2.13b). Thus both the specific main-chain conformation of the loop and specific side chains are required to provide the function of this motif. The helix-loop-helix motif provides a scaffold that holds the calcium ligands in the proper position to bind and release calcium. 

In order to examine whether this sequence gave a fold similar to the template, the corresponding peptide was synthesized and its structure experimentally determined by NMR methods. The result is shown in Figure 17.15 and compared to the design target whose main chain conformation is identical to that of the Zif 268 template. The folds are remarkably similar even though there are some differences in the loop region between the two p strands. The core of the molecule, which comprises seven hydrophobic side chains, is well-ordered whereas the termini are disordered. The root mean square deviation of the main chain atoms are 2.0 A for residues 3 to 26 and 1.0 A for residues 8 to 26. 

Figure 17.15 Schematic diagrams of the main-chain conformations of the second zinc finger domain of Zif 268 (red) and the designed peptide FSD-1 (blue). The zinc finger domain is stabilized by a zinc atom whereas FSD-1 is stabilized by hydrophobic interactions between the p strands and the a helix. (Adapted from B.I. Dahiyat and S.L. Mayo, Science 278 82-87, 1997.)...

Although the main-chain conformations of polysilanes have been described as random coil, 73- (deviant helical), 157 (transoid helical), and 2i (all anti, planar) structures, it is now generally accepted that most polysilanes tend to adopt helical main-chain structures, regardless of side groups and temperature.39 It... 

In this part, two series of 44 copolymers with coiled main-chain structures and 45 copolymers with stiff main-chain conformations were described. It was concluded that both optically inactive 42 and 43 adopt helical conformations with an equal proportion of P and M screw senses by means of UV and CD spectra as well as molecular mechanics calculations. A marked positive cooperative induction effect of the preferential screw sense in 44 and 45 copolymers was found. However, there is a marked difference in the helical cooperativity between 44 and 45, probably because of the differences in their global and local conformations. This difference can be related to the persistence of the helical conformation against defects allowing change of... 

By their nature, and in contrast with microscopic and scattering techniques that are used to elucidate long-ranged structure, spectroscopic methods interrogate short-range structure such as interactions between fixed ions in side chains and counterions, main chain conformations and conformational dynamics, and the fundamental hopping events of water molecules. The most common methods involve infrared (mid-IR and to a much lesser extent near- and far-IR) and solid-state NMR spectroscopies, although other approaches, such as molecular probes, have been utilized. 

The ORD and CD curves of optically active polymers containing chromo-phoric groups show that the chromophores can be asymmetrically perturbed by the chirality of the substituents and of the main chain conformation. This is the case with poly( ec-butyl vinyl ketone) (377), which presents a Cotton effect at 292 nm, its intensity being greater in the prevalently isotactic polymer than in the atactic polymer. 

B. Secondary Structural Elements and Main-Chain Conformations. 109... 

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