Distal Hydrophobic Loop Modulates the Copper Active Site and Reaction of AA13 Polysaccharide Monooxygenases.

Polysaccharide monooxygenases (PMOs) use a type-2 copper center to activate O for the selective hydroxylation of one of the two C-H bonds of glycosidic linkages. Our electron paramagnetic resonance (EPR) analysis and molecular dynamics (MD) simulations suggest the unprecedented dynamic roles of the loop containing the residue G89 (G89 loop) on the active site structure and reaction cycle of starch-active PMOs (AA13 PMOs). In the Cu(II) state, the G89 loop could switch between an "open" and "closed" conformation, which is associated with the binding and dissociation of an aqueous ligand in the distal site, respectively.

Flexible and high-sensitivity sensor based on TiC-MoS MXene composite for the detection of toxic gases.

It is vital to have high sensitivity in gas sensors to allow the exact detection of dangerous gases in the air and at room temperature. In this study, we used 2D MXenes and MoS materials to create a TiC-MoS composite with high metallic conductivity and a wholly functionalized surface for a significant signal. At room temperature, the TiC-MoS composite demonstrated clear signals, cyclic response curves to NO gas, and gas concentration-dependent.

Marine derivatives prevent MUS81 studies.

The winged-helix domain of the methyl methanesulfonate and ultraviolet-sensitive 81 (MUS81) is a potential cancer drug target. In this context, marine fungi compounds were indicated to be able to prevent MUS81 structure via atomistic simulations. Eight compounds such as (), (), (), (), (), (), () and () were indicated that they are able to prevent the conformation of MUS81 via forming a strong binding affinity to the enzyme via perturbation approach.

Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations.

Originating for the first time in Wuhan, China, the outbreak of SARS-CoV-2 has caused a serious global health issue. An effective treatment for SARS-CoV-2 is still unavailable. Therefore, in this study, we have tried to predict a list of potential inhibitors for SARS-CoV-2 main protease (Mpro) using a combination of molecular docking and fast pulling of ligand (FPL) simulations.

Fine Tuning of the Copper Active Site in Polysaccharide Monooxygenases.

Type 2 copper active sites, one of the several important copper active sites in biology, were recently found in the novel superfamily of polysaccharide monooxygenases (PMOs) that cleave recalcitrant polysaccharides via an unprecedented oxidative mechanism. The copper center in PMOs is ligated by the bidentate N-terminal histidine residue and another conserved histidine residue, forming a unique T-shaped core termed as . This core serves as the foundation for diverse structures and electronic properties among PMO families and subfamilies.

Oversampling Free Energy Perturbation Simulation in Determination of the Ligand-Binding Free Energy.

Determination of the ligand-binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate result. However, it is of great interest to improve the accuracy and precision of this method.

Prediction of AChE-ligand affinity using the umbrella sampling simulation.

Acetylcholinesterase (AChE) is characterized as a key target for designing inhibitors to prevent Alzheimer's disease (AD). The binding free energy of a ligand to the AChE enzyme is a critical factor to screen the potential inhibitor in addition to pharmacokinetics and pharmacology estimation. The biased sampling or umbrella sampling (US) method emerges as a reliable technique to estimate the AChE-inhibitor affinity.

Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method.

The binding between two biomolecules is one of the most critical factors controlling many bioprocesses. Therefore, it is of great interest to derive a reliable method to calculate the free binding energy between two biomolecules. In this work, we have demonstrated that the binding affinity of ligands to proteins can be determined through biased sampling simulations.

Co substituted for Bi in BiVO and its enhanced photocatalytic activity under visible LED light irradiation.

We investigated the fabrication of Co-doped BiVO (Bi Co VO , 0.05 < < 0.5) by the substitution of Co ions for Bi sites in BiVO.

Structural and Energetic Impact of Non-natural 7-Deaza-8-azaguanine, 7-Deaza-8-azaisoguanine, and Their 7-Substituted Derivatives on Hydrogen-Bond Pairing with Cytosine and Isocytosine.

The impact of 7-deaza-8-azaguanine (DAG) and 7-deaza-8-azaisoguanine (DAiG) modifications on the geometry and stability of the G:C Watson-Crick (cWW) base pair and the G:iC and iG:C reverse Watson-Crick (tWW) base pairs has been characterized theoretically. In addition, the effect on the same base pairs of seven C7-substituted DAG and DAiG derivatives, some of which have been previously experimentally characterized, has been investigated. Calculations indicate that all of these modifications have a negligible impact on the geometry of the above base pairs, and that modification of the heterocycle skeleton has a small impact on the base-pair interaction energies.

Palladium N-Heterocyclic Carbene Precatalyst Site Isolated in the Core of a Star Polymer.

An approach for supporting a Pd-NHC complex on a soluble star polymer with nanoscale dimensions is described. The resulting star polymer catalyst exhibits excellent activity in cross-coupling reactions, is stable in air and moisture, and is easily recoverable and recyclable. These properties are distinct and unattainable with the small-molecule version of the same catalyst.

One-pot synthesis of Au@SiO(2) catalysts: a click chemistry approach.

Using the copper-catalyzed azide-alkyne cycloaddition "click" reaction, a library of triazole amphiphiles with a variety of functional polar "heads" and hydrophobic or superhydrophobic "tails" was synthesized. The amphiphiles were evaluated for their ability to stabilize small Au nanoparticles, and, at the same time, serve as templates for nanocasting porous SiO2. One of the Au@SiO2 materials thus prepared was found to be a highly active catalyst for the Au nanoparticle-catalyzed regioselective hydroamination of alkynes.