Region-Specific Biomarkers and Their Mechanisms in the Treatment of Lung Adenocarcinoma: A Study of Panax quinquefolius from Wendeng,China

Panax quinquefolius, a popular medicinal herb, has been cultivated in China for many years. In this work, the region-specific profiles of metabolites in P. quinquefolius from Wendeng was investigated using liquid-chromatography–quadrupole–time-of-flight-(LC–Q–TOF)-based metabolomics analysis. The three most abundant biomarkers, identified as ginsenoside Rb₃, notoginsenoside R₁, and ginsenoside Rc, were the representative chemical components employed in the network pharmacology analysis. In addition, molecular docking and western blotting analyses revealed that the three compounds were effective binding ligands with Hsp90α, resulting in the inactivation of SRC and PI3K kinase, which eventually led to the inactivation of the Akt and ERK pathways and lung cancer suppression. The outcomes obtained herein demonstrated the intriguing chemical characteristics and potential functional activities of P. quinquefolius from Wendeng.     

Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies

Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. A topology of secondary structures defines the mapping between a set of sequence segments and a set of traces of secondary structures in three-dimensional space. In order to enhance accuracy in ranking secondary structure topologies, we explored a method that combines three sources of information: a set of sequence segments in 1D, a set of amino acid contact pairs in 2D, and a set of traces in 3D at the secondary structure level. A test of fourteen cases shows that the accuracy of predicted secondary structures is critical for deriving topologies. The use of significant long-range contact pairs is most effective at enriching the rank of the maximum-match topology for proteins with a large number of secondary structures, if the secondary structure prediction is fairly accurate. It was observed that the enrichment depends on the quality of initial topology candidates in this approach. We provide detailed analysis in various cases to show the potential and challenge when combining three sources of information.     

Investigating direct current potentials that affect native protein conformation during trapped ion mobility spectrometry–mass spectrometry

Trapped ion mobility spectrometry–time-of-flight mass spectrometry (TIMS-TOFMS) has emerged as a tool to study protein conformational states. In TIMS, gas-phase ions are guided across the IM stages by applying direct current (DC) potentials (D1–6), which, however, might induce changes in protein structures through collisional activation. To define conditions for native protein analysis, we evaluated the influence of these DC potentials using the metalloenzyme bovine carbonic anhydrase (BCA) as primary test compound. The variation of DC potentials did not change BCA-ion charge and heme content but affected (relative) charge-state intensities and adduct retention. Constructed extracted-ion mobilograms and corresponding collisional cross-section (CCS) profiles gave useful insights in (alterations of) protein conformational state. For BCA, the D3 and D6 potential (which are applied between the deflection transfer and funnel 1 [F1] and the accumulation exit and the start of the ramp, respectively) had most profound effects, showing multimodal CCS distributions at higher potentials indicating gradual unfolding. The other DC potentials only marginally altered the CCS profiles of BCA. To allow for more general conclusions, five additional proteins of diverse molecular weight and conformational stability were analyzed, and for the main protein charge states, CCS profiles were constructed. Principal component analysis (PCA) of the obtained data showed that D1 and D3 exhibit the highest degree of correlation with the ratio of folded and unfolded protein (F/U) as extracted from the mobilograms obtained per set D potential. The correlation of D6 with F/U and protein charge were similar, and D2, D4, and D5 showed an inverse correlation with F/U but were correlated with protein charge. Although DC boundary values for induced conformational changes appeared protein dependent, a set of DC values could be determined, which assured native analysis of most proteins.     

In situ observation of protein-adsorbed stearic acid monolayer by Brewster angle microscopy and fluorescence microscopy

A fluorescence probe, fluorescein isothiocyanate (FITC), was introduced to proteins, and the morphology of protein-adsorbed stearic acid monolayer was observed by fluorescence microscopy and Brewster angle microscopy (BAM) in order to analyze images. At a low protein concentration, the surface pressure increased as shown by a sigmoidal curve. A number of stripe patterns in the BAM images increased and the shapes became clear with increasing concentration of proteins. Simultaneously, the size of circular islands also became small, and finally disappeared. These results suggest that the very large stripe patterns in the BAM image show the assembly of both proteins and stearic acid molecules, and small circular islands show only the stearic acid molecules. © 1998 John Wiley & Sons, Ltd.     

Systematic stepsize variation: Efficient method for searching conformational space of polypeptides

A new and efficient method for overcoming the multiple minima problem of polypeptides, the systematic stepsize variation (SSV) method, is presented. The SSV is based on the assumption that energy barriers can be passed over by sufficiently large rotations about rotatable bonds: randomly chosen dihedral angles are updated starting with a small stepsize (i.e., magnitude of rotation). A new structure is accepted only if it possesses a lower energy than the precedent one. Local minima are passed over by increasing the stepsize systematically. When no new structures are found any longer, the simulation is continued with the starting structure, but other trajectories will be followed due to the random order in updating the torsional angles. First, the method is tested with Met-enkephalin, a peptide with a known global minimum structure; in all runs the latter is found at least once. The global minimum conformations obtained in the simulations show deviations of ±0.0004 kcal/mol from the reference structure and, consequently, are perfectly superposable. For comparison, Metropolis Monte Carlo simulated annealing (MMC-SA) is performed. To estimate the efficiency of the algorithm depending on the complexity of the optimization problem, homopolymers of Ala and Gly of different lengths are simulated, with both the SSV and the MMC-SA method. The comparative simulations clearly reveal the higher efficiency of SSV compared with MMC-SA. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1470–1481, 1998     

Biodegradable hybrid polymer films based on poly(vinyl alcohol) and collagen hydrolyzate

Hybrid blends of poly(vinyl alcohol) (PVA) and collagen hydrolyzate (CH), an added value waste from leather indutry, have been converted by blown molding extrusion, to environmentally degradable films. Blown extruded films comprising 5-15% of CH, were tested as sel fertilizing mulching films and analyzed for their propensity to enviromental degradation. PVA/CH films rapidly disintegrate when buried in soil, and resulted promising for application such as transplanting films, with additional fertilizing action of CH.     

DCMC as a Promising Alternative to Bentonite in White Wine Stabilization. Impact on Protein Stability and Wine Aromatic Fraction

Protein haze in white wine is one of the most common non-microbial defects of commercial wines, with bentonite being the main solution utilized by the winemaking industry to tackle this problem. Bentonite presents some serious disadvantages, and several alternatives have been proposed. Here, an alternative based on a new cellulose derivative (dicarboxymethyl cellulose, DCMC) is proposed. To determine the efficiency of DCMC as a bentonite alternative, three monovarietal wines were characterized, and their protein instability and content determined by a heat stability test (HST) and the Bradford method, respectively. The wines were treated with DCMC to achieve stable wines, as shown by the HST, and the efficacy of the treatments was assessed by determining, before and after treatment, the wine content in protein, phenolic compounds, sodium, calcium, and volatile organic compounds (VOCs) as well as the wine pH. DCMC applied at dosages such as those commonly employed for bentonite was able to reduce the protein content in all tested wines and to stabilize all but the Moscatel de Setúbal varietal wine. In general, DCMC was shown to induce lower changes in the wine pH and phenolic content than bentonite, reducing the wine calcium content. Regarding which VOCs are concerned, DCMC produced a general impact similar to that of bentonite, with differences depending on wine variety. The results obtained suggest that DCMC can be a sustainable alternative to bentonite in protein white wine stabilization.