Solenoid proteins

Here, we will use the term /(-solenoid broadly, as it unites these essentially similar structures in a single structural category, at the same time alluding to their membership of the larger family of solenoid proteins. 

The repeat sequences in solenoid proteins are often so imperfect that it is difficult to identify them without knowledge of the 3D structure or other supplementary information. In highly regular /1-solenoids, such as antifreeze proteins (Leinala et al., 2002 Liou et al., 2000) or YadA adhesin (Nummelin et al., 2004), the repeats are of the same length and sequence similarity between the repeats is discernible (so-called overt repeats). Frequently, however, the repeats in a given /1-solenoid vary in length because additional residues may be inserted at turn sites without disrupting the pattern of /1-strands that stabilizes the structure (Steinbacher et al., 1994 Yoder et al., 1993). In these cases, the structural repeats are not apparent as sequence repeats (covert repeats). 

Fig. 12. A set of recurring /8-arches found in //-solenoid proteins. In these schematized diagrams, the //-strands are shortened and include only one residue from each of the //-strands. Curved black arrows denote the polypeptide backbone. Blue, pink, and green circles show the locations of polar, apolar, and glycine side chains within the //-arches, respectively. Open circles indicate positions that are not preferentially occupied by any particular type of residues. Letters inside some circles indicate certain amino acid residues which occur frequently (>30%) in particular positions. Italic letters describe / -arc conformations (Fig. 10C). The /8-arches cluster into several groups, depending on the value of their turn-angles 90° in violet, 120° in blue, and 180° in orange. The five-residue /8-arch can be represented by two 90° /8-arcs (red) and an inverted /8-arch is in green. The inset demonstrates the locations of these /8-arch modules within T-, O-, R-, and L-type /8-solenoids. Black linear modules indicate /8-strand extensions.

In view of the consideration that /(-solenoids and /(-arcades may also be structural elements of amyloid fibrils (Kajava et al., 2004 Lazo and Downing, 1998 Margittai and Langen, 2004 Pickersgill, 2003), sequence-based detection and structure prediction of /(-solenoid proteins are pertinent to the identification of amyloidogenic sequences and the elucidation of amyloid fibril structures. As with /(-solenoid domains, amyloidogenic regions of... 

An understanding of the relationships between sequence, structure, and function of /l-solenoid proteins also opens the way for successful de novo molecular design of such molecules, with applications in nanotechnology or biomaterial studies. For example, these structures may allow the assembly of rigid and regular nanoscale lattices and display platforms (Hyman et aL, 2002) that are also durable in their resistance to high temperature, proteases, and other extreme conditions. 

Hennetin, J., Jullian, B., Steven, A. C., and Kajava, A. V. (2006). Standard conformations of beta-arches in beta-solenoid proteins. / Mol. Biol. 358, 1094—1105. 

---