Nucleobase carbonyl groups are poor Mg²⁺ inner-sphere binders but excellent monovalent ion binders - A critical PDB survey

Precise knowledge of Mg2+ inner-sphere binding site characteristics is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, that represents the main source of Mg2+ binding sites, contains a significant number of ion assignment issues that significantly blur our understanding of the functions of these ions. Here, following a preceding study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed PDB nucleic acid crystallographic structures with resolutions < 2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether and phosphodiester oxygen atoms to derive a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected given that many of those bind misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide crystallographic evidence that nucleobases are poor inner-sphere Mg2+ binders but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline metal ion stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ should be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments

The Potential of Crude and Partially Purified Black Rice Bran Extracts Obtained by Ultrasound-Assisted Extraction: Anti-Glycemic, Cytotoxicity, Cytoprotective, and Antitumoral Effects

Recovering anthocyanins from black rice bran is a way of valuing this byproduct, by obtaining an extract with biological potential. The objective of this study was to recover anthocyanins using ultrasound-assisted extraction. Some of the extract was partially purified, and both (crude and partially purified) extracts were evaluated for their anthocyanin content, antioxidant activity, antidiabetic and antitumoral activities, cytotoxicity, and oxidative stress. An increase in the laboratory scale was also achieved, making possible to increase the extraction volume up to 20 times without significantly changing the content of anthocyanins (1.85 mg C3G/g DW). It was found that the purified sample presented a 4.2 times higher value of total anthocyanins compared to the crude sample. The best IC50 values for the purified sample were verified by DPPH and ABTS (0.76 and 0.33 mg/mL). The best results for antidiabetic activity were obtained for the partially purified sample: 0.82 µM C3G for α-glucosidase and 12.5 µM C3G for α-amylase. The extracts demonstrated protection (~70%) when subjected to the oxidative stress of L929 cells. An antitumoral effect of 25–30% for both extracts was found in A459 cells. The crude and partially purified extracts of black rice have antidiabetic and anticancer effects and more studies are needed to explore their potential

Leading edge chemical crystallography service provision and its impact on crystallographic data science in the twenty-first century

National facilities provide state-of-the-art crystallographic instrumentation and processes and tend to act as an indicator for the direction of a community in the medium term. There has been a significant step up in terms of instrumentation and approach in the last 10 years which has driven data generation. This has had a significant impact on databases – in turn we observe a substantial change in the use of the Cambridge Structural Database (CSD) from relatively basic search/retrieve to gaining deep understanding about factors that govern the solid state. Databases are now able to drive new science in areas such as crystal engineering. Looking forward, we will see more automated pipelining of the data generation process, and this will require better integration with databases. Databases will provide more predictive power – and this will inform the science/crystallography that should be done