X-ray crystal structures of two non-nucleoside analogue inhibitors bound to hepatitis C virus NS5B RNA-dependent RNA polymerase have been determined to 2.0 and 2.9 Å resolution. These noncompetitive inhibitors bind to the same site on the protein, ∼35 Å from the active site. The common features of binding include a large hydrophobic region and two hydrogen bonds between both oxygen atoms of a carboxylate group on the inhibitor and two main chain amide nitrogen atoms of Ser⁴⁷⁶ and Tyr⁴⁷⁷ on NS5B. The inhibitor-binding site lies at the base of the thumb domain, near its interface with the C-terminal extension of NS5B. The location of this inhibitor-binding site suggests that the binding of these inhibitors interferes with a conformational change essential for the activity of the polymerase.

Clostridium difficile toxins A and B are members of an important class of virulence factors known as large clostridial toxins (LCTs). Toxin action involves four major steps: receptor-mediated endocytosis, translocation of a catalytic glucosyltransferase domain across the membrane, release of the enzymatic moiety by autoproteolytic processing, and a glucosyltransferase-dependent inactivation of Rho family proteins. We have imaged toxin A (TcdA) and toxin B (TcdB) holotoxins by negative stain electron microscopy to show that these molecules are similar in structure. We then determined a 3D structure for TcdA and mapped the organization of its functional domains. The molecule has a “pincher-like” head corresponding to the delivery domain and two tails, long and short, corresponding to the receptor-binding and glucosyltransferase domains, respectively. A second structure, obtained at the acidic pH of an endosome, reveals a significant structural change in the delivery and glucosyltransferase domains, and thus provides a framework for understanding the molecular mechanism of LCT cellular intoxication.

The structural basis of carbohydrate recognition by rat liver mannose-binding protein (MBP-C) has been explored by determining the three-dimensional structure of the C-type carbohydrate-recognition domain (CRD) of MBP-C using x-ray crystallography. The structure was solved by molecular replacement using rat serum mannose-binding protein (MBP-A) as a search model and was refined to maximum Bragg spacings of 1.7 Å. Despite their almost identical folds, the dimeric structures formed by the two MBP CRDs differ dramatically. Complexes of MBP-C with methyl glycosides of mannose, N-acetylglucosamine, and fucose were prepared by soaking MBP-C crystals in solutions containing these sugars. Surprisingly, the pyranose ring of mannose is rotated 180° relative to the orientation observed previously in MBP-A, but the local interactions between sugar and protein are preserved. For each of the bound sugars, vicinal, equatorial hydroxyl groups equivalent to the 3- and 4-OH groups of mannose directly coordinate Ca²⁺ and form hydrogen bonds with residues also serving as Ca²⁺ ligands. Few interactions are observed between other parts of the sugar and the protein. A complex formed between free galactose and MBP-C reveals a similar mode of binding, with the anomeric hydroxyl group serving as one of the Ca²⁺ ligands. A second binding site for mannose has also been observed in one of two copies in the asymmetric unit at a sugar concentration of 1.3 M. These structures explain how MBPs recognize a wide range of monosaccharides and suggest how fine specificity differences between MBP-A and MBP-C may be achieved.

Clostridium difficile is a leading cause of nosocomial infection in North America and a considerable challenge to healthcare professionals in hospitals and nursing homes. The gram-positive bacterium produces two high molecular weight exotoxins, toxin A (TcdA) and toxin B (TcdB), which are the major virulence factors responsible for C. difficile-associated disease and are targets for C. difficile-associated disease therapy. Here, recombinant single-domain antibody fragments (V(H)Hs), which specifically target the cell receptor binding domains of TcdA or TcdB, were isolated from an immune llama phage display library and characterized. Four V(H)Hs (A4.2, A5.1, A20.1, and A26.8), all shown to recognize conformational epitopes, were potent neutralizers of the cytopathic effects of toxin A on fibroblast cells in an in vitro assay. The neutralizing potency was further enhanced when V(H)Hs were administered in paired or triplet combinations at the same overall V(H)H concentration, suggesting recognition of nonoverlapping TcdA epitopes. Biacore epitope mapping experiments revealed that some synergistic combinations consisted of V(H)Hs recognizing overlapping epitopes, an indication that factors other than mere epitope blocking are responsible for the increased neutralization. Further binding assays revealed TcdA-specific V(H)Hs neutralized toxin A by binding to sites other than the carbohydrate binding pocket of the toxin. With favorable characteristics such as high production yield, potent toxin neutralization, and intrinsic stability, these V(H)Hs are attractive systemic therapeutics but are more so as oral therapeutics in the destabilizing environment of the gastrointestinal tract.

The structure of the RNA-dependent RNA polymerase (RdRP) from the rabbit hemorrhagic disease virus has been determined by x-ray crystallography to a 2.5-Å resolution. The overall structure resembles a “right hand,” as seen before in other polymerases, including the RdRPs of polio virus and hepatitis C virus. Two copies of the polymerase are present in the asymmetric unit of the crystal, revealing active and inactive conformations within the same crystal form. The fingers and palm domains form a relatively rigid unit, but the thumb domain can adopt either “closed” or “open” conformations differing by a rigid body rotation of ∼8 degrees. Metal ions bind at different positions in the two conformations and suggest how structural changes may be important to enzymatic function in RdRPs. Comparisons between the structures of the alternate conformational states of rabbit hemorrhagic disease virus RdRP and the structures of RdRPs from hepatitis C virus and polio virus suggest novel structure-function relationships in this medically important class of enzymes.