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The cyclic HCl–(H2O)3 tetramer is the largest observed neutral HCl–(H2O)n cluster. The vibrational predissociation of HCl–(H2O)3 is investigated by theory, quasiclassical trajectory (QCT) calculations, and experiment, following the infrared excitation of the hydrogen-bonded OH-stretch fundamental. The energetically possible dissociation pathways are HCl + (H2O)3 (Pathway 1) and H2O + HCl–(H2O)2 (Pathway 2). The HCl and H2O monomer fragments are observed by 2 + 1 resonance enhanced multiphoton ionization combined with time-of-flight mass spectrometry, and their rotational energy distributions are inferred and compared to the theoretical results. Velocity map images of the monomer fragments in selected rotational levels are used for each pathway to obtain pair-correlated speed distributions. The fragment speed distributions obtained by experiment and QCT calculations are broad and structureless, encompassing the entire range of allowed speeds for each pathway. Bond dissociation energies, D0, are estimated experimentally from the endpoints of the speed distributions: 2100 ± 300 cm−1 and 2400 ± 100 cm−1 for Pathway 1 and Pathway 2, respectively. These values are lower but in the same order as the corresponding calculated D0: 2426 ± 23 cm−1 and 2826 ± 19 cm−1. The differences are attributed to contributions from vibrational hot bands of the clusters that appear in the high-speed tails of the experimental pair-correlated distributions. Satisfactory agreement between theory and experiment is achieved when comparing the monomer fragments’ rotational energies, the shapes of the speed distributions, and the average fragment speeds and center-of-mass translational energies. Insights into the dissociation mechanism and lifetime are gained from QCT calculations performed on a previously reported many-body potential energy surface. It is concluded that the dissociation lifetime is on the order of 10 ps and that the final trimer products are in their lowest energy cyclic forms. [ABSTRACT FROM AUTHOR]

We report on the assembly of a highly ordered array of copper tetrameric clusters, coordinated into a metal-organic network. The ordered cluster array has been achieved by the deposition of tetrahydroxyquinone molecules on the Cu(111) surface at room temperature, and subsequent thermally activated dehydrogenation with the formation of tetraoxyquinone tetra-anions with a 4 × 4 periodicity. The supramolecular organic network acts as a spacer for the highly ordered two-dimensional network of copper tetramers at the very surface. [ABSTRACT FROM AUTHOR]

Lactate Dehydrogenase is an enzyme found in all living cells. The conversion of lactate to pyruvate and vice versa is catalyse by Lactate Dehydrogenase enzyme. The two different sub-units are marked in LDH; notably LDH A is also known as M sub-unit and LDH B is known as H sub-unit. LDH isozymes are found in five common forms, two more mammalian LDH sub-units of tetramers is incorporated namely LDH C and LDH Bx. [ABSTRACT FROM AUTHOR]

Ab initio and density functional theory calculations are used to examine complexes formed between H2CO and H2CS with 1, 2, and 3 molecules of SO2. The nature of the interactions is probed by a variety of means, including electrostatic potentials, natural bond orbital, atoms in molecules, energy decomposition, and electron density redistribution maps. The dimers are relatively strongly bound, with interaction energies exceeding 5 kcal/mol. The structures are cyclic, containing both a O/S· · ·S chalcogen bond and a CH· · ·O H-bond. Addition of a second SO2 molecule leads to a variety of heterotrimer structures, most of which resemble the original dimer, where the second SO2 molecule engages in a chalcogen bond with the first SO2, and a C· · ·O attraction with the H2CX. Some cooperativity is apparent in the trimers and tetramers, with an attractive three-body interaction energy and shortened intermolecular distances. [ABSTRACT FROM AUTHOR]

Tryptocidine C (TpcC, cyclo[D-Phe1-Pro2-Trp3-D-Trp4-Asn5-Gln6-Trp7-Val8-Orn9-Leu10]) is a broad-spectrum antimicrobial peptide in the tyrothricin complex produced by a soil bacterium, Brevibacillus parabrevis. Electrospray mass spectrometric studies reveal the oligomerisation of TpcC into dimers and higher oligomers, analogous to tyrocidine C (TrcC, Trp7 replaced by Tyr7). Ion mobility mass spectrometry (IMMS) further confirms the formation of stable peptide dimers and tetramers with diameters of 2.7 nm and 3.3 nm, respectively, calculated from collisional cross section (CCS). Molecular dynamic simulations and docking studies support the formation of amphipathic dimers, with a diameter of 2.5 ± 0.07 nm calculated from low energy model CCS. Circular dichroism and IMMS studies point towards dynamic hydrogen-bonded conformational changes up to 28–33 μM after which the structures become more static (or in equilibrium). Fluorescence studies indicate aromatic stacking of Trp residues with a CMC of 18 μM in aqueous solutions. The concentration and time dependent interaction of Trp in oligomers indicate cooperativity in the TpcC oligomerisation that leads to the formation of higher order microscopic structures. Scanning electron microscopy studies unequivocally shows that TpcC forms nanospheres with a mean diameter of 25 nm. Repeated smaller oligomeric units, possibly dimers and tetramers, self-assemble to form these nanospheres. Image 1 • Tryptocidine C (TpcC), an antimicrobial cyclodecapeptide from tyrothricin readily oligomerises into nano-assemblies. • Dimers, trimers, tetramers and higher oligomers of TpcC were observed with electrospray – and ion mobility mass spectrometry. • Circular dichroism and fluorescence studies indicated a H-bond network and cooperative aromatic stacking in TpcC oligomers. • Molecular modelling revealed beta-sheet type TpcC monomers and dimers with CCS values correlating with those determined by IMMS. [ABSTRACT FROM AUTHOR]

Advances in quantum computing technology have been made in recent years due to the evolution of spin clusters. Recent studies have tended towards spin cluster subgeometries to understand more complex structures better. These molecular magnets provide a multitude of phenomena via exchange interactions that allow for advancements in spintronics and other magnetic system applications due to the possibility of increasing speed, data storage, memory, and stability of quantum computing systems. Using the Heisenberg spin-spin exchange Hamiltonian and exact diagonalization, we examine the evolution of quantum energy levels and thermodynamic properties for various spin configurations and exchange interactions. The XXYY quantum spin tetramer considered in this study consists of two coupled dimers with exchange interactions a1 J and a'1 J and a dimer--dimer exchange interaction a2 J. By varying spin values and interaction strengths, we determine the exact energy eigenstates that are used to determine closed-form analytic solutions for the heat capacity and magnetic susceptibility of the system and further analyze the evolution of the properties of the system based on the parameter values chosen. Furthermore, this study shows that the Schottky anomaly shifts towards zero as the ground-state of the system approaches a quantum phase transition between spin states. Additionally, we investigate the development of phase transitions produced by the convergence of the Schottky anomaly with both variable exchange interactions and external magnetic field. [ABSTRACT FROM AUTHOR]

In recent years, the field of molecular data storage has emerged from a niche to a vibrant research topic. Herein, we describe a simultaneous and automated read-out of data stored in mixtures of sequence-defined oligomers. Therefore, twelve different sequence-defined tetramers and three hexamers with different mass markers and side chains are successfully synthesised via iterative Passerini three-component reactions and subsequent deprotection steps. By programming a straightforward python script for ESI-MS/MS analysis, it is possible to automatically sequence and thus read-out the information stored in these oligomers within one second. Most importantly, we demonstrate that the use of mass-markers as starting compounds eases MS/MS data interpretation and furthermore allows the unambiguous reading of sequences of mixtures of sequence-defined oligomers. Thus, high data storage capacity considering the field of synthetic macromolecules (up to 64.5 bit in our examples) can be obtained without the need of synthesizing long sequences, but by mixing and simultaneously analysing shorter sequence-defined oligomers. Sequence-defined molecules are promising for data storage applications, but synthesizing long sequences is typically required to achieve a high data storage capacity. Here the authors synthesize a library of different sequence-defined tetramers and hexamers and demonstrate that mixtures of these short sequence-defined oligomers can store up to 64.5 bit. [ABSTRACT FROM AUTHOR]

Eukaryotic histone H3-H4 tetramers contain a putative copper (Cu2+) binding site at the H3-H3′ dimerization interface with unknown function. The coincident emergence of eukaryotes with global oxygenation, which challenged cellular copper utilization, raised the possibility that histones may function in cellular copper homeostasis. We report that the recombinant Xenopus laevis H3-H4 tetramer is an oxidoreductase enzyme that binds Cu2+ and catalyzes its reduction to Cu1+ in vitro. Loss- and gain-of-function mutations of the putative active site residues correspondingly altered copper binding and the enzymatic activity, as well as intracellular Cu1+ abundance and copper-dependent mitochondrial respiration and Sod1 function in the yeast Saccharomyces cerevisiae. The histone H3-H4 tetramer, therefore, has a role other than chromatin compaction or epigenetic regulation and generates biousable Cu1+ ions in eukaryotes. [ABSTRACT FROM AUTHOR]

We investigated the contribution of human leukocyte antigen A2 (HLA-A2) and HLA-E–restricted CD8+ T cells in patients with Mycobacterium tuberculosis and human immunodeficiency virus 1 (HIV-1) coinfection. HIV-1 downregulates HLA-A, -B, and -C molecules in infected cells, thus influencing recognition by HLA class I–restricted CD8+ T cells but not by HLA-E–restricted CD8+ T cells, owing to the inability of the virus to downmodulate their expression. Therefore, antigen-specific HLA-E–restricted CD8+ T cells could play a protective role in Mycobacterium tuberculosis and HIV-1 coinfection. HLA-E– and HLA-A2–restricted Mycobacterium tuberculosis–specific CD8+ T cells were tested in vitro for cytotoxic and microbicidal activities, and their frequencies and phenotypes were evaluated ex vivo in patients with active tuberculosis and concomitant HIV-1 infection. HIV-1 and Mycobacterium tuberculosis coinfection caused downmodulation of HLA-A2 expression in human monocyte–derived macrophages associated with resistance to lysis by HLA-A2–restricted CD8+ T cells and failure to restrict the growth of intracellular Mycobacterium tuberculosis. Conversely, HLA-E surface expression and HLA-E–restricted cytolytic and microbicidal CD8 responses were not affected. HLA-E–restricted and Mycobacterium tuberculosis–specific CD8+ T cells were expanded in the circulation of patients with Mycobacterium tuberculosis/HIV-1 coinfection, as measured by tetramer staining, but displayed a terminally differentiated and exhausted phenotype that was rescued in vitro by anti–PD-1 (programmed cell death protein 1) monoclonal antibody. Together, these results indicate that HLA-E–restricted and Mycobacterium tuberculosis–specific CD8+ T cells in patients with Mycobacterium tuberculosis/HIV-1 coinfection have an exhausted phenotype and fail to expand in vitro in response to antigen stimulation, which can be restored by blocking the PD-1 pathway using the specific monoclonal antibody nivolumab. [ABSTRACT FROM AUTHOR]

The ground-state properties of (NO)2 and (NO)4 have been investigated using multireference second-order perturbation theory (MRMP2) and include a two-tier extrapolation to the complete basis set (CBS) limit. For the NO dimer the MRMP2(18,14)/CBS predicted structure, binding energy (with respect to 2NO; De = 3.46 kcal/mol), and dipole moment (ue = 0.169 D) are in excellent agreement with experimental measurements (De = 2.8-3.8 kcal/mol; ue = 0.171 D). Additionally, three of four intermolecular anharmonic MRMP2(18,14)/CBS-estimated frequencies (143 cm-1, 238 cm-1, 421 cm-1) are in excellent agreement with recent gas-phase experimental measurements (135 cm-1, 239 cm-1, 429/428 cm-1); however, the predicted value of 151 cm-1 for the out-of-plane torsion (A2) is elevated compared to recent experimental estimates of 97-117 cm-1. Our finding that this infrared-forbidden vibration is also predicted to have an extremely low Raman activity (0.04 Å/amu at the MP2/QZ level of theory) conflicts with Raman measurements of a strong intensity for a low frequency band; however, these studies were performed for low temperature solid and liquid phases. Probing the possibility of the presence of higher order clusters we investigated the stability of (NO)4 and discovered three isomers, each resembling pairs of dimers, that were stable to dissociation to 2(NO)2, with the lowest-energy isomer (Ci structure) having a predicted binding energy almost identical to that of the dimer. Computed vibrational frequencies of the Ci isomer indicate that the 12 highest-frequency modes resemble barely shifted NO dimer-combined bands while the 13th highest-frequency mode at ∼100 cm-1 is exclusive to (NO)4. Moreover, this tetramer-unique vibration is infrared inactive but has a very high predicted Raman activity of some 24 Å/amu. Guided by the theoretical results, we reexamined and reassigned experimental Raman and infrared data going back to 1951 and determined that our best predictions of vibrational frequencies of (NO)2 and (NO)4 are consistent with experimental observations. We thus postulate the existence and observation of (NO)4. [ABSTRACT FROM AUTHOR]

Structure and dynamics of acrylodan labeled αA-crystallin tetramer formed in the presence of a bile salt (sodium deoxycholate, NaDC) has been studied using fluorescence correlation spectroscopy (FCS) and femtosecond up-conversion techniques. Using FCS it is shown that, the diffusion constant (Dt) of the αA-crystallin oligomer (mass ∼800 kDa) increases from ∼35 μm2 s-1 to ∼68 μm2 s-1. This corresponds to a decrease in hydrodynamic radius (rh) from ∼6.9 nm to ∼3.3 nm. This corresponds to about 10-fold decrease in molecular mass to ∼80 kDa and suggests formation of a tetramer (since mass of αA-crystallin monomer is ∼20 kDa). The steady state emission maximum and average solvation time (<τs>) of acrylodan labeled at cysteine 131 position of αA-crystallin is markedly affected on addition of NaDC, while the tryptophan (trp-9) becomes more exposed. This suggests that NaDC binds near the cys-131 and makes the terminal region of αA-crystallin exposed. This may explain the enhanced auto-phosphorylation activity of αA-crystallin near the terminus of the 173 amino acid protein (e.g., at the threonine 13, serine 45, or serine 169 and 172) and suggests that phosphorylation at ser-122 (close to cys-131) is relatively less important. [ABSTRACT FROM AUTHOR]

Electronic structure calculations have been carried out for all possible alkali tetramers that can be formed from X2 + X2 → X2X2, X2 + Y2 → X2Y2, and XY + XY → X2Y2 alkali dimer association reactions. Vibrationally stable rhombic (D2h) and planar (Cs) structures are found for all possible tetramers formed from the alkali metals, Li to Cs. All tetramer formation reactions (from ground state singlet homonuclear or heteronuclear dimers) are found to be exothermic with binding energies ranging from 6282 cm-1 for Li2Li2 to 1985 cm-1 for Cs2Cs2. Extensive calculations, carried out at long-range for several reactant pairs, indicate that there are barrier-less pathways for the formation of tetramers from dimer association reactions. At low temperatures, direct formation of tetramers is unlikely, owing to the large exothermicity associated with these association reactions, but atom exchange reactions (X2 + Y2 ↔ XY + XY) are possible for some species. [ABSTRACT FROM AUTHOR]

Hydrogen cyanide polymerizes readily under a variety of conditions and significant prebiotic roles have been suggested for these polymers due to the abundance of HCN in universe. However, the structures of HCN polymers have been more speculative than grounded in experimental data. Here we show that 13C and 15N solid state NMR spectra of polymers formed in neat HCN are inconsistent with the previously proposed structures and suggest instead that the polymers are formed by simple monomer addition, first in head-to-tail fashion to form linear, conjugated chains, and then laterally to form saturated two-dimensional networks. This interpretation of the NMR spectra finds support in other information about the polymerization of neat HCN, including the presence of free radicals. As expected from the literature, formation of the HCN tetramer, diaminomaleonitrile, is also observed, but only when the reaction is catalyzed exclusively by base and then in crystalline form. [ABSTRACT FROM AUTHOR]

We investigate thermal fluctuations in a smectic A phase of an amphiphile–solvent mixture with molecular-dynamics simulations. We use an idealized model system, where solvent particles are represented by simple beads, and amphiphiles by bead-and-spring tetramers. At a solvent bead fraction of 20% and sufficiently low temperature, the amphiphiles self-assemble into a highly oriented lamellar phase. Our study aims at comparing the structure of this phase with the predictions of the elastic theory of thermally fluctuating fluid membrane stacks [Lei et al., J. Phys. II 5, 1155 (1995)]. We suggest a method which permits to calculate the bending rigidity and compressibility modulus of the lamellar stack from the simulation data. The simulation results are in reasonable agreement with the theory. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present a more efficient version of the temperature accelerated dynamics (TAD) method. Without introducing any new approximation, we show how it is possible to make the TAD method faster when a system visits a state more than one time. We demonstrate the method for the diffusion of silver tetramers on Ag(100), obtaining an additional boost (relative to standard TAD) of ∼4 at T= 400 K and ∼11 at T= 200 K. Larger boosts can be obtained at lower temperatures and/or for different systems. This new formalism also offers a way to gain this additional boost in the dynamics on the first visit to a state, provided information is available about the lowest barrier for escape from the state. [ABSTRACT FROM AUTHOR]

Transcription of transposable elements is tightly regulated to prevent genome damage. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) and KRAB-associated protein 1 (KAP1/TRIM28) play a key role in regulating retrotransposons. KRAB-ZFPs recognize specific retrotransposon sequences and recruit KAP1, inducing the assembly of an epigenetic silencing complex, with chromatin remodeling activities that repress transcription of the targeted retrotransposon and adjacent genes. Our biophysical and structural data show that the tripartite motif (TRIM) of KAP1 forms antiparallel dimers, which further assemble into tetramers and higher-order oligomers in a concentration-dependent manner. Structure-based mutations in the B-box 1 domain prevent higher-order oligomerization without significant loss of retrotransposon silencing activity, indicating that, in contrast to other TRIM-family proteins, self-assembly is not essential for KAP1 function. The crystal structure of the KAP1 TRIM dimer identifies the KRAB domain binding site in the coiled-coil domain near the dyad. Mutations at this site abolished KRAB binding and transcriptional silencing activity of KAP1. This work identifies the interaction interfaces in the KAP1 TRIM responsible for self-association and KRAB binding and establishes their role in retrotransposon silencing. [ABSTRACT FROM AUTHOR]

The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom resolution using a single-particle cryo–electron microscopy method. Two classical V-shaped ATP synthase dimers lie antiparallel to each other to form an H-shaped ATP synthase tetramer, as viewed from the matrix. ATP synthase inhibitory factor subunit 1 (IF1) is a well-known in vivo inhibitor of mammalian ATP synthase at low pH. Two IF1 dimers link two ATP synthase dimers, which is consistent with the ATP synthase tetramer adopting an inhibited state. Within the tetramer, we refined structures of intact ATP synthase in two different rotational conformations at 3.34- and 3.45-Å resolution. [ABSTRACT FROM AUTHOR]

The endogenous inhibitor of ATP synthase in mitochondria, called IF1, conserves cellular energy when the proton-motive force collapses by inhibiting ATP hydrolysis. Around neutrality, the 84-amino-acid bovine IF1 is thought to self-assemble into active dimers and, under alkaline conditions, into inactive tetramers and higher oligomers. Dimerization is mediated by formation of an antiparallel a-helical coiled-coil involving residues 44-84. The inhibitory region of each monomer from residues 1-46 is largely a-helical in crystals, but disordered in solution. The formation of the inhibited enzyme complex requires the hydrolysis of two ATP molecules, and in the complex the disordered region from residues 8-13 is extended and is followed by an a-helix from residues 14-18 and a longer a-helix from residue 21, which continues unbroken into the coiled-coil region. From residues 21-46, the long a-helix binds to other a-helices in the C-terminal region of predominantly one of the ß-subunits in the most closed of the three catalytic interfaces. The definition of the factors that influence the self-association of IF1 is a key to understanding the regulation of its inhibitory properties. Therefore, we investigated the influence of pH and salt-types on the self-association of bovine IF1 and the folding of its unfolded region. We identified the equilibrium between dimers and tetramers as a potential central factor in the in vivo modulation of the inhibitory activity and suggest that the intrinsically disordered region makes its inhibitory potency exquisitely sensitive and responsive to physiological changes that influence the capability of mitochondria to make ATP. [ABSTRACT FROM AUTHOR]

Cyclodextrins (CDs) are cyclic oligomers of a-1,4-D-glucopyranoside and are known mainly as hexamers to octamers. The central cavities of CDs can retain small molecules, enabling diverse applications. The smallest members, CD3 and CD4, have ring sizes too small to permit the most stable conformations of glucopyranose and have not been accessible synthetically. In this study, we present methods to chemically synthesize both CD3 and CD4. The main factor in the successful synthesis is the creation of a glucopyranose ring conformationally counterbalanced between equatorial- and axial-rich forms. This suppleness is imparted by a bridge between O-3 and O-6 of glucose, which enables the generation of desirable, albeit deformed, conformers when synthesizing the cyclic trimer and tetramer. [ABSTRACT FROM AUTHOR]

The IKs current has an established role in cardiac action potential repolarization, and provides a repolarization reserve at times of stress. The underlying channels are formed from tetramers of KCNQ1 along with one to four KCNE1 accessory subunits, but how these components together gate the IKs complex to open the pore is controversial. Currently, either a concerted movement involving all four subunits of the tetramer or allosteric regulation of open probability through voltage-dependent subunit activation is thought to precede opening. Here, by using the E160R mutation in KCNQ1 or the F57W mutation in KCNE1 to prevent or impede, respectively, voltage sensors from moving into activated conformations, we demonstrate that a concerted transition of all four subunits after voltage sensor activation is not required for the opening of IKs channels. Tracking voltage sensor movement, via [2-(trimethylammonium)ethyl]methanethiosulfonate bromide (MTSET) modification and fluorescence recordings, shows that E160R-containing voltage sensors do not translocate upon depolarization. E160R, when expressed in all four KCNQ1 subunits, is nonconducting, but if one, two, or three voltage sensors contain the E160R mutation, whole-cell and single-channel currents are still observed in both the presence and absence of KCNE1, and average conductance is reduced proportional to the number of E160R voltage sensors. The data suggest that KCNQ1 + KCNE1 channels gate like KCNQ1 alone. A model of independent voltage sensors directly coupled to open states can simulate experimental changes in IKs current kinetics, including the nonlinear depolarization of the conductance- voltage (G-V) relationship, and tail current acceleration as the number of nonactivatable E160R subunits is increased. [ABSTRACT FROM AUTHOR]

Abstract Streptococcus pyogenes (group A Streptococcus , GAS) has caused a wide variety of human diseases. Its multifunctional surface dehydrogenase (SDH) is crucial for GAS life cycle. Furthermore, GAS infection into human pharyngeal cells has been previously shown to be mediated by the interaction between SDH and host urokinase-type plasminogen activator receptor (uPAR). However, the structural information of SDH remains to be elucidated and there are few detailed studies to characterize its interaction with uPAR. In-depth research on these issues will provide potential targets and strategies for combating GAS. Here, we prepared recombinant SDH tetramer in Escherichia coli BL21 (DE3) cells. After purification and crystallization, we determined its crystal structure at 1.74 Å. The unique characteristics might be potentially explored as drug targets or vaccine immunogen. We subsequently performed gel filtration chromatography, native-polyacrylamide gel electrophoresis (PAGE) and in vitro pull-down analyses. The results showed that their interaction was too weak to form stable complexes and the role of uPAR involved in GAS infection needs further demonstration. Altogether the current work provides the first view of SDH and deepens the knowledge of GAS infection. Highlights • The first crystal structure of SDH was determined at 1.74 Å, serving as a potential GAS target. • The interaction between SDH and uPAR was characterized to be very weak. • The importance of SDH and uPAR in GAS infection demanded in-depth research. [ABSTRACT FROM AUTHOR]

The Ctp1 protein in Schizosaccharomyces pombe is essential for DNA double-strand break (DSB) repair by homologous recombination. Fission yeast Ctp1 and its budding yeast (Sae2) and human (CtIP) homologs control Mre11-Rad50-Nbs1 nuclease complex activity and harbor DNA-binding and -bridging activities. However, the molecular basis for Ctp1-DNA transactions remains undefined. Here, we report atomic force microscopy (AFM) imaging of S. pombe Ctp1-DNA complexes revealing that Ctp1 polymerizes ondsDNAmolecules and forms synaptic filaments that bridge two dsDNA strands.Weobserved that Ctp1 DNA filaments are typified by an average filament length of ~180 bp of dsDNA and a Ctp1 tetramer footprint of ~15 bp. Biochemical results characterizing Ctp1 variants with impaired DNA-binding or -bridging properties were consistent with Ctp1-mediatedDNAbridging requiring the intact and correctly folded Ctp1 tetramer. Furthermore, mutations altering Ctp1 oligomerization and DNA bridging in vitro conferred cell sensitivity to DSB-producing agents. Together, these results support an important role for Ctp1-regulatedDNAstrand coordination required for DNA DSB repair in S. pombe. [ABSTRACT FROM AUTHOR]

Highlights • First DFT study of silver species Ag n (n = 1, 3, 4) bounded to nanoparticulate ceria. • Silver species are oxidized upon adsorption at {100} and {111} nanofacets of ceria. • Adsorption of silver species at {100} facet is ∼0.5–1.0 eV stronger than to {111} one. • Ag 3 are adsorbed as upright triangles; Ag 4 prefer tetrahedral configuration. • Denucleation of silver clusters to atomic species at {100} facet is the most favored. Abstract Silver single atoms and small clusters supported on a model Ce 21 O 42 nanoparticle have been studied computationally at a DFT+U level. It was found that silver atoms, trimers and tetramers are oxidized upon interaction with the {100} and {111} nanofacets of the ceria particle. The most stable surface complexes are formed via interaction of the silver species with two-coordinated O2c atoms of the {100} nanofacet. The binding energies of the silver atom, trimer, and tetramer are calculated to be ∼2.2, ∼2.9 and 3.1 eV, respectively. Binding of these silver species located on the {111} facet is less severe, by 1.0 eV for the single atom and by 0.4–1.1 eV for Ag 3 and Ag 4 clusters. Stability of the lowest-energy supported silver species on the two types of ceria nanofacets decreases in the order of Ag/Ce 21 O 42 {100} > Ag 4 /Ce 21 O 42 {100} > Ag 3 /Ce 21 O 42 {100} > Ag 3 /Ce 21 O 42 {111} > Ag 4 /Ce 21 O 42 {111} > Ag/Ce 21 O 42 {111}, pointing out on the supremacy of the denucleation trend. Graphical abstract Image, graphical abstract [ABSTRACT FROM AUTHOR]

Here we present a calculation scheme which allows us to obtain the electronic structure and exchange interaction parameters of low-dimensional magnetic compounds with subsequent construction of the spin model and verification of this model by comparing the simulated thermodynamic properties with experimental data. This scheme is implemented to quasi-one-dimensional (1D) perovskite KCuF3, the S = 1 spin ladder Rb3Ni2(NO3)7 compound, and potassium dimanganese trivanadate, KMn2V3O10, containing Mn tetramers. [ABSTRACT FROM AUTHOR]

The crystallization of 3‐[4′‐(diethylboryl)phenyl]pyridine (1), which formed a mixture of oligomers in solution with the cyclic trimer as a major component, in acetone at 0 °C afforded a cyclic tetramer that co‐crystallized with solvent molecules. Similarly, solutions of compound 1 in toluene at 10 °C and in benzene at 8 °C furnished the cyclic tetramer with the incorporation of toluene and benzene molecules, respectively, thus suggesting that the cyclic tetramer was the minor component. 13C CP/MAS NMR spectroscopy of precipitates of compound 1 suggested that precipitation from acetone and toluene each afforded mixtures of the cyclic trimer and the cyclic tetramer, whereas precipitation from benzene exclusively furnished the cyclic tetramer. Therefore, it appeared that crystallization readily shifted the equilibrium towards the cyclic tetramer in benzene. The thermodynamic parameters for the equilibrium between these two oligomers in [D6]benzene, as determined from a van′t Hoff plot, were ΔH°=−8.8 kcal mol−1 and ΔS°=−23.7 cal mol−1 K−1, which were coincident with previously reported calculations and observations. Four Your Eyes Only: Precipitates of compound 1 from acetone and toluene solutions contained both the cyclic trimer (13) and the cyclic tetramer (14), whereas precipitation from benzene only furnished the cyclic tetramer. Therefore, it appeared that crystallization readily shifted the equilibrium towards the cyclic tetramer in benzene solution. [ABSTRACT FROM AUTHOR]

The influenza neuraminidase (NA) is a homotetramer with head, stalk, transmembrane and cytoplasmic regions. The structure of the NA head with a stalk has never been determined. The NA head from an N9 subtype influenza A virus, A/tern/Australia/G70C/1975 (H1N9), was expressed with an artificial stalk derived from the tetrabrachion (TB) tetramerization domain from Staphylothermus marinus. The NA was successfully crystallized both with and without the TB stalk, and the structures were determined to 2.6 and 2.3 Å resolution, respectively. Comparisons of the two NAs with the native N9 NA structure from egg‐grown virus showed that the artificial TB stalk maintained the native NA head structure, supporting previous biological observations. This communication is the first to describe the crystal structure, at 2.6 Å resolution, of a recombinant N9 influenza neuraminidase with an artificial stalk formed by the tetrabrachion (TB) tetramerization domain from Staphylothermus marinus. The structure of the N9 head without the TB domain was also determined at 2.3 Å resolution and both were compared with the N9 head derived from egg‐grown virus, which was resolved to 1.4 Å resolution: the highest resolution ever reported for an uncomplexed N9 head. [ABSTRACT FROM AUTHOR]

Celiac disease (CeD) provides an opportunity to study the specificity underlying human T-cell responses to an array of similar epitopes presented by the same human leukocyte antigen II (HLA-II) molecule. Here, we investigated T-cell responses to the two immunodominant and highly homologous HLA-DQ2.5–restricted gluten epitopes, DQ2.5-glia-α1a (PFPQPELPY) and DQ2.5-glia-ω1 (PFPQPEQPF). Using HLA-DQ2.5–DQ2.5-glia-α1a and HLA-DQ2.5–DQ2.5-glia-ω1 tetramers and single-cell αβ T-cell receptor (TCR) sequencing, we observed that despite similarity in biased variable-gene usage in the TCR repertoire responding to these nearly identical peptide–HLA-II complexes, most of the T cells are specific for either of the two epitopes. To understand the molecular basis of this exquisite fine specificity, we undertook Ala substitution assays revealing that the p7 residue (Leu/Gln) is critical for specific epitope recognition by both DQ2.5-glia-α1a– and DQ2.5-glia-ω1–reactive T-cell clones. We determined high-resolution binary crystal structures of HLA-DQ2.5 bound to DQ2.5-glia-α1a (2.0 Å) and DQ2.5-glia-ω1 (2.6 Å). These structures disclosed that differences around the p7 residue subtly alter the neighboring substructure and electrostatic properties of the HLA-DQ2.5–peptide complex, providing the fine specificity underlying the responses against these two highly homologous gluten epitopes. This study underscores the ability of TCRs to recognize subtle differences in the peptide–HLA-II landscape in a human disease setting. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • A new calix[4]arene-like tetramer of resveratrol; • Significant improvement of antioxidative activity; • More stable radical species of calix[4]arene-like tetramer (TSC) than resveratrol; • Synergistic effect of calix[4]arene skeleton and substituent group on upper rim. Abstract Resveratrol is a natural antioxidant in a wide variety of plant species, developing an effective strategy to further improve its antioxidative activity has attracted enormous research attention in recent years. In this work, tetra-(3,5-dihydroxy)styryl-calix[4]arene (TSC, a calix[4]arene-like tetramer of resveratrol) has been theoretically studied at the DFT-BP86/6-311+G(d,p) level of theory. The results demonstrates that TSC has highly symmetrical molecular geometry with four equivalent resveratrol units, the 4′-O H and 4′-C O bonds were elongated and distinct deviation from planarity was observed in four resveratrol units in TSC. More interestingly, TSC has remarkably lower 4′-OH BDE, IP, and PA of 4′-phenolate than those of resveratrol, indicating that TSC exhibits much more excellent antioxidative activities than resveratrol. Spin density in 4′-phenoxyl radical and cation radical are delocalized over whole molecular skeleton of TSC, thus leading to more stable radical species than that of resveratrol. The topologies analysis of unpaired electron occupying orbitals reveals that calix[4]arene skeleton plays very important role in delocalization of unpaired electron. Molecular simplification studies proved that the synergistic effect of calix[4]arene skeleton, the A benzene ring and C C double bonds on the upper rim were responsible for the higher activity of TSC, and calix[4]arene skeleton amongst played the most important role. [ABSTRACT FROM AUTHOR]

Abstract A new Werner type manganese(II) clatharate [Mn(Bz) 2 (H 2 O) 4 ]∙(4–CNpy)∙2H 2 O (1), where Bz = benzoate and 4–CNpy = 4–cyanopyridine, has been synthesized at room temperature and characterized by X-ray crystal structure analysis, FT-IR, electronic spectrum and TGA. The crystal structure of cocrystal hydrate of 1 involves a discrete host monomer with enclathrated water and 4-CNpy molecules. Crystallographic studies on the compound 1 reveal that enclathration of guest water molecules in the Mn(II) host units results in a supramolecular tetramer in the crystal structure of 1 involving weak C H⋯C contacts. The geometry of the supramolecular host tetramer with the guest 4–CNpy molecules has been fully optimized using the crystallographic coordinates and the computational results suggest that the observed C H⋯C interactions are energetically quite significant. It is observed that both electrostatics as well as dispersion interactions are the most dominant contributors towards the stabilization of the C H⋯C interaction. Highlights • A new unusual Werner type clatharate of Mn(II) has been reported. • Mn(II) host units results in a supramolecular tetramer involving weak C H⋯C contacts. • The observed C H⋯C contacts are energetically quite significant. • Both electrostatics and dispersion interactions contribute towards stabilization of the C H⋯C interaction. [ABSTRACT FROM AUTHOR]

Highlights • CD40 ligand expressed by activated T cells forms a homotrimer on the cell surface, which is critical for its biological activities. • Here we have generated a soluble, tetrameric form of CD40L by fusing its extracellular domain with streptavidin (SA). • This SA-CD40L fusion protein exhibits > 25-fold stronger activities than agonistic anti-CD40 antibodies in both mouse and human primary B cells. • This SA-CD40L can be widely used in immunological studies in vitro and in vivo. Abstract CD40 ligand (CD40 L) expressed by activated T cells interacts with CD40 on B cells and triggers B cell survival, proliferation and differentiation. Deficiency in CD40 L or CD40 in humans causes hyper IgM syndrome due to a defect in T-B interaction that is essential for Ig gene class switch recombination (CSR). CD40 L belongs to the tumor necrosis factor family and normally forms a homotrimer on the cell surface, which is important for its biological activity. To generate a multimeric CD40 L that can be used to stimulate both mouse and human B cells, we fused the extracellular domain of mouse CD40 L, which is known to also bind human CD40, with streptavidin (SA) that forms a stable tetramer under physiological conditions. As expected, 293 T cells transiently transfected with an SA-CD40 L expression vector secreted tetrameric SA-CD40 L in the culture supernatant. The secreted SA-CD40 L exhibited > 25-fold stronger activities in inducing the survival, activation and proliferation of both mouse and human primary B cells than did an agonistic anti-mouse or anti-human CD40 antibody. In the presence of IL-4, SA-CD40 L also induced efficient CSR and plasma cell differentiation in both mouse and human B cells. Moreover, administration of SA-CD40 L in mice induced activation and proliferation of spleen B cells in vivo. These results demonstrate that the SA-CD40 L fusion protein generated in the present study recapitulates the function of membrane-bound trimeric CD40 L and has potent biological activities in both mouse and human primary B cells. [ABSTRACT FROM AUTHOR]

In this paper, the synthesis and free-radical scavenging capacity of novel calix[4]arenebased cluster of paracetamol was reported. The phenolic structures of acetaminophen and calix[4]arene prompted us for designing a synthetic route for calix[4]arene-based cyclic tetramer of paracetamol. The present chalice-shaped cluster is the first example of calixarene/acetaminophen hybrid and paracetamol can be considered as ¼ of the synthetic cyclic tetramer. Free-radical scavenging tests were determined by the 2,2-diphenyl-1-picrylhydrazyl radical in methanol. The results of antiradical-testing showed the enhanced free-radical scavenging capacity (~ 10-fold) for the prepared chaliced-shaped cluster with respect to the corresponding single therapeutic drug unit (acetaminophen). It is maybe attributed to the multivalency, spatial preorganization, and synergistic effect of four impacted drug units in the cluster structure (clustering effect). [ABSTRACT FROM AUTHOR]

The vegetation of mainland Southeast Asia is less known to science. This article introduces the studies up to now on the vegetation of mainland Southeast Asia (Indochina peninsula), and describes the main forest vegetation types based on fragmentary information and field visits. Seven main terraneous and wet land forest vegetation types, including coniferous forest, coniferous-broad-leaved mixed forest, tropical montane evergreen broad-leaved forest, tropical rain forest, tropical seasonal moist forest, tropical monsoon forest, and dry thorny thickets/woodland (savanna), are recognized. Of them, the coniferous forest includes two subtypes; temperate coniferous forest and tropical coniferous forest; the coniferous-broad-leaved mixed forest includes also two subtypes; warm temperate and temperate coniferous-broadleaved mixed forests; and the tropical rain forest includes four main vegetation subtypes: tropical lowland evergreen rain forest, tropical seasonal rain forest (tropical lowland semi-evergreen rain forest) , tropical montane rain forest, and peat swamp forest. The study history of the vegetation in the region, its classification, physiognomic characteristics, and dominant species composition, are also concisely introduced. [ABSTRACT FROM AUTHOR]

Graphical abstract Abstract The highly-symmetrical octathia[8]circulene molecule (8S) was synthesized and well studied 10 years ago in Moscow, including X-ray diffraction, IR and Raman spectra assignment on the ground of molecular DFT calculation. Nevertheless, this comprehensive study could not explain a big number of interesting deviations from the DFT predictions based on the molecular D 8h symmetry restriction being specific for a free species in a gas phase. In present work we have performed DFT optimization of the 8S tetramer starting with the X-ray diffraction analysis of a similar crystal structure. DFT calculation of IR and Raman spectra of such a huge system provides a good assignment of the crystal-field splitting and new band occurrence. The force-field distortions, electric charges and polarizability dependence on the tetramer structure are well reproduced by the B3LYP functional with the dispersion correction. Thus, the small shifts of IR and Raman bands, their splitting and intensity redistribution upon weak intermolecular interactions in crystal packing are explained and full assignment of all observed bands is presented. [ABSTRACT FROM AUTHOR]

Examines the coexistence of dipole-bound and valence electron states using photoelectron spectroscopy in pyridine tetramer anion. Difference of states in polarization dependence; Analysis on numerous cases of dipole-bound electrons in cluster system; Thermodynamic stability of the dipole-bound and valence electron.

Presents the quantum four-dimensional (4D) model calculations of coupled intermolecular torsional vibrations of cyclic homodromic water tetrameres. Context of a 4D discrete variable representation approach; Calculation of the lowest 50 torsional levels; Estimation of higher excited pseudorotational states.

Describes studies of the first rotational spectra of mixed noble gas trimers and tetrameres containing neon and argon atoms. Transitions of various isotopomers; Accurate values for rotational constants and centrifugal distortion constants; Determination and characterization of many-body nonadditive interactions; Signal strengths observed.

Ab initio calculations have been carried out to determine the dissociation pathways for the hydrogen fluoride trimer and tetramer that are accessible with single photon excitation of an HF stretching vibration. This requires evaluation of the stabilities of the small HF clusters. Electron correlation effects are found to contribute 1.0 kcal to the stability of the trimer, compared to 0.5 kcal for the dimer. The equilibrium stabilities with respect to dissociation into monomers are 4.6 kcal for the dimer, 14 kcal for the trimer, and 25 kcal for the tetramer. With zero-point vibrational effects, single photon vibrational excitation is sufficient for dissociation of the trimer into three monomers. The orientational structural parameters of the trimer and tetramer, like those of the dimer are found to be well explained by dipole and quadrupole moment interactions. [ABSTRACT FROM AUTHOR]

We use the following approximation to the potential between two 4He atoms—V(r)=4420 exp(-r2/1.69)-1302 exp(-r2/2.44) (V in K, r in Å). We use the hyperspherical harmonics expansion, with Fabre’s optimal subset, to solve for the ground state of the 4He tetramer. The Schrödinger equation is transformed into an infinite set of second order coupled differential equations (CDE), which we truncate to M equations. We test our program for solving CDE in two appendices. We find that the energy for our model is less than -4.3 K. [ABSTRACT FROM AUTHOR]

Ab initio calculations predict the existence of the dimer and tetramer of HXeCCH. The interaction energies are -6.66 and -19.40 kcal mol-1 for the dimer and tetramer, respectively. For both complexes, larger blue shifts of the Xe–H stretching mode are found, while the Xe–C stretching modes are slightly redshifted. The stability and structure of HXeCCH crystals is predicted by density functional theory calculations with periodic boundary conditions. Strong electrostatic interactions are found between the monomers in the crystal. The results are first evidence for the existence of crystalline materials made of a novel class of noble gas molecules. [ABSTRACT FROM AUTHOR]

Type 1 narcolepsy (T1N) is caused by hypocretin/orexin (HCRT) neuronal loss. Association with the HLA DQB1*06:02/DQA1*01:02 (98% vs. 25%) heterodimer (DQ0602), T cell receptors (TCR) and other immune loci suggest autoimmunity but autoantigens are unknown. Onset is seasonal and associated with influenza A, notably pandemic 2009 H1N1 (pH1N1) infection and vaccination (Pandemrix). Peptides derived from HCRT and influenza A, including pH1N1, were screened for DQ0602 binding and presence of cognate DQ0602 tetramer-peptide-specific CD4+ T cells tested in 35 T1N cases and 22 DQ0602 controls. Higher reactivity to influenza pHA273-287 (pH1N1 specific), PR8 (H1N1 pre-2009 and H2N2)-specific NP17-31 and C-amidated but not native version of HCRT54-66 and HCRT86-97 (HCRTNH2) were observed in T1N. Single-cell TCR sequencing revealed sharing of CDR3β TRBV4-2-CASSQETQGRNYGYTF in HCRTNH2 and pHA273-287-tetramers, suggesting molecular mimicry. This public CDR3β uses TRBV4-2, a segment modulated by T1N-associated SNP rs1008599, suggesting causality. TCR-α/β CDR3 motifs of HCRT54-66-NH2 and HCRT86-97-NH2 tetramers were extensively shared: notably public CDR3α, TRAV2-CAVETDSWGKLQF-TRAJ24, that uses TRAJ24, a chain modulated by T1N-associated SNPs rs1154155 and rs1483979. TCR-α/β CDR3 sequences found in pHA273-287, NP17-31, and HCRTNH2 tetramerpositive CD4+ cells were also retrieved in single INF-γ-secreting CD4+ sorted cells stimulatedwith Pandemrix, independently confirming these results. Our results provide evidence for autoimmunity and molecular mimicry with flu antigens modulated by genetic components in the pathophysiology of T1N. [ABSTRACT FROM AUTHOR]

The quaternary structures of the cholinesterases, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), are essential for their localization and function. Of practical importance, BChE is a promising therapeutic candidate for intoxication by organophosphate nerve agents and insecticides, and for detoxification of addictive substances. Efficacy of the recombinant enzyme hinges on its having a long circulatory half-life; this, in turn, depends strongly on its ability to tetramerize. Here, we used cryoelectron microscopy (cryo-EM) to determine the structure of the highly glycosylated native BChE tetramer purified from human plasma at 5.7 Å. Our structure reveals that the BChE tetramer is organized as a staggered dimer of dimers. Tetramerization is mediated by assembly of the C-terminal tryptophan amphiphilic tetramerization (WAT) helices from each subunit as a superhelical assembly around a central lamellipodin-derived oligopeptide with a proline-rich attachment domain (PRAD) sequence that adopts a polyproline II helical conformation and runs antiparallel. The catalytic domains within a dimer are asymmetrically linked to the WAT/PRAD. In the resulting arrangement, the tetramerization domain is largely shielded by the catalytic domains, which may contribute to the stability of the human BChE (HuBChE) tetramer. Our cryo-EM structure reveals the basis for assembly of the native tetramers and has implications for the therapeutic applications of HuBChE. This mode of tetramerization is seen only in the cholinesterases but may provide a promising template for designing other proteins with improved circulatory residence times. [ABSTRACT FROM AUTHOR]

Abstract Parkinson's disease (PD) is multifactorial, likely resulting from an intricate relationship of genetic and environmental factors affecting fundamental cellular processes. Histopathological hallmarks of PD include the development of granular inclusions known as Lewy bodies that are enriched with aggregates of the protein α-synuclein (αS). Historically, αS has been considered a natively unfolded protein prone to amyloidogenic behavior. However, recent studies have revealed a physiologically relevant folded αS tetramer that is both alpha-helical and aggregation-resistant. The two forms are thought to reside in a dynamic coexistence within cells, and it has been suggested that a shift from metastable tetramers to the monomeric form could serve as a mechanism for disease initiation. The underlying pathology causing this type of shift remains unknown, but the importance of understanding tetramer stability and disassembly has therapeutic potential that cannot be overemphasized. Isolation of tetrameric αS is complicated by its dynamic nature, so thorough and detailed biochemical and biophysical studies on this αS conformer have been hampered by accessibility issues. We now report a robust and reliable recombinant expression platform that enables purification of native tetrameric αS without any detergents or other structure-modifying additives. Graphical abstract Image 1 Highlights • Native isolation of recombinant noncovalent tetrameric α-synuclein. • Low pressure separation of tetrameric α-synuclein from disordered monomeric form. • Detergent-free recombinant platform for protein complex isolation and enrichment. • Helical α-synuclein tetramer is stable to flash freezing for long-term storage. • Access to tetrameric α-synuclein may lead to novel Parkinson's disease treatments. [ABSTRACT FROM AUTHOR]

Most excitatory neurotransmission in the mammalian brain is mediated by a family of plasma membrane-bound signaling proteins called ionotropic glutamate receptors (iGluRs). iGluRs assemble at central synapses as tetramers, forming a central ionchannel pore whose primary function is to rapidly transport Na+ and Ca2+ in response to binding the neurotransmitter L-glutamic acid. The pore of iGluRs is also accessible to bulkier cytoplasmic cations, such as the polyamines spermine, spermidine, and putrescine, which are drawn into the permeation pathway, but get stuck and block the movement of other ions. The degree of this polyamine-mediated channel block is highly regulated by processes that control the free cytoplasmic polyamine concentration, the membrane potential, or the iGluR subunit composition. Recently, an additional regulation by auxiliary proteins, most notably transmembrane AMPA (α-amino-3-hydroxy- 5-methyl-4-isoxazolepropionic acid) receptor regulatory proteins (TARPs), cornichons, and neuropilin and tolloid-like proteins (NETOs), has been identified. Here, I review what we have learned of polyamine block of iGluRs and its regulation by auxiliary subunits. TARPs, cornichons, and NETOs attenuate the channel block by enabling polyamines to exit the pore. As a result, polyamine permeation occurs at more negative and physiologically relevant membrane potentials. The structural basis for enhanced polyamine transport remains unresolved, although alterations in both channel architecture and chargescreening mechanisms have been proposed. That auxiliary subunits can attenuate the polyamine block reveals an unappreciated impact of polyamine permeation in shaping the signaling properties of neuronal AMPA- and kainate-type iGluRs. Moreover, enhanced polyamine transport through iGluRs may have a role in regulating cellular polyamine levels. [ABSTRACT FROM AUTHOR]

Atomic resolution characterization of the full-length p53 tetramer has been hampered by its size and the presence of extensive intrinsically disordered regions at both the N and C termini. As a consequence, the structural characteristics and dynamics of the disordered regions are poorly understood within the context of the intact p53 tetramer. Here we apply trans-intein splicing to generate segmentally 15N-labeled full-length p53 constructs in which only the resonances of the N-terminal transactivation domain (NTAD) are visible in NMR spectra, allowing us to observe this region of p53 with unprecedented detail within the tetramer. The N-terminal region is dynamically disordered in the full-length p53 tetramer, fluctuating between states in which it is free and fully exposed to solvent and states in which it makes transient contacts with the DNA-binding domain (DBD). Chemical-shift changes and paramagnetic spin-labeling experiments reveal that the amphipathic AD1 and AD2 motifs of the NTAD interact with the DNA-binding surface of the DBD through primarily electrostatic interactions. Importantly, this interaction inhibits binding of nonspecific DNA to the DBD while having no effect on binding to a specific p53 recognition element. We conclude that the NTAD: DBD interaction functions to enhance selectivity toward target genes by inhibiting binding to nonspecific sites in genomic DNA. This work provides some of the highest-resolution data on the disordered N terminus of the nearly 180-kDa full-length p53 tetramer and demonstrates a regulatory mechanism by which the N terminus of p53 transiently interacts with the DBD to enhance target site discrimination. [ABSTRACT FROM AUTHOR]

Azobenzene is a prototypical molecular switch that can be reversibly photoisomerized between the nearly planar and apolar trans form, and the distorted, polar cis form. Most studies related to azobenzene derivatives have focused on planar adsorbed molecules. We present herein the study of a three‐dimensional shape‐persistent molecular architecture consisting of four tetrahedrally arranged azobenzene units that is adsorbed on a Ag(111) surface. While the azobenzenes of the tripod in contact with the surface lost their switching ability, different isomers of the upright standing arm of the tetramer were obtained reversibly and efficiently by illumination at different wavelengths, revealing time constants of only a few minutes. Diffusion on the surface was dependent on the isomeric state—trans or cis—of the upright oriented azobenzene group. Hence, molecular mobility can be modulated by its isomeric state, which suggests that molecular growth processes could be controlled by external stimuli. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Geometry optimization of camptothecin lactone pi-aggregates up to tetramers. • Comparison of 5 DFT functionals in DMSO and aqueous solutions. • Comparison of TD-B3LYP electron transitions with experimental data. • Evaluation of BSSE corrected free reaction energies of aggregation reactions. • Only 2 DFT functionals with Grimme dispersion correction produce reliable results. Abstract The structures of camptothecin (CPT) lactone head-to-tail π-aggregates up to tetramers were optimized in DMSO and aqueous solutions using various DFT functionals with cc-pVDZ basis sets. Solvent effects were estimated using the Integral Equation Formalism Polarizable Continuum Model. The calculated reaction equilibria indicate that the higher π-aggregates formation is more preferred in DMSO than in aqueous solutions. TD-B3LYP calculated electron transitions ascribe two strong peaks over 300 nm in UV–Vis spectra to the CPT monomer (at lower wavelength) and to higher CPT head-to-tail π-aggregates (at higher wavelengths). Only B3LYP with D2 dispersion correction of Grimme and ωB97XD functionals are able to produce reliable results. [ABSTRACT FROM AUTHOR]

Controlled protein assembly provides a means to regulate function. Supramolecular building blocks, including rigid macrocycles, are versatile triggers of protein assembly. Now it is shown that sulfonato‐calix[8]arene (sclx8) mediates the formation of cytochrome c tetramers in solution. This tetramer spontaneously disassembles at ≥2 equivalents of sclx8, providing a remarkable example of auto‐regulation. Using X‐ray crystallography the sclx8 binding sites on cytochrome c were characterized. Crystal structures at different protein–ligand ratios reveal varying degrees (up to 35 %) of protein surface coverage by the flexible calixarene and suggest a mechanism for oligomer disassembly. The solution structure of the oligomer was characterized by small‐angle X‐ray scattering. Overall, the data indicate calixarene‐controlled protein assembly and disassembly without the requirement for a competitive inhibitor, and point to protein encapsulation by a flexible macrocycle. Calixarene‐controlled assembly and disassembly of a protein tetramer is demonstrated. The flexible sulfonato‐calix[8]arene acts as a scaffold for the assembly of cytochrome c. High concentrations of the calixarene mask the protein surface and prevent oligomerization, providing a means to control assembly without the need for competitive inhibitors. [ABSTRACT FROM AUTHOR]

Background Phosphodiesterases (PDEs) are a superfamily of evolutionary conserved cyclic nucleotides (cAMP/cGMP) hydrolysing enzymes, components of transduction pathways regulating crucial aspects of cell life. PDE5, one of these families, is the molecular target of several drugs used to treat erectile dysfunction and pulmonary hypertension. Despite its medical relevance, PDE5 macromolecular structure has only been solved for the isolated regulatory and catalytic domains. The definition of the quaternary structure of the full length PDE5 (MmPDE5A1), produced in large amounts in the yeast Kluyveromyces lactis , could greatly enhance the knowledge on its assembly/allosteric regulation and the development of new inhibitors for clinical-therapeutic applications. Methods Small-angle X-ray scattering (SAXS), analytical ultracentrifugation (AUC), size exclusion chromatography (SEC), native polyacrylamide gel electrophoresis (PAGE) and western blot (WB) were used to assess the assembly of PDE5A1. Results The full length MmPDE5A1 isoform is a mixture of dimers and tetramers in solution. We also report data showing that dimers and tetramers also coexist in vivo in platelets, blood components naturally containing high levels of PDE5. Conclusions This is the first time that structural studies on the full length protein evidenced the assembly of PDE5 in tetramers in addition to the expected dimers. General Significance The assembly of PDE5 in tetramers in platelets, beside the dimers, opens the possibility to alternative assembly/allosteric regulation of this enzyme, as component of large signaling complexes, in all cellular districts in which PDE5 is present. [ABSTRACT FROM AUTHOR]

Nicotinamide adenine dinucleotide (NAD) is the redox cofactor of many enzymes, including the vast aldehyde dehydrogenase (ALDH) superfamily. Although the function of NAD(H) in hydride transfer is established, its influence on protein structure is less understood. Herein, we show that NAD+‐binding promotes assembly of the ALDH7A1 tetramer. Multiangle light scattering, small‐angle X‐ray scattering, and sedimentation velocity all show a pronounced shift of the dimer–tetramer equilibrium toward the tetramer when NAD+ is present. Furthermore, electron microscopy shows that cofactor binding enhances tetramer formation even at the low enzyme concentration used in activity assays, suggesting the tetramer is the active species. Altogether, our results suggest that the catalytically active oligomer of ALDH7A1 is assembled on demand in response to cofactor availability. [ABSTRACT FROM AUTHOR]

Besides multiple life-threatening diseases like lung cancer and cardiovascular disease, cigarette smoking is known to produce hypoxia, a state of inadequate oxygen supply to tissues. Hypoxia plays a pivotal role in the development of chronic obstructive pulmonary disease. Smoking during pregnancy imposes risk for the unborn child. In addition to carbon monoxide, conjugation of para-benzoquinone (pBQ), derived from cigarette smoke, with human hemoglobin (HbA) was also reported to contribute in hypoxia. In fact, conjugation of pBQ is more alarming than carbon monoxide as it is an irreversible covalent modification. In the present study, the functional assay of Hb-pBQ, performed through oxygen equilibrium curve, showed a significant decrease in both P50 and cooperativity. However, the structural changes associated with the observed functional perturbation of the hemoglobin conjugate (Hb-pBQ) are unknown to date. Enhanced sensitivity and high resolution of nano-ESI mass spectrometry platform have enabled to investigate the native structure of oligomers of hemoglobin in a single scan. The structural integrity of Hb-pBQ measured through the dissociation equilibrium constants (Kd) indicated that compared to HbA, Kd of tetramer-dimer and dimer-monomer equilibria were increased by 4.98- and 64.3-folds, respectively. Using isotope exchange mass spectrometry, we observed perturbations in the inter-subunit interactions of deoxy and oxy states of Hb-pBQ. However, the three-dimensional architecture of Hb-pBQ, monitored through collision cross-sectional area, did not show any change. We propose that the significant destabilization of the functionally active structure of hemoglobin upon conjugation with pBQ results in tighter oxygen binding that leads to hypoxia.ᅟ [ABSTRACT FROM AUTHOR]