The structure of a tetrameric septin complex reveals a hydrophobic element essential for NC-interface integrity

The septins of the yeast Saccharomyces cerevisiae assemble into hetero-octameric rods by alternating interactions between neighboring G-domains or N- and C-termini, respectively. These rods polymerize end to end into apolar filaments, forming a ring beneath the prospective new bud that expands during the cell cycle into an hourglass structure. The hourglass finally splits during cytokinesis into a double ring. Understanding these transitions as well as the plasticity of the higher order assemblies requires a detailed knowledge of the underlying structures. Here we present the first X-ray crystal structure of a tetrameric Shs1-Cdc12-Cdc3-Cdc10 complex at a resolution of 3.2 Å. Close inspection of the NC-interfaces of this and other septin structures reveals a conserved contact motif that is essential for NC-interface integrity of yeast and human septins in vivo and in vitro. Using the tetrameric structure in combination with AlphaFold-Multimer allowed us to propose a model of the octameric septin rod.

Structural Basis for Inhibition of ROS-Producing Respiratory Complex I by NADH-OH

NADH:ubiquinone oxidoreductase, respiratory complex I, plays a central role in cellular energy metabolism. As a major source of reactive oxygen species (ROS) it affects ageing and mitochondrial dysfunction. The novel inhibitor NADH-OH specifically blocks NADH oxidation and ROS production by complex I in nanomolar concentrations. Attempts to elucidate its structure by NMR spectroscopy have failed. Here, by using X-ray crystallographic analysis, we report the structure of NADH-OH bound in the active site of a soluble fragment of complex I at 2.0 Å resolution. We have identified key amino acid residues that are specific and essential for binding NADH-OH. Furthermore, the structure sheds light on the specificity of NADH-OH towards the unique Rossmann-fold of complex I and indicates a regulatory role in mitochondrial ROS generation. In addition, NADH-OH acts as a lead-structure for the synthesis of a novel class of ROS suppressors.

Structural basis of O-methylation of (2-heptyl-)1-hydroxyquinolin-4(1H)-one and related compounds by the heterocyclic toxin methyltransferase Rv0560c of Mycobacterium tuberculosis

The S-adenosyl-L-methionine-dependent methyltransferase Rv0560c of Mycobacterium tuberculosis belongs to an orthologous group of heterocyclic toxin methyltransferases (Htm) which likely contribute to resistance of mycobacteria towards antimicrobial natural compounds as well as drugs. Htm_M.t. catalyzes the methylation of the Pseudomonas aeruginosa toxin 2-heptyl-1-hydroxyquinolin-4(1H)-one (also known as 2-heptyl-4-hydroxyquinoline N-oxide), a potent inhibitor of respiratory electron transfer, its 1-hydroxyquinolin-4(1H)-one core (QNO), structurally related (iso)quinolones, and some mycobactericidal compounds. In this study, crystal structures of Htm_M.t. in complex with S-adenosyl-L-homocysteine (SAH) and the methyl-accepting substrates QNO or 4-hydroxyisoquinoline-1(2H)-one, or the methylated product 1-methoxyquinolin-4(1H)-one, were determined at < 1.9 Å resolution. The monomeric protein exhibits the typical Rossmann fold topology and conserved residues of class I methyltransferases. Its SAH binding pocket is connected via a short tunnel to a large solvent-accessible cavity, which accommodates the methyl-accepting substrate. Residues W44, F168, and F208 in connection with F212 form a hydrophobic clamp around the heteroaromatic ring of the methyl-accepting substrate and likely play a major role in substrate positioning. Structural and biochemical data suggest that H139 and T136 are key active site residues, with H139 acting as general base that activates the methyl-accepting hydroxy group. Our structural data may contribute to the design of Htm inhibitors or of antimycobacterial drugs unamenable for methylation.

A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I

Respiratory complex I plays a central role in cellular energy metabolism coupling NADH oxidation to proton translocation. In humans its dysfunction is associated with degenerative diseases. Here we report the structure of the electron input part of Aquifex aeolicus complex I at up to 1.8 Å resolution with bound substrates in the reduced and oxidized states. The redox states differ by the flip of a peptide bond close to the NADH binding site. The orientation of this peptide bond is determined by the reduction state of the nearby [Fe-S] cluster N1a. Fixation of the peptide bond by site-directed mutagenesis led to an inactivation of electron transfer and a decreased reactive oxygen species (ROS) production. We suggest the redox-gated peptide flip to represent a previously unrecognized molecular switch synchronizing NADH oxidation in response to the redox state of the complex as part of an intramolecular feed-back mechanism to prevent ROS production.

Respiratory complex I plays a central role in cellular energy metabolism coupling NADH oxidation to proton translocation. Here, the authors report the structure of the electron input part of Aquifex aeolicus complex I at up to 1.8 Å resolution with bound substrates in the reduced and oxidized states.

Beyond the BET Family: Targeting CBP/p300 with 4-Acyl Pyrroles

Bromodomain and extra-terminal domain (BET) inhibitors are widely used both as chemical tools to study the biological role of their targets in living organisms and as candidates for drug development against several cancer variants and human disorders. However, non-BET bromodomains such as those in p300 and CBP are less studied. XDM-CBP is a highly potent and selective inhibitor for the bromodomains of CBP and p300 derived from a pan-selective BET BRD-binding fragment. Along with X-ray crystal-structure analysis and thermodynamic profiling, XDM-CBP was used in screenings of several cancer cell lines in vitro to study its inhibitory potential on cancer cell proliferation. XDM-CBP is demonstrated to be a potent and selective CBP/p300 inhibitor that acts on specific cancer cell lines, in particular malignant melanoma, breast cancer, and leukemia.

Deterministic implementation of a bright, on-demand single photon source with near-unity indistinguishability via quantum dot imaging

Deterministic techniques enabling the implementation and engineering of bright and coherent solid-state quantum light sources are key for the reliable realization of a next generation of quantum devices. Such a technology, at best, should allow one to significantly scale up the number of implemented devices within a given processing time. In this work, we discuss a possible technology platform for such a scaling procedure, relying on the application of nanoscale quantum dot imaging to the pillar microcavity architecture, which promises to combine very high photon extraction efficiency and indistinguishability. We discuss the alignment technology in detail, and present the optical characterization of a selected device which features a strongly Purcell-enhanced emission output. This device, which yields an extraction efficiency of η = (49 ± 4) %, facilitates the emission of photons with (94 ± 2.7) % indistinguishability.

Biocatalytic Properties and Structural Analysis of Phloroglucinol Reductases

Phloroglucinol reductases (PGRs) are involved in anaerobic degradation in bacteria, in which they catalyze the dearomatization of phloroglucinol into dihydrophloroglucinol. We identified three PGRs, from different bacterial species, that are members of the family of NAD(P)H-dependent short-chain dehydrogenases/reductases (SDRs). In addition to catalyzing the reduction of the physiological substrate, the three enzymes exhibit activity towards 2,4,6-trihydroxybenzaldehyde, 2,4,6-trihydroxyacetophenone, and methyl 2,4,6-trihydroxybenzoate. Structural elucidation of PGRcl and comparison to known SDRs revealed a high degree of conservation. Several amino acid positions were identified as being conserved within the PGR subfamily and might be involved in substrate differentiation. The results enable the enzymatic dearomatization of monoaromatic phenol derivatives and provide insight into the functional diversity that may be found in families of enzymes displaying a high degree of structural homology.

Preparation data of the bromodomains BRD3(1), BRD3(2), BRD4(1), and BRPF1B and crystallization of BRD4(1)-inhibitor complexes

This article presents detailed purification procedures for the bromodomains BRD3(1), BRD3(2), BRD4(1), and BRPF1B. In addition we provide crystallization protocols for apo BRD4(1) and BRD4(1) in complex with numerous inhibitors. The protocols described here were successfully applied to obtain affinity data by isothermal titration calorimetry (ITC) and by differential scanning fluorimetry (DSF) as well as structural characterizations of BRD4(1) inhibitor complexes (PDB codes: PDB: 4LYI, PDB: 4LZS, PDB: 4LYW, PDB: 4LZR, PDB: 4LYS, PDB: 5D24, PDB: 5D25, PDB: 5D26, PDB: 5D3H, PDB: 5D3J, PDB: 5D3L, PDB: 5D3N, PDB: 5D3P, PDB: 5D3R, PDB: 5D3S, PDB: 5D3T). These data have been reported previously and are discussed in more detail elsewhere [1], [2].

Highly indistinguishable on-demand resonance fluorescence photons from a deterministic quantum dot micropillar device with 74% extraction efficiency

The implementation and engineering of bright and coherent solid state quantum light sources is key for the realization of both on chip and remote quantum networks. Despite tremendous efforts for more than 15 years, the combination of these two key prerequisites in a single, potentially scalable device is a major challenge. Here, we report on the observation of bright single photon emission generated via pulsed, resonance fluorescence conditions from a single quantum dot (QD) deterministically centered in a micropillar cavity device via cryogenic optical lithography. The brightness of the QD fluorescence is greatly enhanced on resonance with the fundamental mode of the pillar, leading to an overall device efficiency of η = (74 ± 4) % for a single photon emission as pure as g⁽²⁾(0) = 0.0092 ± 0.0004. The combination of large Purcell enhancement and resonant pumping conditions allows us to observe a two-photon wave packet overlap up to ν = (88 ± 3) %.

4-Acyl Pyrrole Derivatives Yield Novel Vectors for Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1)

Several human diseases, including cancer, show altered signaling pathways resulting from changes in the activity levels of epigenetic modulators. In the past few years, small-molecule inhibitors against specific modulators, including the bromodomain and extra-terminal (BET) bromodomain family of acetylation readers, have shown early promise in the treatment of the genetically defined midline carcinoma and hematopoietic malignancies. We have recently developed a novel potent inhibitor of BET proteins, 1 (XD14[ Angew. Chem., Int. Ed. 2013, 52, 14055]), which exerts a strong inhibitory potential on the proliferation of specific leukemia cell lines. In the study presented here, we designed analogues of 1 to study the potential of substitutions on the 4-acyl pyrrole backbone to occupy additional sites within the substrate recognition site of BRD4(1). The compounds were profiled using ITC, DSF, and X-ray crystallography. We could introduce several substitutions that address previously untargeted areas of the substrate recognition site. This work may substantially contribute to the development of therapeutics with increased target specificity against BRD4-related malignancies.

Assembly of methylated KDM1A and CHD1 drives androgen receptor-dependent transcription and translocation

Prostate cancer evolution is driven by a combination of epigenetic and genetic alterations such as coordinated chromosomal rearrangements, termed chromoplexy. TMPRSS2-ERG gene fusions found in human prostate tumors are a hallmark of chromoplexy. TMPRSS2-ERG fusions have been linked to androgen signaling and depend on androgen receptor (AR)-coupled gene transcription. Here, we show that dimethylation of KDM1A at K114 (to form K114me2) by the histone methyltransferase EHMT2 is a key event controlling androgen-dependent gene transcription and TMPRSS2-ERG fusion. We identified CHD1 as a KDM1A K114me2 reader and characterized the KDM1A K114me2-CHD1 recognition mode by solving the cocrystal structure. Genome-wide analyses revealed chromatin colocalization of KDM1A K114me2, CHD1 and AR in prostate tumor cells. Together, our data link the assembly of methylated KDM1A and CHD1 with AR-dependent transcription and genomic translocations, thereby providing mechanistic insight into the formation of TMPRSS2-ERG gene fusions during prostate-tumor evolution.

Crystal structure of Cdc11, a septin subunit from Saccharomyces cerevisiae

Septins are a conserved family of GTP-binding proteins that assemble into a highly ordered array of filaments at the mother bud neck in Saccharomyces cerevisiae cells. Many molecular functions and mechanisms of the septins in S. cerevisiae were already uncovered. However, structural information is only available from modeling the crystallized subunits of the human septins into the EM cryomicroscopy data of the yeast hetero-octameric septin rod. Octameric rods are the building block of septin filaments in yeast. We present here the first crystal structure of Cdc11, the terminal subunit of the octameric rod and discuss its structure in relation to its human homologues. Size exclusion chromatography analysis revealed that Cdc11 forms homodimers through its C-terminal coiled coil tail.

Deterministic generation of bright single resonance fluorescence photons from a Purcell-enhanced quantum dot-micropillar system

We report on the observation of bright emission of single photons under pulsed resonance fluorescence conditions from a single quantum dot (QD) in a micropillar cavity. The brightness of the QD fluorescence is greatly enhanced via the coupling to the fundamental mode of a micropillar, allowing us to determine a single photon extraction efficiency of (20.7 ± 0.8) % per linear polarization basis. This yields an overall extraction efficiency of (41.4 ± 1.5) % in our device. We observe the first Rabi-oscillation in a weakly coupled quantum dot-micropillar system under coherent pulsed optical excitation, which enables us to deterministically populate the excited QD state. In this configuration, we probe the single photon statistics of the device yielding g(2)(0) = 0.072 ± 0.011 at a QD-cavity detuning of 75 μeV.

A Conformational Switch Triggers Nitrogenase Protection from Oxygen Damage by Shethna Protein II (FeSII)

The two-component metalloprotein nitrogenase catalyzes the reductive fixation of atmospheric dinitrogen into bioavailable ammonium in diazotrophic prokaryotes. The process requires an efficient energy metabolism, so that although the metal clusters of nitrogenase rapidly decompose in the presence of dioxygen, many free-living diazotrophs are obligate aerobes. In order to retain the functionality of the nitrogen-fixing enzyme, some of these are able to rapidly "switch-off" nitrogenase, by shifting the enzyme into an inactive but oxygen-tolerant state. Under these conditions the two components of nitrogenase form a stable, ternary complex with a small [2Fe:2S] ferredoxin termed FeSII or the "Shethna protein II". Here we have produced and isolated Azotobacter vinelandii FeS II and have determined its three-dimensional structure to 2.1 Å resolution by X-ray diffraction. In the crystals, the dimeric protein was present in two distinct states that differ in the conformation of an extended loop in close proximity to the iron-sulfur cluster. We show that this rearrangement is redox-dependent and forms the molecular basis for oxygen-dependent conformational protection of nitrogenase. Protection assays highlight that FeSII binds to a preformed complex of MoFe and Fe protein upon activation, primarily through electrostatic interactions. The surface properties and known complexes of nitrogenase component proteins allow us to propose a model of the conformationally protected ternary complex of nitrogenase.

Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking

Sirtuins constitute a family of NAD(+)-dependent enzymes that catalyse the cleavage of various acyl groups from the ℇ-amino group of lysines. They regulate a series of cellular processes and their misregulation has been implicated in various diseases, making sirtuins attractive drug targets. To date, only a few sirtuin modulators have been reported that are suitable for cellular research and their development has been hampered by a lack of structural information. In this work, microseed matrix seeding (MMS) was used to obtain crystals of human Sirt3 in its apo form and of human Sirt2 in complex with ADP ribose (ADPR). Crystal formation using MMS was predictable, less error-prone and yielded a higher number of crystals per drop than using conventional crystallization screening methods. The crystals were used to solve the crystal structures of apo Sirt3 and of Sirt2 in complex with ADPR at an improved resolution, as well as the crystal structures of Sirt2 in complex with ADPR and the indoles EX527 and CHIC35. These Sirt2-ADPR-indole complexes unexpectedly contain two indole molecules and provide novel insights into selective Sirt2 inhibition. The MMS approach for Sirt2 and Sirt3 may be used as the basis for structure-based optimization of Sirt2/3 inhibitors in the future.

The goal of making friends for youth with disabilities: creating a goal menu

BACKGROUND

Clinicians working with youth with disabilities have acknowledged making friends as a commonly identified client goal. Clinicians find this goal difficult to address, as there are no measures that provide a breakdown of making friends into functional steps. In addition, research on friendship has traditionally focused on characteristics and quality of friendships rather than the friend-making process as a whole. A goal menu, comprised of a variety of steps that address the goal of making friends, would provide guidance to clinicians challenged with this goal in practice.

PURPOSE

To develop an understanding of the friend-making process as a first step towards the development of a goal menu for the goal of making friends.

METHODS

A literature review, youth focus group and expert clinician semi-structured interviews and consultation were used to generate a comprehensive data set. Established qualitative methods were used to sort and group the data into categories. A thematic analysis of the categories was performed.

RESULTS

Analysis revealed four themes integral to the friend-making process: person factors influencing friend-making, making friend-making a priority, opportunity for friend-making and motivation to make friends. An additional theme identified as occasionally involved in the process was a little bit of luck in making friends.

CONCLUSIONS

The themes generated by this research indicate that actionable target areas exist for the somewhat abstract notion of friend-making and the authors recommend that clinicians explore beyond person factors when addressing the goal of making friends. As a next step, the identified themes will provide the foundation for a goal menu, ultimately enabling clinicians to address the goal of making friends in a more efficient and effective manner.

Structural characterization of O- and C-glycosylating variants of the landomycin glycosyltransferase LanGT2

The structures of the O-glycosyltransferase LanGT2 and the engineered, C-C bond-forming variant LanGT2S8Ac show how the replacement of a single loop can change the functionality of the enzyme. Crystal structures of the enzymes in complex with a nonhydrolyzable nucleotide-sugar analogue revealed that there is a conformational transition to create the binding sites for the aglycon substrate. This induced-fit transition was explored by molecular docking experiments with various aglycon substrates.

Improving coiled coil stability while maintaining specificity by a bacterial hitchhiker selection system

The design and selection of peptides targeting cellular proteins is challenging and often yields candidates with undesired properties. Therefore we deployed a new selection system based on the twin-arginine translocase (TAT) pathway of Escherichia coli, named hitchhiker translocation (HiT) selection. A pool of α-helix encoding sequences was designed and selected for interference with the coiled coil domain (CC) of a melanoma-associated basic-helix-loop-helix-leucine-zipper (bHLHLZ) protein, the microphthalmia associated transcription factor (MITF). One predominant sequence (iM10) was enriched during selection and showed remarkable protease resistance, high solubility and thermal stability while maintaining its specificity. Furthermore, it exhibited nanomolar range affinity towards the target peptide. A mutation screen indicated that target-binding helices of increased homodimer stability and improved expression rates were preferred in the selection process. The crystal structure of the iM10/MITF-CC heterodimer (2.1Å) provided important structural insights and validated our design predictions. Importantly, iM10 did not only bind to the MITF coiled coil, but also to the markedly more stable HLHLZ domain of MITF. Characterizing the selected variants of the semi-rational library demonstrated the potential of the innovative bacterial selection approach.

High-harmonic fast-wave power flow along magnetic field lines in the scrape-off layer of NSTX

A significant fraction of high-harmonic fast-wave (HHFW) power applied to NSTX can be lost to the scrape-off layer (SOL) and deposited in bright and hot spirals on the divertor rather than in the core plasma. We show that the HHFW power flows to these spirals along magnetic field lines passing through the SOL in front of the antenna, implying that the HHFW power couples across the entire width of the SOL rather than mostly at the antenna face. This result will help guide future efforts to understand and minimize these edge losses in order to maximize fast-wave heating and current drive.

Discovery of a potent, selective, and orally bioavailable acidic 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) inhibitor: discovery of 2-[(3S)-1-[5-(cyclohexylcarbamoyl)-6-propylsulfanylpyridin-2-yl]-3-piperidyl]acetic acid (AZD4017)

Inhibition of 11β-HSD1 is an attractive mechanism for the treatment of obesity and other elements of the metabolic syndrome. We report here the discovery of a nicotinic amide derived carboxylic acid class of inhibitors that has good potency, selectivity, and pharmacokinetic characteristics. Compound 11i (AZD4017) is an effective inhibitor of 11β-HSD1 in human adipocytes and exhibits good druglike properties and as a consequence was selected for clinical development.

MacA is a second cytochrome c peroxidase of Geobacter sulfurreducens

The metal-reducing δ-proteobacterium Geobacter sulfurreducens produces a large number of c-type cytochromes, many of which have been implicated in the transfer of electrons to insoluble metal oxides. Among these, the dihemic MacA was assigned a central role. Here we have produced G. sulfurreducens MacA by recombinant expression in Escherichia coli and have solved its three-dimensional structure in three different oxidation states. Sequence comparisons group MacA into the family of diheme cytochrome c peroxidases, and the protein indeed showed hydrogen peroxide reductase activity with ABTS(-2) as an electron donor. The observed K(M) was 38.5 ± 3.7 μM H(2)O(2) and v(max) was 0.78 ± 0.03 μmol of H(2)O(2)·min(-1)·mg(-1), resulting in a turnover number k(cat) = 0.46 · s(-1). In contrast, no Fe(III) reductase activity was observed. MacA was found to display electrochemical properties similar to other bacterial diheme peroxidases, in addition to the ability to electrochemically mediate electron transfer to the soluble cytochrome PpcA. Differences in activity between CcpA and MacA can be rationalized with structural variations in one of the three loop regions, loop 2, that undergoes conformational changes during reductive activation of the enzyme. This loop is adjacent to the active site heme and forms an open loop structure rather than a more rigid helix as in CcpA. For the activation of the protein, the loop has to displace the distal ligand to the active site heme, H93, in loop 1. A H93G variant showed an unexpected formation of a helix in loop 2 and disorder in loop 1, while a M297H variant that altered the properties of the electron transfer heme abolished reductive activation.

Selective non zinc binding inhibitors of MMP13

Directed screening has identified a novel series of MMP13 inhibitors that possess good levels of activity whilst possessing excellent selectivity over related MMPs. The binding mode of the series has been solved by co-crystallisation and demonstrates an interesting mode of inhibition without interaction with the catalytic zinc atom.

Structure of GlnK1, a signalling protein from Archaeoglobus fulgidus

GlnB and GlnK are ancient signalling proteins that play a crucial role in the regulation of nitrogen assimilation. Both protein types can be present in the same genome as either single or multiple copies. However, the gene product of glnK is always found in an operon together with an amt gene encoding an ammonium-transport (Amt) protein. Complex formation between GlnK and Amt blocks ammonium uptake and depends on the nitrogen level in the cell, which is regulated through the binding of specific effector molecules to GlnK. In particular, an ammonium shock to a cell culture previously starved in this nitrogen source or the binding of ATP to purified GlnK can stimulate effective complex formation. While the binding of ATP/ADP and 2-oxoglutarate (as a signal for low intracellular nitrogen) to GlnK have been reported and several GlnB/K protein structures are available, essential functional questions remain unanswered. Here, the crystal structure of A. fulgidus GlnK1 at 2.28 Å resolution and a comparison with the crystal structures of other GlnK proteins, in particular with that of its paralogue GlnK2 from the same organism, is reported.

Demonstration of Tokamak ohmic flux saving by transient coaxial helicity injection in the national spherical torus experiment

Transient coaxial helicity injection (CHI) started discharges in the National Spherical Torus Experiment (NSTX) have attained peak currents up to 300 kA and when coupled to induction, it has produced up to 200 kA additional current over inductive-only operation. CHI in NSTX has shown to be energetically quite efficient, producing a plasma current of about 10 A/J of capacitor bank energy. In addition, for the first time, the CHI-produced toroidal current that couples to induction continues to increase with the energy supplied by the CHI power supply at otherwise similar values of the injector flux, indicating the potential for substantial current generation capability by CHI in NSTX and in future toroidal devices.

Structural basis of the action of glucosyltransferase Lgt1 from Legionella pneumophila

The glucosyltransferase Lgt1 is one of three glucosylating toxins of Legionella pneumophila, the causative agent of Legionnaires disease. It acts through specific glucosylation of a serine residue (S53) in the eukaryotic elongation factor 1A and belongs to type A glycosyltransferases. High-resolution crystal structures of Lgt1 show an elongated shape of the protein, with the binding site for uridine disphosphate glucose at the bottom of a deep cleft. Lgt1 shows only a low sequence identity with other type A glycosyltransferases, and structural conservation is limited to a central folding core that is usually observed within this family of proteins. Domains and protrusions added to the core motif represent determinants for the specific recognition and binding of the target. Manual docking experiments based on the crystal structures of toxin and target protein suggest an obvious mode of binding to the target that allows for efficient transfer of a glucose moiety.