Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-ß signaling.

TGF-ß receptors phosphorylate SMAD2 and SMAD3 transcription factors, which then form heterotrimeric complexes with SMAD4 and cooperate with context-specific transcription factors to activate target genes. Here we provide biochemical and structural evidence showing that binding of SMAD2 to DNA depends on the conformation of the E3 insert, a structural element unique to SMAD2 and previously thought to render SMAD2 unable to bind DNA. Based on this finding, we further delineate TGF-ß signal transduction by defining distinct roles for SMAD2 and SMAD3 with the forkhead pioneer factor FOXH1 as a partner in the regulation of differentiation genes in mouse mesendoderm precursors. FOXH1 is prebound to target sites in these loci and recruits SMAD3 independently of TGF-ß signals, whereas SMAD2 remains predominantly cytoplasmic in the basal state and set to bind SMAD4 and join SMAD3:FOXH1 at target promoters in response to Nodal TGF-ß signals. The results support a model in which signal-independent binding of SMAD3 and FOXH1 prime mesendoderm differentiation gene promoters for activation, and signal-driven SMAD2:SMAD4 binds to promoters that are preloaded with SMAD3:FOXH1 to activate transcription.

The Doping Mechanism of Halide Perovskite Unveiled by Alkaline Earth Metals.

Halide perovskites are a strong candidate for the next generation of photovoltaics. Chemical doping of halide perovskites is an established strategy to prepare the highest efficiency and most stable perovskite-based solar cells. In this study, we unveil the doping mechanism of halide perovskites using a series of alkaline earth metals. We find that low doping levels enable the incorporation of the dopant within the perovskite lattice, whereas high doping concentrations induce surface segregation. The threshold from low to high doping regime correlates to the size of the doping element. We show that the low doping regime results in a more n-type material, while the high doping regime induces a less n-type doping character. Our work provides a comprehensive picture of the unique doping mechanism of halide perovskites, which differs from classical semiconductors. We proved the effectiveness of the low doping regime for the first time, demonstrating highly efficient methylammonium lead iodide based solar cells in both n-i-p and p-i-n architectures.

Fragment-Based Discovery of Non-bisphosphonate Binders of Trypanosoma brucei Farnesyl Pyrophosphate Synthase.

Trypanosoma brucei is the causative agent of human African trypanosomiasis (HAT). Nitrogen-containing bisphosphonates, a current treatment for bone diseases, have been shown to block the growth of the T. brucei parasites by inhibiting farnesyl pyrophosphate synthase (FPPS); however, due to their poor pharmacokinetic properties, they are not well suited for antiparasitic therapy. Recently, an allosteric binding pocket was discovered on human FPPS, but its existence on trypanosomal FPPS was unclear. We applied NMR and X-ray fragment screening to T. brucei FPPS and report herein on four fragments bound to this previously unknown allosteric site. Surprisingly, non-bisphosphonate active-site binders were also identified. Moreover, fragment screening revealed a number of additional binding sites. In an early structure-activity relationship (SAR) study, an analogue of an active-site binder was unexpectedly shown to bind to the allosteric site. Overlaying identified fragment binders of a parallel T. cruzi FPPS fragment screen with the T. brucei FPPS structure, and medicinal chemistry optimisation based on two binders revealed another example of fragment "pocket hopping". The discovery of binders with new chemotypes sets the framework for developing advanced compounds with pharmacokinetic properties suitable for the treatment of parasitic infections by inhibition of FPPS in T. brucei parasites.

Structure of p300 in complex with acyl-CoA variants.

Histone acetylation plays an important role in transcriptional activation. Histones are also modified by chemically diverse acylations that are frequently deposited by p300, a transcriptional coactivator that uses a number of different acyl-CoA cofactors. Here we report that while p300 is a robust acetylase, its activity gets weaker with increasing acyl-CoA chain length. Crystal structures of p300 in complex with propionyl-, crotonyl-, or butyryl-CoA show that the aliphatic portions of these cofactors are bound in the lysine substrate-binding tunnel in a conformation that is incompatible with substrate transfer. Lysine substrate binding is predicted to remodel the acyl-CoA ligands into a conformation compatible with acyl-chain transfer. This remodeling requires that the aliphatic portion of acyl-CoA be accommodated in a hydrophobic pocket in the enzymes active site. The size of the pocket and its aliphatic nature exclude long-chain and charged acyl-CoA variants, presumably explaining the cofactor preference for p300.

Calcium-dependent oligomerization of CAR proteins at cell membrane modulates ABA signaling.

Regulation of ion transport in plants is essential for cell function. Abiotic stress unbalances cell ion homeostasis, and plants tend to readjust it, regulating membrane transporters and channels. The plant hormone abscisic acid (ABA) and the second messenger Ca(2+) are central in such processes, as they are involved in the regulation of protein kinases and phosphatases that control ion transport activity in response to environmental stimuli. The identification and characterization of the molecular mechanisms underlying the effect of ABA and Ca(2+) signaling pathways on membrane function are central and could provide opportunities for crop improvement. The C2-domain ABA-related (CAR) family of small proteins is involved in the Ca(2+)-dependent recruitment of the pyrabactin resistance 1/PYR1-like (PYR/PYL) ABA receptors to the membrane. However, to fully understand CAR function, it is necessary to define a molecular mechanism that integrates Ca(2+) sensing, membrane interaction, and the recognition of the PYR/PYL interacting partners. We present structural and biochemical data showing that CARs are peripheral membrane proteins that functionally cluster on the membrane and generate strong positive membrane curvature in a Ca(2+)-dependent manner. These features represent a mechanism for the generation, stabilization, and/or specific recognition of membrane discontinuities. Such structures may act as signaling platforms involved in the recruitment of PYR/PYL receptors and other signaling components involved in cell responses to stress.

C2-domain abscisic acid-related proteins mediate the interaction of PYR/PYL/RCAR abscisic acid receptors with the plasma membrane and regulate abscisic acid sensitivity in Arabidopsis.

Membrane-delimited abscisic acid (ABA) signal transduction plays a critical role in early ABA signaling, but the molecular mechanisms linking core signaling components to the plasma membrane are unclear. We show that transient calcium-dependent interactions of PYR/PYL ABA receptors with membranes are mediated through a 10-member family of C2-domain ABA-related (CAR) proteins in Arabidopsis thaliana. Specifically, we found that PYL4 interacted in an ABA-independent manner with CAR1 in both the plasma membrane and nucleus of plant cells. CAR1 belongs to a plant-specific gene family encoding CAR1 to CAR10 proteins, and bimolecular fluorescence complementation and coimmunoprecipitation assays showed that PYL4-CAR1 as well as other PYR/PYL-CAR pairs interacted in plant cells. The crystal structure of CAR4 was solved, which revealed that, in addition to a classical calcium-dependent lipid binding C2 domain, a specific CAR signature is likely responsible for the interaction with PYR/PYL receptors and their recruitment to phospholipid vesicles. This interaction is relevant for PYR/PYL function and ABA signaling, since different car triple mutants affected in CAR1, CAR4, CAR5, and CAR9 genes showed reduced sensitivity to ABA in seedling establishment and root growth assays. In summary, we identified PYR/PYL-interacting partners that mediate a transient Ca(2+)-dependent interaction with phospholipid vesicles, which affects PYR/PYL subcellular localization and positively regulates ABA signaling.

The strawberry pathogenesis-related 10 (PR-10) Fra a proteins control flavonoid biosynthesis by binding to metabolic intermediates.

Pathogenesis-related 10 (PR-10) proteins are involved in many aspects of plant biology but their molecular function is still unclear. They are related by sequence and structural homology to mammalian lipid transport and plant abscisic acid receptor proteins and are predicted to have cavities for ligand binding. Recently, three new members of the PR-10 family, the Fra a proteins, have been identified in strawberry, where they are required for the activity of the flavonoid biosynthesis pathway, which is essential for the development of color and flavor in fruits. Here, we show that Fra a proteins bind natural flavonoids with different selectivity and affinities in the low µm range. The structural analysis of Fra a 1 E and a Fra a 3-catechin complex indicates that loops L3, L5, and L7 surrounding the ligand-binding cavity show significant flexibility in the apo forms but close over the ligand in the Fra a 3-catechin complex. Our findings provide mechanistic insight on the function of Fra a proteins and suggest that PR-10 proteins, which are widespread in plants, may play a role in the control of secondary metabolic pathways by binding to metabolic intermediates.

Atomic structure of a nanobody-trapped domain-swapped dimer of an amyloidogenic beta2-microglobulin variant.

Atomic-level structural investigation of the key conformational intermediates of amyloidogenesis remains a challenge. Here we demonstrate the utility of nanobodies to trap and characterize intermediates of ß2-microglobulin (ß2m) amyloidogenesis by X-ray crystallography. For this purpose, we selected five single domain antibodies that block the fibrillogenesis of a proteolytic amyloidogenic fragment of ß2m (ΔN6ß2m). The crystal structure of ΔN6ß2m in complex with one of these nanobodies (Nb24) identifies domain swapping as a plausible mechanism of self-association of this amyloidogenic protein. In the swapped dimer, two extended hinge loops--corresponding to the heptapetide NHVTLSQ that forms amyloid in isolation--are unmasked and fold into a new two-stranded antiparallel ß-sheet. The ß-strands of this sheet are prone to self-associate and stack perpendicular to the direction of the strands to build large intermolecular ß-sheets that run parallel to the axis of growing oligomers, providing an elongation mechanism by self-templated growth.

Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining.

Cernunnos/XLF is a core protein of the nonhomologous DNA end-joining (NHEJ) pathway that processes the majority of DNA double-strand breaks in mammals. Cernunnos stimulates the final ligation step catalyzed by the complex between DNA ligase IV and Xrcc4 (X4). Here we present the crystal structure of the X4(1-157)-Cernunnos(1-224) complex at 5.5-Å resolution and identify the relative positions of the two factors and their binding sites. The X-ray structure reveals a filament arrangement for X4(1-157) and Cernunnos(1-224) homodimers mediated by repeated interactions through their N-terminal head domains. A filament arrangement of the X4-Cernunnos complex was confirmed by transmission electron microscopy analyses both with truncated and full-length proteins. We further modeled the interface and used structure-based site-directed mutagenesis and calorimetry to characterize the roles of various residues at the X4-Cernunnos interface. We identified four X4 residues (Glu(55), Asp(58), Met(61), and Phe(106)) essential for the interaction with Cernunnos. These findings provide new insights into the molecular bases for stimulatory and bridging roles of Cernunnos in the final DNA ligation step.

Crystal structure of (E)-1-(2-nitro-benzyl-idene)-2,2-di-phenyl-hydrazine.

The title compound, C19H15N3O2, shows an E conformation of the imine bond. The dihedral angle between the planes of the phenyl rings in the di-phenyl-hydrazine groups is 88.52 (4)°. The 2-nitro-benzene ring shows a torsion angle of 10.17 (8)° with the C=N-N plane. A short intra-molecular C-H⋯O contact occurs. In the crystal, only van der Waals contacts occur between the mol-ecules.

Purification, crystallization and preliminary X-ray analysis of the strawberry allergens Fra a 1E and Fra a 3 in the presence of catechin.

The strawberry Fra a proteins belong to the pathogenesis-related PR-10 protein family and share a common fold with the Bet v 1 major pollen allergen and the START/PYR/PYL proteins, which are characterized by the presence of a central cavity and are often involved in the binding of a variety of natural compounds. The Fra a proteins play a key role in the control of flavonoid biosynthesis in strawberries and are essential for pigment formation in fruits. In order to understand Fra a protein function, full-length Fra a 1E and Fra a 3 cDNAs were cloned and expressed in Escherichia coli, and the proteins were purified to homogeneity using metal-affinity chromatography. Diffraction-quality crystals of Fra a 1E and of Fra a 3 in the presence of (+)-catechin were obtained by the sitting-drop vapour-diffusion method. X-ray diffraction data from single crystals of Fra a 1E and Fra a 3 were processed to 2.2 and 3.0 Šresolution in space groups P212121 and P2221, with unit-cell parameters a = 70.02, b = 74.42, c = 84.04 Šand a = 137.91, b = 206.61, c = 174.7 Šfor Fra a 1E and Fra a 3, respectively.

Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition.

Proton-dependent oligopeptide transporters (POTs) are promiscuous transporters of the major facilitator superfamily that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several POT homologs have been studied extensively at the structural and molecular level. However, the molecular basis of recognition and transport of diverse peptide substrates has remained elusive. We present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe whether all 8400 natural di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides with compact hydrophobic residues are the best DtpB binders.

Modulation of abscisic acid signaling in vivo by an engineered receptor-insensitive protein phosphatase type 2C allele.

The plant hormone abscisic acid (ABA) plays a crucial role in the control of the stress response and the regulation of plant growth and development. ABA binding to PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS intracellular receptors leads to inhibition of key negative regulators of ABA signaling, i.e. clade A protein phosphatases type 2C (PP2Cs) such as ABA-INSENSITIVE1 and HYPERSENSITIVE TO ABA1 (HAB1), causing the activation of the ABA signaling pathway. To gain further understanding on the mechanism of hormone perception, PP2C inhibition, and its implications for ABA signaling, we have performed a structural and functional analysis of the PYR1-ABA-HAB1 complex. Based on structural data, we generated a gain-of-function mutation in a critical residue of the phosphatase, hab1(W385A), which abolished ABA-dependent receptor-mediated PP2C inhibition without impairing basal PP2C activity. As a result, hab1(W385A) caused constitutive inactivation of the protein kinase OST1 even in the presence of ABA and PYR/PYL proteins, in contrast to the receptor-sensitive HAB1, and therefore hab1(W385A) qualifies as a hypermorphic mutation. Expression of hab1(W385A) in Arabidopsis (Arabidopsis thaliana) plants leads to a strong, dominant ABA insensitivity, which demonstrates that this conserved tryptophan residue can be targeted for the generation of dominant clade A PP2C alleles. Moreover, our data highlight the critical role of molecular interactions mediated by tryptophan-385 equivalent residues for clade A PP2C function in vivo and the mechanism of ABA perception and signaling.

Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARS-CoV-2.

Although vaccines are greatly mitigating the worldwide pandemic diffusion of SARS-Cov-2, therapeutics should provide many distinct advantages as complementary approach to control the viral spreading. Here, we report the development of new tripeptide derivatives of AT1001 against SARS-CoV-2 Mpro. By molecular modeling, a small compound library was rationally designed and filtered for enzymatic inhibition through FRET assay, leading to the identification of compound 4. X-ray crystallography studies provide insights into its binding mode and confirm the formation of a covalent bond with Mpro C145. In vitro antiviral tests indicate the improvement of biological activity of 4 respect to AT1001. In silico and X-ray crystallography analysis led to 58, showing a promising activity against three SARS-CoV-2 variants and a valuable safety in Vero cells and human embryonic lung fibroblasts. The drug tolerance was also confirmed by in vivo studies, along with pharmacokinetics evaluation. In summary, 58 could pave the way to develop a clinical candidate for intranasal administration.

Slot-Die Coated Triple-Halide Perovskites for Efficient and Scalable Perovskite/Silicon Tandem Solar Cells.

Wide bandgap halide perovskite materials show promising potential to pair with silicon bottom cells. To date, most efficient wide bandgap perovskites layers are fabricated by spin-coating, which is difficult to scale up. Here, we report on slot-die coating for an efficient, 1.68 eV wide bandgap triple-halide (3halide) perovskite absorber, (Cs0.22FA0.78)Pb(I0.85Br0.15)3 + 5 mol % MAPbCl3. A suitable solvent system is designed specifically for the slot-die coating technique. We demonstrate that our fabrication route is suitable for tandem solar cells without phase segregation. The slot-die coated wet halide perovskite is dried by a "nitrogen (N2)-knife" with high reproducibility and avoiding antisolvents. We explore varying annealing conditions and identify parameters allowing crystallization of the perovskite film into large grains reducing charge collection losses and enabling higher current density. At 150 °C, an optimized trade-off between crystallization and the PbI2 aggregates on the film's top surface is found. Thus, we improve the cell stability and performance of both single-junction cells and tandems. Combining the 3halide top cells with a 120 µm thin saw damage etched commercial Czochralski industrial wafer, a 2-terminal monolithic tandem solar cell with a PCE of 25.2% on a 1 cm2 active area is demonstrated with fully scalable processes.

A thermal stability assay can help to estimate the crystallization likelihood of biological samples.

The identification of crystallization conditions for biological molecules largely relies on a trial-and-error process in which a number of parameters are explored in large screening experiments. Currently, construct design and sample formulation are recognized as critical variables in this process and often a number of protein variants are assayed for crystallization either sequentially or in parallel, which adds complexity to the screening process. Significant effort is dedicated to sample characterization and quality-control experiments in order to identify at an early stage and prioritize those samples which would be more likely to crystallize. However, large-scale studies relating crystallization success to sample properties are generally lacking. In this study, the thermal stability of 657 samples was estimated using a simplified Thermofluor assay. These samples were also subjected to automated vapour-diffusion crystallization screening under a constant protocol. Analysis of the data shows that samples with an apparent melting temperature (T(m)) of 318 K or higher crystallized in 49% of cases, while the crystallization success rate decreased rapidly for samples with lower T(m). Only 23% of samples with a T(m) below 316 K produced crystals. Based on this analysis, a simple method for estimation of the crystallization likelihood of biological samples is proposed. This method is easy, rapid and consumes very small amounts of sample. The results of this assay can be used to determine optimal incubation temperatures for crystallization experiments or to prioritize certain constructs. More generally, this work provides an objective test that can contribute to making decisions in both focused and structural genomics crystallography projects.

Probing the Origin of the Open Circuit Voltage in Perovskite Quantum Dot Photovoltaics.

Perovskite quantum dots (PQDs) have many properties that make them attractive for optoelectronic applications, including expanded compositional tunability and crystallographic stabilization. While they have not achieved the same photovoltaic (PV) efficiencies of top-performing perovskite thin films, they do reproducibly show high open circuit voltage (VOC) in comparison. Further understanding of the VOC attainable in PQDs as a function of surface passivation, contact layers, and PQD composition will further progress the field and may lend useful lessons for non-QD perovskite solar cells. Here, we use photoluminescence-based spectroscopic techniques to understand and identify the governing physics of the VOC in CsPbI3 PQDs. In particular, we probe the effect of the ligand exchange and contact interfaces on the VOC and free charge carrier concentration. The free charge carrier concentration is orders of magnitude higher than in typical perovskite thin films and could be tunable through ligand chemistry. Tuning the PQD A-site cation composition via replacement of Cs+ with FA+ maintains the background carrier concentration but reduces the trap density by up to a factor of 40, reducing the VOC deficit. These results dictate how to improve PQD optoelectronic properties and PV device performance and explain the reduced interfacial recombination observed by coupling PQDs with thin-film perovskites for a hybrid absorber layer.

Influence of the Rear Interface on Composition and Photoluminescence Yield of CZTSSe Absorbers: A Case for an Al2O3 Intermediate Layer.

The rear interface of kesterite absorbers with Mo back contact represents one of the possible sources of nonradiative voltage losses (ΔVoc,nrad) because of the reported decomposition reactions, an uncontrolled growth of MoSe2, or a nonoptimal electrical contact with high recombination. Several intermediate layers (IL), such as MoO3, TiN, and ZnO, have been tested to mitigate these issues, and efficiency improvements have been reported. However, the introduction of IL also triggers other effects such as changes in alkali diffusion, altered morphology, and modifications in the absorber composition, all factors that can also influence ΔVoc,nrad. In this study, the different effects are decoupled by designing a special sample that directly compares four rear structures (SLG, SLG/Mo, SLG/Al2O3, and SLG/Mo/Al2O3) with a Na-doped kesterite absorber optimized for a device efficiency >10%. The IL of choice is Al2O3 because of its reported beneficial effect to reduce the surface recombination velocity at the rear interface of solar cell absorbers. Identical annealing conditions and alkali distribution in the kesterite absorber are preserved, as measured by time-of-flight secondary ion mass spectrometry and energy-dispersive X-ray spectroscopy. The lowest ΔVoc,nrad of 290 mV is measured for kesterite grown on Mo, whereas the kesterite absorber on Al2O3 exhibits higher nonradiative losses up to 350 mV. The anticipated field-effect passivation from Al2O3 at the rear interface could not be observed for the kesterite absorbers prepared by the two-step process, further confirmed by an additional experiment with air annealing. Our results suggest that Mo with an in situ formed MoSe2 remains a suitable back contact for high-efficiency kesterite devices.