Biochemie und Chemie
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The title co-crystal, 1,3,5,7-tetraazatricyclo[3.3.1.13,7]decane (HMTA, 1)–4-fluorophenol (4-FP) (1/1), C6H12N4·C6H5FO, shows an unusual asymmetric unit that comprises eight independent molecules (Z′′ = 8), four for each component, with four formula units per asymmetric unit (Z′ = 4). In the molecular packing, each HMTA molecule bridges one 4-FP molecule via an O−H···N hydrogen bond to form a two-molecule aggregate. Differences can be observed between the bond lengths and angles of the independent HMTA and 4-FP molecules and those of the molecules in the aggregate. The C−N bonds exhibit different bond lengths in the tetrahedral cage-like structure of the HMTA molecules, but the largest differences between the molecular aggregates are in the bond lengths in the 4-fluorophenol ring. In the crystal, the HMTA and 4-FP molecules form two hydrogen-bonded (O−H···N, C−H···F and C−H···O) dimers of HMTA and 4-FP molecules, A···D and B···C inversion dimers, which generate enlarged R88(34) ring motifs in both supramolecular structures. In both structures, the crystal packing also features additional C−H···F and C−H···O interactions. The A···D and B···C dimers are linked by additional C−H···F and C−H···O hydrogen bonds, forming columns along the a and b axes, respectively. The importance of the C−H···F interaction to the structure and crystal packing has been demonstrated.
In every established species, protein-protein interactions have evolved such that they are fit for purpose. However, the molecular details of the evolution of new protein-protein interactions are poorly understood. We have used nuclear magnetic resonance spectroscopy to investigate the changes in structure and dynamics during the evolution of a protein-protein interaction involving the intrinsically disordered CREBBP (CREB-binding protein) interaction domain (CID) and nuclear coactivator binding domain (NCBD) from the transcriptional coregulators NCOA (nuclear receptor coactivator) and CREBBP/p300, respectively. The most ancient low-affinity “Cambrian-like” [540 to 600 million years (Ma) ago] CID/NCBD complex contained less secondary structure and was more dynamic than the complexes from an evolutionarily younger “Ordovician-Silurian” fish ancestor (ca. 440 Ma ago) and extant human. The most ancient Cambrian-like CID/NCBD complex lacked one helix and several interdomain interactions, resulting in a larger solvent-accessible surface area. Furthermore, the most ancient complex had a high degree of millisecond-to-microsecond dynamics distributed along the entire sequences of both CID and NCBD. These motions were reduced in the Ordovician-Silurian CID/NCBD complex and further redistributed in the extant human CID/NCBD complex. Isothermal calorimetry experiments show that complex formation is enthalpically favorable and that affinity is modulated by a largely unfavorable entropic contribution to binding. Our data demonstrate how changes in structure and motion conspire to shape affinity during the evolution of a protein-protein complex and provide direct evidence for the role of structural, dynamic, and frustrational plasticity in the evolution of interactions between intrinsically disordered proteins.
The combination of high-throughput sequencing and in vivo crosslinking approaches leads to the progressive uncovering of the complex interdependence between cellular transcriptome and proteome. Yet, the molecular determinants governing interactions in protein-RNA networks are not well understood. Here we investigated the relationship between the structure of an RNA and its ability to interact with proteins. Analysing in silico, in vitro and in vivo experiments, we find that the amount of double-stranded regions in an RNA correlates with the number of protein contacts. This relationship —which we call structure-driven protein interactivity— allows classification of RNA types, plays a role in gene regulation and could have implications for the formation of phase-separated ribonucleoprotein assemblies. We validate our hypothesis by showing that a highly structured RNA can rearrange the composition of a protein aggregate. We report that the tendency of proteins to phase-separate is reduced by interactions with specific RNAs.
Formation of the anteroposterior and dorsoventral body axis in Caenorhabditis elegans depends on cortical flows and advection of polarity determinants. The role of this patterning mechanism in tissue polarization after formation of cell-cell contacts is not fully understood. Here, we demonstrate that planar asymmetries are established during left-right symmetry breaking: Centripetal cortical flows asymmetrically and differentially advect anterior polarity determinants (aPARs) from contacts to the medial cortex, resulting in their unmixing from apical myosin. Contact localization and advection of PAR-6 requires balanced CDC-42 activation, while asymmetric retention and advection of PAR-3 can occur independently of PAR-6. Concurrent asymmetric retention of PAR-3, E-cadherin/HMR-1 and opposing retention of antagonistic CDC-42 and Wnt pathway components leads to planar asymmetries. The most obvious mark of planar asymmetry, retention of PAR-3 at a single cell-cell contact, is required for proper cytokinetic cell intercalation. Hence, our data uncover how planar polarity is established in a system without the canonical planar cell polarity pathway through planar asymmetric retention of aPARs.
1H-detected solid-state NMR experiments feasible at fast magic-angle spinning (MAS) frequencies allow accessing 1H chemical shifts of proteins in solids, which enables their interpretation in terms of secondary structure. Here we present 1H and 13C-detected NMR spectra of the RNA polymerase subunit Rpo7 in complex with unlabeled Rpo4 and use the 13C, 15N, and 1H chemical-shift values deduced from them to study the secondary structure of the protein in comparison to a known crystal structure. We applied the automated resonance assignment approach FLYA including 1H-detected solid-state NMR spectra and show its success in comparison to manual spectral assignment. Our results show that reasonably reliable secondary-structure information can be obtained from 1H secondary chemical shifts (SCS) alone by using the sum of 1Hα and 1HN SCS rather than by TALOS. The confidence, especially at the boundaries of the observed secondary structure elements, is found to increase when evaluating 13C chemical shifts, here either by using TALOS or in terms of 13C SCS.
The synergetic effects of combining structural biology and epr spectroscopy on membrane proteins
(2017)
Protein structures as provided by structural biology such as X-ray crystallography, cryo-electron microscopy and NMR spectroscopy are key elements to understand the function of a protein on the molecular level. Nonetheless, they might be error-prone due to crystallization artifacts or, in particular in case of membrane-imbedded proteins, a mostly artificial environment. In this review, we will introduce different EPR spectroscopy methods as powerful tools to complement and validate structural data gaining insights in the dynamics of proteins and protein complexes such that functional cycles can be derived. We will highlight the use of EPR spectroscopy on membrane-embedded proteins and protein complexes ranging from receptors to secondary active transporters as structural information is still limited in this field and the lipid environment is a particular challenge.
The tetracycline-binding RNA aptamer (TC-aptamer) is a synthetic riboswitch that binds the antibiotic tetracycline (TC) with exceptionally high affinity. Although a crystal structure exists of the TC-bound state, little is known about the conformational dynamics and changes upon ligand binding. In this study, pulsed electron paramagnetic resonance techniques for measuring distances (PELDOR) in combination with rigid nitroxide spin labels (Çm spin label) were used to investigate the conformational flexibility of the TC-aptamer in the presence and absence of TC at different Mg2+ concentrations. TC was found to be the essential factor for stabilizing the tertiary structure at intermediate Mg2+ concentrations. At higher Mg2+ concentrations, Mg2+ alone is sufficient to stabilize the tertiary structure. In addition, the orientation of the two spin-labeled RNA helices with respect to each other was analyzed with orientation-selective PELDOR and compared to the crystal structure. These results demonstrate for the first time the unique value of the Çm spin label in combination with PELDOR to provide information about conformational flexibilities and orientations of secondary structure elements of biologically relevant RNAs.
Enhanced labeling density and whole-cell 3D dSTORM imaging by repetitive labeling of target proteins
(2018)
With continuing advances in the resolving power of super-resolution microscopy, the inefficient labeling of proteins with suitable fluorophores becomes a limiting factor. For example, the low labeling density achieved with antibodies or small molecule tags limits attempts to reveal local protein nano-architecture of cellular compartments. On the other hand, high laser intensities cause photobleaching within and nearby an imaged region, thereby further reducing labeling density and impairing multi-plane whole-cell 3D super-resolution imaging. Here, we show that both labeling density and photobleaching can be addressed by repetitive application of trisNTA-fluorophore conjugates reversibly binding to a histidine-tagged protein by a novel approach called single-epitope repetitive imaging (SERI). For single-plane super-resolution microscopy, we demonstrate that, after multiple rounds of labeling and imaging, the signal density is increased. Using the same approach of repetitive imaging, washing and re-labeling, we demonstrate whole-cell 3D super-resolution imaging compensated for photobleaching above or below the imaging plane. This proof-of-principle study demonstrates that repetitive labeling of histidine-tagged proteins provides a versatile solution to break the "labeling barrier" and to bypass photobleaching in multi-plane, whole-cell 3D experiments.
The group of neurodegenerative diseases, Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA) all exhibit inclusions containing amyloid-type α-synuclein (α-syn) aggregates within degenerating brain cells. α-syn also exists as soluble oligomeric species that are hypothesized to represent intermediates between its native and aggregated states. These oligomers are present in brain extracts from patients suffering from synucleinopathies and hold great potential as biomarkers. Although easily prepared in vitro, oligomers are metastable and dissociate over time, thereby complicating α-syn oligomer research. Using the small amine-reactive cross-linker, formaldehyde (FA), we successfully stabilized α-syn oligomers without affecting their size, overall structure or antigenicity towards aggregate-conformation specific α-syn antibodies FILA and MJFR-14-6-4-2. Further, cross-linked α-syn oligomers show resistance towards denaturant like urea and SDS treatment and remain fully functional as internal standard in an aggregation-specific enzyme-linked immunosorbent assay (ELISA) despite prior incubation with urea. We propose that FA cross-linked α-syn oligomers could serve as important calibrators to facilitate comparative and standardized α-syn biomarker studies going forward.
Iodo(triphenyl)silane
(2019)
The molecular structure of the title compound, C18H15ISi, which crystallizes in the space group C2/c, does not exhibit any unusual features. Two weak C—H⋯π interactions may help to consolidate the packing. The present structure is not isostructural with the known Ph3SiX (X = F, Cl or Br) compounds.
From a global viewpoint, a lot of time is spent within the indoor air compartment of vehicles. A German study on mobility has revealed that, on average, people spend 45 minutes per day inside vehicles. In recent years the number of cars has increased to around 43 million vehicles in private households. This means that more than one car can be used in every household. The ratio has been growing, especially in eastern Germany and rural areas. "Overall and especially outside the cities, the car remains by far number one mode of transport, especially in terms of mileage". Therefore, numerous international studies have addressed different aspects of indoor air hygiene, in the past years. In this paper, meaningful original studies on car indoor air pollution, related to VOCs, COx, PMs, microbials, BFRs, OPFRs, cigarettes, electronic smoking devices, high molecular weight plasticizer, and NOx are summarized in the form of a review. This present review aimed to summarize recently published studies in this important field of environmental medicine and points to the need for further studies with special recommendations for optimizing the interior air hygiene.
Although intrinsically disordered proteins or protein domains (IDPs or IDD) are less abundant in bacteria than in eukaryotes, their presence in pathogenic bacterial proteins is important for protein-protein interactions. The protein tyrosine kinase A (PtkA) from Mycobacterium tuberculosis possesses an 80-residue disordered region (IDDPtkA ) of unknown function, located N-terminally to the well-folded kinase core domain. Here, we characterize the conformation of IDDPtkA under varying biophysical conditions and phosphorylation using NMR-spectroscopy. Our results confirm that the N-terminal domain of PtkA exists as an IDD at physiological pH. Furthermore, phosphorylation of IDDPtkA increases the activity of PtkA. Our findings will complement future approaches in understanding molecular mechanisms of key proteins in pathogenic virulence.
Telomeric G-quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G-quadruplex that adopts the biologically relevant hybrid-2 conformation in a ligand-bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G-quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G-quadruplex. The ligand is sandwiched between one terminal G-tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G-quadruplex structure as observed for other G-quadruplexes in different conformations, invalidating simple docking approaches to ligand-G-quadruplex structure determination
The impact of the incorporation of a non-natural amino acid (NNAA) on protein structure, dynamics, and ligand binding has not been studied rigorously so far. NNAAs are regularly used to modify proteins post-translationally in vivo and in vitro through click chemistry. Herein, structural characterisation of the impact of the incorporation of azidohomoalanine (AZH) into the model protein domain PDZ3 is examined by means of NMR spectroscopy and X-ray crystallography. The structure and dynamics of the apo state of AZH-modified PDZ3 remain mostly unperturbed. Furthermore, the binding of two PDZ3 binding peptides are unchanged upon incorporation of AZH. The interface of the AZH-modified PDZ3 and an azulene-linked peptide for vibrational energy transfer studies has been mapped by means of chemical shift perturbations and NOEs between the unlabelled azulene-linked peptide and the isotopically labelled protein. Co-crystallisation and soaking failed for the peptide-bound holo complex. NMR spectroscopy, however, allowed determination of the protein-ligand interface. Although the incorporation of AZH was minimally invasive for PDZ3, structural analysis of NNAA-modified proteins through the methodology presented herein should be performed to ensure structural integrity of the studied target.
The interaction of fibroblast growth factors (FGFs) with their fibroblast growth factor receptors (FGFRs) are important in the signaling network of cell growth and development. SSR128129E (SSR),[1, 2] a ligand of small molecular weight with potential anti-cancer properties, acts allosterically on the extracellular domains of FGFRs. Up to now, the structural basis of SSR binding to the D3 domain of FGFR remained elusive. This work reports the structural characterization of the interaction of SSR with one specific receptor, FGFR3, by NMR spectroscopy. This information provides a basis for rational drug design for allosteric FGFR inhibitors.
We have encountered two polymorphs of the title compound, C24H16B2OS2, both of which display almost the same unit-cell parameters. Compound (I) crystallizes in the non-centrosymmetric space group P21 with four molecules in the asymmetric unit. These molecules are related by pseudosymmetry. As a result, the space group looks like P21/c, but the structure cannot be refined successfully in that space group. Compound (II) on the other hand crystallizes in the centrosymmetric space group P21/c with only two molecules in the asymmetric unit. The crystals studied for (I) and (II) were both non-merohedral twins.
A(syn)-U/T and G(syn)-C+ Hoogsteen (HG) base pairs (bps) are energetically more disfavored relative to Watson–Crick (WC) bps in A-RNA as compared to B-DNA by >1 kcal/mol for reasons that are not fully understood. Here, we used NMR spectroscopy, optical melting experiments, molecular dynamics simulations and modified nucleotides to identify factors that contribute to this destabilization of HG bps in A-RNA. Removing the 2′-hydroxyl at single purine nucleotides in A-RNA duplexes did not stabilize HG bps relative to WC. In contrast, loosening the A-form geometry using a bulge in A-RNA reduced the energy cost of forming HG bps at the flanking sites to B-DNA levels. A structural and thermodynamic analysis of purine-purine HG mismatches reveals that compared to B-DNA, the A-form geometry disfavors syn purines by 1.5–4 kcal/mol due to sugar-backbone rearrangements needed to sterically accommodate the syn base. Based on MD simulations, an additional penalty of 3–4 kcal/mol applies for purine-pyrimidine HG bps due to the higher energetic cost associated with moving the bases to form hydrogen bonds in A-RNA versus B-DNA. These results provide insights into a fundamental difference between A-RNA and B-DNA duplexes with important implications for how they respond to damage and post-transcriptional modifications.
The lysosomal polypeptide transporter TAPL belongs to the superfamily of ATP-binding cassette transporters. TAPL forms a homodimeric transport complex, which translocates oligo- and polypeptides into the lumen of lysosomes driven by ATP hydrolysis. Although the structure and the function of ABC transporters were intensively studied in the past, details about the single steps of the transport cycle are still elusive. Therefore, we analyzed the coupling of peptide binding, transport and ATP hydrolysis for different substrate sizes. Although longer and shorter peptides bind with the same affinity and are transported with identical Km values, they differ significantly in their transport rates. This difference can be attributed to a higher activation energy for the longer peptide. TAPL shows a basal ATPase activity, which is inhibited in the presence of longer peptides. Uncoupling between ATP hydrolysis and peptide transport increases with peptide length. Remarkably, also the type of nucleotide determines the uncoupling. While GTP is hydrolyzed as good as ATP, peptide transport is significantly reduced. In conclusion, TAPL does not differentiate between transport substrates in the binding process but during the following steps in the transport cycle, whereas, on the other hand, not only the coupling efficiency but also the activation energy varies depending on the size of peptide substrate.
The transcriptional regulator far upstream binding protein 1 (FUBP1) is essential for fetal and adult hematopoietic stem cell (HSC) self-renewal, and the constitutive absence of FUBP1 activity during early development leads to embryonic lethality in homozygous mutant mice. To investigate the role of FUBP1 in murine embryonic stem cells (ESCs) and in particular during differentiation into hematopoietic lineages, we generated Fubp1 knockout (KO) ESC clones using CRISPR/Cas9 technology. Although FUBP1 is expressed in undifferentiated ESCs and during spontaneous differentiation following aggregation into embryoid bodies (EBs), absence of FUBP1 did not affect ESC maintenance. Interestingly, we observed a delayed differentiation of FUBP1-deficient ESCs into the mesoderm germ layer, as indicated by impaired expression of several mesoderm markers including Brachyury at an early time point of ESC differentiation upon aggregation to EBs. Coculture experiments with OP9 cells in the presence of erythropoietin revealed a diminished differentiation capacity of Fubp1 KO ESCs into the erythroid lineage. Our data showed that FUBP1 is important for the onset of mesoderm differentiation and maturation of hematopoietic progenitor cells into the erythroid lineage, a finding that is supported by the phenotype of FUBP1-deficient mice.
The adaptive response of Sorghum bicolor landraces from Egypt to drought stress and following recovery was analyzed using two-dimensional difference gel electrophoresis, 2D-DIGE. Physiological measurements and proteome alterations of accession number 11434, drought tolerant, and accession number 11431, drought sensitive, were compared to their relative control values after drought stress and following recovery. Differentially expressed proteins were analysed by Matrix assisted laser desorption ionisation time-of-flight mass spectrometry, MALDI-TOF-MS. Alterations in protein contents related to the energy balance, metabolism (sensu Mewes et al. 1997), and chaperons were the most apparent features to elucidate the differences between the drought tolerant and sensitive accessions. Further alterations in the levels of proteins related to transcription and protein synthesis are discussed.
Photofragmentation spectroscopy—the study of "half collisions" with polarized light of subdoppler line width—opens a window to look into the structure of molecules. The energy partitioning among the particular degrees of freedom of the products of the fragmentation reaction is described by the scalar properties, the direction and magnitude of a particular type of motion is described by the vector properties. The measurement of the scalar and vector properties allows a pictorial view of the intermediate state. The forces which make the fragments fly apart or rotate and vibrate can be "seen" from the line shapes. Information on the unstable intermediate state is gained from the stable fragments long after the dissociation of the parent molecule. In particular, information on the "lifetime" of the intermediate on a femtosecond time scale can be obtained.
A number of molecules, mainly three and four atomic, have been studied by this technique. Hydrogen peroxide has shown up as a textbook example. A complete analysis was possible including not only correlation of different types of fragment motion but also a correlation of the two coincident particles formed from the same parent molecule. The experimental results are in full agreement with recent calculations of the dynamics of the fragmentation on newly obtained potential energy surfaces. Hydrogen peroxide shows a strong dependence of its potential energy on the dihedral angle in the two electronic states amenable to laser excitation. This experiment further demonstrates that an analysis is also possible if two states are excited simultaneously.
Another good example is the fragmentation of hydrazoic acid for which also coincident pair correlation has been treated. Here again the results agree excellently with a qualitative picture which can be drawn from recently calculated ab initio potential energy surfaces. The HN3 example is much more complicated than the former one due to its higher structured upper potential energy surface. Strong rotational excitation is observed in the N2 fragment leaving the NH fragment rotationally cold.
The treatment of vector correlations in molecular photofragmentation is a powerful tool for the study of the dynamics of molecular dissociation reactions.
The excellent results of dispersion‐corrected density functional theory (DFT‐D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT‐D calculations is a target, especially for the field of molecular NMR crystallography. Four 13C ss‐NMR calibration compounds are investigated by single‐crystal X‐ray diffraction, molecular dynamics and DFT‐D calculations. The crystal structure of 3‐methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated 13C chemical shifts of these compounds are in excellent agreement with experiment, with a root‐mean‐square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT‐D chemical shift calculation improves the accuracy of calculated chemical shifts.
Live-cell labelling techniques to visualize proteins with minimal disturbance are important; however, the currently available methods are limited in their labelling efficiency, specificity and cell permeability. We describe high-throughput protein labelling facilitated by minimalistic probes delivered to mammalian cells by microfluidic cell squeezing. High-affinity and target-specific tracing of proteins in various subcellular compartments is demonstrated, culminating in photoinduced labelling within live cells. Both the fine-tuned delivery of subnanomolar concentrations and the minimal size of the probe allow for live-cell super-resolution imaging with very low background and nanometre precision. This method is fast in probe delivery (∼1,000,000 cells per second), versatile across cell types and can be readily transferred to a multitude of proteins. Moreover, the technique succeeds in combination with well-established methods to gain multiplexed labelling and has demonstrated potential to precisely trace target proteins, in live mammalian cells, by super-resolution microscopy.
Retrograde transport of NF-κB from the synapse to the nucleus in neurons is mediated by the dynein/dynactin motor complex and can be triggered by synaptic activation. The caliber of axons is highly variable ranging down to 100 nm, aggravating the investigation of transport processes in neurites of living neurons using conventional light microscopy. We quantified for the first time the transport of the NF-κB subunit p65 using high-density single-particle tracking in combination with photoactivatable fluorescent proteins in living mouse hippocampal neurons. We detected an increase of the mean diffusion coefficient (Dmean) in neurites from 0.12±0.05 to 0.61±0.03 μm2/s after stimulation with glutamate. We further observed that the relative amount of retrogradely transported p65 molecules is increased after stimulation. Glutamate treatment resulted in an increase of the mean retrograde velocity from 10.9±1.9 to 15±4.9 μm/s, whereas a velocity increase from 9±1.3 to 14±3 μm/s was observed for anterogradely transported p65. This study demonstrates for the first time that glutamate stimulation leads to an increased mobility of single NF-κB p65 molecules in neurites of living hippocampal neurons.
A current challenge in life sciences is to image cell membrane receptors while characterizing their specific interactions with various ligands. Addressing this issue has been hampered by the lack of suitable nanoscopic methods. Here we address this challenge and introduce multifunctional high-resolution atomic force microscopy (AFM) to image human protease-activated receptors (PAR1) in the functionally important lipid membrane and to simultaneously localize and quantify their binding to two different ligands. Therefore, we introduce the surface chemistry to bifunctionalize AFM tips with the native receptor-activating peptide and a tris-N-nitrilotriacetic acid (tris-NTA) group binding to a His10-tag engineered to PAR1. We further introduce ways to discern between the binding of both ligands to different receptor sites while imaging native PAR1s. Surface chemistry and nanoscopic method are applicable to a range of biological systems in vitro and in vivo and to concurrently detect and localize multiple ligand-binding sites at single receptor resolution.
The discovery of antibiotics represented a key milestone in the history of medicine. However, with the rise of these life-saving drugs came the awareness that bacteria deploy defense mechanisms to resist these antibiotics, and they are good at it. Today, we appear at a crossroads between discovery of new potent drugs and omni-resistant superbugs. Moreover, the misuse of antibiotics in different industries has increased the rate of resistance development by providing permanent selective pressure and, subsequently, enrichment of multidrug resistant pathogens. As a result, antimicrobial resistance has now become an urgent threat to public health worldwide (http:// www.who.int/drugresistance/documents/surveillancereport/en/). The development of multidrug resistance (MDR) in an increasing number of pathogens, including Pseudomonas, Acinetobacter, Klebsiella, Salmonella, Burkholderia, and other Gram-negative bacteria is a serious issue. Membrane efflux pump complexes of the Resistance-Nodulation-Division (RND) superfamily play a key role in the development of MDR in these bacteria. These pumps, together with other transporters, contribute to intrinsic and acquired resistance of bacteria toward most, if not all, of the compounds available in our antimicrobial arsenal. Given the enormous drug polyspecificity of MDR efflux pumps, studies on their mechanism of action are extremely challenging, and this has negatively impacted both on the development of new antibiotics that are able to evade these efflux pumps and on the design of pump inhibitors. The collection of articles in this eBook, published as a Research Topic in Frontiers in Microbiology, section of Antimicrobials, Resistance, and Chemotherapy, aims to update the reader about the latest advances on the structure and function of RND efflux transporters, their roles in the overall multidrug resistance phenotype of Gram-negative pathogens, and on the strategies to inhibit their activities. ...
Corneal topometric, aberrometric and biomechanical parameters in mucopolysaccharidosis patients
(2019)
Aims: To report corneal topometric and aberrometric values in mucopolysaccharidosis (MPS) and to investigate their correlation with biomechanical corneal parameters.
Methods: One randomly chosen eye of 20 MPS patients with no to moderate corneal clouding and one eye of 23 healthy controls with comparable age were prospectively included into this study. Corneal surface regularity was assessed by index of surface variance (ISV), -vertical asymmetry (IVA), -height asymmetry (IHA), -height decentration (IHD); keratoconus index (KI), central keratoconus index (CKI) and Zernike indices of anterior and posterior corneal surface using Scheimpflug imaging (Pentacam). Corneal resistance factor (CRF) and corneal hysteresis (CH) were assessed by Ocular Response Analyzer. Statistical analyses were performed using Mann-Whitney-Test and Spearman Correlation Coefficients.
Results: IVA, ISV, IHD, IHA, but not KI and CKI were significantly higher in MPS patients compared to age matched healthy controls. Spherical aberration and asphericity coefficients either at the anterior or at the posterior corneal surface differed significantly between both groups. The grade of the MPS-associated corneal opacity correlated significantly with ISV (rho = 0.52), IVA (rho = 0.54), IHA (rho = 0.57) and IHD (rho = 0.48). Density of the MPS-affected corneas correlated significantly with ISV (rho = 0.52), IVA (rho = 0.72), IHA (rho = 0.57), IHD (rho = 0.69), 3rd order horizontal trefoil aberration at the posterior (rho = 0.62) and anterior surface (rho = 0.48) as well as with CH (rho = 0.55) and CRF (rho = 0.57). Spherical aberration at the back surface correlated with CRF and CH in MPS and in healthy controls.
Conclusions: This is the first study analyzing shape of the corneal surface in MPS patients. Topometric indices of corneal asymmetry are significantly increased and correlate with MPS-related corneal opacity and density. Spherical aberration and asphericity coefficient at the front and at the back corneal surface differ significantly between MPS and healthy controls.
Mechanistic and structural studies of membrane proteins require their stabilization in specific conformations. Single domain antibodies are potent reagents for this purpose, but their generation relies on immunizations, which impedes selections in the presence of ligands typically needed to populate defined conformational states. To overcome this key limitation, we developed an in vitro selection platform based on synthetic single domain antibodies named sybodies. To target the limited hydrophilic surfaces of membrane proteins, we designed three sybody libraries that exhibit different shapes and moderate hydrophobicity of the randomized surface. A robust binder selection cascade combining ribosome and phage display enabled the generation of conformation-selective, high affinity sybodies against an ABC transporter and two previously intractable human SLC transporters, GlyT1 and ENT1. The platform does not require access to animal facilities and builds exclusively on commercially available reagents, thus enabling every lab to rapidly generate binders against challenging membrane proteins.
PfEMP1 (erythrocyte membrane protein 1) adhesins play a pivotal role in the pathophysiology of falciparum malaria, by mediating sequestration of Plasmodium falciparum-infected erythrocytes in the microvasculature. PfEMP1 variants are expressed by var genes and are presented on membrane elevations, termed knobs. However, the organization of PfEMP1 on knobs is largely unclear. Here, we use super-resolution microscopy and genetically altered parasites expressing a modified var2csa gene in which the coding sequence of the photoactivatable mEOS2 was inserted to determine the number and distribution of PfEMP1 on single knobs. The data were verified by quantitative fluorescence-activated cell sorting analysis and immuno-electron microscopy together with stereology methods. We show that knobs contain 3.3 ± 1.7 and 4.3 ± 2.5 PfEMP1 molecules, predominantly placed on the knob tip, in parasitized erythrocytes containing wild type and sickle haemoglobin, respectively. The ramifications of our findings for cytoadhesion and immune evasion are discussed.
Secondary multidrug (Mdr) transporters utilize ion concentration gradients to actively remove antibiotics and other toxic compounds from cells. The model Mdr transporter MdfA from Escherichia coli exchanges dissimilar drugs for protons. The transporter should open at the cytoplasmic side to enable access of drugs into the Mdr recognition pocket. Here we show that the cytoplasmic rim around the Mdr recognition pocket represents a previously overlooked important regulatory determinant in MdfA. We demonstrate that increasing the positive charge of the electrically asymmetric rim dramatically inhibits MdfA activity and sometimes even leads to influx of planar, positively charged compounds, resulting in drug sensitivity. Our results suggest that unlike the mutants with the electrically modified rim, the membrane-embedded wild-type MdfA exhibits a significant probability of an inward-closed conformation, which is further increased by drug binding. Since MdfA binds drugs from its inward-facing environment, these results are intriguing and raise the possibility that the transporter has a sensitive, drug-induced conformational switch, which favors an inward-closed state.
Hydride transfers play a crucial role in a multitude of biological redox reactions and are mediated by flavin, deazaflavin or nicotinamide adenine dinucleotide cofactors at standard redox potentials ranging from 0 to –340 mV. 2-Naphthoyl-CoA reductase, a key enzyme of oxygen-independent bacterial naphthalene degradation, uses a low-potential one-electron donor for the two-electron dearomatization of its substrate below the redox limit of known biological hydride transfer processes at E°’ = −493 mV. Here we demonstrate by X-ray structural analyses, QM/MM computational studies, and multiple spectroscopy/activity based titrations that highly cooperative electron transfer (n = 3) from a low-potential one-electron (FAD) to a two-electron (FMN) transferring flavin cofactor is the key to overcome the resonance stabilized aromatic system by hydride transfer in a highly hydrophobic pocket. The results evidence how the protein environment inversely functionalizes two flavins to switch from low-potential one-electron to hydride transfer at the thermodynamic limit of flavin redox chemistry.
Background: Esophageal cancer (EC) is one of the deadliest cancers worldwide. The contemporary strong increase of the adenocarcinomas in Western countries and the high mortality rates require the intensification of prospective multinational studies.
Methods: Therefore, this global health issue has been chosen for the bibliometric review of the global publication output. As source for meta and citation data, the Web of Science has been used and Density Equalizing Maps were applied for visualization.
Results: 17,387 articles on EC could be identified. The years with publication and citation maxima correspond to the appearance of the most prolific articles. China is the most publishing country, followed by Japan and the USA. Germany and the UK ranked 4th and 5th. The analysis of the ratios articles and socio-economic parameters emphasizes the leading position of the Scandinavian countries and Japan. Here, the high-income countries come out on top. The high incidence regions are mainly represented by Chinese and Japanese research. The association of the publication output and the overall research funding could be shown.
Conclusions: A strengthened international network increasingly consisting of the scientifically best positioned countries as well as more of the high incidence countries worldwide is mandatory for future research. The findings deliver scientists, clinicians and decision makers backgrounds for future decisions all over the world.
Rhodopsins are the most universal biological light-energy transducers and abundant phototrophic mechanisms that evolved on Earth and have a remarkable diversity and potential for biotechnological applications. Recently, the first sodium-pumping rhodopsin KR2 from Krokinobacter eikastus was discovered and characterized. However, the existing structures of KR2 are contradictory, and the mechanism of Na+ pumping is not yet understood. Here, we present a structure of the cationic (non H+) light-driven pump at physiological pH in its pentameric form. We also present 13 atomic structures and functional data on the KR2 and its mutants, including potassium pumps, which show that oligomerization of the microbial rhodopsin is obligatory for its biological function. The studies reveal the structure of KR2 at nonphysiological low pH where it acts as a proton pump. The structure provides new insights into the mechanisms of microbial rhodopsins and opens the way to a rational design of novel cation pumps for optogenetics.
Identifizierung und Charakterisierung neuer Inhibitoren der C2-ähnlichen Domäne der 5-Lipoxygenase
(2011)
Die 5-Lipoxygenase (5-LO) katalysiert die ersten beiden Schritte der Leukotrien (LT)-Biosynthese (Samuelsson et al., 1987). Das Substrat Arachidonsäure (AA) wird im ersten Schritt zu einem Fettsäurehydroperoxid, der 5(S)-Hydroperoxy-6-trans-8,11,14-cis-Eikosatetraensäure (5-HpETE) oxidiert. Durch Dehydrierung entsteht im zweiten Reaktionsschritt das instabile Epoxid LTA4. Weiter wandeln zwei Synthasen das LTA4 zum einen in LTB4 oder zum anderen in die Cysteinyl-LTs C4, D4 und E4 um (Samuelsson et al., 1987). Die 5-LO wird in Zellen myeloiden Ursprungs exprimiert und kommt vor allem in reifen Leukozyten vor.
LTs spielen eine wichtige Rolle bei der angeborenen Immunantwort und vermitteln vor allem entzündliche und allergische Reaktionen (Funk 2001; Peters-Golden & Henderson, 2007). Asthma bronchiale, kardiovaskuläre Erkrankungen wie Atherosklerose, Osteoporose oder verschiedene Krebsarten werden im Zusammenhang mit der 5-LO untersucht (Werz & Steinhilber, 2006). Die Inhibition der LT-Biosynthese oder die Senkung der LT-Spiegel stellt eine Möglichkeit dar, den entzündungsfördernden Eigenschaften entgegenzuwirken. Inhibitoren der LT-Biosynthese lassen sich in indirekte und direkte 5-LO-Inhibitoren gliedern. Zu den indirekten 5-LO-Inhibitoren zählen FLAP-Antagonisten (Young, 1991; Evans et al., 2008) sowie CysLT1-Rezeptorantagonisten (Darzen, 1998). Von den vier Gruppen der direkten 5-LO-Inhibitoren (redoxaktive, Eisenligand-, nichtredox- sowie diverse Inhibitoren (Pergola & Werz, 2010)) ist bisher nur Zileuton (Carter et al., 1991), ein Eisenligand-Inhibitor, als Wirkstoff zur Behandlung von Asthma bronchiale in den USA zugelassen.
Das Ziel der vorliegenden Arbeit war es, die neuartige Klasse der Imidazo[1,2-a]pyridine hinsichtlich ihrer 5-LO-Inhibition, ihrer Löslichkeit sowie ihrer Effekte auf die Zellviabilität zu evaluieren und zu optimieren. Dabei stand das Verständnis der Rezeptor-Ligand-Wechselwirkung im Fokus. Ausgehend von Substanz A14, der potentesten Substanz eines virtuellen Screenings nach dualen COX/5-LO-Inhibitoren (Hofmann et al., 2008), wurden 78 Substanzen in ionophor-stimulierten intakten polymorphkernigen Leukozyten (PMNL) sowie im zellfreien System, dem Überstand nach 100.000 × g Zentrifugation (S100) von homogenisierten PMNL, bezüglich ihrer inhibitorischen Aktivität untersucht. Die Effekte auf die Zellviabilität nach Inkubation mit den Substanzen für 48 h auf die humane leukämische Monozytenvorläufer Zelllinie U937 wurden mit Hilfe eines WST-Assays, der die mitochondriale Aktivität misst, sowie eines LDH-Assays, zur Bestimmung der Freisetzung von LDH als Folge von Nekrose, evaluiert.
Innerhalb der Struktur-Aktivitäts-Beziehung (SAR) der 78 Derivate konnte kein eindeutiges Substitutionsmuster, das sowohl in intakten PMNL als auch in zellfreiem S100 zu den gleichen Schlüssen führt, festgestellt werden. Ausgehend von Substanz A14 konnte die inhibitorische Aktivität verbessert werden, wobei Substanzen mit nanomolaren IC50-Werten in beiden Assaysystemen resultierten. Die Substanzen lassen sich in drei strukturelle Teile gliedern: Einen oberen Teil am sekundären Amin, ein bizyklisches N-fusioniertes Imidazopyridin (Teil A) sowie einen Teil B am aromatischen Kern. Nur für den oberen Teil ließ sich ein allgemein-gültiges Substitutionsmuster feststellen. Am sekundären Amin führen in intakten PMNL größere Substituenten zu einer Verbesserung der inhibitorischen Aktivität, wobei dies bis zu einer Cyclohexylgruppe gilt und eine Adamantyl-Substitution eine Ausnahme bildet. Allgemein lässt sich feststellen, dass bei einer Cyclohexylgruppe am sekundären Amin und einer Methylgruppe an Position 6 in Teil A, die Substituenten in Teil B stark variieren können, ohne an inhibitorischer Aktivität zu verlieren. Werden innerhalb des oberen Teils oder in Teil A die Substituenten polarer, sind in Teil B weniger Variationen möglich. Es werden insbesondere lipophile Reste toleriert. Beim Versuch, die Löslichkeit zu verbessern, zeigte sich, dass ein Gleichgewicht zwischen polaren und unpolaren Substituenten vorliegen muss. Auch die Einflüsse der Substituenten auf die Zellviabilität konnten nicht einem allgemein-gültigen Muster unterworfen werden. Mit Substanz 15 konnte ein Derivat identifiziert werden, das verglichen mit der Ausgangssubstanz A14 eine verbesserte inhibitorische Aktivität aufweist (IC50-Werte von 0,16 µM (PMNL) und 0,1 µM (S100)), löslicher ist (clogP-Wert von 4,6) und keine Nekrose auslöst. Weiter zeigten auch die Substanzen 31 und 50 eine Verbesserung der inhibitorischen Aktivität (IC50-Werte von 0,26 µM bzw. 0,58 µM (PMNL) und 0,8 µM bzw. 0,16 µM (S100)) ohne Nekrose auszulösen, wobei Substanz 50 zusätzlich eine verringerte Lipophilie (clogP-Wert von 4,2) aufweist. Substanz 76 ist mit einem IC50-Wert von 6 nM die im zellfreien System aktivste Substanz unter den 78 getesteten Derivaten.
Ein vielversprechender Vertreter dieser neuartigen Klasse der Imidazo[1,2-a]pyridine, Substanz 15 (EP6), wurde in verschiedenen Assaysystemen charakterisiert. EP6 ist ein hochwirksamer Inhibitor der 5-LO mit einem IC50-Wert von 0,16 µM in intakten PMNL und weist im zellfreien S100 von PMNL einen IC50-Wert von 0,1 µM, am partiell gereinigten Enzym einen IC50-Wert von 0,05 µM auf. Die vergleichbare inhibitorische Aktivität in intakten Zellen sowie im zellfreien System lässt auf eine direkte Inhibition der 5-LO schließen. Die Zugabe der allosterischen Faktoren ATP oder Calcium hat keinen Einfluss auf die Potenz von EP6. Auch ist die Inhibition nicht vom Redoxzustand der Zelle abhängig, wie im Falle bekannter nichtredox-Inhibitoren (Werz et al., 1998). Die Zugabe von steigenden Mengen an exogenem Substrat AA zu S100 von PMNL führt zu keiner Beeinträchtigung der Potenz von EP6, was im Vergleich zu den nichtredox-Inhibitoren einen Vorteil bei entzündlichen Prozessen mit erhöhten Lipidhydroperoxid-Spiegeln darstellt. Bei ionophor-stimulierten PMNL ohne die Zugabe von exogenem Substrat resultiert ein sechsfach höherer IC50-Wert von 1,2 µM, der auf eine allosterische Inhibition durch EP6 hinweist, bei der Substrat in ausreichenden Mengen vorliegen muss, damit EP6 mit dem 5-LO-AA-Komplex interagieren kann. Darüber hinaus inhibiert EP6 die LT-Bildung unabhängig von der Art der 5-LO-Stimulation bei einer Zugabe von 20 µM exogener AA. Der physiologische Stimulus in PMNL über N-Formylmethionyl-Leucyl-Phenylalanin (fMLP) führt zu einem höheren IC50-Wert von 0,76 µM mit Zugabe von 20 µM AA und bestätigt die Ergebnisse von ionophor-stimulierten PMNL ohne Zugabe von exogenem Substrat. Für EP6 konnte weiterhin eine allosterische Bindestelle an der C2-ähnlichen Domäne der 5-LO postuliert werden. Die Zugabe von Phosphatidylcholin führte zu einer verminderten inhibitorischen Aktivität. Durch Experimente mit einer Mutante der 5-LO, bei der die Tryptophane, welche die Membranbindung vermitteln, ausgetauscht sind (3W-Mutante), konnte die Interaktion dieser Aminosäuren mit EP6 gezeigt werden. Über einen Kompetitionsassay mit der C2-ähnlichen Domäne, Mutations- und Docking-Studien, wurden die Aminosäuren Y81, Y100 und Y383 des Interfaces der beiden Domänen der 5-LO als essentiell für die Bindung identifiziert. Somit zählt EP6 als Vertreter der Klasse der Imidazo[1,2-a]pyridine neben Hyperforin und AKBA zu den einzigen mit der C2-ähnlichen Domäne interagierenden 5-LO-Inhibitoren.
EP6 ist ein selektiver Inhibitor der 5-LO, der die 15-LO1, 15-LO2 und 12-LO nicht inhibiert. Weiterhin werden drei weitere Enzyme der AA-Kaskade, die Cyclooxygenase-1 und -2 sowie die mikrosomale Prostaglandin E2 Synthase-1 nicht durch EP6 beeinflusst. Neben der humanen 5-LO wird auch die murine 5-LO, in intakten RAW 264.7 Zellen und deren S100 getestet, mit niedrig mikromolarem bzw. nanomolarem IC50-Wert inhibiert, was die erste Voraussetzung für potentielle in vivo Studien darstellt.
Die Inhibition der 5-LO-Produktbildung in humanem Vollblut konnte jedoch bis zu einer Konzentration von 30 µM EP6 nicht gehemmt werden. EP6 ist lipophil (clogP-Wert von 4,6) und weist eine hohe Plasmaproteinbindung (Bindung an humanes Serumalbumin von 97,5 ± 0,7% bei 10 µg/ml EP6) auf, was die Unwirksamkeit in humanem Vollblut erklären könnte.
Abschließend wurden die Effekte von EP6 auf die Zellviabilität untersucht. Die Experimente wurden zunächst in U937 bei einer Inkubationszeit von 48 h mit einer maximalen Konzentration von 30 µM EP6 durchgeführt. EP6 führt zu keinen unmittelbaren zytotoxischen Effekten innerhalb der Inkubationszeit der in dieser Arbeit durchgeführten Aktivitätsassays (gezeigt in PMNL). Weiter wurde jedoch gezeigt, dass die mitochondriale Aktivität nach Inkubation für 48 h mit einem EC50-Wert von 14 µM beeinträchtigt wird (WST-Assay). Dieser Effekt ist jedoch nicht auf Nekrose zurückzuführen, da die gemessene Konzentration an freigesetztem LDH gering bleibt. Über ein Langzeitexperiment wurde die Abnahme der Lebendzellzahl nach Inkubation mit 30 µM EP6 nach 24 h festgestellt. Über Detektion von PARP-Spaltung, einem Marker für späte Apoptose, stellte sich heraus, dass EP6 in U937 Apoptose induziert. Zusätzlich zu den Untersuchungen der leukämischen Zelllinie wurden humane nicht-tumor Zellen (RPE) im Langzeitexperiment sowie im BrdU-Assay untersucht. EP6 beeinträchtigt die Lebendzellzahl der nicht-tumor Zelllinie RPE nicht und führt nur zu geringen antiproliferativen Effekten.
The on-surface synthesis of bisheptahelicene by Ullmann coupling of 9-bromoheptahelicene on Au(111) and its temperature-induced dehydrogenation is studied using temperature-programmed reaction spectroscopy and time-of-flight secondary ion mass spectrometry. Specific dehydrogenation products of bisheptahelicene after loss of 6, 8 and 10 hydrogen atoms are identified, corresponding to molecules having undergone Diels–Alder transformations and intramolecular C–C coupling reactions. By combining with atomic hydrogen produced by dehydrogenation, the Ullmann coupling side-product bromine desorbs as HBr. H2 desorption emerges only after all Br has desorbed. Such characteristic behavior is explained by a kinetic model which explicitly considers the coverage of transient atomic H on the surface. Heating experiments performed with saturated layers of different Br-containing molecules reveal that the onset of HBr desorption depends strictly on the dehydrogenation step and therefore on the structure of the molecules.
The immune system makes use of major histocompatibility complex class I (MHC I) molecules to present peptides to other immune cells, which can evoke an immune response. Within this process of antigen presentation, the MHC I peptide loading complex, consisting of a transporter associated with antigen processing TAP, MHC I, and chaperones, is key to the initiation of immune response by shuttling peptides from the cytosol into the ER lumen. However, it is still enigmatic how the flux of antigens is precisely coordinated in time and space, limiting our understanding of antigen presentation pathways. Here, we report on the development of a synthetic viral TAP inhibitor that can be cleaved by light. This photo-conditional inhibitor shows temporal blockade of TAP-mediated antigen translocation, which is unleashed upon illumination. The recovery of TAP activity was monitored at single-cell resolution both in human immune cell lines and primary cells. The development of a photo-conditional TAP inhibitor thus expands the repertoire of chemical intervention tools for immunological processes.
LILBID and nESI : different native mass spectrometry techniques as tools in structural biology
(2018)
Native mass spectrometry is applied for the investigation of proteins and protein complexes worldwide. The challenge in native mass spectrometry is maintaining the features of the proteins of interest, such as oligomeric state, bound ligands, or the conformation of the protein complex, during transfer from solution to gas phase. This is an essential prerequisite to allow conclusions about the solution state protein complex, based on the gas phase measurements. Therefore, soft ionization techniques are required. Widely used for the analysis of protein complexes are nanoelectro spray ionization (nESI) mass spectrometers. A newer ionization method is laser induced liquid bead ion desorption (LILBID), which is based on the release of protein complexes from solution phase via infrared (IR) laser desorption. We use both methods in our lab, depending on the requirements of the biological system we are interested in. Here we benchmark the performance of our LILBID mass spectrometer in comparison to a nESI instrument, regarding sample conditions, buffer and additive tolerances, dissociation mechanism and applicability towards soluble and membrane protein complexes.
Electron cryo-microscopy analyzes the structure of proteins and protein complexes in vitrified solution. Proteins tend to adsorb to the air-water interface in unsupported films of aqueous solution, which can result in partial or complete denaturation. We investigated the structure of yeast fatty acid synthase at the air-water interface by electron cryo-tomography and single-particle image processing. Around 90% of complexes adsorbed to the air-water interface are partly denatured. We show that the unfolded regions face the air-water interface. Denaturation by contact with air may happen at any stage of specimen preparation. Denaturation at the air-water interface is completely avoided when the complex is plunge-frozen on a substrate of hydrophilized graphene.
Die Tumorprotein-Familie des Proteins p53 besteht aus drei Familienmitgliedern p53, p63 und p73 mit diversen Funktionen als Transkriptionsfaktoren. p53 war das erste Mitglied dieser Familie, das im Jahre 1979 entdeckt wurde und wurde zunächst als krebsverursachendes Protein eingeordnet, weil es in vielen Tumorgeweben in erhöhter Menge vorgefunden wurde. Es wurde allerdings festgestellt, dass der Großteil dieser gefundenen p53-Proteine funktionsunfähig durch Mutationen in ihrer Aminosäuresequenz waren. Unmutiertes p53 hingegen führt zu einem Stopp von Zellteilung oder sogar Zelltod, sofern die Zellen genetischem Stress durch Strahlung oder mutagene Chemikalien ausgesetzt sind. Heute wird p53 als eines der wichtigsten Tumor-Unterdrückungsproteine betrachtet. Die beiden anderen Familienmitglieder p63 und p73 existieren in einer Vielzahl von Isoformen. Neben carboxyterminaler alternativer mRNA-Prozessierung (α, β, γ, usw. Isoformen) führen zwei unabhängige Promotoren auch zu zwei unterschiedlichen Aminotermini. Hier wird zwischen ΔN- und TA-Isoformen unterschieden. Im Falle von p63 treten zwei dominante Isoformen auf, ΔNp63α und TAp63α. Während ΔNp63α eine Rolle in der Differenzierung von Haut spielt, wurde TAp63α bisher ausschließlich in Eizellen gefunden. Dort hat es die Funktion eines Sensors, der die genetische Integrität der weiblichen Keimbahn sicherstellt. Es liegt in Eizellen in hoher Konzentration vor, allerdings in einer komplett inaktiven Form. Werden Schäden im der Erbgut der Eizelle festgestellt, so wird das Protein aktiviert und kann so den Prozess des Zelltods der Eizelle einleiten. Mutationen oder das Fehlen des p63-Genes führen zu Missbildungen während der Entwicklung und zu unvollständig ausgebildeter Haut. Im Falle von p73 gibt es ebenfalls mehrere Isoformen, wobei die Funktionen und Relevanzen der einzelnen Isoformen bisher nicht komplett geklärt werden konnten. Eine p73-negative Maus hat einen diffusen Phänotyp, der sich durch niedrige Intelligenz, fast sterile Männchen und chronische bronchiale Infektion auszeichnet. Generell sind alle Mitglieder der p53-Familie tetramere Proteine und sind nur in diesem Zustand auch aktiv. Die einzige Ausnahme stellt, wie oben beschrieben, TAp63α dar, das in einem inaktiven dimeren Zustand vorliegt und nur durch Modifikation durch zwei unabhängige Kinasen aktiviert werden kann. Dabei geht es in den tetrameren Zustand über und ist daraufhin aktiv.
Alle drei Proteine haben (anhand ihrer längsten Isoform beschrieben) eine konservierte Domänenstruktur. Am Aminoterminus befindet sich zunächst die transaktivierende-Domäne (TAD), die für Interaktionen mit transkriptionellen Koaktivatioren relevant ist. Danach folgt die stark konservierte Desoxyribonukleinsäure (DNA) bindende Domäne (DBD). Sie stellt sicher, dass der Transkriptionsfaktor sequenzspezifisch an der richtigen Stelle auf die DNA bindet. Weitergehend folgt die Tetramerisierungsdomäne (TD), welche den oligomeren Zustand des Proteins herstellt. Im Falle von p53 endet das Protein an dieser Stelle, bei p63 und p73 folgen noch das Sterile-Alpha-Motiv (SAM) und die Transkription-inhibierende Domäne (TID). Die SAM Domäne wird generell als Interaktionsdomäne beschrieben, es konnte allerdings bis dato kein Interaktionspartner gefunden werden. Die TID hat einen negativen Einfluss auf die transkriptionelle Aktivität der Proteine. Im Falle von TAp63α interagiert sie zusätzlich mit der TAD um den Dimeren Zustand zu stabilisieren.
Histon Acetylasen
Die Acetylierung von Histonen ist neben deren Methylierung die wichtigste Modifikation. Sie ist essenziell für die Transkription innerhalb aller eukaryontischen Lebewesen, da sie durch die Modifikation von Histonen die DNA für die DNA-Polymerase II zugänglich macht. Es gibt insgesamt fünf verschiedene, nicht näher miteinander verwandte Familien von Histonacetylasen. Diese Studie beschäftigt sich ausschließlich mit der KAT3 Familie, bestehend aus den Proteinen p300 und CBP. Beide sind hochgradig konserviert, in gefalteten Bereichen der Proteine erreicht die Sequenzidentität fast 100%. Beide Proteine scheinen sehr ähnliche Aufgaben zu erfüllen, die jedoch nicht komplett identisch sind. Die Fehlfunktion von einem Allel von CBP führt zum Krankheitsbild des Rubinstein-Taybi-Syndrom (RTS), während ein Mangel an p300 sich in Mäusen auf das Gedächtnis auswirkt. Der komplette Verlust beider Allele eines der Proteine ist immer tödlich, genauso wie auch Verlust jeweils eines Allels bei beiden Proteinen. Insgesamt vier unabhängige Domänen in p300/CBP sind in der Lange die transaktivierende Domänen der p53-Familie zu binden. Bei zwei der Domänen handelt es sich um Zinkfinger-Proteine (Taz1 und Taz2), die anderen beiden sind kleine, ausschließlich α-helikale Domänen (Kix und IBiD).
Diese Studie beschäftigt sich mit der Lösung von Strukturen von der transaktivierenden Domäne von p63 und p73 mit der p300-Domäne Taz2. Außerdem wurden die Auswirkungen von direkten Acetylierungen von TAp63α charakterisiert und der Effekt von einem potenten p300/CBP Inhibitor auf Oozyten unter genotoxischem Stress analysiert. Zusätzlich wurde die Phosphorylierungskinetiken von Tap63α wärend der Aktivierung durch Kinasen untersucht.
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Infections with multidrug resistant bacterial strains like Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa or Acinetobacter baumanii that can accumulate resistance mechanisms against different groups of drugs cause increasing problems for the health care system. Multidrug efflux pumps are able to transport different classes of substances, providing a basic resistance to different antibiotics. Especially when they are overexpressed they can keep bacterial cells alive under antibiotic pressure unless other high level resistance mechanisms like expression of β-lactamases are established. One example for a clinically relevant multidrug efflux pump is the AcrAB/TolC tripartite system of E. coli, that transports a variety of different substrates, including besides antibiotics dyes, detergents, bile salts and organic compounds from the periplasm or the inner membrane out of the cell. AcrB is the inner membrane component of the protein complex that determines not only the substrate specificity of the tripartite system but energises the transport through the whole system process via proton transduction as well. TolC is the outer membrane spanning protein that forms a pore in the outer membrane enabling the system to transport drugs over the latter out of the cell. The periplasmic membrane fusion protein AcrA connects AcrB and TolC in the periplasm completing the channel from the periplasm, respective the inner membrane to the extracellular space. AcrB assembles as trimers, in asymmetric crystal structures each of the protomers adapts a different conformation designated L(oose), T(ight) and O(pen). In the protomers tunnels open up and collaps in different conformations. In the L protomer a periplasmic cleft opens up that can initially bind substrates to the periplasmic part of AcrB. In the T conformation the deep binding pocket opens that is assumed to bind substrates tightly that were bound to the access pocket before. As well in the T conformation a second pathway leading to the deep binding pocket opens that can guide substrates from a groove between transmembrane helices TM7, TM8 and TM9, the TM8 groove, that is connected with socalled tunnel 1 that ends in the deep binding pocket. In the O conformation a new tunnel opens that connects the collapsing deep binding pocket with the periplasmic space, respective the channel through the periplasmic space formed from AcrA and TolC. Substrates were cocrystallised in access and deep binding pocket verifying their role in substrate transport. In the TM8 groove in high resolution crystal structures DDM molecules were cocrystallised in L and T conformation, indicating that the AcrB substrate DDM may utilise this entrance to the deep binding pocket. The asymmetry observed in the AcrB trimers trongly suggests a peristaltic pump mechanism. The functional rotation cycle demands communication between the subunits and tight control of substrate load of protomers during the transport to optimise the ration between protons that are transduced and substrates transported. Indeed it was shown that AcrB transport mechanism is positively cooperative for some β-lactam substrates. For the communication between the subunits it was assumed that ionic interaction between ion pairs established between charged amino acids at the interfaces of protomers in different conformations are of special importance. Thus the amino acids engaged in ionic interactions, respective ion pairs D73-K131, E130-K110, D174-K110, R168, R259-E734 were substituted with non-charged amino acids pairwise and phenotypes were determined in plate dilution assays and MIC experiments. No evidence for a general, substrate independent, reduction of AcrB activity, that would be expected when the ionic residues are of special importance for AcrB function, could be found with the methods applied. Substitutions were not only combined pairwise according to the putative ion pairs but as well in combinations of R168A with D174N, E130Q and K131M. AcrB activity is reduced for the variant R168A_D174N significantly, activity decreases further for quadruple variant E130Q_K131M_ R168A_D174N. Because the reduced activity is only observed in this combination of substitutions the phenotype must result from accumulation of small effects of the single substitutions. R168A may destabilise the protomer interfaces, as its side chain is oriented in direction to the neighbouring protomer at all interfaces, enhancing substratespecific effects of substitutions E130Q, K131M, D174N that are not in all conformations oriented towards the neighbouring protomer but as well along the substrate transport pathway. Further investigations to figure out the details of the effects observed were not conducted because fluctuating expression of the variants hindered experimental procedures.
In another approach TM8 was in focus of the interest. As mentioned above it is a possible substrate entrance in the inner membrane. The linker between TM8 and the periplasmic PC2 subdomain undergoes a coil-to-helix transition when AcrB cycles through L, T and O conformations. Linking the transmembrane part of AcrB that provides the energy for the transport process via proton transduction with the periplasmic part harbouring the major part of the substrate pathway assignes TM8 and the periplasmic linker (859-876) an important role in the function of AcrB. Thus it was investigated with an alanine-scan of residues 859 to 884 and G/P respective P/G exchange followed by phenotype characterisation in growth curve and plate dilution assays of selected variants. In the phenotype determinations none of the variants, except G861P that seems to cause massive sterical restriction in an α-helical region, displayed a general, substrate independent decrease of AcrB activity. Thus it is concluded that the individual properties of amino acids in TM8 and the periplasmic linker are not of general importance for the mechanism of AcrB. The substitution of individual amino acids had impact on uptake of different substrates in plate dilution assays in a substrate dependent manner. The uptake of some substrates, like erythromycin or chloramphenicol is more affected than that of others with rhodamine 6G resistance being only reduced for the G861P variant. A relation between the PSA of substrates and reduced activity of AcrB was observed. in Substrates with higher PSA values are more affected by substitutions in TM8 or periplasmic linker, resulting in the conclusion that substrates with higher PSA are more likely to be taken up via the TM8 groove/tunnel 1 pathway than those with lower PSA values.
Site-specific cleavage of RNAs derived from the PIM1 3′-UTR by a metal-free artificial ribonuclease
(2019)
Oligonucleotide conjugates of tris(2-aminobenzimidazole) have been reported previously to cleave complementary RNA strands with high levels of sequence and site specificity. The RNA substrates used in these studies were oligonucleotides not longer than 29-mers. Here we show that ~150–400-mer model transcripts derived from the 3′-untranslated region of the PIM1 mRNA reacted with rates and specificities comparable to those of short oligonucleotide substrates. The replacement of DNA by DNA/LNA mixmers further increased the cleavage rate. Tris(2-aminobenzimidazoles) were designed to interact with phosphates and phosphate esters. A cell, however, contains large amounts of phosphorylated species that may cause competitive inhibition of RNA cleavage. It is thus important to note that no loss in reaction rates was observed in phosphate buffer. This opens the way to in-cell applications for this type of artificial nuclease. Furthermore, we disclose a new synthetic method giving access to tris(2-aminobenzimidazoles) in multigram amounts.
Der gezielte, effiziente Aufbau komplexer Struktureinheiten, die mehrere Stereozentren besitzen, ist bis heute eine der größten Herausforderungen in der organischen Synthese. Gerade hinsichtlich der Wirkstoffentwicklung ist es von großer Bedeutung alle möglichen Stereoisomere einer Verbindung zugänglich zu machen. Die 1,3-Diamin-Struktureinheit ist Bestandteil interessanter Naturstoffe, biologisch aktiver Substanzen oder chiraler Liganden. Zusammenfassend konnte erfolgreich eine neue hoch modulare, stereokonvergente, Enamid/Acylimin-basierte Methode zur Synthese von 1,3-Diaminen mit drei fortlaufenden Stereozentren entwickelt werden. Diese Route bietet Zugang zur kompletten Tetrade möglicher Diastereomere, ausgehend von einfach zugänglichen Startmaterialien. Die Konfiguration der beiden zuerst gebildeten Stereozentren kann durch die Enamid-Geometrie kontrolliert werden ((E) -> 1,2 anti, (Z) -> 1,2-syn-Konfiguration). Die 2,3 Konfiguration kann hingegen über die geschickte Wahl der Reagenzien und den damit assoziierten Reaktionsbedingungen gesteuert werden. Weiterhin konnte eine Bi(OTf)3-katalysierte Ein-Topf-Sequenz zur diastereoselektiven Synthese von 1,2-anti-2,3-anti-1,3-Diaminen 6 etabliert werden. Darüber hinaus konnte die Synthese der N,O-Acetale, als auch die der Enamide optimiert und bzgl. der Synthesen im Multigrammmaßstab verbessert werden. Die N,O-Acetale konnten erfolgreich aus Amiden, Aldehyden und Alkoholen dargestellt werden. Die Enamide wurden unter Zuhilfenahme luftunempfindlicher Ni-Katalystoren aus Allylamiden mittels Isomerisierung zugänglich gemacht.