An Attempt of Seeking Favorable Binding Free Energy Prediction Schemes Considering the Entropic Effect on Fis-DNA Binding

Protein–DNA binding mechanisms in a complex manner are essential for understanding many biological processes. Over the past decades, numerous experiments and calculations have analyzed the specificity of protein–DNA binding. However, the accuracy of binding free energy prediction for multi-base DNA systems still needs to be improved. Fis is a DNA-binding protein that regulates various transcription and recombination reactions. In the present work, we tested several methods of predict binding free energy based on this system to find a favorable prediction scheme and explore the binding mechanism of Fis protein and DNA. Two solvent models (explicit and implicit solvent models) were chosen for the dynamics process, and the predicted binding free energy was more accurate under the explicit solvent model. When different Poisson–Boltzmann/Generalized Born (PB/GB) models were tested for DNA force fields (BSC1 and OL15), it was found that the binding free energy predicted by the selected OL15 force field performed better and the correlation between predicted and experimental values was improved with the increasing interior dielectric constant (Dk). Finally, using Dk = 8, the GBOBC1 model combined with interaction entropy (IE), which was calculated for entropic contribution (GBOBC1_IE_8), was screened out for the binding free energy prediction and analysis of the Fis–DNA system, and the validity of the method was further verified by testing the Cren7–DNA system. By performing conformational analysis of the minor groove, it was found that mutation of the DNA central sequence A/T to C/G and deletion of the guanine 2-amino group would change the minor groove width and thus affect the formation of the major groove, altering the interaction and atomic contact between the protein and the major groove, thus changing the binding affinity of Fis and DNA. Hopefully, the series of tests in this work can shed some light on the related studies of protein and DNA systems

Organic Matter Transfer Caused by Concentration Difference Creates TC4 Surfaces with Switchable Wettability

In this paper, low-cost electrochemical processing and heat treatment were adopted to fabricate titanium alloy surfaces with switchable wettability. Meanwhile, surface structure, roughness, and oxide content were regulated by electrochemical processing voltage. The effects of surface structure, roughness, oxide content, temperature, and time of heat treatment on switchable wettability were investigated. In addition to suitable structural conditions, surface chemistry is also crucial to preparing metal surfaces with switchable wettability. The surface chemistry of electrochemical processed surfaces was changed by organic matter transfer during heat treatment. In a certain voltage range, suitable surface structure, high roughness, and surface oxide content by high voltage contribute to the organic matter transfer. In a certain range of heating temperature and time, the concentration difference of organic matter is the premise of organic matter transfer. Concurrently, the higher the temperature, the faster the speed of organic matter transfer. Different from other relevant studies, the hypothesis that the concentration difference promotes organic matter transfer is proposed and verified by interesting experiments. The difference concentration of organic matter between the environment and the samples, as well as between the two samples, was created to promote organic matter transfer. Therefore, the electrochemical processed surfaces with switchable wettability were obtained by organic matter transfer in two ways

Molecular Mechanism of the Non-Covalent Orally Targeted SARS-CoV‑2 M^pro Inhibitor S‑217622 and Computational Assessment of Its Effectiveness against Mainstream Variants

Convenient and efficient therapeutic agents are urgently needed to block the continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, the mechanism for the novel orally targeted SARS-CoV-2 main protease (Mpro) inhibitor S-217622 is revealed through a molecular dynamics simulation. The difference in the movement modes of the S-217622–Mpro complex and apo-Mpro suggested S-217622 could inhibit the motility intensity of Mpro, thus maintaining their stable binding. Subsequent energy calculations showed that the P2 pharmacophore possessed the highest energy contribution among the three pharmacophores of S-217622. Additionally, hot-spot residues H41, M165, C145, E166, and H163 have strong interactions with S-217622. To further investigate the resistance of S-217622 to six mainstream variants, the binding modes of S-217622 with these variants were elucidated. The subtle differences in energy compared to that of the wild type implied that the binding patterns of these systems were similar, and S-217622 still inhibited these variants. We hope this work will provide theoretical insights for optimizing novel targeted Mpro drugs

Table_1_Effectiveness of online caries management platform in children's caries prevention: A randomized controlled trial.DOC

PurposeTo construct an online caries management platform and evaluate its efficacy in children's caries prevention based on caries risk.MethodsThe study participants were second-grade pupils. The caries risk assessment tool (CAT) was used to grade caries risk for all participants, who were randomly divided into the experimental (114 pupils) and control (111 pupils) groups. The experimental group used the Internet for caries management, while the control group was managed by traditional lecturing in classroom. The caries status of each surface of the first permanent molars was recorded. The basic information and oral health knowledge, attitude, and behaviors of participants were collected by questionnaire. One year later, outcome data were collected. Pearson's chi-squared test was used to analyze the caries risk assessment items and oral health behaviors. The Mann-Whitney U-test was used to analyze the decayed-missing-filled surfaces (DMFS) index, plaque index, and scores of oral health knowledge and attitude. P ResultsAfter 1 year, the oral health knowledge score was improved by 20.58% (P ConclusionsThe online caries management platform showed more advantages than traditional lecturing in improving oral health knowledge and behaviors (oral hygiene practice, sugar consumption behavior, and medical treatment behavior). This platform provides a reliable implementation path for the occurrence and continuous improvement of oral health-related behaviors.</p

Scheme of this experimental study.

<p>Rats were treated by intraperitoneal injection of normal saline [control group (n = 13)] or CCl₄ [fibrosis group (n = 25)] (50% CCl₄/olive oil; 1 mL/kg body weight twice a week) for 4 to 13 weeks to produce different degrees of liver fibrosis. Starting from the fourth week, two or three rats in each group were examined in a 3 Tesla MR scanner. CCI₄ = carbon tetrachloride.</p

The results of serial combined examination for blood markers and DCE-MRI parameters.

<p>ALT = alanine transaminase; AST = aspartate transaminase; K^trans = transfer constant, iAUC = initial area under the gadolinium concentration-time curve.</p><p>The results of serial combined examination for blood markers and DCE-MRI parameters.</p

Immune Escape Mechanisms of SARS-CoV‑2 Delta and Omicron Variants against Two Monoclonal Antibodies That Received Emergency Use Authorization

Multiple-site mutated SARS-CoV-2 Delta and Omicron variants may trigger immune escape against existing monoclonal antibodies. Here, molecular dynamics simulations combined with the interaction entropy method reveal the escape mechanism of Delta/Omicron variants to Bamlanivimab/Etesevimab. The result shows the significantly reduced binding affinity of the Omicron variant for both antibodies, due to the introduction of positively charged residues that greatly weaken their electrostatic interactions. Meanwhile, significant structural deflection induces fewer atomic contacts and an unstable binding mode. As for the Delta variant, the reduced binding affinity for Bamlanivimab is owing to the alienation of the receptor-binding domain to the main part of this antibody, and the binding mode of the Delta variant to Etesevimab is similar to that of the wild type, suggesting that Etesevimab could still be effective against the Delta variant. We hope this work will provide timely theoretical insights into developing antibodies to prevalent and possible future variants of SARS-CoV-2

Parameters of DCE-MRI in different groups.

<p>Note.—Data are mean ± standard deviations.</p><p>*<i>P</i><0.05,</p><p>**<i>P</i><0.01 for comparison with rats in normal group.</p><p>^#<i>P</i><0.05 for comparison with rats in mild group.</p><p>K^trans = transfer constant, K_ep = rate constant, V_e = extravascular extracellular volume fraction; iAUC = initial area under the gadolinium concentration-time curve.</p><p>Parameters of DCE-MRI in different groups.</p

Table_5_[18F]PBR146 and [18F]DPA-714 in vivo Imaging of Neuroinflammation in Chronic Hepatic Encephalopathy Rats.docx

Neuroinflammation is an important pathogenesis of hepatic encephalopathy (HE). The upregulation of translocator protein (TSPO) during neuroinflammation provides an imaging molecular target to evaluate the severity of neuroinflammation in chronic HE rats. [18F]DPA-714 and [18F]PBR146 targeting TSPO are often used for neuroinflammation imaging. This study performed bile duct ligation (BDL) in rats to simulate chronic HE model, tested the behavioral experiments, and conducted [18F]PBR146 and [18F]DPA-714 micro-PET/CT scans followed analyzing the average %ID/g values of the whole brain, brain regions and main organs of subjects. After sacrifice the rats, the blood plasma samples were taken for blood biochemical indexes and plasma inflammatory factor levels examination, the liver and brain specimens were obtained for pathological analysis. The BDL rats showed chronic liver failure with defects in cognition, motor coordination ability and mental state. [18F]PBR146 and [18F]DPA-714 micro-PET/CT imaging results were similar in whole brain of BDL group and Sham group. Besides, some regional brain areas in BDL rats were found abnormal uptakes mainly located in basal ganglia area, auditory cortex, motor cortex, cingulate gyrus, somatosensory cortex, hippocampus, thalamus, midbrain, and medulla oblongata, and these regions also correlated with behavioral alterations. In conclusion, both [18F]PBR146 and [18F]DPA-714 had the similar imaging effects in hepatic encephalopathy models could quantitatively evaluate neuroinflammation load and distribution. The difference brain regions with higher uptake values of radiotracers in BDL rats were correlated with behavioral alterations.</p

Table_3_[18F]PBR146 and [18F]DPA-714 in vivo Imaging of Neuroinflammation in Chronic Hepatic Encephalopathy Rats.docx

Neuroinflammation is an important pathogenesis of hepatic encephalopathy (HE). The upregulation of translocator protein (TSPO) during neuroinflammation provides an imaging molecular target to evaluate the severity of neuroinflammation in chronic HE rats. [18F]DPA-714 and [18F]PBR146 targeting TSPO are often used for neuroinflammation imaging. This study performed bile duct ligation (BDL) in rats to simulate chronic HE model, tested the behavioral experiments, and conducted [18F]PBR146 and [18F]DPA-714 micro-PET/CT scans followed analyzing the average %ID/g values of the whole brain, brain regions and main organs of subjects. After sacrifice the rats, the blood plasma samples were taken for blood biochemical indexes and plasma inflammatory factor levels examination, the liver and brain specimens were obtained for pathological analysis. The BDL rats showed chronic liver failure with defects in cognition, motor coordination ability and mental state. [18F]PBR146 and [18F]DPA-714 micro-PET/CT imaging results were similar in whole brain of BDL group and Sham group. Besides, some regional brain areas in BDL rats were found abnormal uptakes mainly located in basal ganglia area, auditory cortex, motor cortex, cingulate gyrus, somatosensory cortex, hippocampus, thalamus, midbrain, and medulla oblongata, and these regions also correlated with behavioral alterations. In conclusion, both [18F]PBR146 and [18F]DPA-714 had the similar imaging effects in hepatic encephalopathy models could quantitatively evaluate neuroinflammation load and distribution. The difference brain regions with higher uptake values of radiotracers in BDL rats were correlated with behavioral alterations.</p