The three-dimensional structure of the human immunodeficiency virus–type 1 (HIV-1) nucleocapsid protein (NC) bound to the SL3 stem-loop recognition element of the genomic Ψ RNA packaging signal has been determined by heteronuclear magnetic resonance spectroscopy. Tight binding (dissociation constant, ∼100 nM) is mediated by specific interactions between the amino- and carboxyl-terminal CCHC-type zinc knuckles of the NC protein and the G ⁷ and G ⁹ nucleotide bases, respectively, of the G ⁶ -G ⁷ -A ⁸ -G ⁹ RNA tetraloop. A ⁸ packs against the amino-terminal knuckle and forms a hydrogen bond with conserved Arg ³² , and residues Lys ³ to Arg ¹⁰ of NC form a 3 ₁₀ helix that binds to the major groove of the RNA stem and also packs against the amino-terminal zinc knuckle. The structure provides insights into the mechanism of viral genome recognition, explains extensive amino acid conservation within NC, and serves as a basis for the development of inhibitors designed to interfere with genome encapsidation.

The structure of the water-soluble, periplasmic domain of the fumarate sensor DcuS (DcuS-pd) has been determined by NMR spectroscopy in solution. DcuS is a prototype for a sensory histidine kinase with transmembrane signal transfer. DcuS belongs to the CitA family of sensors that are specific for sensing di- and tricarboxylates. The periplasmic domain is folded autonomously and shows helices at the N and the C terminus, suggesting direct linking or connection to helices in the two transmembrane regions. The structure constitutes a novel fold. The nearest structural neighbor is the Per-Arnt-Sim domain of the photoactive yellow protein that binds small molecules covalently. Residues Arg¹⁰⁷, His¹¹⁰, and Arg¹⁴⁷ are essential for fumarate sensing and are found clustered together. The structure constitutes the first periplasmic domain of a two component sensory system and is distinctly different from the aspartate sensory domain of the Tar chemotaxis sensor.

An NMR-based structure is presented for a 20 mer hairpin model of the SL3 stem-loop from the HIV-1 packaging signal. The stem has an A-family structure. However, the GGAG tetraloop appears to be flexible with the second (G10) and fourth (G12) bases extruded from the normal stacking arrangement. The A-base (A11) occupies a cavity large enough for it to jump rapidly between stacking upon G9 (in the loop) and G13 (from the base-pair adjacent to the loop). The H-bonding loci of G10, A11, and G12 are unoccupied in the free RNA structure. The loop should be easily adaptable to binding by the HIV-1 nucleocapsid protein or loop receptors.

Pomegranate is rich in high value nutritional substances known to be beneficial against several diseases and its use in medicine is known since ancient times. Due to its properties and delicious taste, pomegranate fresh fruit juices demand has been growing worldwide and its adulteration is becoming a problem. Low-cost, user friendly and fast detection methods are therefore desirable in order to easily and rapidly detect adulteration of short shelf-life fresh fruit juices. For this purpose fresh squeezed arils pomegranate juice samples adulterated with less expensive apple juice concentrate were investigated by UV–visible spectroscopy combined with multivariate statistical analysis. Unsupervised principle component analysis (PCA), supervised projection to latent structure discriminant analysis (PLS-DA) and orthogonal projection to latent structure discriminant analysis (OPLS-DA) were performed on the full spectra. OPLS-DA analysis of UV–visible spectra proved to be a suitable method to detect pomegranate juices adulterated by more than 20% v/v apple juice concentrate.