motif identified for proteins of the right-handed β-helix family (Fig. 4) (46, 47). This correspondence led to a suggestion that the internalins would form a β-helix structure rather than the observed LRR structure (47). The β-helix structure is found in pectate lyases and forms a distinctive L-shaped repeat containing three β-strands. The greatest difference between the two repeat motifs occurs at position 19, which faces outward and is variable in the internalin LRR but is occupied by an inward-facing conserved hydrophobic residue in the β-helix motif. The close correspondence of these two motifs suggests a means by which to probe the basis for their formation.
Two structural positions of the InlB LRR are unique to the internalin family. Position 14 is outward facing and is usually occupied by an Asp that hydrogen bonds to main-chain atoms at the beginning of 310-helices (Fig. 3). Other residues capable of hydrogen bonding, including Ser, Thr, Asn, and Gln, are also found at this position (Fig. 1). Position 17 is generally occupied by a small amino acid, usually Gly, Pro, Ala, or Ser. It is located on the 310-helix, and a larger residue at this position would sterically clash with the preceding 310-helix. These two positions add to the eight inward-facing ones to yield the 10 positions conserved for structural reasons.
More than half the residues of the internalin LRR face outward, are variable, and can serve to define protein–protein interaction surfaces specific to each internalin. As with other LRR proteins, the interaction surfaces of the internalins are likely to be formed by the β-strand regions that constitute the concave faces of these molecules. The concave face has been observed to form the major binding surface in complexes of RI and U2LRR with their target proteins (41, 43) and is inferred to form the binding surface for rna1p (44). The sides of RI adjacent to the concave face are also involved in binding. In InlB, the concave face contains separate patches of hydrophobic and negatively charged residues that could constitute protein–protein interaction surfaces (39).
Sequence characteristics of the internalins also point to the concave face as being important to protein–protein interactions. Three-quarters of the hydrophobic residues predicted to be surface exposed in the L. monocytogenes internalins are located on the concave face (positions 3, 4, 6, 8, and 9) (Fig. 1). Likewise, greater than three-quarters of the negatively charged residues predicted to be surface exposed are also located on the concave face (Fig. 1). In general, the concave faces of the internalins possess the hydrophobic and negative charge characteristics observed for InlB. The sides adjacent to the concave face (positions 11 and 13 on one side, and positions 21 and 1 on the other) are highly enriched in positively charged residues, as also observed in InlB. In contrast to the distinctive pattern of residues found on the concave face and sides, the convex face (positions 16, 19, and 20) of the internalins appears to be relatively featureless (Fig. 1). The exception to this is InlC, for which the convex face is predicted to contain a small hydrophobic patch. Although the high sequence conservation of the internalin LRR allows strong predictions about protein–protein interaction sites based on the InlB structure, it does not lead as easily to predictions about target specificity.
The challenge for the future will be in identifying binding partners for individual internalins and in determining how the LRR structural motif is used to generate a variety of specific functional interactions.
M.M. was supported by National Institutes of Health Training Grant GM07240-24. This work was in part supported by a W. M. Keck Distinguished Young Scholar award and an American Heart Association grant (9930135N) to P.G.
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