Human Cellular Retinol Binding Protein II Forms a Domain;#8208;Swapped Trimer Representing a Novel F
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Ghanbarpour, Alireza↗
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Observation of the Low‐Frequency Spectrum of the Water Trimer as a Sensitive Test of the Water‐Trimer Potential and the Dipole‐Moment Surface
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Raffael Schwan↗
Observation of the Low‐Frequency Spectrum of the Water Trimer as a Sensitive Test of the Water‐Trimer Potential and the Dipole‐Moment Surface
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Raffael Schwan↗
Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines
Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.
60 APPLIED LIFE SCIENCES↗
Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine regimens
HIV-1 vaccine immunofocusing strategies may be able to induce broadly-reactive neutralizing antibodies (NAbs). Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets—the V2 apex and fusion peptide (FP). Selection criteria included i) high expression and ii) infectious function, so that trimer neutralization sensitivity can be profiled in pseudovirus (PV) assays. Initially, we boosted the expression of 17 candidate trimers by truncating gp41 and introducing a gp120-gp41 SOS disulfide to prevent gp120 shedding. "Repairs" were made to fill glycan holes and eliminate other strain-specific aberrations. A new neutralization assay allowed PV infection when our standard assay was insufficient. Trimers with exposed V3 loops, a target of non-NAbs, were discarded. To try to increase V2-sensitivity, we removed clashing glycans and modified the C-strand. Notably, a D167N mutation improved V2-sensitivity in several cases. Glycopeptide analysis of JR-FL trimers revealed near complete sequon occupation and that filling the N197 glycan hole was well-tolerated. In contrast, sequon optimization and inserting/removing glycans at other positions frequently had global "ripple" effects on glycan maturation and sequon occupation throughout the gp120 outer domain and gp41. V2 MAb CH01 selectively bound to trimers with small high mannose glycans near the base of the V1 loop, thereby avoiding clashes. Knocking in a rare N49 glycan was found to perturb gp41 glycans, increasing FP NAb sensitivity—and sometimes improving expression. Finally, a biophysical analysis of VLPs revealed that i) ~25% of particles bear Env spikes, ii) spontaneous particle budding is high and only increases 4-fold upon Gag transfection, and iii) Env+ particles express ~30–40 spikes. Taken together, we identified 7 diverse trimers with a range of sensitivities to two targets to allow rigorous testing of immunofocusing vaccine concepts.
60 APPLIED LIFE SCIENCES↗
Noncollinear magnetic configurations and substrate-mediated interactions in Mn trimers on the GaN (000$\bar{1}$) surface
Collinear and noncollinear calculations based on density functional theory are carried out to elucidate the magnetic ordering of Mn trimers on a GaN ($000\bar{1}$) substrate. These trimers had previously been observed in $3a \times 3a$ surface reconstructions through Mn deposition onto the N-polar face of wurtzite GaN($000\bar{1}$). In this work, we start off by studying the effect of spin orbit coupling for the case of monomers and dimers of Mn atoms on top of a GaN surface. Based on an effective spin Hamiltonian, we estimate the magnetic anisotropy energy (MAE) for those cases and found that it is four orders of magnitude weaker than the exchange magnetic coupling between Mn adatoms. In the Mn trimer case, the magnetic ground state has the Mn spins in-plane with the GaN surface in which the relative spin orientation within each trimer is noncollinear due to the competition between the two antiferromagnetic interactions that affect each Mn spin in the trimer, which leads to the found energy minimum with 120 degree angles between the spins. By exploring the nature and fundamental mechanisms for the magnetic interaction among the Mn trimers, we find that the surface states of the substrate play a key role, involving a Ruderman-Kittel-Kasuya-Yosida (RKKY)-type interaction. We report on an electron-mediated long-distance exchange coupling between localized magnetic moments on a GaN($000\bar{1}$) surface.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Tunable Metal–Organic Frameworks Based on 8-Connected Metal Trimers for High Ethane Uptake
Metal trimers [M 3 (O/OH)](OOCR) 6 are among the most important structural building blocks. From these trimers, a great success has been achieved in the design of 6- or 9-connected framework materials with various topological features and outstanding gas-sorption properties. In comparison, 8-connected trimer-based MOFs are rare. Given multiple competitive pathways for the formation of 6- or 9-connected frameworks, it remains challenging to identify synthetic or structural parameters that can be used to direct self-assembly process towards trimer-based 8-connected materials. Here, we reveal a viable strategy called angle bending modulation for creating a prototypical MOF type based on 8-connected M 3 (OH)(OOCR) 5 (Py-R) 3 trimers, M = Zn, Co, Fe). As a proof of concept, we synthesized six members in this family using three types of ligands (CPM-80, -81, and -82). These materials do not possess open-metal sites and show excellent uptake capacity for various hydrocarbon gas molecules and inverse C 2 H 6 /C 2 H 4 selectivity. CPM-81-Co, made from 2,5-furandicarboxylate and isonicotinate, features selectivity of 1.80 with high uptake capacity for ethane (123 cm 3 /g -1 ) and ethylene (113 cm 3 /g -1 ) at 298 K and 1 bar.
36 MATERIALS SCIENCE↗
Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes
Higher plants synthesize cellulose using membrane-bound, six-lobed cellulose synthase complexes, each lobe containing trimeric cellulose synthases (CESAs). Although molecular biology reports support heteromeric trimers composed of different isoforms, a homomeric trimer was reported for in vitro studies of the catalytic domain of CESA1 of Arabidopsis (AtCESA1CatD) and confirmed in cryoEM structures of full-length CESA8 and CESA7 of poplar and cotton, respectively. In both structures, a small portion of the plant-conserved region (P-CR) forms the only contacts between catalytic domains of the monomers. Here, we report inter-subunit lysine-crosslinks that localize to the small P-CR, negative-stain EM structure, and modeling data for homotrimers of AtCESA1CatD. Molecular dynamics simulations for AtCESA1CatD trimers based on the CESA8 cryoEM structure were stable and dependent upon a small set of residue contacts. The results suggest that homomeric CESA trimers may be important for the synthesis of primary and secondary cell walls and identify key residues for future mutagenic studies.
59 BASIC BIOLOGICAL SCIENCES↗
Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer
Broadly-neutralizing antibodies (bNAbs) against HIV-1 Env can protect from infection. We characterize Ab1303 and Ab1573, heterologously-neutralizing CD4-binding site (CD4bs) antibodies, isolated from sequentially-immunized macaques. Ab1303/Ab1573 binding is observed only when Env trimers are not constrained in the closed, prefusion conformation. Fab-Env cryo-EM structures show that both antibodies recognize the CD4bs on Env trimer with an ‘occluded-open’ conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4. The occluded-open Env trimer conformation includes outwardly-rotated gp120 subunits, but unlike CD4-bound Envs, does not exhibit V1V2 displacement, 4-stranded gp120 bridging sheet, or co-receptor binding site exposure. Inter-protomer distances within trimers measured by double electron-electron resonance spectroscopy suggest an equilibrium between occluded-open and closed Env conformations, consistent with Ab1303/Ab1573 binding stabilizing an existing conformation. Studies of Ab1303/Ab1573 demonstrate that CD4bs neutralizing antibodies that bind open Env trimers can be raised by immunization, thereby informing immunogen design and antibody therapeutic efforts.
59 BASIC BIOLOGICAL SCIENCES↗
Cyclically conjugated porphyrin trimers linked through benzo[4,5]imidazo[2,1- a ]isoindole bridges
Cyclically conjugated porphyrin trimers were prepared via a concise synthetic method. Zn-Trimer-1 displayed strong exciton coupling, suggesting the presence of effective electronic interactions. UV-Vis absorption and fluorescence spectra obtained through titration studies on the donor–acceptor adduct (Zn-Trimer-1–C60Im) indicate the occurrence of excited state photo-events. Inspired by nature's photosynthetic process of plants and bacteria, electronically interacting multiporphyrinic systems have long been investigated as synthetic models of natural photosynthetic systems. Remarkable successes have been achieved with cyclic porphyrin arrays, where porphyrins are arranged in a wheel-like structure or nanoring as photosynthetic antennae. Considerable efforts have also been devoted to constructing other porphyrin arrays such as molecular wires for potential applications in sensors, solar energy conversion, non-linear optical (NLO) materials, and more. Due to synthetic difficulties, cyclically conjugated porphyrin arrays in which porphyrins are arranged in planar geometry are very rare. Very recently, Anderson and coworkers have reported unprecedented β,β-directly linked porphyrin trimers and tetramers with different geometries, propeller and saddle, respectively, which result in distinct photophysical and electrochemical properties (Fig. 1a). In this paper, we present novel cyclically conjugated porphyrin trimers, which feature planar geometry with porphyrins assembled around the aromatic triphenylene at the center (Fig. 1b).
Han, Ting↗
Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire
The generation of broadly neutralizing antibodies (bnAbs) to conserved epitopes on HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The animal models commonly used for HIV do not reliably produce a potent broadly neutralizing serum antibody response, with the exception of cows. Cows have previously produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models, other engineered immunogens were shown to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n = 4) with two regimens of V2-apex focusing Env immunogens to investigate whether antibody responses could be generated to the V2-apex on Env. Group 1 was immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 was immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows, respectively, and showed moderate breadth and potency. Potent and broad responses in this study developed much later than previous cow immunizations that elicited CD4bs bnAbs responses and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target more than one broadly neutralizing epitope on the HIV surface reveals the generality of elongated structures for the recognition of highly glycosylated proteins. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response.
Microbiology↗
The 12-layer trimer-based hexagonal perovskite Cs 4 Ca 0.7 Mn 3.3 Cl 12
Here, we describe the crystal structure and basic magnetic properties of Cs 4 Ca 0.7 Mn 3.3 Cl 12 , a previously unreported twelve layer (12L-) hexagonal (R-3m) chloride perovskite. Its crystal structure features face sharing MnCl 6 octahedra that form Mn 3 Cl 12 trimers. The trimers, which form a triangular array, are separated by corner sharing to layers of disordered single Ca(Mn)Cl 6 octahedra. The decreased intratrimer Mn–Mn distance yields stronger magnetic coupling within trimers than between trimers. The dominant magnetic interactions are antiferromagnetic (θ CW = –105 K), the effective magnetic moment per Mn 2+ is 6.5 μ B , and potential signatures of magnetic frustration are observed. Behavior consistent with short- and long-range magnetic order is exhibited at approximately 37 and 0.7 K, respectively.
12L-hexagonal perovskite↗
Effects of HLA single chain trimer design on peptide presentation and stability
MHC class I “single-chain trimer” molecules, coupling MHC heavy chain, β 2 -microglobulin, and a specific peptide into a single polypeptide chain, are widely used in research. To more fully understand caveats associated with this design that may affect its use for basic and translational studies, we evaluated a set of engineered single-chain trimers with combinations of stabilizing mutations across eight different classical and non-classical human class I alleles with 44 different peptides, including a novel human/murine chimeric design. While, overall, single-chain trimers accurately recapitulate native molecules, care was needed in selecting designs for studying peptides longer or shorter than 9-mers, as single-chain trimer design could affect peptide conformation. In the process, we observed that predictions of peptide binding were often discordant with experiment and that yields and stabilities varied widely with construct design. We also developed novel reagents to improve the crystallizability of these proteins and confirmed novel modes of peptide presentation.
59 BASIC BIOLOGICAL SCIENCES↗
Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines
Ebola virus (EBOV) glycoprotein (GP) can be recognized by neutralizing antibodies (NAbs) and is the main target for vaccine design. Here, we first investigate the contribution of the stalk and heptad repeat 1-C (HR1 C ) regions to GP metastability. Specific stalk and HR1 C modifications in a mucin-deleted form (GPΔmuc) increase trimer yield, whereas alterations of HR1 C exert a more complex effect on thermostability. Crystal structures are determined to validate two rationally designed GPΔmuc trimers in their unliganded state. We then display a modified GPΔmuc trimer on reengineered protein nanoparticles that encapsulate a layer of locking domains (LD) and a cluster of helper T-cell epitopes. In mice and rabbits, GP trimers and nanoparticles elicit cross-ebolavirus NAbs, as well as non-NAbs that enhance pseudovirus infection. Repertoire sequencing reveals quantitative profiles of vaccine-induced B-cell responses. This study demonstrates a promising vaccine strategy for filoviruses, such as EBOV, based on GP stabilization and nanoparticle display.
60 APPLIED LIFE SCIENCES↗
Ultrafast optical melting of trimer superstructure in layered 1T′-TaTe2
Abstract Quasi-two-dimensional transition-metal dichalcogenides are a key platform for exploring emergent nanoscale phenomena arising from complex interactions. Access to the underlying degrees-of-freedom on their natural time scales motivates the use of advanced ultrafast probes sensitive to self-organised atomic-scale patterns. Here, we report the ultrafast investigation of TaTe 2 , which exhibits unique charge and lattice trimer order characterised by a transition upon cooling from stripe-like chains into a (3 × 3) superstructure of trimer clusters. Utilising MeV-scale ultrafast electron diffraction, we capture the photo-induced TaTe 2 structural dynamics – exposing a rapid ≈ 1.4 ps melting of its low-temperature ordered state followed by recovery via thermalisation into a hot cluster superstructure. Density-functional calculations indicate that the initial quench is triggered by intra-trimer Ta charge transfer which destabilises the clusters, unlike melting of charge density waves in other TaX 2 compounds. Our work paves the way for further exploration and ultimately rapid optical and electronic manipulation of trimer superstructures.
36 MATERIALS SCIENCE↗
Quantum Monte Carlo studies of a trimer scaling function with microscopic two- and three-body interactions
Here, we present an energy scaling function to predict, in a specific range, the energy of bosonic trimers with large scattering lengths and finite range interactions, which is validated by quantum Monte Carlo calculations using microscopic Hamiltonians with two- and three-body potentials. The proposed scaling function depends on the scattering length, effective range, and a reference energy, which we chose as the trimer energy at unitarity. We obtained the scaling function as a limit cycle from the solution of the renormalized zero-range model with effective range corrections. We proposed a simple parametrization of the energy scaling function. Besides the intrinsic interest in theoretical and experimental investigations, this scaling function allows one to probe Efimov physics with only the trimer ground states, which may open opportunities to identify Efimov trimers whenever access to excited states is limited.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Antibody Recognition of CD4-Induced Open HIV-1 Env Trimers
Human immunodeficiency virus type 1 (HIV-1) envelope (Env), a heterotrimer of gp120-gp41 subunits, mediates fusion of the viral and host cell membranes after interactions with the host receptor CD4 and a coreceptor. CD4 binding induces rearrangements in Env trimer, resulting in a CD4-induced (CD4i) open Env conformation. Structural studies of antibodies isolated from infected donors have defined antibody-Env interactions, with one class of antibodies specifically recognizing the CD4i open Env conformation. In this study, we characterized a group of monoclonal antibodies isolated from HIV-1 infected donors (V2i MAbs) that displayed characteristics of CD4i antibodies. Binding experiments demonstrated that the V2i MAbs preferentially recognize CD4-bound open Env trimers. Structural characterizations of V2i MAb-Env-CD4 trimer complexes using single-particle cryo-electron microscopy showed recognition by V2i MAbs using different angles of approach to the gp120 V1V2 domain and the β2/β3 strands on a CD4i open conformation Env with no direct interactions of the MAbs with CD4. We also characterized CG10, a CD4i antibody that was raised in mice immunized with a gp120-CD4 complex, bound to an Env trimer plus CD4. CG10 exhibited characteristics similar to those of the V2i antibodies, i.e., recognition of the open Env conformation, but showed direct contacts to both CD4 and gp120. Structural comparisons of these and previously characterized CD4i antibody interactions with Env provide a suggested mechanism for how these antibodies are elicited during HIV-1 infection.
60 APPLIED LIFE SCIENCES↗
Catalytic trimerization of aromatic nitriles for synthesis of polyimide matrix resins
Aromatic nitriles may be trimerized at moderate temperature and pressure with p-toluenesulfonic acid as catalyst. Studies were conducted to establish the effect of the reaction temperature, pressure, time, and catalyst concentration on yield of the trimerized product. Trimerization studies were also conducted to establish the effect of substituting electron donating or withdrawing groups on benzonitrile. Preliminary results of using the catalytic trimerization approach to prepare s-triazine cross-linked polyimide/graphite fiber composites are presented.
Hsu, L. C.↗