CH-π hydrogen bonds in biological macromolecules

Structure-aided function assignment to the transcriptomic conopeptide Am931

Implementation of the next-generation technologies for gene sequencing of venom duct transcriptome has provided a large number of peptide sequences of marine cone snails. Emerging technologies on computational platforms are now rapidly evolving for the accurate predictions of the 3D structure of the polypeptide using the primary sequence. The current report aims to integrate the information derived from these two technologies to develop the concept of structure-aided function assignment of Conus peptides. The proof of the concept was demonstrated using the transcriptomic peptide Am931 of C. amadis. The 3D structure of Am931 was computed using Density Functional Theory (DFT) and the quality of the predicted structure was confirmed using 2D NMR spectroscopy of the corresponding synthetic peptide. The computed structure of Am931 aligns with the active site motif of thioredoxins, possess catalytic disulfide conformation of (+, -)AntiRHHook and selectively modulate the N-terminal Cys3 thiol. These structural features indicate that Am931 may act as a disulfide isomerase and modulate the oxidative folding of conotoxins. Synthetic peptide Am931 provides proof-of-function by exhibiting catalytic activity on the oxidative folding of α-conotoxin ImI and improving the yield of native globular fold. The approach of integration of new technologies in the Conus peptide research may help to accelerate the discovery pipeline of new/improved conotoxin functional.

Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction

In a continuing effort to understand reaction mechanisms of terpene synthases catalyzing initial anti-Markovnikov cyclization reactions, we solved the X-ray crystal structure of (+)-caryolan-1-ol synthase (CS) from Streptomyces griseus, with and without an inactive analog of the farnesyl diphosphate (FPP) substrate, 2-fluorofarnesyl diphosphate (2FFPP), bound in the active site of the enzyme. The CS-2FFPP structure was solved to 2.65 Å resolution and showed the ligand in an elongated orientation, incapable of undergoing the initial cyclization event to form a C1-C11 bond. Intriguingly, the apo CS structure (2.2 Å) also had electron density in the active site, in this case, well fit by a curled-up tetraethylene glycol molecule recruited, presumably, from the crystallization medium. The density was also well fit by a molecule of farnesene suggesting that the structure may mimic an intermediate along the reaction coordinate. The curled-up conformation of tetraethylene glycol was accompanied by dramatic rotation of some active-site residues in comparison to the 2FFPP-structure. Most notably, W56 and F183 undergo 90° rotations between the 2FFPP complex and apoenzyme structures, suggesting that these residues provide interactions that help curl the tetraethylene glycol molecule in the active site, and by extension perhaps also a derivative of the FPP substrate in the normal course of the cyclization reaction. In support of this proposal, the CS W56L and F183A variants were observed to be severely restricted in their ability to catalyze C1-C11 cyclization of the FPP substrate and instead produced predominantly acyclic terpene products dominated by farnesol, β-farnesene, and nerolidol.

Structure-based mapping of the histone-binding pocket of KDM4D using functionalized tetrazole and pyridine core compounds

KDM4 histone demethylases became an exciting target for inhibitor development as the evidence linking them directly to tumorigenesis mounts. In this study, we set out to better understand the binding cavity using an X-ray crystallographic approach to provide a detailed landscape of possible interactions within the under-investigated region of KDM4. Our design strategy was based on utilizing known KDM binding motifs, such as nicotinic acid and tetrazolylhydrazides, as core motifs that we decided to enrich with flexible tails to map the distal histone binding site. The resulting X-ray structures of the novel compounds bound to KDM4D, a representative of the KDM4 family, revealed the interaction pattern with distal residues in the histone-binding site. The most prominent protein rearrangement detected upon ligand binding is the loop movement that blocks the accessibility to the histone binding site. Apart from providing new sites that potential inhibitors can target, the novel compounds may prove helpful in exploring the capacity of ligands to bind in sites distal to the cofactor-binding site of other KDMs or 2-oxoglutarate (2OG)-dependent oxygenases. The case study proves that combining a strong small binding motif with flexible tails to probe the binding pocket will facilitate lead discovery in classical drug-discovery campaigns, given the ease of accessing X-ray quality crystals.

Aromatic Residues in Proteins: Re-Evaluating the Geometry and Energetics of π-π, Cation-π, and CH-π Interactions

Aromatic residues can participate in various biomolecular interactions, such as π-π, cation-π, and CH-π interactions, which are essential for protein structure and function. Here, we re-evaluate the geometry and energetics of these interactions using quantum mechanical (QM) calculations, focusing on pairwise interactions involving the aromatic amino acids Phe, Tyr, and Trp and the cationic amino acids Arg and Lys. Our findings reveal that π-π interactions, while energetically favorable, are less abundant in structured proteins than commonly assumed and are often overshadowed by previously underappreciated, yet prevalent, CH-π interactions. Cation-π interactions, particularly those involving Arg, show strong binding energies and a specific geometric preference toward stacked conformations, despite the global QM minimum, suggesting that a rather perpendicular T-shape conformation should be more favorable. Our results support a more nuanced understanding of protein stabilization via interactions involving aromatic residues. On the one hand, our results challenge the traditional emphasis on π-π interactions in structured proteins by showing that CH-π and cation-π interactions contribute significantly to their structure. On the other hand, π-π interactions appear to be key stabilizers in solvated regions and thus may be particularly important to the stabilization of intrinsically disordered proteins.

Quantification of CH and NH/π-Stacking Interactions in Cells Using Nuclear Magnetic Resonance Spectroscopy

π-Stacking, a type of noncovalent interactions involving aromatic residues, plays an important role in protein folding and function. In this work, an attempt has been made to measure CH/π and NH/π stacking interactions in a protein in Escherichia coli cells using a combined double-mutant cycle and nuclear magnetic resonance spectroscopy method. The results show that the CH/π and NH/π stacking interactions are generally weaker in cells than those in the buffer. The transient intermolecular noncovalent interactions between the protein and the complex cellular environment may compete with and thus weaken the stacking interactions in the protein. The weakening of stacking interactions can enhance the local conformational opening of proteins in E. coli cells. This is evident from the faster rates of amide hydrogen/deuterium exchange observed in cells than in the buffer, for residues that undergo local conformational opening. This study highlights the influence of the cellular environment on π-stacking and the conformational dynamics of proteins.

Organic Chimeras based on Selenosugars, Steroids, and Fullerenes as Potential Inhibitors of the β-amyloid Peptide Aggregation

The aggregation of β-amyloid peptide (Aβ) is associated with neurodegenerative diseases such as Alzheimer's disease (AD). Several therapies aimed at reducing the aggregation of this peptide have emerged as potential strategies for the treatment of AD. This paper describes the design and preparation of new hybrid molecules based on steroids, selenosugars, and [60]fullerene as potential inhibitors of Aβ oligomerization. These moieties were selected based on their antioxidant properties and possible areas of interaction with the Aβ. Cyclopropanations between C60 and malonates bearing different steroid and selenosugar moieties using the Bingel-Hirsch protocol have enabled the synthesis of functionalized molecular hybrids. The obtained derivatives were characterized by physical and spectroscopic techniques. Theoretical calculations for all the selenium compounds were performed using the density functional theory DFT/B3LYP-D3(BJ)/6-311G(2d,p) predicting the most stable conformations of the synthesized derivatives. Relevant geometrical parameters were investigated to relate the stereochemical behavior and the spectroscopic data obtained. The affinity of the compounds for Aβ-peptide was estimated by molecular docking simulation, which predicted an increase in affinity and interactions for Aβ for the hybrids containing the C60 core. In addition, parameters such as lipophilicity, polar surface area, and dipole moment were calculated to predict their potential interaction with membrane cells.

Probing Protein-Ligand Methyl-π Interaction Geometries through Chemical Shift Measurements of Selectively Labeled Methyl Groups

Fragment-based drug design is heavily dependent on the optimization of initial low-affinity binders. Herein we introduce an approach that uses selective labeling of methyl groups in leucine and isoleucine side chains to directly probe methyl-π contacts, one of the most prominent forms of interaction between proteins and small molecules. Using simple NMR chemical shift perturbation experiments with selected BRD4-BD1 binders, we find good agreement with a commonly used model of the ring-current effect as well as the overall interaction geometries extracted from the Protein Data Bank. By combining both interaction geometries and chemical shift calculations as fit quality criteria, we can position dummy aromatic rings into an AlphaFold model of the protein of interest. The proposed method can therefore provide medicinal chemists with important information about binding geometries of small molecules in fast and iterative matter, even in the absence of high-resolution experimental structures.

Differing Effects of Nonlinearity around the Proton Acceptor on CH··O and NH··O H-Bond Strength within Proteins

The effects of deviations from nonlinearity around the carbonyl proton acceptor of an amide group are assessed by DFT quantum chemical calculations for both CH··O and NH··O H-bonds. The proton donors are the imidazole functional group of His and the indole of Trp, which are paired respectively with N-methylacetamide and acetamide. The displacement of either CH or NH group toward the carbonyl O sp2 lone pairs stabilizes the system and strengthens the H-bond. But the two donor groups differ in their response to a shift out of the amide plane. While the NH··O H-bond is weakened by this displacement, a substantial strengthening is observed when the CH donor is moved out of this plane, in one direction versus the other. This pattern is explained on the basis of simple Coulombic considerations.

Dynamics of CH/n hydrogen bond networks probed by time-resolved CARS spectroscopy

Hydrogen bond (HB) networks are essential for stabilizing molecular structures in solution and govern the solubility and functionality of molecules in an aqueous environment. HBs are important in biological processes such as enzyme-substrate interactions, protein folding, and DNA replication. However, the exact role of weakly polarized C-H bonds as HB proton donors in solution, such as CH/n HBs, remains mostly unknown. Here, we employ a novel approach focusing on vibrational dephasing to investigate the coherence relaxation of induced dipoles in C-H bonds within CH/n HB networks, utilizing time-resolved coherent anti-Stokes Raman scattering (T-CARS) spectroscopy. Using a representative binary system of dimethyl sulfoxide (DMSO)-water, known for its C-H backboned HB system (i.e., C-H⋯S), we observed an increase in the dephasing time of the C-H bending mode with increasing water content until a percolation threshold at a 6 : 1 water : DMSO molar ratio, where the trend is reversed. These results provide compelling evidence for the existence of C-H⋯S structures and underscore the presence of a percolation effect, suggesting a critical threshold where long-range connectivity is disputed.

Structural Characterization of Disulfide-Linked p53-Derived Peptide Dimers

Disulfide bonds provide a convenient method for chemoselective alteration of peptide and protein structure and function. We previously reported that mild oxidation of a p53-derived bisthiol peptide (CTFANLWRLLAQNC) under dilute non-denaturing conditions led to unexpected disulfide-linked dimers as the exclusive product. The dimers were antiparallel, significantly α-helical, resistant to protease degradation, and easily reduced back to the original bisthiol peptide. Here we examine the intrinsic factors influencing peptide dimerization using a combination of amino acid substitution, circular dichroism (CD) spectroscopy, and X-ray crystallography. CD analysis of peptide variants suggests critical roles for Leu6 and Leu10 in the formation of stable disulfide-linked dimers. The 1.0 Å resolution crystal structure of the peptide dimer supports these data, revealing a leucine-rich LxxLL dimer interface with canonical knobs-into-holes packing. Two levels of higher-order oligomerization are also observed in the crystal: an antiparallel "dimer of dimers" mediated by Phe3 and Trp7 residues in the asymmetric unit and a tetramer of dimers mediated by Trp7 and Leu10. In CD spectra of Trp-containing peptide variants, minima at 227 nm provide evidence for the dimer of dimers in dilute aqueous solution. Importantly, and in contrast to the original dimer model, the canonical leucine-rich core and robust dimerization of most peptide variants suggests a tunable molecular architecture to target various proteins and evaluate how folding and oligomerization impact various properties, such as cell permeability.

Functionalized Chiral Materials for Use in Chiral Sensors

Chirality represents a fundamental attribute within living systems and is a pervasive phenomenon in the natural world. The identification and analysis of chiral materials within natural environments and biological systems hold paramount importance in clinical, chemical, and biological sciences. Within chiral analysis, there is a burgeoning focus on developing chiral sensors exhibiting exceptional selectivity, sensitivity, and stability, marking it as a forefront area of research. In the past decade (2013-2023), approximately 1990 papers concerning the application of various chiral materials in chiral sensors have been published. Biological materials and nanomaterials have important applications in the development of chiral sensors, which accounting for 26.67% and 45.24% of the material-related applications in these sensors, respectively; moreover, the development of chiral nanomaterials is closely related to the development of portable and stable chiral sensors. Natural chiral materials, utilized as selective recognition units, are combined with carriers characterized by good physical and chemical properties through functionalization to form various functional chiral materials, which improve the recognition efficiency of chiral sensors. In this article, from the perspective of biological materials, polymer materials, nanomaterials, and other functional chiral materials, the applications of chiral sensors are summarized and the research prospects of chiral sensors are discussed.

Structural and Functional Analyses of Inhibition of Human Dihydroorotate Dehydrogenase by Antiviral Furocoumavirin

Natural products are important sources of seed compounds for drug discovery. However, it has become difficult in recent years to discover new compounds with valuable pharmacological activities. On the other hand, among the vast number of natural products that have been isolated so far, a considerable number of compounds with specific biological activities are thought to be overlooked in screening that uses biological activity as an index. Therefore, it is conceivable that such overlooked useful compounds may be found by screening compound libraries that have been amassed previously through specific assays. Previously, NPD723, a member of the Natural Products Depository library comprised of a mixture of natural and non-natural products developed at RIKEN, and its metabolite H-006 were found to inhibit growth of various cancer cells at low nanomolar half-maximal inhibitory concentration. Subsequent analysis revealed that H-006 strongly inhibited human dihydroorotate dehydrogenase (DHODH), the rate-limiting enzyme in the de novo pyrimidine biosynthetic pathway. Here, we elucidated the crystal structure of the DHODH-flavin mononucleotide-orotic acid-H-006 complex at 1.7 Å resolution to determine that furocoumavirin, the S-enantiomer of H-006, was the actual inhibitor. The overall mode of interaction of furocoumavirin with the inhibitor binding pocket was similar to that described for previously reported tight-binding inhibitors. However, the structural information together with kinetic characterizations of site-specific mutants identified key unique features that are considered to contribute to the sub-nanomolar inhibition of DHODH by furocoumavirin. Our finding identified new chemical features that could improve the design of human DHODH inhibitors.

Synergistic modification of hot-melt extrusion and nobiletin on the multi-scale structures, interactions, thermal properties, and in vitro digestibility of rice starch

Background

Rice starch has high digestibility due to its large carbohydrate content. Synergistic modification of hot-melt extrusion (HME) and additives such as flavonoids, hydrocolloids, proteins, lipids, and other additives has the tendency to retard the rate of starch hydrolysis. Hence, the current investigation aimed to study the combined effect of the HME-assisted addition of nobiletin (NOB, 0, 2, 4, and 6%) on the multi-scale structures, interactions, thermal, and digestibility characteristics of rice starch.

Methods

The study employed density functional theory calculations and an infrared second derivative of an Fourier-transform infrared (FTIR) spectrometer to analyze the interactions between NOB and starch. The physicochemical properties of the starch extrudates were characterized by FTIR, 13C nuclear magnetic resonance, X-ray diffraction, and differential scanning calorimetry, while the digestibility was evaluated using an in vitro digestion model.

Results

HME was found to disrupt the crystalline structure, helix structure, short-ordered structure, and thermal properties of starch. The interaction between NOB and starch involved hydrophobic interactions and hydrogen bonds, effectively preventing the molecular chains of starch from interacting with each other and disrupting their double helix structure. The addition of NOB led to the formation of a highly single-helical V-type crystalline structure, along with the formation of ordered structural domains. Consequently, the combined treatment significantly enhanced the ordered structure and thermal stability of starch, thus effectively leading to an increase in resistant starch and slowly digestion starch.

Discussion

The study underscores that synergistic modification of HME and NOB holds promise for enhancing both the nutritional value and functional properties of rice starch. These findings offer valuable insights for developing high-quality rice starch products with broader applications.

Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery

In the pursuit of novel antiretroviral therapies for human immunodeficiency virus type-1 (HIV-1) proteases (PRs), recent improvements in drug discovery have embraced machine learning (ML) techniques to guide the design process. This study employs ensemble learning models to identify crucial substructures as significant features for drug development. Using molecular docking techniques, a collection of 160 darunavir (DRV) analogs was designed based on these key substructures and subsequently screened using molecular docking techniques. Chemical structures with high fitness scores were selected, combined, and one-dimensional (1D) screening based on beyond Lipinski's rule of five (bRo5) and ADME (absorption, distribution, metabolism, and excretion) prediction implemented in the Combined Analog generator Tool (CAT) program. A total of 473 screened analogs were subjected to docking analysis through convolutional neural networks scoring function against both the wild-type (WT) and 12 major mutated PRs. DRV analogs with negative changes in binding free energy (ΔΔ G bind ) compared to DRV could be categorized into four attractive groups based on their interactions with the majority of vital PRs. The analysis of interaction profiles revealed that potent designed analogs, targeting both WT and mutant PRs, exhibited interactions with common key amino acid residues. This observation further confirms that the ML model-guided approach effectively identified the substructures that play a crucial role in potent analogs. It is expected to function as a powerful computational tool, offering valuable guidance in the identification of chemical substructures for synthesis and subsequent experimental testing.

Tri-fluoro-methane-sulfonate salt of 5,10,15,20-tetra-kis-(1-benzyl-pyridin-1-ium-4-yl)-21H,23H-porphyrin and its CaII complex

The synthesis, crystallization and characterization of a tri-fluoro-methane-sulfonate salt of 5,10,15,20-tetra-kis-(1-benzyl-pyridin-1-ium-4-yl)-21H,23H-por-phy-rin, C68H54N8 4+·4CF3SO3 -·4H2O, 1·OTf, are reported in this work. The reaction between 5,10,15,20-tetra-kis-(pyridin-4-yl)-21H,23H-porphyrin and benzyl bromide in the presence of 0.1 equiv. of Ca(OH)2 in CH3CN under reflux with an N2 atmosphere and subsequent treatment with silver tri-fluoro-methane-sulfonate (AgOTf) salt produced a red-brown solution. This reaction mixture was filtered and the solvent was allowed to evaporate at room temperature for 3 d to give 1·OTf. Crystal structure determination by single-crystal X-ray diffraction (SCXD) revealed that 1·OTf crystallizes in the space group P21/c. The asymmetric unit contains half a porphyrin mol-ecule, two tri-fluoro-methane-sulfonate anions and two water mol-ecules of crystallization. The macrocycle of tetra-pyrrole moieties is planar and unexpectedly it has coordinated CaII ions in occupational disorder. This CaII ion has only 10% occupancy (C72H61.80Ca0.10F12N8O16S4). The pyridinium rings bonded to methyl-ene groups from porphyrin are located in two different arrangements in almost orthogonal positions between the plane formed by the porphyrin and the pyridinium rings. The crystal structure features cation⋯π inter-actions between the CaII atom and the π-system of the phenyl ring of neighboring mol-ecules. Both tri-fluoro-methane-sulfonate anions are found at the periphery of 1, forming hydrogen bonds with water mol-ecules.

Regulation of RAS palmitoyltransferases by accessory proteins and palmitoylation

Palmitoylation of cysteine residues at the C-terminal hypervariable regions in human HRAS and NRAS, which is necessary for RAS signaling, is catalyzed by the acyltransferase DHHC9 in complex with its accessory protein GCP16. The molecular basis for the acyltransferase activity and the regulation of DHHC9 by GCP16 is not clear. Here we report the cryo-electron microscopy structures of the human DHHC9-GCP16 complex and its yeast counterpart-the Erf2-Erf4 complex, demonstrating that GCP16 and Erf4 are not directly involved in the catalytic process but stabilize the architecture of DHHC9 and Erf2, respectively. We found that a phospholipid binding to an arginine-rich region of DHHC9 and palmitoylation on three residues (C24, C25 and C288) were essential for the catalytic activity of the DHHC9-GCP16 complex. Moreover, we showed that GCP16 also formed complexes with DHHC14 and DHHC18 to catalyze RAS palmitoylation. These findings provide insights into the regulatory mechanism of RAS palmitoyltransferases.

Removal of glyphosate (GLY) and aminomethylphosphonic acid (AMPA) by ultrafiltration with permeate-side polymer-based spherical activated carbon (UF-PBSAC)

Glyphosate (GLY) is the most commonly used herbicide worldwide, and aminomethylphosphonic acid (AMPA) is one of its main metabolites. GLY and AMPA are toxic to humans, and their complex physicochemical properties present challenges in their removal from water. Several technologies have been applied to remove GLY and AMPA such as adsorption, filtration, and degradation with varied efficiencies. In previous works, an ultrafiltration membrane with permeate-side polymer-based spherical activated carbon (UF-PBSAC) showed the feasibility of removing uncharged micropollutants via adsorption in a flow-through configuration. The same UF-PBSAC was investigated for GLY and AMPA adsorption to assess the removal of charged and lower molecular weight micropollutants. The results indicated that both surface area and hydraulic residence time were limiting factors in GLY/AMPA adsorption by UF-PBSAC. The higher external surface of PBSAC with strong affinity for GLY and AMPA showed higher removal in a dynamic process where the hydraulic residence time was short (tens of seconds). Extending hydraulic residence times (hundreds of seconds) resulted in higher GLY/AMPA removal by allowing GLY/AMPA to diffuse into the PBSAC pores and reach more surfaces. Enhancement was achieved by minimising both limiting factors (external surface and hydraulic residence time) with a low flux of 25 L/m2.h, increased PBSAC layer of 6 mm, and small PBSAC particle size of 78 µm. With this configuration, UF-PBSAC could remove 98 % of GLY and 95 % of AMPA from an initial concentration of 1000 ng/L at pH 8.2 ± 0.2 and meet European Union (EU) regulation for herbicides (100 ng/L for individuals and 500 ng/L for total herbicides). The results implied that UF-PBSAC was able to remove charged micropollutants to the required levels and had potential for application in wastewater treatment and water reuse.

Introducing fluorescent probe technology for detecting microcystin-LR in the water and cells

BACKGROUND

For a long time, the environment hazards caused by cyanobacteria bloom and associated microcystins have attracted attention worldwide. Microcystin-LR (MC-LR) is the most widely distributed and most toxic toxin. At present, numerous MC-LR detection methods exist many drawbacks. Therefore, a quick and accurate method for identifying and detecting MC-LR is crucial and necessary. In this work, we strived to introduce a novel fluorescence assay to detect MC-LR in the water and cells.

RESULTS

According to the special spatial configuration and physicochemical properties of MC-LR, we designed and constructed six fluorescent probes. The design concepts of the probes were exhaustively elaborated. MC-YdTPA, MC-YdTPE, MC-RdTPA, and MC-RdTPE could show significant fluorescence enhancement in MC-LR solution. Significantly, MC-YdTPA, MC-YdTPE, and MC-RdTPA could also response well in the cells treated with MC-LR, demonstrating these fluorescent probes' values. The recognition mechanism between probes and MC-LR were also deeply explored: (1) The polyphenylene ring structure of probes may have nested or hydrogen bond weak interaction with the ring structure of MC-LR. (2) The probes can generate a reaction to the hydrogen ions ionized by MC-LR.

SIGNIFICANCE

We proposed the novel ideas for designing MC-LR probes. This research can provide valuable experiences and important assistance in synthesizing MC-LR fluorescent probes. We expect that this work may bring new ideas to develop fluorescent probes for researching MC-LR in vivo and in vitro.

Reticulons bind sphingolipids to activate the endoplasmic reticulum cell cycle checkpoint, the ER surveillance pathway

The inheritance of a functional endoplasmic reticulum (ER) is ensured by the ER stress surveillance (ERSU) pathway. Here, we made the unexpected discovery that reticulon 1 (Rtn1) and Yop1, well-known ER-curvature-generating proteins, each possess two sphingolipid-binding motifs within their transmembrane domains and that these motifs recognize the ER-stress-induced sphingolipid phytosphingosine (PHS), resulting in an ER inheritance block. Upon binding PHS, Rtn1/Yop1 accumulate on the ER tubule, poised to enter the emerging daughter cell, and cause its misdirection to the bud scars (i.e., previous cell division sites). Amino acid changes in the conserved PHS-binding motifs preclude Rtn1 or Yop1 from binding PHS and diminish their enrichment on the tubular ER, ultimately preventing the ER-stress-induced inheritance block. Conservation of these sphingolipid-binding motifs in human reticulons suggests that sphingolipid binding to Rtn1 and Yop1 represents an evolutionarily conserved mechanism that enables cells to respond to ER stress.

Polymorphism and Light-Driven Forward Movement of TPE Derivative Micro-Crystal due to ArH-pi Interactions Difference

Aggregation-induced emission (AIE) and aggregation-caused quenching (ACQ) are two classes of opposite luminescence phenomena. It is almost impossible to show both AIE and ACQ effect simultaneously by the same molecule. However, here we report that a simple TPE derivative TAP-TPE grows into both AIE crystals and ACQ ones. It is found that equatorial, contact distance-longer and weak ArH-π interactions exist in AIE crystals while vertical, contact distance-shorter and strong ArH-π interactions appear in ACQ crystals. Theoretical calculation of electron density on the interaction atoms unveils that ACQ crystals have much larger change in electron density than AIE ones, suggesting that the intermolecular electron transfer aroused by the strong ArH-π hydrogen bonds leads to ACQ phenomenon. This result provides a new insight into the emission mechanism in aggregation state. Interestingly, due to the ArH-pi interactions difference, only one of five kinds of crystals shows rapid photochromism, and can act as multimode anti-counterfeiting materials. Very exceptionally, for the first time we find that the photochromic micrometric rod-like crystal even makes forward rolling movement as it repeatedly bends and straightens by responding to on and off of the ultraviolet light irradiation, displaying potential for photo-actuator and light-driven micro-vehicle.

Impact of Peptide Sequence on Functional siRNA Delivery and Gene Knockdown with Cyclic Amphipathic Peptide Delivery Agents

Short-interfering RNA (siRNA) oligonucleotide therapeutics that modify gene expression by accessing RNA-interference (RNAi) pathways have great promise for the treatment of a range of disorders; however, their application in clinical settings has been limited by significant challenges in cellular delivery. Herein, we report a structure-function study using a series of modified cyclic amphipathic cell-penetrating peptides (CAPs) to determine the impact of peptide sequence on (1) siRNA-binding efficiency, (2) cellular delivery and knockdown efficiency, and (3) the endocytic uptake mechanism. Nine cyclic peptides of the general sequence Ac-C[XZ]4CG-NH2 in which X residues are hydrophobic/aromatic (Phe, Tyr, Trp, or Leu) and Z residues are charged/hydrophilic (Arg, Lys, Ser, or Glu) are assessed along with one acyclic peptide, Ac-(WR)4G-NH2. Cyclization is enforced by intramolecular disulfide bond formation between the flanking Cys residues. Binding analyses indicate that strong cationic character and the presence of aromatic residues that are competent to participate in CH-π interactions lead to CAP sequences that most effectively interact with siRNA. CAP-siRNA binding increases in the following order as a function of CAP hydrophobic/aromatic content: His < Phe < Tyr < Trp. Both cationic charge and disulfide-constrained cyclization of CAPs improve uptake of siRNA in vitro. Net neutral CAPs and an acyclic peptide demonstrate less-efficient siRNA translocation compared to the cyclic, cationic CAPs tested. All CAPs tested facilitated efficient siRNA target gene knockdown of at least 50% (as effective as a lipofectamine control), with the best CAPs enabling >80% knockdown. Significantly, gene knockdown efficiency does not strongly correlate with CAP-siRNA internalization efficiency but moderately correlates with CAP-siRNA-binding affinity. Finally, utilization of small-molecule inhibitors and targeted knockdown of essential endocytic pathway proteins indicate that most CAP-siRNA nanoparticles facilitate siRNA delivery through clathrin- and caveolin-mediated endocytosis. These results provide insight into the design principles for CAPs to facilitate siRNA delivery and the mechanisms by which these peptides translocate siRNA into cells. These studies also demonstrate the nature of the relationships between peptide-siRNA binding, cellular delivery of siRNA cargo, and functional gene knockdown. Strong correlations between these properties are not always observed, which illustrates the complexity in the design of optimal next-generation materials for oligonucleotide delivery.

Insights into the Mechanism of Tryptophan Fluorescence Quenching due to Synthetic Crowding Agents: A Combined Experimental and Computational Study

Intrinsic tryptophan fluorescence spectroscopy is an important tool for examining the effects of molecular crowding and confinement on the structure, dynamics, and function of proteins. Synthetic crowders such as dextran, ficoll, polyethylene glycols, polyvinylpyrrolidone, and their respective monomers are used to mimic crowded intracellular environments. Interactions of these synthetic crowders with tryptophan and the subsequent impact on its fluorescence properties are therefore critically important for understanding the possible interference created by these crowders. In the present study, the effects of polymer and monomer crowders on tryptophan fluorescence were assessed by using experimental and computational approaches. The results of this study demonstrated that both polymer and monomer crowders have an impact on the tryptophan fluorescence intensity; however, the molecular mechanisms of quenching were different. Using Stern-Volmer plots and a temperature variation study, a physical basis for the quenching mechanism of commonly used synthetic crowders was established. The quenching of free tryptophan was found to involve static, dynamic, and sphere-of-action mechanisms. In parallel, computational studies employing Kohn-Sham density functional theory provided a deeper insight into the effects of intermolecular interactions and solvation, resulting in differing quenching modes for these crowders. Taken together, the study offers new physical insights into the quenching mechanisms of some commonly used monomer and polymer synthetic crowders.

Synthesis and Conformational Analysis of FR901464-Based RNA Splicing Modulators and Their Synergism in Drug-Resistant Cancers

FR901464 is a cytotoxic natural product that binds splicing factor 3B subunit 1 (SF3B1) and PHD finger protein 5A (PHF5A), the components of the human spliceosome. The amide-containing tetrahydropyran ring binds SF3B1, and it remains unclear how the substituents on the ring contribute to the binding. Here, we synthesized meayamycin D, an analogue of FR901464, and three additional analogues to probe the conformation through methyl scanning. We discovered that the amide-containing tetrahydropyran ring assumes only one of the two possible chair conformations and that methylation of the nitrogen distorts the chair form, dramatically reducing cytotoxicity. Meayamycin D induced alternative splicing of MCL-1, showed strong synergism with venetoclax in drug-resistant lung cancer cells, and was cancer-specific over normal cells. Meayamycin D incorporates an alkyl ether and shows a long half-life in mouse plasma. The characteristics of meayamycin D may provide an approach to designing other bioactive L-shaped molecules.

Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally Determined Enthalpic and Entropic Contributions to Interactions of Amide sp2O, N, C and sp3C Unified Atoms with Naphthalene sp2C Atoms in Water

In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp2 atoms of amides, aromatics, and other groups occur in protein self-assembly processes including folding, oligomerization, and condensate formation. These interactions also occur in aqueous solutions of amide and aromatic compounds, where they can be quantified. Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp2O with amide sp2N unified atoms (presumably C═O···H-N hydrogen bonds) and amide/aromatic sp2C (lone pair π, n-π*) are particularly favorable. Sp3C-sp3C (hydrophobic), sp3C-sp2C (hydrophobic, CH-π), sp2C-sp2C (hydrophobic, π-π), and sp3C-sp2N interactions are favorable, sp2C-sp2N interactions are neutral, while sp2O-sp2O and sp2N-sp2N self-interactions and sp2O-sp3C interactions are unfavorable. Here, from determinations of favorable effects of 14 amides on naphthalene solubility at 10, 25, and 45 °C, we dissect amide-aromatic interaction free energies into enthalpic and entropic contributions and find these vary systematically with amide composition. Analysis of these results yields enthalpic and entropic contributions to intrinsic strengths of interactions of amide sp2O, sp2N, sp2C, and sp3C unified atoms with aromatic sp2C atoms. For each interaction, enthalpic and entropic contributions have the same sign and are much larger in magnitude than the interaction free energy itself. The amide sp2O-aromatic sp2C interaction is enthalpy-driven and entropically unfavorable, consistent with direct chemical interaction (e.g., lone pair-π), while amide sp3C- and sp2C-aromatic sp2C interactions are entropy-driven and enthalpically unfavorable, consistent with hydrophobic effects. These findings are relevant for interactions involving π-bonded sp2 atoms in protein processes.

AQcalc: A web server that identifies weak molecular interactions in protein structures

Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion-quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein-protein, protein-nucleic acids, and protein-lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation-π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation-π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen-bonded AQ (HBAQ) in fibril structures and protein-lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.

Visualization Tools for Detecting Microcystin-LR in the Biological System via Near-Infrared Fluorescent Probes

Numerous toxicological and epidemiological studies have shown that microcystin-LR (MC-LR) could cause a variety of toxicity to humans and animals. However, the absence of effective methods to trace MC-LR in biological systems has hindered the in-depth understanding of the mechanism of MC-LR toxicity. Near-infrared (NIR) fluorescent probes are crucial tools for accurate visualization and in-depth study of specific molecules in biological systems. Due to the lack of effective design strategies, NIR fluorescent probes for imaging MC-LR specifically in biological systems have not been reported yet. In order to address this pressing issue, herein, we have introduced a new and facile strategy to improve MC-LR detection and imaging in biological systems, and based on this design strategy, three NIR fluorescence probes (MC-RdTPA1, MC-RdTPA2, and MC-RdTPE1) have been constructed. These probes have several advantages: (i) have long emission wavelength and large Stokes shifts, which have great potential in vivo imaging applications; (ii) could selectively visualize MC-LR in cells; and (iii) showed stable fluorescence intensity in the pH range of 5.0-7.0. This work may provide a new avenue for the detection of MC-LR in biological systems and new tool to advance our knowledge of the mechanism of MC-LR toxicity.

Functional diversity of c-di-GMP receptors in prokaryotic and eukaryotic systems

Cyclic bis-(3', 5')-dimeric guanosine monophosphate (c-di-GMP) is ubiquitous in many bacterial species, where it functions as a nucleotide-based secondary messenger and is a vital regulator of numerous biological processes. Due to its ubiquity, most bacterial species possess a wide range of downstream receptors that has a binding affinity to c-di-GMP and elicit output responses. In eukaryotes, several enzymes and riboswitches operate as receptors that interact with c-di-GMP and transduce cellular or environmental signals. This review examines the functional variety of receptors in prokaryotic and eukaryotic systems that exhibit distinct biological responses after interacting with c-di-GMP. Evolutionary relationships and similarities in distance among the c-di-GMP receptors in various bacterial species were evaluated to understand their specificities. Furthermore, residues of receptors involved in c-di-GMP binding are summarized. This review facilitates the understanding of how distinct receptors from different origins bind c-di-GMP equally well, yet fulfill diverse biological roles at the interspecies, intraspecies, and interkingdom levels. Furthermore, it also highlights c-di-GMP receptors as potential therapeutic targets, particularly those found in pathogenic microorganisms. Video Abstract.

Strong structuring arising from weak cooperative O-H···π and C-H···O hydrogen bonding in benzene-methanol solution

Weak hydrogen bonds, such as O-H···π and C-H···O, are thought to direct biochemical assembly, molecular recognition, and chemical selectivity but are seldom observed in solution. We have used neutron diffraction combined with H/D isotopic substitution to obtain a detailed spatial and orientational picture of the structure of benzene-methanol mixtures. Our analysis reveals that methanol fully solvates and surrounds each benzene molecule. The expected O-H···π interaction is highly localised and directional, with the methanol hydroxyl bond aligned normal to the aromatic plane and the hydrogen at a distance of 2.30 Å from the ring centroid. Simultaneously, the tendency of methanol to form chain and cyclic motifs in the bulk liquid is manifest in a highly templated solvation structure in the plane of the ring. The methanol molecules surround the benzene so that the O-H bonds are coplanar with the aromatic ring while the oxygens interact with C-H groups through simultaneous bifurcated hydrogen bonds. This demonstrates that weak hydrogen bonding can modulate existing stronger interactions to give rise to highly ordered cooperative structural motifs that persist in the liquid phase.

Neuroprotective Properties of Oleanolic Acid-Computational-Driven Molecular Research Combined with In Vitro and In Vivo Experiments

Oleanolic acid (OA), as a ubiquitous compound in the plant kingdom, is studied for both its neuroprotective and neurotoxic properties. The mechanism of acetylcholinesterase (AChE) inhibitory potential of OA is investigated using molecular dynamic simulations (MD) and docking as well as biomimetic tests. Moreover, the in vitro SH-SY5Y human neuroblastoma cells and the in vivo zebrafish model were used. The inhibitory potential towards the AChE enzyme is examined using the TLC-bioautography assay (the IC50 value is 9.22 μM). The CH-π interactions between the central fragment of the ligand molecule and the aromatic cluster created by the His440, Phe288, Phe290, Phe330, Phe331, Tyr121, Tyr334, Trp84, and Trp279 side chains are observed. The results of the in vitro tests using the SH-SY5Y cells indicate that the viability rate is reduced to 71.5%, 61%, and 43% at the concentrations of 100 µg/mL, 300 µg/mL, and 1000 µg/mL, respectively, after 48 h of incubation, whereas cytotoxicity against the tested cell line with the IC50 value is 714.32 ± 32.40 µg/mL. The in vivo tests on the zebrafish prove that there is no difference between the control and experimental groups regarding the mortality rate and morphology (p > 0.05).

Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally-determined Enthalpic and Entropic Contributions to Interactions of Amide sp 2 O, N, C and sp 3 C Unified Atoms with Naphthalene sp 2 C Atoms in Water

In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp 2 atoms of amides, aromatics and other groups occur in protein self-assembly processes including folding, oligomerization and condensate formation. These interactions also occur in aqueous solutions of amide and aromatic compounds, where they can be quantified. Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp 2 O with amide sp 2 N unified atoms (presumably C=O···H-N hydrogen bonds) and amide/aromatic sp 2 C (lone pair-π, n-π * ) are particularly favorable. Sp 3 C-sp 3 C (hydrophobic), sp 3 C-sp 2 C (hydrophobic, CH-π), sp 2 C-sp 2 C (hydrophobic, π-π) and sp 3 C-sp 2 N interactions are favorable, sp 2 C-sp 2 N interactions are neutral, while sp 2 O-sp 2 O and sp 2 N-sp 2 N self-interactions and sp 2 O-sp 3 C interactions are unfavorable. Here, from determinations of favorable effects of fourteen amides on naphthalene solubility at 10, 25 and 45 °C, we dissect amide-aromatic interaction free energies into enthalpic and entropic contributions and find these vary systematically with amide composition. Analysis of these results yields enthalpic and entropic contributions to intrinsic strengths of interactions of amide sp 2 O, sp 2 N, sp 2 C and sp 3 C unified atoms with aromatic sp 2 C atoms. For each interaction, enthalpic and entropic contributions have the same sign and are much larger in magnitude than the interaction free energy itself. The amide sp 2 O-aromatic sp 2 C interaction is enthalpy-driven and entropically unfavorable, consistent with direct chemical interaction (e.g. lone pair-π) while amide sp 3 C- and sp 2 C-aromatic sp 2 C interactions are entropy-driven and enthalpically unfavorable, consistent with hydrophobic effects. These findings are relevant for interactions involving π-bonded sp 2 atoms in protein processes.

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The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function

Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.

Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin

The rational structural and computational studies of a blue copper protein, pseudoazurin (PAz), and its Met16X (X = Phe, Leu, Val, Ile) variants gave clear functional meanings of the noncovalent interaction (NCI) through the second coordination sphere. The high-resolution X-ray crystal structures of Met16X PAz demonstrated that the active site geometry is significantly affected by the substitution of Met16, which is located within the NCI distance from the His81 imidazole ring at the copper active site. The computational chemistry calculations based on the crystal structure analyses confirmed that the NCI of S-π/CH-π (wild-type), π-π (Met16Phe), double CH-π (Met16Leu), and single CH-π (Met16Val and Met16Ile). The estimated interaction energies for the NCI demonstrated that the fine-tuning of the protein stability and Cu site properties form the second coordination sphere of PAz.

Antidepressant Effects of Essential Oils: A Review of the Past Decade (2012-2022) and Molecular Docking Study of Their Major Chemical Components

Depression is a mental disorder that affects more than 300 million people worldwide. The medications available for treatment take a long time to exhibit therapeutic results and present several side effects. Furthermore, there is a decrease in the quality of life of people suffering from this affliction. Essential oils are traditionally used to relieve the symptoms of depression due to the properties of the constituents of these oils to cross the blood-brain barrier acting on depression-related biological receptors associated with reduced toxicity and side effects. In addition, compared to traditional drugs, they have several administration forms. This review provides a comprehensive assessment of studies on plants whose essential oil has exhibit antidepressant activity in the past decade and the mechanism of action of the major components and models tested. An additional in silico study was conducted with the frequent compounds in the composition of these essential oils, providing a molecular approach to the mechanism of action that has been reported in the past decade. This review is valuable for the development of potential antidepressant medications in addition to providing a molecular approach to the antidepressant mechanism of action of the major volatile compounds that have been reported in the past decade.

Identification of Catechins' Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations

The assembly of the amyloid-β peptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer's disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the Aβ monomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of Aβ, standard computational tools cannot be easily applied for high-throughput structure-based virtual screening in drug discovery projects. In the current study, we propose a computational pipeline-in the framework of the ensemble docking strategy-to identify catechins' binding sites in monomeric Aβ₄₂. It is shown that both hydrophobic aromatic interactions and hydrogen bonding are crucial for the binding of catechins to Aβ₄₂. Additionally, it has been found that all the studied ligands, especially EGCG, can act as potent inhibitors against amyloid aggregation by blocking the central hydrophobic region of Aβ. Our findings are evaluated and confirmed with multi-microsecond MD simulations. Finally, it is suggested that our proposed pipeline, with low computational cost in comparison with MD simulations, is a suitable approach for the virtual screening of ligand libraries against Aβ.

Infinitenes as the Most Stable Form of Cycloarenes: The Interplay among π Delocalization, Strain, and π-π Stacking

The recent successful preparation of infinitene has sparked widespread attention due to its aesthetic appeal and synthetic challenge. Spectroscopic measurements and follow-up computational investigations suggest that infinitene holds fundamental significance and potential applications in chiroptics, optoelectronics, asymmetric synthesis, and supramolecular chemistry. However, unlike other looped polyarenes enriched with sizes and shapes, the infinitene molecule seems, so far, the only known example of this fascinating new form of nanocarbons, whose further exploitation would be considerably limited because of the lack of molecular diversity. Here, we introduce a whole new family of generalized infinitenes with different sizes and topologies. Three types of infinitene structures are rationally designed by joining two units of coronene, kekulene, or their extended analogs. The constructed molecules of varying sizes, each with a large number of possible topoisomers, are systematically studied by DFT calculations. Comprehensive analysis using a simple energy decomposition model uncovers that the stability of infinitenes is governed by the interplay among π delocalization, steric strain, and π-π stacking. While the first two factors are crucial to the stability of smaller infinitenes, the latter is the primary stabilizing interaction for larger infinitenes. Most importantly, we show that larger-sized infinitenes are actually the energetically most favorable form among all known looped polyarenes; their substantial thermodynamic stability surpassing that of circulenes, various carbon nanobelts, and kekulene-like macrocycles renders them promising targets for synthesis. The simulated ¹H NMR, UV-vis, and circular dichroism spectra along with optical rotations for the most stable infinitene species may help their identification in future synthetic efforts.

Ring-and-Lock Interactions in Self-Healable Styrenic Copolymers

Commodity copolymers offer many useful applications, and their durability is critical in maintaining desired functions and retaining sustainability. These studies show that primarily alternating styrene/n-butyl acrylate [p(Sty/nBA)] copolymers self-heal without external intervention when monomer molar ratios are within the 45:55-53:47 range. This behavior is attributed to the favorable interchain interactions between aliphatic nBA side groups being sandwiched by aromatic rings forming ring-and-lock associations driven by pi-sigma-pi (π-σ-π) interactions. Guided by molecular dynamics (MD) simulations combined with spectroscopic and thermomechanical analysis, the ring-and-lock interchain van der Waals forces between π orbitals of aromatic rings and sigma components of aliphatic side groups are responsible for self-healing. Despite the frequent occurrence of these interactions in biological systems (proteins, nucleic acids, lipids, and polysaccharides), these largely unexplored weak and ubiquitous molecular forces between the soft acid aliphatic and soft base aromatic electrons may be valuable assets in the development of polymeric materials with sustainable properties.

Coating peanut shell lignin nanospheres with gelatin via non-covalent adsorption: Key parameters, consequences, and underlying interactions

In the present work, lignin nanospheres (LNS, average diameter 166.43 nm) were prepared and the affecting parameters, the absorbed types, and mechanisms of their interactions with type-A gelatin (AG) were explored. The findings demonstrated that upon AG coating, the ζ-potential of LNS sharply decreased and concluded a negative-to-positive shift, while the average diameter and polydispersity index increased significantly. AG presented the highest coating capacity (0.32 mg/mg, db) onto LNS (0.5 mg/mL) at an optimum pH of 4.0 and an AG concentration of 1.0 mg/mL. The adsorption of AG onto LNS could be well described by the Hill model (R² = 0.9895), which was characterized as positive synergistic adsorption by the Hill coefficient (1.32) and physical adsorption by the free energy (3.70 kJ/mg). The spectral analysis revealed that the interactions between AG and LNS were mainly driven by electrostatic forces (ΔG < 0, ΔH < 0, and ΔS > 0) together with the assistance of hydrogen bonds and hydrophobic interactions, which companied a decrease of α-helix (4.04 %) and β-turn (0.60 %) and an increase of β-sheet (3.10 %) and random coil (1.53 %) of the secondary structure of AG. The results herein certainly favored the hydrophilic/hydrophobic change of LNS/AG and the quality control of a binary system consisting of lignin and gelatin.

Structural basis of botulinum neurotoxin serotype A1 binding to human SV2A or SV2C receptors

Botulinum neurotoxin A1 (BoNT/A1) is the most potent natural poison in human. BoNT/A1 recognize the luminal domain of SV2A (LD-SV2A) and its glycosylation at position N573 (N573g) or the luminal domain of SV2C (LD-SV2C) and its glycosylation at position N559 (N559g) to bind neural membrane. Our computational data suggest that the N-glycan at position 480 (N480g) in the luminal domain of SV2C (LD-SV2C) indirectly enhanced the contacts of the neurotoxin surface with the second N-glycan at position 559 (N559g) by acting as a shield to prevent N559g to interact with residues of LD-SV2C. The absence of an N-glycan homologous to N480g in LD-SV2A leads to a decrease of the binding of N573g to the surface of BoNT/A1. Concerning the intermolecular interactions between BoNT/A and the protein part of LD-SV2A or LD-SV2C, we showed that the high affinity of the neurotoxin for binding LD-SV2C are mediated by a better compaction of its F557-F562 part provided by a π-π network mediated by residues F547, F552, F557 and F562 coupled with the presence of two aromatic residues at position 563 and 564 that optimize the binding of BoNT/A1 via cation-pi and CH-pi interaction. Finally, in addition to the well-known ganglioside binding site which accommodates a ganglioside on the surface of BoNT/A1, we identified a structure we coined the ganglioside binding loop defined by the sequence 1253-HQFNNIAK-1260 that is conserved across all subtypes of BoNT/A and is predicted to has a high affinity to interact with gangliosides. These data solved the puzzle generated by mutational studies that could be only partially understood with crystallographic data that lack both a biologically relevant membrane environment and a full glycosylation of SV2.

Structures and Supramolecular Properties of Inclusion Complexes of Anthracene-Triptycene Nanocages with Fullerene Guests and Their Dynamic Motion as Molecular Gyroscopes

Three derivatives of macrocyclic cage compounds consisting of diarylanthracene and triptycene units were synthesized. These nanocages formed host-guest complexes with C₆₀ and other fullerene guests as confirmed by ¹ H NMR and fluorescence spectroscopy. The association constant of the mesityl and 2,4,6-tributoxyphenyl derivatives with C₆₀ was determined to be 2.2 × 10⁴  L mol^-1 , which was larger than that of the pentafluorophenyl derivative. Direct experimental evidence of the complexation was obtained by X-ray diffraction analysis: the guest C₆₀ molecule was included in the cavity via multipoint CH⋅⋅⋅π interactions. Dynamic disorders of the included C₆₀ molecule in variable-temperature X-ray analysis indicated uniaxial motion, such as gyroscopic motion. The unique dynamic behavior of the spherical C₆₀ rotor anchored by the cage stator via CH⋅⋅⋅π interactions in the crystal, as well as substituent effects on the association properties, are discussed with the aid of DFT calculations.

A critical comparison of CH⋯π versus π⋯π interactions in the benzene dimer: obtaining benchmarks at the CCSD(T) level and assessing the accuracy of lower scaling methods

We have established CCSD(T)/CBS (Complete Basis Set) limits for 3 stationary points on the benzene dimer potential energy surface, corresponding to the π⋯π (parallel displaced or PD(C_2h), minimum) and CH⋯π (T-shaped or T(C_2v), transition state) and tilted T-shaped (or TT(C_s), minimum) bonding scenarios considering both the structure and binding energy. The CCSD(T)/CBS binding energies are -2.65 ± 0.02 (PD), -2.74 ± 0.03 (T), and -2.83 ± 0.01 kcal mol^-1 (TT). To this end, the CH⋯π is ∼0.2 kcal mol^-1 stronger than the π⋯π interaction, whereas the tilting of the CH donating benzene molecule with respect to the other benzene is worth 0.1 kcal mol^-1. As previously discussed in the literature, the MP2 level of theory does not provide a close match for either the energy or structure, yet the SCS-MP2 yields structures in excellent agreement with respect to the CCSD(T) result. It is found that the SCS-MI-MP2 also gives optimized structures very close to SCS-MP2 (within ∼0.01 Å of the benchmark). Despite the closer match in structure, the spin-biased MP2 methods (SCS-, SCS-MI-, and SOS-MP2) incorrectly predict the relative stabilities of the isomers. That said, none of the spin biased MP2 methods offers a good compromise between energy and structure for the systems examined. Finally, the CCSD(T)/CBS benchmarks were used to assess the performance of 13 DFT functionals selected from different rungs of Jacob's ladder. Several functionals such as TPSS-D3, B3LYP-D3, B97-D, B97-D3, and B2PLYP-D3 provided a good description of the binding energies for both CH⋯π and π⋯π interactions, yielding values within 6% of the CCSD(T)/CBS benchmark values. Unlike the MP2 methods, these functionals correctly predict the relative stability of the PD(C_2h) and T(C_2v) dimers. Further, we find that there is no systematic improvement as Jacob's ladder is ascended (increased complexity of functional). The best functionals that result in a good compromise between structure and energy accuracy are B97-D3 and B2PLYP-D3 for both the CH⋯π and π⋯π interaction. Despite the impressive performance of these functionals, a challenge that remains is ensuring the transferability of these density functionals in accurately describing the interaction between dimers of larger aromatic molecules, the latter requiring high-level benchmarks for these systems.

An impact resistant hydrogel enabled by bicontinuous phase structure and hierarchical energy dissipation

High performance hydrogels have essential applications in many fields such as tissue engineering and soft robot. Herein, we develop an impact resistant hydrogel composed of bicontinuous structures of polymer-hard phase and polymer-soft phase. This unique bicontinuous phase structure is formed by modulating various hydrogen bonding interactions. During loading, the polymer-hard phase is broken accompanied by the dissociation of hydrogen bonds to dissipate energy, while the polymer-soft phase distributes the load to avoid stress concentration, thus enabling the bicontinuous hydrogel to achieve excellent strength and toughness simultaneously. Furthermore, the fracture of hierarchical energy dissipation structures efficiently reduces impact strength and increases buffer time. Owing to the synergy of the bicontinuous phase structure and hierarchical energy dissipation, the resulting bicontinuous hydrogel remains intact even if it undergoes impact at a strain rate of ∼13 000 s^-1. Based on these findings, it is expected that the bicontinuous hydrogel has a potential application in the field of articular cartilage repair.

Structural and Energetic Origin of Different Product Specificities and Activities for SETD3 and Its Mutants on the Methylation of the β-Actin H73K Peptide: Insights from a QM/MM Study

The methylation of the lysine residue can affect some fundamental biological processes, and specific biological effects of the methylations are often related to product specificity of methyltransferases. The question remains concerning how active-site structural features and dynamics control the activity as well as the number (1, 2, or 3) of methyl groups on methyl lysine products. SET domain containing protein 3 (SETD3) has been identified recently as the β-actin histidine73-N₃ methyltransferase, and also, it has a weak methylation activity on the H73K β-actin peptide for which the target H73 residue is mutated into K73. Interestingly, the K73 methylation activity of SETD3 increases significantly as a result of the N255 → A or N255 → F/W273 → A mutation, and the N255A product specificity also differs from that of wild-type. Here, we performed QM/MM molecular dynamics and potential of mean force (PMF) simulations for SETD3 and its mutants (N255A and N255F/W273A) to study how SETD3 and its mutants could have different product specificities and activities for the K73 methylation. The PMF simulations show that the barrier for the first methylation of K73 is higher compared to the barrier of the H73 methylation in SETD3. Moreover, the second methylation of K73 has been found to have a barrier from the free energy simulation that is higher by 2.2 kcal/mol compared to the barrier of the first methyl transfer to K73, agreeing with the suggestion that SETD3 is a monomethylase. For the first, second, and third methylations of K73 in the N255A mutant, the barriers obtained from the PMF simulations for transferring the second and third methyl groups are found to be lower relative to the barrier for the first methyl transfer. Thus, N255A can be considered as a trimethyl lysine methyltransferase. In addition, for the first K73 methylation, the activities from the PMF simulations follow the order of N255F/W273A > N255A > WT, in agreement with experiments. The examination of the structural and dynamic results at the active sites provides better understanding of different product specificities and activities for the K73 methylations in SETD3 and its mutants. It is demonstrated that the existence of well-balanced interactions at the active site leading to the near attack conformation is of crucial importance for the efficient methyl transfers. Moreover, the presence of potential interactions (e.g., the C-H···O and cation-π interactions) that are strengthening at the transition state can also be important. Furthermore, the activity as well as product specificity of the K73 methylation also seems to be controlled by certain active-site water molecules which may be released to provide extra space for the addition of more methyl groups on K73.

Effect of non-covalent self-dimerization on the spectroscopic and electrochemical properties of mixed Cu(i) complexes

A series of six new Cu(i) complexes with ([Cu(N-{4-R}pyridine-2-yl-methanimine)(PPh₃)Br]) formulation, where R corresponds to a donor or acceptor p-substituent, have been synthesized and were used to study self-association effects on their structural and electrochemical properties. X-ray diffraction results showed that in all complexes the packing is organized from a dimer generated by supramolecular π stacking and hydrogen bonding. ¹H-NMR experiments at several concentrations showed that all complexes undergo a fast-self-association monomer-dimer equilibrium in solution, while changes in resonance frequency towards the high or low field in specific protons of the imine ligand allow establishing that dimers have similar structures to those found in the crystal. The thermodynamic parameters for this self-association process were calculated from dimerization constants determined by VT-¹H-NMR experiments for several concentrations at different temperatures. The values for K _D (4.0 to 70.0 M^-1 range), ΔH (-1.4 to -2.6 kcal mol^-1 range), ΔS (-0.2 to 2.1 cal mol^-1 K^-1 range), and ΔG ₂₉₈ (-0.8 to -2.0 kcal mol^-1 range) are of the same order and indicate that the self-dimerization process is enthalpically driven for all complexes. The electrochemical profile of the complexes shows two redox Cu(ii)/Cu(i) processes whose relative intensities are sensitive to concentration changes, indicating that both species are in chemical equilibrium, with the monomer and the dimer having different electrochemical characteristics. We associate this behaviour with the structural lability of the Cu(i) centre that allows the monomeric molecules to reorder conformationally to achieve a more adequate assembly in the non-covalent dimer. As expected, structural properties in the solid and in solution, as well as their electrochemical properties, are not correlated with the electronic parameters usually used to evaluate R substituent effects. This confirms that the properties of the Cu(i) complexes are usually more influenced by steric effects than by the inductive effects of substituents of the ligands. In fact, the results obtained showed the importance of non-covalent intermolecular interactions in the structuring of the coordination geometry around the Cu centre and in the coordinative stability to avoid dissociative equilibria.

Radiationless deactivation pathways versus H-atom elimination from the N-H bond photodissociation in PhNH2-(Py)n (n = 1,2) complexes

Minimum energy structures of the ground and lowest excited states of aniline (PhNH₂) solvated by pyridine (Py) show that the clusters formed are stabilized by hydrogen bonds in which only one or both hydrogen atoms of the NH₂ group take part. Two different N-H bonds photodissociation in PhNH₂-(Py)_n (n = 1,2) complexes, free and hydrogen bonded have been studied by analyzing excited state potential energy surfaces. In the first one, only N-H bonds engaged in hydrogen bonding in these complexes are considered. RICC2 calculations of potential energy (PE) profiles indicate that all photochemical reaction paths along N-H stretching occur mainly via the proton-coupled electron transfer (PCET) mechanism. The repulsive charge transfer ¹ππ*(CT) state dominates the PE profiles, leading to low-lying ¹ππ*(CT)/S₀ conical intersections and thus provide channels for ultrafast radiationless deactivation of the electronic excitation or stabilization to biradical complexes. The second photoreaction consists of a direct dissociation along the free N-H bond of the NH₂ group. It has been shown that this process is played by excited singlet states of ¹πσ* character having repulsive potential energy profiles with respect to the stretching of N-H bond, which dissociates over an exit barrier about 0.5 eV giving rise to the formation of a ¹πσ*/S₀ conical intersection. This may cause an internal conversion to the ground state or may lead to H-atom elimination. This photophysical process is the same in both planar and T-shaped conformers of the PhNH₂-Py monomer complex. Our findings reveal that there is no single dominating path in the photodissociation of N-H bonds in PhNH₂-(Py)_n complexes, but rather a variety of paths involving H-atom elimination and several quenching mechanisms.

Dynamic Long-Range Interactions Influence Substrate Binding and Catalysis by Human Histidine Triad Nucleotide-Binding Proteins (HINTs), Key Regulators of Multiple Cellular Processes and Activators of Antiviral ProTides

Human histidine triad nucleotide-binding (hHINT) proteins catalyze nucleotide phosphoramidase and acyl-phosphatase reactions that are essential for the activation of antiviral proTides, such as Sofosbuvir and Remdesivir. hHINT1 and hHINT2 are highly homologous but exhibit disparate roles as regulators of opioid tolerance (hHINT1) and mitochondrial activity (hHINT2). NMR studies of hHINT1 reveal a pair of dynamic surface residues (Q62, E100), which gate a conserved water channel leading to the active site 13 Å away. hHINT2 crystal structures identify analogous residues (R99, D137) and water channel. hHINT1 Q62 variants significantly alter the steady-state k_cat and K_m for turnover of the fluorescent substrate (TpAd), while stopped-flow kinetics indicate that K_D also changes. hHINT2, like hHINT1, exhibits a burst phase of adenylation, monitored by fluorescent tryptamine release, prior to rate-limiting hydrolysis and nucleotide release. hHINT2 exhibits a much smaller burst-phase amplitude than hHINT1, which is further diminished in hHINT2 R99Q. Kinetic simulations suggest that amplitude variations can be accounted for by a variable fluorescent yield of the E·S complex from changes in the environment of bound TpAd. Isothermal titration calorimetry measurements of inhibitor binding show that these hHINT variants also alter the thermodynamic binding profile. We propose that these altered surface residues engender long-range dynamic changes that affect the orientation of bound ligands, altering the thermodynamic and kinetic characteristics of hHINT active site function. Thus, studies of the cellular roles and proTide activation potential by hHINTs should consider the importance of long-range interactions and possible protein binding surfaces far from the active site.

Structural Basis of Botulinum Toxin Type F Binding to Glycosylated Human SV2A: In Silico Studies at the Periphery of a Lipid Raft

Botulinum neurotoxins are the deadliest microbial neurotoxins in humans, with a lethal dose of 1 ng/kg. Incidentally, these neurotoxins are also widely used for medical and cosmetic purposes. However, little is known about the molecular mechanisms that control binding of botulinum neurotoxin type F1 (BoNT/F1) to its membrane receptor, glycosylated human synaptic vesicle glycoprotein A (hSV2Ag). To elucidate these mechanisms, we performed a molecular dynamics simulation (MDS) study of initial binding kinetics of BoNT/F1 to SV2A. Since this toxin also interacts with gangliosides, the simulations were performed at the periphery of a lipid raft in the presence of both SV2A and gangliosides. Our study suggested that interaction of BoNT/F1 with SV2A is exclusively mediated by N-glycan moiety of SV2A, which interacts with aromatic residues Y898, Y910, F946, Y1059 and H1273 of this toxin. Thus, in contrast with botulinum neurotoxin A1 (BoNT/A1), BoNT/F1 does not interact with protein content of SV2A. We attributed this incapability to a barrage effect exerted by neurotoxin residues Y1132, Q1133 and K1134, which prevent formation of long-lasting intermolecular hydrogen bonds. We also provided structural elements that suggest that BoNT/F1 uses the strategy of BoNT/A1 combined with the strategy of botulinum neurotoxin type E to bind N-glycan of its glycoprotein receptor. Overall, our study opened a gate for design of a universal inhibitor aimed at disrupting N-glycan-toxin interactions and for bioengineering of a BoNT/F1 protein that may be able to bind protein content of synaptic vesicle glycoprotein for therapeutic purposes.

Molecular duplexes featuring NH···N, CH···O and CH···π interactions in solid-state self-assembly of triazine-based compounds

Synthetic supramolecular structures constructed through the cooperative action of numerous non-covalent forces are highly desirable as models to unravel and understand the complexity of systems created in nature via self-assembly. Taking advantage of the low cost of 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) and the sequential nucleophilic substitution reactions with almost all types of nucleophiles, a series of six structurally related novel s-triazine derivatives 1-6 were synthesized and structurally characterized based on their physical, spectral and crystallographic data. The solid-state structures of all the six compounds showed intriguing and unique molecular duplexes featuring NH···N, CH···O and CH···π interactions. Careful analysis of different geometric parameters of the involved H-bonds indicates that they are linear, significant and are therefore responsible for guiding the three-dimensional structure of these compounds in the solid state. The prevalence of sextuple hydrogen bond array-driven molecular duplexes and the possibility of structural modifications on the s-triazine ring render these novel triazine derivatives 1-6 attractive as a platform to create heteroduplex constructs and their subsequent utility in the field of supramolecular chemistry and crystal engineering.