Helix definition

Different side chains have been found to have weak but definite preferences either for or against being in a helices. Thus Ala (A), Glu (E), Leu (L), and Met (M) are good a-helix formers, while Pro (P), Gly (G), Tyr (Y), and Ser (S) are very poor. Such preferences were central to all early attempts to predict secondary structure from amino acid sequence, but they are not strong enough to give accurate predictions. 

The three-dimensional conformation of a protein is called its tertiary structure. An a-helix can be either twisted, folded, or folded and twisted into a definite geometric pattern. These structures are stabilized by dispersion forces, hydrogen bonding, and other intermo-lecular forces. 

While it is reasonable to assume that kinks are formed at the site of the covalent binding of BaPDE (34), it is also possible that such bends arise elsewhere on the double helix, due to the known formation of nicks and single-strand breaks (35,36). Therefore, the existence of kinks in the DNA helix at site I or site II binding sites should be further investigated, before such a model can be adopted definitively. 

The reflections include a particular g in which the dislocation is invisible (i.e., g b = 0 when b is normal to the reflecting plane). With these criteria in diffraction contrast, one can determine the character of the defect, e.g., screw (where b is parallel to the screw dislocation line or axis), edge (with b normal to the line), or partial (incomplete) dislocations. The dislocations are termed screw or edge, because in the former the displacement vector forms a helix and in the latter the circuit around the dislocation exhibits its most characteristic feature, the half-plane edge. By definition, a partial dislocation has a stacking fault on one side of it, and the fault is terminated by the dislocation (23-25). The nature of dislocations is important in understanding how defects form and grow at a catalyst surface, as well as their critical role in catalysis (3,4). 

Another basic property of solenoids is their twist. This parameter reflects the fact that successive coils are not stacked exactly above one another but with a small angular offset. Twist may be defined in relation to reference points at corresponding positions in consecutive coils (Fig. 1A). When connected, these points form a helix. The sense of the twist is given by the hand of this helix as it winds around the solenoid axis. Note that the definition of protein solenoid twist (Kobe and Kajava, 2000) differs from the usual definition of the twist in /1-sheets which is defined by the twist of /(-strands... 

With 3.6 residues per turn, side chains protrude from the a-helix at about every 100° in azimuth. Since the commonest location for a helix is along the outside of the protein, there is a tendency for side chains to change from hydrophobic to hydrophilic with a periodicity of three to four residues (Schiffer and Edmundson, 1967). This trend can sometimes be seen in the sequence, but it is not strong enough for reliable prediction by itself. Different residues have weak but definite preferences either for or against being in a-helix Ala, Glu, Leu,... 

When the helix amount increases the medium changes from a viscous liquid (sol) to an elastic solid (gel). The kinetics of gelation depends strongly on the quenching temperature. The rheological measurements that we performed are particularly focused on the sol-gel transition and on the definition of the "gel point". The greatest difficulty encountered is due to the weakness of the bonds which can easily be destroyed by the mechanical stress. 

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