The severe acute respiratory syndrome (SARS) virus belongs to the Coronaviridea family of viruses. Its virion encodes several proteins including a replicase and four structural proteins. Here we describe the three-dimensional structure of the N-terminal domain of the SARS coronavirus (CoV) nucleocapsid protein. The protein consists of a five-stranded beta sheet with a folding topology distinct from other RNA-binding proteins. Single-stranded RNAs bind to the protein surface at the junction between a flexible, positively charged beta hairpin and the core structure. NMR-based screening was used to identify low molecular weight compounds that bind to this site.

A method is described for NMR-based screening that involves monitoring the 13 C/ 1 H chemical shift changes of a protein selectively labeled with 13 C at the methyl groups of valine, leucine, and isoleucine (δ1 only). Using this approach, the sensitivity is increased by nearly 3-fold compared with that of NMR-based screening using 1 H/ 15 N chemical shifts. A synthetic route is described for the inexpensive production of the labeled amino acid precursors [3,3′-13 C]-R-ketoisovalerate and [3-13 C]-R-ketobutyrate, making the cost of protein preparation comparable to that of uniform 15 N labeling. In addition to enhancing the NMR-based screening efforts directed against low molecular weight proteins (MW e 30 kDa), the use of the selective methyl labels in combination with deuterium labeling is advantageous for screening high molecular weight protein targets (MW g 100 kDa).

The three-dimensional structure of the anti-apoptotic protein Bcl-xL complexed to a 25-residue peptide from the death promoting region of Bad was determined using NMR spectroscopy. Although the overall structure is similar to Bcl-xL bound to a 16-residue peptide from the Bak protein (Sattler et al., 1997), the Bad peptide forms additional interactions with Bcl-xL. However, based upon site-directed mutagenesis experiments, these additional contacts do not account for the increased affinity of the Bad 25-mer for Bcl-xL compared to the Bad 16-mer. Rather, the increased helix propensity of the Bad 25-mer is primarily responsible for its greater affinity for Bcl-xL. Based on this observation, a pair of 16-residue peptides were designed and synthesized that were predicted to have a high helix propensity while maintaining the interactions important for complexation with Bcl-xL. Both peptides showed an increase in helix propensity compared to the wild-type and exhibited an enhanced affinity for Bcl-xL.