X-ray crystallography at macromolecular resolution: A solution of the phase problem

The problem of crystal structure analysis at macromolecular resolution is tackled using notions borrowed from small-angle solution-scattering studies. The mathematical procedure - essentially a pattern recognition approach - consists of generating all the phase combinations compatible with the data and screening them: the critical steps are the choice of the “pattern” and of the criteria which preside the “recognition”. Two strategies are adopted. One is based upon use of the histogram of the electron density maps, a function more dependent on chemical composition than on physical structure: the histograms of samples of different structure and similar chemical composition are compared in search for similarity. The other strategy operates on the electron density maps and involves the principle of maximum smoothness. From the practical viewpoint, one single parameter, (Δp)⁴, is found to play an outstanding role in the two cases. Algorithms are worked out, implemented on the computer and tested using a variety of lipid-water phases. The comparison of samples of different structure and similar chemical composition is found to provide a powerful screening criterion. The principle of maximum smoothness is also of great help, at least to the extent that the electron density distribution is a fairly smooth function, devoid of sharp peaks (associated with heavy atoms). The practical aspects of the algorithms are discussed, as well as their possible application to crystallographic problems of more general interest.     

Phenolic Characterization and Neuroprotective Properties of Grape Pomace Extracts

Vitis vinifera (grape) contains various compounds with acknowledged phytochemical and pharmacological properties. Among the different parts of the plant, pomace is of particular interest as a winemaking industry by-product. A characterization of the water extract from grape pomace from Montepulciano d’Abruzzo variety (Villamagna doc) was conducted, and the bioactive phenolic compounds were quantified through HPLC-DAD-MS analysis. HypoE22, a hypothalamic cell line, was challenged with an oxidative stimulus and exposed to different concentrations (1 µg/mL⁻¹ mg/mL) of the pomace extract for 24, 48, and 72 h. In the same conditions, cells were exposed to the sole catechin, in a concentration range (5–500 ng/mL) consistent with the catechin level in the extract. Cell proliferation was investigated by MTT assay, dopamine release through HPLC-EC method, PGE₂ amount by an ELISA kit, and expressions of neurotrophin brain-derived neurotrophic factor (BDNF) and of cyclooxygenase-2 (COX-2) by RT-PCR. The extract reverted the cytotoxicity exerted by the oxidative stimulus at all the experimental times in a dose-dependent manner, whereas the catechin was able to revert the oxidative stress-induced depletion of dopamine 48 h and 72 h after the stimulus. The extract and the catechin were also effective in preventing the downregulation of BDNF and the concomitant upregulation of COX-2 gene expression. In accordance, PGE₂ release was augmented by the oxidative stress conditions and reverted by the administration of the water extract from grace pomace and catechin, which were equally effective. These results suggest that the neuroprotection induced by the extract could be ascribed, albeit partially, to its catechin content.     

Small‐Angle Neutron Scattering Studies of Hemoglobin Confined Inside Silica Tubes of Varying Sizes

In addition to the chemical nature of the surface, the dimensions of the confining host exert a significant influence on confined protein structures; this results in immense biological implications, especially those concerning the enzymatic activities of the protein. This study probes the structure of hemoglobin (Hb), a model protein, confined inside silica tubes with pore diameters that vary by one order of magnitude (≈20–200 nm). The effect of confinement on the protein structure is probed by comparison with the structure of the protein in solution. Small‐angle neutron scattering (SANS), which provides information on protein tertiary and quaternary structures, is employed to study the influence of the tube pore diameter on the structure and configuration of the confined protein in detail. Confinement significantly influences the structural stability of Hb and the structure depends on the Si‐tube pore diameter. The high radius of gyration (R_g) and polydispersity of Hb in the 20 nm diameter Si‐tube indicates that Hb undergoes a significant amount of aggregation. However, for Si‐tube diameters greater or equal to 100 nm, the R_g of Hb is found to be in very close proximity to that obtained from the protein data bank (PDB) reported structure (R_g of native Hb=23.8 Å). This strongly indicates that the protein has a preference for the more native‐like non‐aggregated state if confined inside tubes of diameter greater or equal to 100 nm. Further insight into the Hb structure is obtained from the distance distribution function, p(r), and ab initio models calculated from the SANS patterns. These also suggest that the Si‐tube size is a key parameter for protein stability and structure.