Near-adjacent heavy lanthanide separation and sensing using dimerizing lanmodulins
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Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA
Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. Furthermore, the relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein–Frenkel Hamiltonian model.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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, in this work, 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.
36 MATERIALS SCIENCE↗
A split luciferase system for studying coronavirus Mpro dimerization in vitro and in living cells
The main protease enzyme (Mpro) of coronaviruses cleaves the viral polyprotein into functional units essential for virus replication. Prior work has demonstrated that Mpro functions as a homodimer. However, studies on the mechanism of dimerization have been challenging because the purified protease is mostly dimeric, dimerization-defective mutants lack proteolytic activity, and robust cell-based assays have yet to be reported. To enable work on Mpro dimerization, we have developed a quantitative luciferase-based SARS-CoV-2 (SARS2) Mpro biosensor that accurately reports protein dimerization in living cells and, upon purification, also in vitro. Co-transfection of cells with a construct expressing Mpro fused to the 18 kDa LargeBiT of luciferase (LgBiT) and a second construct with Mpro fused to the 1 kDa SmallBiT of luciferase (SmBiT) results in a reconstitution of luciferase activity in a dose-dependent manner that requires conserved residues within the dimerization interface. Proteolytic activity is dispensable for dimerization and, uniquely, a C145A catalytically inactive mutant exhibits enhanced dimerization signal likely due to lower cytotoxicity. Mpro enzymes from multiple different coronaviruses also dimerize in this system, indicating mechanistic conservation. Interestingly, this dimerization biosensor also provides a quantitative read-out of inhibitor-facilitated dimerization. Covalent SARS2 Mpro inhibitors such as nirmatrelvir cause a 3- to 5-fold increase in luciferase activity. Together with corroborating structural, biophysical, and molecular dynamics experiments, our studies support a model in which covalent Mpro inhibitors such as nirmatrelvir simultaneously block catalytic activity and induce allosteric stabilization of the dimeric complex.
SARS-CoV-2 main protease (Mpro/3CLpro)↗
Unveiling a Family of Dimerized Quantum Magnets, Conventional Antiferromagnets, and Nonmagnets in Ternary Metal Borides
Dimerized quantum magnets are exotic crystalline materials where Bose–Einstein condensation of magnetic excitations can happen. However, known dimerized quantum magnets are limited to only a few oxides and halides. Here, we unveil 9 dimerized quantum magnets and 11 conventional antiferromagnets in ternary metal borides MTB 4 (M = Sc, Y, La, Ce, Lu, Mg, Ca, and Al; T = V, Cr, Mn, Fe, Co, and Ni), where T atoms are arranged in structural dimers. Quantum magnetism in these compounds is dominated by strong antiferromagnetic (AFM) interactions between Cr (Cr and Mn for M = Mg and Ca) atoms within the dimers, with much weaker interactions between the dimers. These systems are proposed to be close to a quantum critical point between a disordered singlet spin-dimer phase, with a spin gap, and the ordered conventional Néel AFM phase. They greatly enrich the materials inventory that allows investigations of the spin-gap phase. Conventional antiferromagnetism in these compounds is dominated by ferromagnetic Mn (Fe for M = Mg and Ca) interactions within the dimers. The predicted stable and nonmagnetic (NM) YFeB 4 phase is synthesized and characterized, providing a scarce candidate to study Fe dimers and Fe ladders in borides. The identified quantum, conventional, and NM systems provide a platform with abundant possibilities to tune the magnetic exchange coupling by doping and study the unconventional quantum phase transition and conventional magnetic transitions. Finally, this work opens new avenues for studying novel magnetism in borides arising from spin dimers and establishes a theoretical workflow for future searches for dimerized quantum magnets in other families of materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold
Abstract Infected cell protein 0 (ICP0) is an immediate‐early regulatory protein of herpes simplex virus 1 (HSV‐1) that possesses E3 ubiquitin ligase activity. ICP0 transactivates viral genes, in part, through its C‐terminal dimer domain (residues 555–767). Deletion of this dimer domain results in reduced viral gene expression, lytic infection, and reactivation from latency. Since ICP0's dimer domain is associated with its transactivation activity and efficient viral replication, we wanted to determine the structure of this specific domain. The C‐terminus of ICP0 was purified from bacteria and analyzed by X‐ray crystallography to solve its structure. Each subunit or monomer in the ICP0 dimer is composed of nine β‐strands and two α‐helices. Interestingly, two adjacent β‐strands from one monomer “reach” into the adjacent subunit during dimer formation, generating two β‐barrel‐like structures. Additionally, crystallographic analyses indicate a tetramer structure is formed from two β‐strands of each dimer, creating a “stacking” of the β‐barrels. The structural protein database searches indicate the fold or structure adopted by the ICP0 dimer is novel. The dimer is held together by an extensive network of hydrogen bonds. Computational analyses reveal that ICP0 can either form a dimer or bind to SUMO1 via its C‐terminal SUMO‐interacting motifs but not both. Understanding the structure of the dimer domain will provide insights into the activities of ICP0 and, ultimately, the HSV‐1 life cycle.
Biochemistry & Molecular Biology↗
Understanding the Competition between Alcohol Formation and Dimerization during Electrochemical Reduction of Aromatic Carbonyl Compounds
The electrochemical reductive dimerization of small aromatic carbonyl compounds derived from lignocellulosic biomass is a crucial C−C coupling reaction for upgrading small molecules to longchain hydrocarbons, particularly in the synthesis of drop-in sustainable aviation fuels. Although other electrochemical reduction reactions of these reactants (i.e., hydrogenation and hydrogenolysis) have undergone extensive mechanistic investigation, the understanding of dimerization remains relatively underdeveloped. Most importantly, there is a lack of understanding of the selectivity-determining step between dimerization and monomer reduction and critical factors that can affect this step. In this study, we provide a comprehensive mechanistic model to explain the competition between dimerization and monomer reduction of benzaldehyde under various conditions. Our model proposes that the selectivity between dimerization and monomer reduction depends on the competition between desorption of a ketyl radical from the electrode, necessary for dimerization, and further reduction of the ketyl radical to an alcohol on the electrode by proton-coupled electron transfer (PCET). Computationally comparing the adsorption/desorption energy and PCET activation barrier energy is challenging because conventional DFT calculations substantially underestimate the PCET kinetic barriers. In this study, we employed constrained DFTbased configuration interaction (CDFT-CI) to obtain a reliable comparison of these energies. Our mechanistic model was tested and supported by experimental results obtained with four electrodes (Cu, Pb, Bi, graphite), three pH conditions (acidic, neutral, basic), and three potentials. Our study offers a coherent mechanistic foundation that can explain how each of these conditions impacts the desorption and PCET processes and the selectivities for dimerization and alcohol production.
09 BIOMASS FUELS↗
Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes
FAM111A, a serine protease, plays roles in DNA replication and antiviral defense. Missense mutations in the catalytic domain cause hyper-autocleavage and are associated with genetic disorders with developmental defects. Despite the enzyme’s biological significance, the molecular architecture of the FAM111A serine protease domain (SPD) is unknown. Here, we show that FAM111A is a dimerization-dependent protease containing a narrow, recessed active site that cleaves substrates with a chymotrypsin-like specificity. X-ray crystal structures and mutagenesis studies reveal that FAM111A dimerizes via the N-terminal helix within the SPD. This dimerization induces an activation cascade from the dimerization sensor loop to the oxyanion hole through disorder-to-order transitions. Dimerization is essential for proteolytic activity in vitro and for facilitating DNA replication at DNA-protein crosslink obstacles in cells, while it is dispensable for autocleavage. These findings underscore the role of dimerization in FAM111A’s function and highlight the distinction in its dimerization dependency between substrate cleavage and autocleavage.
59 BASIC BIOLOGICAL SCIENCES↗
Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Mononucleotides
Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2- methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2(+) in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MelmpU and 2-MelmpC produce about 65% of oligomers including 4% of the 3',5'-Iinked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of intemucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MelmpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.
Kanavarioti, Anastassia↗
Cleavage at the nsp5–nsp6 site of SARS-CoV-2 main protease intermediate precursor is faster from a monomer than a dimer form
Our previous studies of severe acute respiratory syndrome coronavirus 2 main protease (MPro) precursor monomer indicate that the initial N-terminal nonstructural protein (nsp)4/nsp5 cleavage occurs intramolecularly, with a small fraction of the active site loop equilibrium being in the active state. To understand the influence of dimer formation of MPro upon N-terminal cleavage on the subsequent C-terminal nsp5/nsp6 intermolecular cleavage kinetics, the stepwise processing of a monomeric, inactive precursor containing the native terminal cleavage sites of MPro (MBP- (−6) MPro C145A(+3) -GB1-6H, 86.2 kDa) by mature WT MPro (MPro WT ) was investigated. Differential scanning fluorimetry and analytical ultracentrifugation measurements of various MPro constructs suggest that the C145A mutation decreases the dimer dissociation constant (K dimer ) by ∼26-fold, relative to WT C145 and H41A. The monomeric precursor’s nsp4–nsp5 site appears to saturate MProWT’s active sites and cleave faster, followed by a slower first-order cleavage at the C-terminal site. No detectable product resulting from the C-terminal cleavage is observed until most of the N-terminal cleavage is complete. The initial intermediate product (termed MPro C145A-IP ) is a homodimer with an estimated K dimer of <0.05 μM. In contrast, the first-order kinetics observed for the cleavage of the monomeric form of the intermediate product is at least 300 times faster than that of the dimer form. Room-temperature X-ray structure of the MPro C145A-IP –ensitrelvir complex is like that of the MPro WT –ensitrelvir complex and reveals a dynamic C-terminal region including MPro residues 302 to 306. These results are interpreted from the point of view of a mechanism in which nsp5–nsp6 cleavage may occur from a monomeric intermediate, and dimer formation restricts this cleavage.
60 APPLIED LIFE SCIENCES↗
Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease
N-terminal autoprocessing from its polyprotein precursor enables creating the mature-like stable dimer interface of SARS-CoV-2 main protease (MPro), concomitant with the active site oxyanion loop equilibrium transitioning to the active conformation (E*) and onset of catalytic activity. Here, through mutagenesis of critical interface residues and evaluating noncovalent inhibitor (ensitrelvir, ESV) facilitated dimerization through its binding to MPro, we demonstrate that residues extending from Ser1 through Glu14 are critical for dimerization. Combined mutations G11A, E290A and R298A (MPro™) restrict dimerization even upon binding of ESV to monomeric MPro™ with an inhibitor dissociation constant of 7.4 ± 1.6 µM. Contrasting the covalent inhibitor NMV or GC373 binding to monomeric MPro, ESV binding enabled capturing the transition of the oxyanion loop conformations in the absence of a reactive warhead and independent of dimerization. Characterization of complexes by room-temperature X-ray crystallography reveals ESV bound to the E* state of monomeric MPro as well as an intermediate approaching the inactive state (E). It appears that the E* to E equilibrium shift occurs initially from G138-F140 residues, leading to the unwinding of the loop and formation of the 3 10 -helix. Finally, we describe a transient dimer structure of the MPro precursor held together through interactions of residues A5-G11 with distinct states of the active sites, E and E*, likely representing an intermediate in the autoprocessing pathway.
59 BASIC BIOLOGICAL SCIENCES↗
Synthesis of (oxo)chlorin dimers chelated with thallium(III)
Two target dimers have been prepared for fundamental studies of hole/electron transfer. Metalation with thallium(III) enables clocking of the rate of hole/electron transfer between the two macrocycles. Each dimer contains a diphenylethyne linker joining two identical hydroporphyrins (chlorin or oxochlorin). The linker is substituted at the 4,4′-positions whereas each (oxo)chlorin is joined at the 10-position. Each (oxo)chlorin is equipped with a gem-dimethyl group at the 18-position to stabilize the hydroporphyrin chromophore toward adventitious dehydrogenation and a 3,5-di-tert-butyl group at the 5-position to achieve increased solubilization in organic media. The dimers parallel a prior set of diphenylethyne-linked (oxo)chlorin constructs containing zinc-free base, zinc-zinc, and copper-copper metalation states that have been examined in studies of electronic communication. The building block (oxo)chlorins for preparing the thallium-containing dimers have been prepared in quantities of 32–404 mg, a scale up to 14-fold larger than previously. Thallation of the free base (oxo)chlorin dimers was achieved with excess TlCl 3 ⋅4H 2 O in CH 2 Cl 2 /CH 3 OH (3–4:1) upon overnight reaction at room temperature. The long-wavelength (Q[Formula: see text] absorption band of (oxo)chlorins lies between that of the zinc(II) and free base counterparts. Absorption spectral comparisons are provided of the thallium(III) and free base (oxo)chlorin monomers and dimers.
Chemistry↗
Impact of Linker Engineering in Core‐Linked Dimeric Acceptors for High‐Performance Organic Solar Cells
Abstract The dimerization of small molecule acceptors (SMAs) is a promising strategy for enhancing the long‐term stability and power conversion efficiency (PCE) of organic solar cells (OSCs). However, the reported DSMAs are primarily limited to end‐linked molecular configurations, highlighting the need for further exploration of various dimer architectures. Herein, the development of two distinct core‐linked dimerized SMAs (DYF‐V and DYF‐E) are reported with tailored linker structures (vinylene and ethynyl, respectively), achieving high‐performance OSCs (PCE = 18.53%). Interestingly, a subtle change in the linker structures results in markedly different molecular properties and photovoltaic performances of the dimer acceptors. DYF‐E with an ethynyl linker exhibits more twisted backbone conformation and mitigated aggregation property compared to DYF‐V, inducing desirable blend morphologies with a polymer donor including high crystallinity, face‐on oriented packing structures, and well‐intermixed domains. Thus, the DYF‐E‐based OSCs exhibit a high PCE (17.02%), which significantly outperforms the DYF‐V‐based OSCs (PCE = 9.98%). Furthermore, the ternary OSCs based on DYF‐E achieve a higher PCE of 18.53%. Thus, this study highlights the significance of selecting an appropriate linker in core‐linked dimerized SMAs for producing high‐performance OSCs.
Oh, Shinbee↗
Unconventional bipartite entanglement in the quantum dimer magnet Yb2Be 2 SiO 7
The quantum dimer magnet, with antiferromagnetic intradimer and interdimer Heisenberg exchange between spin-1/2 moments, is known to host an (|$\uparrow$$\downarrow$$\rangle$ - |$\downarrow$$\uparrow$$\rangle$)/$\sqrt{2}$ singlet ground state when the intradimer exchange is dominant. Rare-earth-based quantum dimer systems with strong spin-orbit coupling offer the opportunity for tuning their magnetic properties by using magnetic anisotropy as a control knob. Here, we present bulk characterization and neutron scattering measurements of the quantum dimer magnet Yb 2 Be 2 SiO 7 . We find that the Yb3+ ions can be described by an effective spin-1/2 model at low temperatures and the system does not show signs of magnetic order down to 50 mK. The magnetization, heat capacity, and neutron spectroscopy data can be well-described by an isolated dimer model with highly anisotropic exchange that stabilizes a singlet ground state with a wavefunction (|$\uparrow$$\uparrow$$\rangle$ - |$\downarrow$$\downarrow$$\rangle$)/$\sqrt{2}$ or (|$\uparrow$$\uparrow$$\rangle$ + |$\downarrow$$\downarrow$$\rangle$)/$\sqrt{2}$. Our results show that strong spin-orbit coupling can induce unusual entangled states of matter in quantum dimer magnets.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Interactions that define the arrangement of sugar-binding sites in BDCA-2 and dectin-2 dimers
The sugar-binding receptors dectin-2 and blood dendritic cell antigen 2 (BDCA-2) bind oligosaccharide ligands through extracellular carbohydrate-recognition domains (CRDs) and initiate intracellular signaling through Fc receptor γ adapters (FcRγ). Dectin-2 stimulates macrophages in response to pathogen binding while BDCA-2 modulates cytokine production in plasmacytoid dendritic cells. The oligomeric states of these receptors and the orientations of their CRDs have been investigated by analysis of a naturally occurring disulfide-bonded variant of BDCA-2 and by replacement of transmembrane domains with N-terminal dimerization domains to create extracellular domain dimers of both dectin-2 and BDCA-2. Analysis of these constructs, as well as previously described crystal structures of the CRDs from these proteins and a novel structure of an extended version of the extracellular domain of dectin-2, showed that there is only limited interaction of the CRDs in the dimers, but interactions can be stabilized by the presence of the neck region. The resulting orientation of sugar-binding sites in the dimers would favor crosslinking of multiple dimers by oligosaccharide ligands, causing clustering of FcRγ to initiate signaling.
carbohydrate-binding protein↗
Dimer piling problems and interacting field theory
The dimer tiling problem asks in how many ways can the edges of a graph be covered by dimers so that each site is covered once. In the special case of a planar graph, this problem has a solution in terms of a free fermionic field theory. We rediscover and explore an expression for the number of coverings of an arbitrary graph by arbitrary objects in terms of an interacting fermionic field theory first proposed by Samuel. Generalizations of the dimer tiling problem, which we call “dimer piling problems,” demand that each site be covered N times by indistinguishable dimers. Our field theory provides a solution of these problems in the large- N limit. We give a similar path integral representation for certain lattice coloring problems. Published by the American Physical Society 2024
Astronomy & Astrophysics↗
Condensation in CO2 free jet expansions. I - Dimer formation.
A theoretical and experimental investigation of the kinetics of CO2 dimer formation in the adiabatically expanding core of a free jet expansion has been carried out. The theoretical analysis is based on dimer formation by an efficient termolecular process and dimer destruction by bimolecular collisions. Account is taken of the expected variation of the specific heat ratio during the expansion and of the effective increase in the termolecular collision rate at low temperatures due to the presence of loosely bound orbiting pairs. Experimental dimer concentrations were measured mass spectrometrically by forming a molecular beam from the expanded gas mixture after the onset of molecular flow. Observed dimer concentrations, for a range of pre-expansion conditions of 400 to 900 torr pressure and room temperature, are in good agreement with the theoretical analysis, provided that account is taken of the effect of loosely bound orbiting pairs at low temperatures.
Dorfeld, W. G.↗