Asparagine-ladders

Fig. 2. Ball-and-stick representations of two differently oriented asparagine ladders of (A) W-arcade taken from the crystal structures of pectate lyase C (Lietzke et al., 1996) and (b) ppl-arcade taken from l DP-.V-aretylglucosamine acyltransferase (Raetz and Roderick, 1995). b, l, and so on refer to a one-letter conformational code (Fig. IOC). The ladders are viewed from within the respective /(-solenoids. The arrow shows the orientation (N- to C-terminal) of the solenoid. Oxygen atoms are in red, nitrogen in blue, and carbon in green. Dotted lines designate H-bonds of side chains (red) and inter-coil H-bonds of the polypeptide backbone (black). Except for the ladder-forming asparagines, only the backbones of the coils are shown. Panels are reprinted from Hennetin et al. (2006) with the permission of the publisher.

I-Solenoid repeats usually have several x or x x sequence patterns that correspond to the /1-strands (here, denotes an apolar residue, and x is mostly polar but can be any residue except pro line). The middle -position in x x usually has a bulky apolar residue, while -residues in positions close to turns are often alanine, glycine, serine, or threonine. These positions are also occupied by asparagine residues that stack to form H-bonded ladders inside the /1-solenoid. The strand-associated x and x x patterns are interrupted by regions enriched in polar residues and glycine (Hennetin et al., 2006). These are regions of turns and loops. The long loops frequently contain proline residues. In several /1-solenoids, the alternation of apolar and polar residues that is typical for /1-strands is not well observed and outside positions are occupied by apolar residues. 

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