The structure assessment web server: for proteins, complexes and more.

The 'structure assessment' web server is a one-stop shop for interactive evaluation and benchmarking of structural models of macromolecular complexes including proteins and nucleic acids. A user-friendly web dashboard links sequence with structure information and results from a variety of state-of-the-art tools, which facilitates the visual exploration and evaluation of structure models. The dashboard integrates stereochemistry information, secondary structure information, global and local model quality assessment of the tertiary structure of comparative protein models, as well as prediction of membrane location. In addition, a benchmarking mode is available where a model can be compared to a reference structure, providing easy access to scores that have been used in recent CASP experiments and CAMEO. The structure assessment web server is available at https://swissmodel.expasy.org/assess.

Inhibition of ALDH2 by quercetin glucuronide suggests a new hypothesis to explain red wine headaches.

The consumption of red wine induces headaches in some subjects who can drink other alcoholic beverages without suffering. The cause for this effect has been attributed to a number of components, often the high level of phenolics in red wine, but a mechanism has been elusive. Some alcohol consumers exhibit flushing and experience headaches, and this is attributed to a dysfunctional ALDH2 variant, the enzyme that metabolizes acetaldehyde, allowing it to accumulate. Red wine contains much higher levels of quercetin and its glycosides than white wine or other alcoholic beverages. We show that quercetin-3-glucuronide, a typical circulating quercetin metabolite, inhibits ALDH2 with an IC50 of 9.6 µM. Consumption of red wine has been reported to result in comparable levels in circulation. Thus, we propose that quercetin-3-glucoronide, derived from the various forms of quercetin in red wines inhibits ALDH2, resulting in elevated acetaldehyde levels, and the subsequent appearance of headaches in susceptible subjects. Human-subject testing is needed to test this hypothesis.

Uncovering new families and folds in the natural protein universe.

We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database1. These models cover nearly all proteins that are known, including those challenging to annotate for function or putative biological role using standard homology-based approaches. In this study, we examine the extent to which the AlphaFold database has structurally illuminated this 'dark matter' of the natural protein universe at high predicted accuracy. We further describe the protein diversity that these models cover as an annotated interactive sequence similarity network, accessible at https://uniprot3d.org/atlas/AFDB90v4 . By searching for novelties from sequence, structure and semantic perspectives, we uncovered the ß-flower fold, added several protein families to Pfam database2 and experimentally demonstrated that one of these belongs to a new superfamily of translation-targeting toxin-antitoxin systems, TumE-TumA. This work underscores the value of large-scale efforts in identifying, annotating and prioritizing new protein families. By leveraging the recent deep learning revolution in protein bioinformatics, we can now shed light into uncharted areas of the protein universe at an unprecedented scale, paving the way to innovations in life sciences and biotechnology.

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.

While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modeling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify what models can best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank.

Wine Closure Performance of Three Common Closure Types: Chemical and Sensory Impact on a Sauvignon Blanc Wine.

A Napa Valley Sauvignon blanc wine was bottled with 200 each of a natural cork, a screw cap, and a synthetic cork. As browning is an index for wine oxidation, we assessed the brown color of each bottle with a spectrophotometer over 30 months. A random-effects regression model for longitudinal data on all bottles and closure groups found a browning growth trajectory for each closure group. Changes in the wine's browning behavior at 18 months and 30 months showed that the browning of the wine bottles appeared to slow down later in the storage period, especially for natural corks. The between-bottle variation was the highest for the natural cork. At 30 months, we separated the bottles by the extent of browning and samples were pulled from the high, mid, and low levels of browning levels for each closure. The degree of browning is inversely correlated with free SO2 levels ranging from 5 to 12 mg/L. However, a Quantitative Descriptive Analysis (QDA™) sensory panel could not detect any difference in their aroma and flavor profile between closure types regardless of browning level. Even low levels of free SO2 retain protection against strong oxidation aromas, and visual browning detected by spectrophotometer seemed to precede oxidative aroma and flavor changes of the aging Sauvignon blanc.

A novel method combining stable isotopic labeling and high-resolution mass spectrometry to trace the quinone reaction products in wines.

Quinone formation is a key initial step of wine oxidation. Nucleophiles sacrificially react with quinones to sustain color and aroma, but due to the complexity of wine, determining the identity of the constitutive nucleophile has been challenging. Here we apply a novel stable-isotope labelling approach combined with high-resolution mass spectrometry, using 13C6-labelled ortho-quinone. This allows for the specific detection of quinone reaction products with M and M + 6x peak feature-pairs in real wines. Analysis using MetExtract II successfully identified 225 quinone reaction suspects in negative mode in Sauvignon blanc wine, and 120 in Cabernet Sauvignon. Ten quinone reaction products with the most abundant peak areas were tentatively identified using a mass/structure workflow. It appears that sulfides largely quench quinones in white wines, whereas flavonoids are the dominant reactants in red wines. The latter result demonstrates how skin/seed extraction preserves red wine.

Acid complexation of iron controls the fate of hydrogen peroxide in model wine.

At a key branchpoint in wine oxidation, hydrogen peroxide reacts either with iron(II), leading to the Fenton oxidation of ethanol, or with sulfur dioxide, precluding oxidation. The fate of H2O2 was investigated in anoxic model wines with different pH and acid buffers. In the absence of SO2, anoxic conditions allowed the stoichiometric production of acetaldehyde from H2O2 despite iron(II) being limiting, indicating efficient iron redox cycling. Acetaldehyde production was faster at pH 4.0 than at pH 3.0, attributable largely to increased iron complexation. Citrate allowed the most rapid acetaldehyde formation, while the comparative effects of tartrate and malate were pH-dependent, likely due to differences in their iron-chelating abilities. The inclusion of SO2 greatly diminished acetaldehyde formation, but did not prevent it, and reduced the differential effects of pH and acid composition. Findings overall suggest management of wine acidity can significantly affect the rate and outcome of oxidation.

Evaluation of the potential of total proanthocyanidin content in feces as an intake biomarker.

Due to the health benefits associated with proanthocyanidins (PAs), it is useful to identify dietary PA biomarkers that can be determined by simple methods. Since increased levels of circulating PA metabolites are associated with increased fecal PA content, this study explores the spectrophotometric measurement of fecal PA content and its use as a biomarker of PA intake. To this end, fecal PA content was measured using an adaptation of Porter's spectrophotometric method in samples from a preclinical study and an observational study. In the former, excretion of 250-400 mg PA polymer equivalents/100 g feces was observed during supplementation and the day after, together with a significant association (p < 0.05) between PA intake and the excretion of both intact PAs and some PA metabolites, i.e., (+)-catechin, (-)-epicatechin and syringic acid. No relationship between intake and excretion was found in the observational study, either for the entire group (mean excretion of 240 ± 226 mg PA polymer equivalents/100 g feces) or after stratification into tertiles of consumption. In conclusion, the spectrophotometric determination of total PA content in feces proved to be a valid compliance marker in a preclinical study, but it was not associated with PA intake in free-living subjects. The potential of total PA excretion in observational studies, determined in fecal samples collected the day before dietary recall or in several fecal samples from the same subject, remains to be elucidated, as does a complete validation of the method proposed here.

Anthocyanin Addition Alters Tannin Extraction from Grape Skins in Model Solutions via Chemical Reactions.

Condensed tannin extraction and stable color formation are two of the cornerstones of red wine production. Without condensed tannin, red wine would lack the tactile feeling of astringency, and without the formation of modified pigments, it would lack color stability for long-term aging. To understand how malvidin-3,5-diglucoside interacts with condensed tannin under nonoxidative conditions, an experiment was designed conducting model-wine skin extractions of Sauvignon blanc grapes harvested at various dates of maturity. Monomeric malvidin-3,5-diglucoside was isolated from color concentrate and added during these extractions. Following a 72 h extraction, solutions were evaluated for recovery of monomeric anthocyanins, skin tannin concentration, skin tannin extractability, and impact of anthocyanins on condensed tannin size. Anthocyanins showed a significant impact on the extraction of flavan-3-ol material in the early stages of ripening that declined in the latter stages of ripening. Furthermore, anthocyanins significantly decreased the size of the condensed tannin extracted. These results suggest that anthocyanins are not only enhancing the extractability of condensed tannin but also readily incorporating into the polymeric material, leading to a decrease in the average molecular mass of the condensed tannin polymer. The extent of reaction in 72 h suggests that the rate of interflavan bond cleavage may be higher than previously reported and merits closer scrutiny.

Can Chemical Analysis Predict Wine Aging Capacity?

Oxidation is the limiting factor in wine aging, and recently some famous wines have exhibited unexpected premature oxidation. Antioxidant assays may provide a means to assess a wine's aging potential by measuring its capacity to chemically reduce reagent components. Correlations between antioxidant activity and wine components have the highest value with flavanols, notable for their catechol and phloroglucinol moieties. Both FRAP and DPPH based methods respond strongly to catechol groups, but these functional groups do not protect wine from oxidation. An ideal assay for wine aging capacity would respond selectively to thiols, phloroglucinol moieties, SO2 and other antioxidants capable of reducing quinones. A definitive test will be to compare the various assays against the shelf life of a number of commercial wines.

Normal-phase chromatographic separation of pigmented wine tannin by nano-HPLC quadrupole time-of-flight tandem mass spectrometry and identification of candidate molecular features.

BACKGROUND: As a wine ages, altered sensory properties lead to changes in perceived quality and value. Concurrent modifications of anthocyanin and tannin occur forming pigmented tannin, softening astringency and retaining persistent color. Wine tannin extracts of 1990 and 2010 vintages of Oakville Station Cabernet Sauvignon have been analyzed using normal-phase chromatography with tandem quadrupole time-of-flight mass spectrometry (QToF) to investigate the compositional differences in their pigmented tannin fractions. RESULTS: The older wine demonstrates much greater structural diversity and a range of more polar compounds, while the younger wine contains fewer observed ion peaks. Several hundred molecular features are observable, and, as expected, there is progression to higher molecular weights after long aging. Between 7% and 16% of molecular features could be matched to a database of anticipated pigmented tannin compounds. Many signals had multiple possible isomeric identities, but fragmentation to resolve their identity was stymied by low sensitivity of the tandem mass spectrometric capability provided by QToF, so isomeric disambiguation is incomplete. CONCLUSIONS: The chromatography displayed a high degree of resolution in aged wines, separating many of the known pigment types, including aldehyde bridged compounds, pyranoanthocyanins and direct condensation products among others, as well as resolving a great number of unknown compounds. Expanding our understanding of red wine pigments will lead to better wines as winemakers will be able to associate quality with particular wine pigment profiles once we can distinguish the relevant patterns in those pigments. © 2021 Society of Chemical Industry.

Yeasts Induce Acetaldehyde Production in Wine Micro-oxygenation Treatments.

Micro-oxygenation (Mox) is a common technique used to stabilize color and reduce harsh astringency in red wines. Here, we investigate the role of residual sugars, phenolics, SO2, and yeast on the oxidation of wine in three studies. In a Mox experiment, populations of yeasts emerged after the loss of SO2, and this was associated with sharp increases in oxygen consumption and acetaldehyde production. No acetaldehyde production was observed without the presence of yeast. In an oxygen saturation experiment, unfiltered wines, in particular those with residual sugar >3 g/L, consumed oxygen more quickly and produced more acetaldehyde than filtered wines. In a final experiment, the reincorporation of oxygen and glucose immediately after the completion of fermentation of an otherwise dry synthetic wine resulted in significant acetaldehyde production. These experiments highlighted the importance of yeast metabolism in determining a wine's response to Mox and suggested that the role of chemical oxidation to produce acetaldehyde during Mox may not be very important. It appears that control of microbial populations and residual sugar levels may be key to managing Mox treatments in winemaking, and production scale experiments should be conducted.

A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0.

(1) Background: Virtual screening studies on the therapeutically relevant proteins of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) require a detailed characterization of their druggable binding sites, and, more generally, a convenient pocket mapping represents a key step for structure-based in silico studies; (2) Methods: Along with a careful literature search on SARS-CoV-2 protein targets, the study presents a novel strategy for pocket mapping based on the combination of pocket (as performed by the well-known FPocket tool) and docking searches (as performed by PLANTS or AutoDock/Vina engines); such an approach is implemented by the Pockets 2.0 plug-in for the VEGA ZZ suite of programs; (3) Results: The literature analysis allowed the identification of 16 promising binding cavities within the SARS-CoV-2 proteins and the here proposed approach was able to recognize them showing performances clearly better than those reached by the sole pocket detection; and (4) Conclusions: Even though the presented strategy should require more extended validations, this proved successful in precisely characterizing a set of SARS-CoV-2 druggable binding pockets including both orthosteric and allosteric sites, which are clearly amenable for virtual screening campaigns and drug repurposing studies. All results generated by the study and the Pockets 2.0 plug-in are available for download.

Effects of initial oxygenation on chemical and aromatic composition of wine in mixed starters of Hanseniaspora vineae and Saccharomyces cerevisiae.

The use of Saccharomyces and non-Saccharomyces yeast species as mixed starters has potential advantages over pure culture fermentation due to increased wine complexity based on modification of metabolites of oenological interest. In this work, the effects of initial oxygenation on fermentation performance, chemical and volatile composition of French Colombard wine fermented with Hanseniaspora vineae and Saccharomyces cerevisiae in sequential inoculations were investigated in 1 L flasks. Although dominated by S. cerevisiae at the middle-end of fermentation, initial aeration for 1 day boosted H. vineae populations, and allowed H. vineae to coexist longer with S. cerevisiae in mixed cultures compared to no aeration, and suppressed S. cerevisiae later in the fermentation, which resulted in extended fermentation time. More important, the major fermentation products and volatile compounds were significantly modified by aeration and different from no aeration fermentation. The wines produced by aeration of mixed fermentations were characterized with higher amounts of glycerol, lactic acid and acetate esters, and lower levels of ethanol, higher alcohol and ethyl fatty acid esters. The aeration had more potential to shape the quality of wines and diversify the aromatic characteristics relative to simple mixed inoculation, as indicated by PCA analysis. Our results suggested that the impact of early aeration on yeast physiology extends beyond the aeration phase and influences fermentation activity, chemical and aromatic compounds in the following anaerobic stage. The aeration for a short time during the cell growth stage in mixed fermentation is therefore a potential means to increase the aromatic diversity and quality of wine, possibly providing an alternative approach to meet the expectations of wine consumers for diverse aromatic qualities.

A quarter century of wine pigment discovery.

The red grape berry pigments, anthocyanins, were characterized in the early 20th century, but investigations of wine pigments were stymied during that era. The question of their identity was a major challenge for wine chemists. A number of techniques showed that the pigments were polymeric in nature. Some structures were postulated by mid-century based on reactions between anthocyanins and condensed tannin, and later postulated wine pigments were observed in model reactions. Some related compounds were then observed in wine. By the end of the 20th century, the ionization of non-volatiles for mass spectrometry opened the door to these compounds. In addition, a new class of compounds was observed, the pyranoanthocyanins, a product of fermentation and aging metabolites with anthocyanins. These compounds possess the pigment stability to SO2 and pH change that is characteristic of aged red wine. Aging experiments show a dynamic situation with shifts in the population of pigment classes over time. The very large number of diverse pigments explains why it has been so difficult to answer the century-old question of the structure of wine pigments. Our current understanding is founded on the use of mass spectral analysis using electrospray and related ionization techniques over the last 25 years. Future progress will rely on more sophisticated analysis of this very complex mixture of substances. © 2019 Society of Chemical Industry.