Dimer Association Research Articles

Preformed mincle dimers stabilized by an interchain disulfide bond in the neck region.

The sugar-binding receptor mincle stimulates macrophages when it encounters surface glycans on pathogens, such as trehalose dimycolate glycolipid in the outer membrane of mycobacteria. Binding of oligosaccharide ligands to the extracellular C-type carbohydrate-recognition domain (CRD) in mincle initiates intracellular signaling through the common Fc receptor γ (FcRγ) adapter molecule associated with mincle. One potential mechanism for initiation of signaling involves clustering of receptors, so it is important to understand the oligomeric state of mincle. Affinity purification of mincle from transfected mammalian cells has been used to show that mincle exists as a pre-formed, disulfide-linked dimer. Deletion of cysteine residues and chemical crosslinking further demonstrate that the dimers of mincle are stabilized by a disulfide bond between cysteine residues in the neck sequence that links the CRD to the membrane. In contrast, cysteine residues in the transmembrane region of mincle are not required for dimer formation or association with FcRγ. A protocol has been developed for efficient production of a disulfide-linked extracellular domain fragment of mincle in a bacterial expression system by appending synthetic dimerization domains to guide dimer formation in the absence of the membrane anchor.

Synthesis and Dynamic Behaviors of 5,7,8,10-Tetraphenyl-1,14-dianilinotripyrrins

Abstract5,7,8,10-Tetraphenyl-1,14-di(arylamino)tripyrrins have been synthesized via 5,7,8,10-tetraphenyltripyrrane. The structures and dynamic equilibrium between single helical monomer and double helical dimer were analyzed by 1H NMR spectra and X-ray diffraction analysis. Their dimerization association constants in CDCl3 are larger than those of previously reported dianilinotripyrrin derivatives. In DMSO, they exhibited luminescence around 700 nm as a consequence of restricted rotational relaxation by the phenyl groups installed at the 7,8-positions.

Cryo-EM structure of bacterial nitrilase reveals insight into oligomerization, substrate recognition, and catalysis

Many enzymes can self-assemble into higher-order structures with helical symmetry. A particularly noteworthy example is that of nitrilases, enzymes in which oligomerization of dimers into spiral homo-oligomers is a requirement for their enzymatic function. Nitrilases are widespread in nature where they catalyze the hydrolysis of nitriles into the corresponding carboxylic acid and ammonia. Here, we present the Cryo-EM structure, at 3 Å resolution, of a C-terminal truncate nitrilase from Rhodococcus sp. V51B that assembles in helical filaments. The model comprises a complete turn of the helical arrangement with a substrate-intermediate bound to the catalytic cysteine. The structure was solved having added the substrate to the protein. The length and stability of filaments was made more substantial in the presence of the aromatic substrate, benzonitrile, but not for aliphatic nitriles or dinitriles. The overall structure maintains the topology of the nitrilase family, and the filament is formed by the association of dimers in a chain-like mechanism that stabilizes the spiral. The active site is completely buried inside each monomer, while the substrate binding pocket was observed within the oligomerization interfaces. The present structure is in a closed configuration, judging by the position of the lid, suggesting that the intermediate is one of the covalent adducts. The proximity of the active site to the dimerization and oligomerization interfaces, allows the dimer to sense structural changes once the benzonitrile was bound, and translated to the rest of the filament, stabilizing the helical structure.

First Sublimation Thermodynamics and First Gas‐Phase Experimental Molecular Structure of Heteroporphyrins: 5,10,15,20‐Tetraphenyl‐21‐X, 23‐Y‐Porphyrins (X=O or S; Y=N or S)

AbstractFirst sublimation enthalpies of heteroporphyrins: 10,15,20‐tetraphenyl‐21‐oxa‐ (HOPP), 5,10,15,20‐tetraphenyl‐21‐thia‐ (HSPP) and 5,10,15,20‐tetraphenyl‐21,23‐dithia‐ (S2PP) were measured by Knudsen effusion mass spectrometry: ΔsublH (T)=209±2 (561 K), 224±2 (552 K) and 219±2 (577 K) kJ/mol, respectively. Geometry and force field of a free molecule of HSPP was studied by quantum chemistry, and first gas‐phase experimental molecular structure of heteroporphyrins was derived by gas‐phase electron diffraction. Theoretically observed changes of the coordination cavity geometries due to heteroatomic intracavity substitution were experimentally confirmed with good agreement. Molecular structures of the dimeric associates of the heteroporphyrins were tested simulated to reveal tendencies in sublimation thermodynamics.

Nitrate Radicals Suppress Biogenic New Particle Formation from Monoterpene Oxidation.

Highly oxygenated organic molecules (HOMs) are a major source of new particles that affect the Earth's climate. HOM production from the oxidation of volatile organic compounds (VOCs) occurs during both the day and night and can lead to new particle formation (NPF). However, NPF involving organic vapors has been reported much more often during the daytime than during nighttime. Here, we show that the nitrate radicals (NO3), which arise predominantly at night, inhibit NPF during the oxidation of monoterpenes based on three lines of observational evidence: NPF experiments in the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber at CERN (European Organization for Nuclear Research), radical chemistry experiments using an oxidation flow reactor, and field observations in a wetland that occasionally exhibits nocturnal NPF. Nitrooxy-peroxy radicals formed from NO3 chemistry suppress the production of ultralow-volatility organic compounds (ULVOCs) responsible for biogenic NPF, which are covalently bound peroxy radical (RO2) dimer association products. The ULVOC yield of α-pinene in the presence of NO3 is one-fifth of that resulting from ozone chemistry alone. Even trace amounts of NO3 radicals, at sub-parts per trillion level, suppress the NPF rate by a factor of 4. Ambient observations further confirm that when NO3 chemistry is involved, monoterpene NPF is completely turned off. Our results explain the frequent absence of nocturnal biogenic NPF in monoterpene (α-pinene)-rich environments.

Comment on “Limonene as a renewable unsaturated hydrocarbon solvent for living anionic polymerization of β-myrcene” by A. Dev, A. Rösler and H. Schlaad, Polym. Chem., 2021, 12, 3084

Polymyrcenyllithium chains in dl-limonene solution are present as dimeric associates and not as single chains.

Zinc and cadmium thioamidate complexes: rational design of single-source precursors for the AACVD of ZnS.

A series of zinc(II) thioamidate complexes [Zn{SC(iPr)NR}2]n for R = iPr (n = 2) (2), tBu (3) (n = 1), Ph (4) (n = 2) and Cy (5) (n = 2) and one cadmium(II) thioamidate complex [Cd{SC(iPr)NtBu}2]3, (6), were designed and synthesised as single-source precursors for AACVD ZnS and CdS. Solid-state structures of all four zinc(II) compounds revealed distorted tetrahedral or trigonal bipyramidal geometries, with varying tendencies for dimeric association, mediated by {Zn-S} bridging bonds. The thermogravimetric analysis identified the {tBu} derivertive, 3, as the most promising precursor based on its low decomposition onset (118 °C) and clean conversion to ZnS. This was attributed to the greater availability of β-hydrogen atoms promoting the pyrolysis mechanism. The corresponding cadmium thioamide 6 was found to crystallise as a trimetallic molecule which lacked the thermal stability to be considered viable for AACVD. Hence, 3 was used to deposit ZnS thin films by AACVD at 200-300 °C. Powder X-ray diffraction confirmed phase-pure growth of hexagonal wurtzite ZnS, with approximate crystallite sizes of 15-20 nm. Scanning electron microscopy revealed densely packed spherical nanoclusters. The morphology and crystallinity were most consistent for depositions between 250-300 °C. Energy dispersive X-ray spectroscopy indicated slightly sulfur-deficient stoichiometries.

The Allosteric Regulation of Β-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces.

The activity of β-ureidopropionase, which catalyses the last step in the degradation of uracil, thymine, and analogous antimetabolites, is cooperatively regulated by the substrate and product of the reaction. This involves shifts in the equilibrium of the oligomeric states of the enzyme, but how these are achieved and result in changes in enzyme catalytic competence has yet to be determined. Here, the regulation of human β-ureidopropionase was further explored via site-directed mutagenesis, inhibition studies, and cryo-electron microscopy. The active-site residue E207, as well as H173 and H307 located at the dimer-dimer interface, are shown to play crucial roles in enzyme activation. Dimer association to larger assemblies requires closure of active-site loops, which positions the catalytically crucial E207 stably in the active site. H173 and H307 likely respond to ligand-induced changes in their environment with changes in their protonation states, which fine-tunes the active-site loop stability and the strength of dimer-dimer interfaces and explains the previously observed pH influence on the oligomer equilibrium. The correlation between substrate analogue structure and effect on enzyme assembly suggests that the ability to favourably interact with F205 may distinguish activators from inhibitors. The cryo-EM structure of human β-ureidopropionase assembly obtained at low pH provides first insights into the architecture of its activated state. and validates our current model of the allosteric regulation mechanism. Closed entrance loop conformations and dimer-dimer interfaces are highly conserved between human and fruit fly enzymes.

Crystal Structure of the Brugia malayi Thymidylate Kinase-dTMP Complex and Small Angle X-ray Scattering Experiments Identifies Changes in the Dimeric Association Compared to the Human Homolog

Crystal Structure of the Brugia malayi Thymidylate Kinase-dTMP Complex and Small Angle X-ray Scattering Experiments Identifies Changes in the Dimeric Association Compared to the Human Homolog

Enabling Carbonized Polymer Dots with Color‐tunable Time‐dependent Room Temperature Phosphorescence through Confining Carboxyl Dimer Association

AbstractDeveloping a facile strategy to realize fine‐tuning of phosphorescence color in time‐dependent room temperature phosphorescence (RTP) materials is essential but both theoretically and practically rarely exploited. Through simultaneously confining carboxyl dimer association and isolated carboxyl into the particle via a simple hydrothermal treatment of polyacrylic acid, a dual‐peak emission of red phosphorescence (645 nm) and green phosphorescence (550 nm) was observed from carbonized polymer dots (CPDs). The ratio of the two luminescent species can be well regulated by hydrochloric acid inhibiting the dissociation of carboxyl to promote hydrogen bond. Due to comparable but different lifetimes, color‐tunable time‐dependent RTP with color changing from yellow to green or orange to green were obtained. Based on the crosslinking enhanced emission effect, the phosphorescence visible time was even extended to 7 s through introducing polyethylenimide. This study not only proposes a novel and facile method for developing CPDs with color‐tunable time‐dependent RTP, but also provides a bran‐new non‐conjugated red phosphorescence unit and its definite structure.

Enabling Carbonized Polymer Dots with Color-tunable Time-dependent Room Temperature Phosphorescence through Confining Carboxyl Dimer Association.

Developing a facile strategy to realize fine-tuning of phosphorescence color in time-dependent room temperature phosphorescence (RTP) materials is essential but both theoretically and practically rarely exploited. Through simultaneously confining carboxyl dimer association and isolated carboxyl into the particle via a simple hydrothermal treatment of polyacrylic acid, a dual-peak emission of red phosphorescence (645 nm) and green phosphorescence (550 nm) was observed from carbonized polymer dots (CPDs). The ratio of the two luminescent species can be well regulated by hydrochloric acid inhibiting the dissociation of carboxyl to promote hydrogen bond. Due to comparable but different lifetimes, color-tunable time-dependent RTP with color changing from yellow to green or orange to green were obtained. Based on the crosslinking enhanced emission effect, the phosphorescence visible time was even extended to 7 s through introducing polyethylenimide. This study not only proposes a novel and facile method for developing CPDs with color-tunable time-dependent RTP, but also provides a bran-new non-conjugated red phosphorescence unit and its definite structure.

DNA major versus minor groove occupancy of monomeric and dimeric crystal violet derivatives. Toward structural correlations

Six monomeric (1a-1f) and five dimeric (2a-2e) derivatives of the triphenylmethane dye crystal violet (CV) have been prepared. Evaluation of the binding of these compounds to CT DNA by competitive fluorescent intercalator displacement (FID) assays, viscosity experiments, and UV and CD spectroscopy suggest that monomeric derivative 1a and dimeric derivative 2d likely associate with the major groove of DNA, while dimeric derivatives 2a and 2e likely associate with the minor groove of DNA. Additional evidence for the groove occupancy assignments of these derivatives was obtained from ITC experiments and from differential inhibition of DNA cleavage by the major groove binding restriction enzyme BamHI, as revealed by agarose gel electrophoresis. The data indicate that major groove ligands may be optimally constructed from dye units containing a sterically bulky 3,5-dimethyl-N,N-dimethylaniline group; furthermore, the groove-selectivity of olefin-tethered dimer 2d suggests that stereoelectronic interactions (n → π*) between the ligand and DNA are also an important design consideration in the crafting of major-groove binding ligands.

Glutathione and Glutaredoxin-Key Players in Cellular Redox Homeostasis and Signaling.

This Special Issue of Antioxidants on Glutathione (GSH) and Glutaredoxin (Grx) was designed to collect review articles and original research studies focused on advancing the current understanding of the roles of the GSH/Grx system in cellular homeostasis and disease processes. The tripeptide glutathione (GSH) is the most abundant non-enzymatic antioxidant/nucleophilic molecule in cells. In addition to various metabolic reactions involving GSH and its oxidized counterpart GSSG, oxidative post-translational modification (PTM) of proteins has been a focal point of keen interest in the redox field over the last few decades. In particular, the S-glutathionylation of proteins (protein-SSG formation), i.e., mixed disulfides between GSH and protein thiols, has been studied extensively. This reversible PTM can act as a regulatory switch to interconvert inactive and active forms of proteins, thereby mediating cell signaling and redox homeostasis. The unique architecture of the GSH molecule enhances its relative abundance in cells and contributes to the glutathionyl specificity of the primary catalytic activity of the glutaredoxin enzymes, which play central roles in redox homeostasis and signaling, and in iron metabolism in eukaryotes and prokaryotes under physiological and pathophysiological conditions. The class-1 glutaredoxins are characterized as cytosolic GSH-dependent oxidoreductases that catalyze reversible protein S-glutathionylation specifically, thereby contributing to the regulation of redox signal transduction and/or the protection of protein thiols from irreversible oxidation. This Special Issue includes nine other articles: three original studies and six review papers. Together, these ten articles support the central theme that GSH/Grx is a unique system for regulating thiol-redox hemostasis and redox-signal transduction, and the dysregulation of the GSH/Grx system is implicated in the onset and progression of various diseases involving oxidative stress. Within this context, it is important to appreciate the complementary functions of the GSH/Grx and thioredoxin systems not only in thiol-disulfide regulation but also in reversible S-nitrosylation. Several potential clinical applications have emerged from a thorough understanding of the GSH/Grx redox regulatory system at the molecular level, and in various cell types in vitro and in vivo, including, among others, the concept that elevating Grx content/activity could serve as an anti-fibrotic intervention; and discovering small molecules that mimic the inhibitory effects of S-glutathionylation on dimer association could identify novel anti-viral agents that impact the key protease activities of the HIV and SARS-CoV-2 viruses. Thus, this Special Issue on Glutathione and Glutaredoxin has focused attention and advanced understanding of an important aspect of redox biology, as well as spawning questions worthy of future study.

N‐(aminobenzyliden)phthalimides as a New Redox Mediator Family for the Selective Indirect Reduction of Benzyl or Allyl Halides

AbstractThe chemical stability of the electrogenerated radical anion of N‐(aminobenzyl) phthalimide 1 in aprotic organic media at room temperature is reported in this work. The redox couples 1/1⋅− and its imine precursor 2/2⋅− can carry out reductive redox catalysis of benzyl or allyl halides indirectly. This reaction gives easy access to reactive alkyl radicals, which in the presence of diethyl fumarate yields 2‐benzylsuccinate diethyl ester in moderate yields; this reaction is unattainable by direct electrochemical reduction. Spin density calculations at the DFT level of theory showed that the spin density of 1⋅− and 2⋅− is located on the phtalimide ring, and a dimeric association was evidenced (Eint=23.47 kcal/mol and Eint=80.42 kcal/mol respectively), via π−π stacking interactions. The redox mediators presented here showed good functional group selectivity, redox potential tunability and easy preparation from readily available commercial materials with excellent yields.

Assembly dynamics and structure of an aegerolysin, ostreolysin A6

Ostreolysin A6 (OlyA6) is an oyster mushroom-derived membrane-binding protein that, upon recruitment of its partner protein, pleurotolysin B, forms a cytolytic membrane pore complex. OlyA6 itself is not cytolytic but has been reported to exhibit pro-apoptotic activities in cell culture. Here we report the formation dynamics and the structure of OlyA6 assembly on a lipid membrane containing an OlyA6 high-affinity receptor, ceramide phosphoethanolamine, and cholesterol. High-speed atomic force microscopy revealed the reorganization of OlyA6 dimers from initial random surface coverage to 2D protein crystals composed of hexameric OlyA6 repeat units. Crystal growth took place predominantly in the longitudinal direction by the association of OlyA6 dimers, forming a hexameric unit cell. Molecular-level examination of the OlyA6 crystal elucidated the arrangement of dimers within the unit cell and the structure of the dimer that recruits pleurotolysin B for pore formation.

A Free Energy Decomposition Analysis: Insight into Binding Thermodynamics from Absolutely Localized Molecular Orbitals.

Traditional energy decomposition analysis (EDA) methods can provide an interpretive decomposition of non-covalent electronic binding energies. However, by definition, they neglect entropic effects and nuclear contributions to the enthalpy. With the objective of revealing the chemical origins of trends in free energies of binding, we introduce the concept of a Gibbs decomposition analysis (GDA) by coupling the absolutely localized molecular orbital treatment of electrons in non-covalent interactions with the simplest possible quantum rigid rotor-harmonic oscillator treatment of nuclear motion at finite temperature. The resulting pilot GDA is employed to decompose enthalpic and entropic contributions to the free energy of association of the water dimer, fluoride-water dimer, and water binding to an open metal site in the metal-organic framework Cu(I)-MFU-4l. The results show enthalpic trends that generally track the electronic binding energy and entropic trends that reveal the increasing price of loss of translational and rotational degrees freedom with temperature.

Effects of aluminum ion on particle sizes and surface charges of exopolysaccharides from Rhizobium tropici and pH effects

Exopolysaccharides (EPS) are ubiquitous and important extracellular macromolecular biopolymers produced by soil microorganisms. Aluminum (Al) is a major element in earth crust and Al toxicity is one of the major limitations inhibiting plant growth in acidic soils. EPS strongly affects soil microaggregate structure, soil moisture and bioavailability of nutrients and heavy metals. The objectives of this study are to investigate the effect of Al ion on particle sizes and zeta potential of EPS and EPS-Al complexes. Results show that Al ions strongly interact with EPS and the interaction was affected by pH. Al ion binding in EPS was involved in multilayer binding sites, i.e., inside/within the macromolecular and intermolecular bridging. This was confirmed by Al binding isotherm, the change of the particle size and zeta potentials of EPS-Al complexes. Al ions significantly increased the particle sizes and zeta potentials of EPS-Al became less negative. At the lower molar ratio of Al/EPS, EPS-Al may form mono-complexation within molecule while at higher molar ratios EPS-Al may form dimers/multimerization/lateral association of dimers of EPS, significantly increasing the particle sizes. When the molar ratio of binding Al/EPS was 72, the zeta potential of EPS-Al complexes was almost zero. With continuing increase in Al ion/EPS molar ratios to 336, EPS-Al complexes reached the positive charge at +2.0 mV. The particle sizes of EPS-Al complexes correlated well with the zeta potentials. pH significantly affected the particle sizes and zeta potential of EPS alone and EPS-Al complexes. The size of the EPS particles decreased with pH while the particle size of the EPS-Al complexes increased with pH. pH not only controlled protonation and deprotonation of carboxylic and phenol functional groups of EPS, but also shifted the speciation of Al ions, thus significantly controlling particle sizes of EPS and EPS-Al. This study provides an insight understanding of the interaction of Al3+ with EPS for controlling toxicity of Al ion in water and soils affected by microbial-excreted exopolysaccharides.

Self-Complementary Dimer of Zinc(II) Porphyrins through Coordination with Oxygen Ligands

AbstractOxygen ligands have been shown to play a critical role in the formation and organization of metalloporphyrin assemblies and natural chlorosomes. In this work, mutually complementary head-to-tail dimers of zinc(II) porphyrins were synthesized through the coordination of zinc with the imide group and 7-oxanorbornene oxygen ligands. UV/Vis absorption and emission, 1H NMR as well as FT-IR analyses were used to determine the structure. The dimerization association constant K has been determined to be 5.6 M–1 and 29 M–1, respectively, by the dilution experiment.

Structural basis of mitochondrial membrane bending by the I–II–III2–IV2 supercomplex

Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane1. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I–II–III2–IV2 supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.

Observation of coherent oscillations in the association of dimers from a thermal gas of ultracold atoms

We report the observation of coherent oscillations in conversion efficiency of weakly-bound dimers formed from a thermal gas of ultracold atoms. Finite thermal energy of the gas causes loss of coherence when a broad continuum is resonantly coupled to a discrete bound state. Restoration of the coherence can be achieved through non-adiabatic transitions of the dressed molecular energy level that are induced by a strong modulation pulse with fast envelope dynamics. Conditions to observe coherent oscillations are verified, and control of their properties is demonstrated. The main experimental findings are supported by theoretical modeling and numerical calculations. The observed results may lead to a renewed interest in general studies of a discrete energy level coupled to a broadband continuum when the properties of both are fully controlled.