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WW domains are small protein modules composed of approximately 40 amino acids. These domains fold as a stable, triple stranded β-sheet and recognize proline-containing ligands. WW domains are found in many different signaling and structural proteins, often localized in the cytoplasm as well as in the cell nucleus. Based on analyses of seven structures of WW domains, we discuss their diverse binding preferences and sequence conservation patterns. While modeling WW domains for which structures have not been determined we uncovered a case of potential molecular and functional convergence between WW and SH3 domains. The binding surface of the modeled WW domain of Npw38 protein shows a remarkable similarity to the SH3 domain of Sem5 protein, confirming biochemical data on similar binding predilections of both domains.

A three-dimensional model of the human class IV alcohol dehydrogenase has been calculated based upon the X-ray structure of the class I enzyme. As judged from the model, the substrate-binding site is wider than in class I, compatible with the differences in substrate specificities and the large difference in Km value for ethanol. Substrate docking performed for the class I structure and the class IV model show all-trans-retinol and 11-cis-retinol to bind better to the class IV enzyme. The calculations also indicate that 16-hydroxyhexadecanoic acid binds in a different manner for the two enzyme classes. A simulation of coenzyme-binding indicates that the adenine ring of the coenzyme might be differently bound in class IV than in class I, decreasing the interactions with Asp-223 which is compatible with the higher kcat values for class IV.

A three-dimensional structure of Schistosoma mansoni cathepsin B was modelled using the coordinates of the crystal structure of the human liver enzyme. Both enzymes appear to share remarkable structural similarity. However, an examination of the models complexed with two synthetic inhibitors revealed differences in inhibitor binding, as confirmed by differences in the 50% inhibitory concentration of the same inhibitor.

The amino acid sequence of a large form of inhibin-like peptide in human seminal plasma was determined, and compared with structures reported for similar inhibin preparations and a seminal plasma globulin. The data confirm and correlate previous reports on this form of inhibin-like peptide. The structural comparisons further suggest that the peptide is closely similar to or possibly identical to a sperm-coating antigen reported to be synthesized from prostatic epithelium. This may correlate with non-gonadal origins of inhibin-like material and will help to elucidate the biological roles of inhibin(s).

The nature of the factors leading to the conversion of the cellular prion protein (PrPC) into its amyloidogenic isoform (PrPSc) is still matter of debate in the field of structural biology. The NMR structures of non-mammalian PrPC (non-mPrP) from frog, chicken and turtle [Calzolai, L., Lysek, D.A., Perez, D.R., Guntert, P. and Wuthrich, K. (2005) Prion protein NMR structures of chickens, turtles, and frogs. Proc. Natl. Acad. Sci. USA 102, 651-655] have provided some new and valuable information on the scaffolding elements that preserve the PrPC folding, despite their low sequence identity with the mammalian prions (mPrP). The present molecular dynamics study of non-mPrPC focuses on the hydration properties of these proteins in comparison with the mammalian ones. The data reveal new insights in the PrP hydration and focus on the implications for PrPC folding stability and its propensity for interactions. In addition, for the first time, a role in disfavoring the PrPC aggregation is suggested for a conserved β-bulge which is stabilized by the local hydration. © 2006 Federation of European Biochemical Societies.