Effect of Disulfide Bridge on the Binding of SARS-CoV‑2 Fusion Peptide to Cell Membrane: A Coarse-Grained Study

In this paper, we present the parameterization of the CAVS coarse-grained (CG) force field for 20 amino acids, and our CG simulations show that the CAVS force field could accurately predict the amino acid tendency of the secondary structure. Then, we used the CAVS force field to investigate the binding of a severe acute respiratory syndrome-associated coronavirus fusion peptide (SARS-CoV-2 FP) to a phospholipid bilayer: a long FP (FP-L) containing 40 amino acids and a short FP (FP-S) containing 26 amino acids. Our CAVS CG simulations displayed that the binding affinity of the FP-L to the bilayer is higher than that of the FP-S. We found that the FP-L interacted more strongly with membrane cholesterol than the FP-S, which should be attributed to the stable helical structure of the FP-L at the C-terminus. In addition, we discovered that the FP-S had one major and two minor membrane-bound states, in agreement with previous all-atom molecular dynamics (MD) studies. However, we found that both the C-terminal and N-terminal amino acid residues of the FP-L can strongly interact with the bilayer membrane. Furthermore, we found that the disulfide bond formed between Cys840 and Cys851 stabilized the helices of the FP-L at the C-terminus, enhancing the interaction between the FP-L and the bilayer membrane. Our work indicates that the stable helical structure is crucial for binding the SARS-CoV-2 FP to cell membranes. In particular, the helical stability of FP should have a significant influence on the FP–membrane binding

Data collection and refinement statistics.

a<p>the highest resolution shell.</p>b<p> </p>c<p><b><i>R</i></b>_crystal = </p>d<p><b><i>R</i></b>_free, calculated the same as <b><i>R</i></b>_crystal, but from a test set containing 5% of data excluded from the refinement calculation.</p

Crystal structure of NMB0315.

<p>(<b>A</b>) Overall topology of NMB0315. (<b>B</b>) Cartoon representation of NMB0315. The metal atom is shown as a red ball. Domains I, II and III are colored in orange, blue and green, respectively.</p

Structure comparison of NMB0315 with other M23 metallopeptidases.

<p>(<b>A</b>) Comparison of the overall structure of NMB0315 (left) and Vly (right). Each domain from one protein resembles the corresponding domain in the other; however, the spatial arrangements of the three domains between the two proteins are different. (<b>B</b>) Stereoview of the superposition of NMB0315 onto Vly (yellow), LytM (magenta) (<b>C</b>), or LasA (orange) (<b>D</b>).</p

The auto-inhibition mechanism of NMB0315.

<p>(<b>A</b>) The inhibition loop of Domain I of NMB0315 is stabilized by numerous interactions with Domain III. The main chains of Domain I and Domain III are colored orange and green, respectively. The hydrogen bonds are shown as dashed magenta lines. The substrate binding grooves are blocked in NMB0315 (<b>B</b>), Vly (<b>C</b>), and LytM (<b>D</b>) but open in LasA (<b>E</b>). The catalytic domains of these four proteins are shown as surfaces in (<b>B</b>), (<b>C</b>), (<b>D</b>) and (<b>E</b>), and the inhibiting domains are shown as cartoons. The metal ions (M²⁺) in the active sites of these enzymes are represented as cyan spheres. A tartrate molecule is colored as magenta in the open catalytic site of LasA.</p

The catalytic pocket of NMB0315.

<p>(<b>A</b>) The metal ion binding site. Nitrogen, oxygen and carbon atoms are colored blue, red and cyan, respectively. The metal ion and water molecules are shown as red and yellow balls, respectively. The initial experimental electron density map calculated from the SAD phases is shown contoured at 14σ in black. Hydrogen bonds are shown as red dashed lines. (<b>B</b>) The superposition of the active site of NMB0315 onto LasA. The side chains of conserved residues are shown as sticks, and the main chain is shown as loops. NMB0315 is colored cyan, with the nitrogen and oxygen atoms of the side chains colored blue and red, respectively. LasA is colored gray. The metal ions of NMB0315 and LasA in the active sites are represented as red and light pink spheres, respectively. (<b>C</b>) Sequence alignment of NMB0315, Vly and LytM. Secondary structure elements of NMB0315 are shown as arrows (β-strands). The amino acids highlighted in red and denoted with asterisks are key residues in the active site that are conserved across the three proteins. (<b>D,E</b>) The atomic absorption spectrum for the different metal elements in the purified NMB0315 protein solution. (<b>F</b>) ITC measurement of the binding affinity between Zn²⁺ and NMB0315.</p

Englerins: A Comprehensive Review

In the decade since the discovery of englerin A (<b>1</b>) and its potent activity in cancer models, this natural product and its analogues have been the subject of numerous chemical, biological, and preclinical studies by many research groups. This review summarizes published findings and proposes further research directions required for entry of an englerin analogue into clinical trials for kidney cancer and other conditions

Effect of Cholesterol on Membrane Dipole Potential: Atomistic and Coarse-Grained Molecular Dynamics Simulations

The effect of cholesterol on membrane dipole potential has been the subject of a great number of experimental and theoretical investigations, but these studies have yielded different findings and interpretations at high cholesterol concentrations. This suggests that the underlying mechanism of the cholesterol effect is not well addressed. Moreover, as far as we know, none of the previously proposed coarse-grained (CG) models (including MARTINI and its improved versions) have been successfully used to probe the effect of cholesterol on membrane dipole potential, owing to either an inaccurate description of water-cholesterol electrostatics or the neglect of the contribution of cholesterol to membrane dipole potential. In our previous works, we proposed a CG model CAVS (charge attached to virtual site) for lipid and water, showing the advantage of the CAVS model in the calculations of membrane dipole potential as compared to the MARTINI model. In this work, we present the CAVS model for cholesterol in order to enable us to investigate the effect of cholesterol on membrane dipole potential at large spatial scale. Our works showed that the CAVS and CHARMM models produced similar results in the study of the effects of cholesterol on lipid bilayer structures and membrane dipole potential. In particular, by combining the CHARMM and CAVS simulations, we explicitly calculated the individual contributions of membrane components (cholesterol, water, and lipid) to membrane dipole potential at different cholesterol concentrations, and we discovered that an increase in cholesterol content would result in a nonlinear variation of the individual contributions of water and lipid with cholesterol concentration. On the other side, we observed that the individual contribution of cholesterol to membrane dipole potential would nonlinearly increase with increasing cholesterol concentration. Thus, the effect of cholesterol on membrane dipole potential is complicated owing to the different variation of individual contributions of membrane components (water, lipid, and cholesterol) with cholesterol concentration

Modulating Catalytic Activity and Stability of Atomically Precise Gold Nanoclusters as Peroxidase Mimics via Ligand Engineering

Metal nanoclusters (NCs), composed of a metal core and protecting ligands, show promising potentials as enzyme mimics for producing fuels, pharmaceuticals, and valuable chemicals, etc. Herein, we explore the critical role of ligands in modulating the peroxidase mimic activity and stability of Au NCs. A series of Au15(SR)13 NCs with various thiolate ligands [SR = N-acetyl-l-cysteine (NAC), 3-mercaptopropionic acid (MPA), or 3-mercapto-2-methylpropanoic acid (MMPA)] are utilized as model catalysts. It is found that Au15(NAC)13 shows higher structural stability than Au15(MMPA)13 and Au15(MPA)13 against external stimuli (e.g., pH, oxidants, and temperature) because of the intramolecular hydrogen bonds. More importantly, detailed enzymatic kinetics data show that the catalytic activity of Au15(NAC)13 is about 4.3 and 2.7 times higher than the catalytic activity of Au15(MMPA)13 and Au15(MPA)13, respectively. Density functional theory (DFT) calculations reveal that the Au atoms on the motif of Au NCs should be the active centers, whereas the superior peroxidase mimic activity of Au15(NAC)13 should originate from the emptier orbitals of Au atoms because of the electron-withdrawing effect of acetyl amino group in NAC. This work demonstrates the ligand-engineered electronic structure and functionality of atomically precise metal NCs, which afford molecular and atomic level insights for artificial enzyme design

Additional file 1: of The polycomb group protein EZH2 induces epithelial–mesenchymal transition and pluripotent phenotype of gastric cancer cells by binding to PTEN promoter

Materials and Methods. Table S1. Relationship between EZH2 expression and clinicopathologic parameters of gastric cancer patients. Table S2. Univariate and multivariate analysis of clinicopathological factors for disease-free survival in gastric cancer (qRT-PCR cohort). Table S3. Univariate and multivariate analysis of clinicopathological factors for overall survival in gastric cancer (qRT-PCR cohort). Table S4. Univariate and multivariate analysis of clinicopathological factors for overall survival in gastric cancer (IHC cohort). Table S5. Correlation analysis of expression of stem cell related factors with EZH2. Table S6. Primers and siRNA sequences used in this study. (DOCX 67 kb