Cellular Scent of Influenza Virus Infection.

Volatile organic compounds (VOCs) emanating from humans have the potential to revolutionize non‐invasive diagnostics. Yet, little is known about how these compounds are generated by complex biological systems, and even less is known about how these compounds are reflective of a particular physiological state. In this proof‐of‐concept study, we examined VOCs produced directly at the cellular level from B lymphoblastoid cells upon infection with three live influenza virus subtypes: H9N2 (avian), H6N2 (avian), and H1N1 (human). Using a single cell line helped to alleviate some of the complexity and variability when studying VOC production by an entire organism, and it allowed us to discern marked differences in VOC production upon infection of the cells. The patterns of VOCs produced in response to infection were unique for each virus subtype, while several other non‐specific VOCs were produced after infections with all three strains. Also, there was a specific time course of VOC release post infection. Among emitted VOCs, production of esters and other oxygenated compounds was particularly notable, and these may be attributed to increased oxidative stress resulting from infection. Elucidating VOC signatures that result from the host cells response to infection may yield an avenue for non‐invasive diagnostics and therapy of influenza and other viral infections.     

Rapid Total Synthesis of DARPin pE59 and Barnase

We report the convergent total synthesis of two proteins: DARPin pE59 and Bacillus amyloliquefaciens RNase (Barnase). Leveraging our recently developed fast‐flow peptide‐synthesis platform, we rapidly explored numerous conditions for the assembly of long polypeptides, and were able to mitigate common side reactions, including deletion and aspartimide products. We report general strategies for improving the synthetic quality of difficult peptide sequences with our system. High‐quality protein fragments produced under optimal synthetic conditions were subjected to convergent native chemical ligation, which afforded native full‐length proteins after a final desulfurization step. Both DARPin and Barnase were folded and found to be as active as their recombinant analogues.     

Combined Mutagenesis and Kinetics Characterization of the Bilin‐Binding GAF Domain of the Protein Slr1393 from the Cyanobacterium Synechocystis PCC6803

The gene slr1393 from Synechocystis sp. PCC6803 encodes a protein composed of three GAF domains, a PAS domain, and a histidine kinase domain. GAF3 is the sole domain able to bind phycocyanobilin (PCB) as chromophore and to accomplish photochemistry: switching between a red‐absorbing parental and a green‐absorbing photoproduct state (λ_max=649 and 536 nm, respectively). Conversions in both directions were followed by time‐resolved absorption spectroscopy with the separately expressed GAF3 domain of Slr1393. Global fit analysis of the recorded absorbance changes yielded three lifetimes (3.2 μs, 390 μs, and 1.5 ms) for the red‐to‐green conversion, and 1.2 μs, 340 μs, and 1 ms for the green‐to‐red conversion. In addition to the wild‐type (WT) protein, 24 mutated proteins were studied spectroscopically. The design of these site‐directed mutations was based on sequence alignments with related proteins and by employing the crystal structure of AnPixJg2 (PDB ID: 3W2Z), a Slr1393 orthologous from Anabaena sp. PCC7120. The structure of AnPixJg2 was also used as template for model building, thus confirming the strong structural similarity between the proteins, and for identifying amino acids to target for mutagenesis. Only amino acids in close proximity to the chromophore were exchanged, as these were considered likely to have an impact on the spectral and dynamic properties. Three groups of mutants were found: some showed absorption features similar to the WT protein, a second group showed modified absorbance properties, and the third group had lost the ability to bind the chromophore. The most unexpected result was obtained for the exchange at residue 532 (N532Y). In vivo assembly yielded a red‐absorbing, WT‐like protein. Irradiation, however, not only converted it into the green‐absorbing form, but also produced a 660 nm, further‐red‐shifted absorbance band. This photoproduct was fully reversible to the parental form upon green light irradiation.     

Small‐Molecule Proteomimetic Inhibitors of the HIF‐1α–p300 Protein–Protein Interaction

The therapeutically relevant hypoxia inducible factor HIF‐1α–p300 protein–protein interaction can be orthosterically inhibited with α‐helix mimetics based on an oligoamide scaffold that recapitulates essential features of the C‐terminal helix of the HIF‐1α C‐TAD (C‐terminal transactivation domain). Preliminary SAR studies demonstrated the important role of side‐chain size and hydrophobicity/hydrophilicity in determining potency. These small molecules represent the first biophysically characterised HIF‐1α–p300 PPI inhibitors and the first examples of small‐molecule aromatic oligoamide helix mimetics to be shown to have a selective binding profile. Although the compounds were less potent than HIF‐1α, the result is still remarkable in that the mimetic reproduces only three residues from the 42‐residue HIF‐1α C‐TAD from which it is derived.     

Using Singular Value Decomposition to Characterize Protein–Protein Interactions by In‐cell NMR Spectroscopy

Distinct differences between how model proteins interact in‐cell and in vitro suggest that the cytosol might have a profound effect in modulating protein–protein and/or protein–ligand interactions that are not observed in vitro. Analyses of in‐cell NMR spectra of target proteins interacting with physiological partners are further complicated by low signal‐to‐noise ratios, and the long overexpression times used in protein–protein interaction studies may lead to changes in the in‐cell spectra over the course of the experiment. To unambiguously resolve the principal binding mode between two interacting species against the dynamic cellular background, we analyzed in‐cell spectral data of a target protein over the time course of overexpression of its interacting partner by using single‐value decomposition (SVD). SVD differentiates between concentration‐dependent and concentration‐independent events and identifies the principal binding mode between the two species. The analysis implicates a set of amino acids involved in the specific interaction that differs from previous NMR analyses but is in good agreement with crystallographic data.     

Adsorption of naphthalene and indole on F300 MOF in liquid phase by the complementary spectroscopic,kinetic and DFT studies

Metal–organic frameworks (MOFs) are the promising functional materials for adsorption in liquid phase. It is important to understand the details of chemical bonding between the aromatic and heteroaromatic adsorbates and major structural units in the MOF sorbent—metal coordinatively unsaturated sites (CUS) and organic linkers. In this paper, we report the mechanistic studies of adsorption of naphthalene and indole on F300 Basolite MOF by two complementary spectroscopic methods and density functional theory (DFT) calculations. Fluorescence spectra, the near-UV/visible diffuse reflectance spectroscopy (near-UV/VIS DRS) and DFT calculations suggest that naphthalene forms an adsorption complex with F300 MOF where naphthalene is quantum confined within the cavity of the F300, weakly electronically bound to the Fe(III) CUS, and strongly dispersively stabilized by side interactions with the benzene rings of the linker of F300. On the other hand, indole forms an adsorption complex with F300 MOF in which indole is electronically bound to the Fe(III) CUS and dispersively stabilized by the side interactions with benzene rings of the linker. Coordination bonds between indole and F300 MOF in the adsorption complex are detected by geometry optimization using the DFT method, and electronic spectra are calculated by the time-dependent-DFT method. The direct spectroscopic proof of the formation of adsorption complex with coordination bonds between indole and F300 MOF is provided by the complementary near-UV/VIS DRS spectroscopy (new absorption bands at 460–660 nm), the wavelength-dependent fluorescence spectroscopy (new fluorescence bands at 410 and 430 nm) and by the time-dependent fluorescence spectroscopy.     

Structural and Biochemical Studies of Actin in Complex with Synthetic Macrolide Tail Analogues

The actin filament‐binding and filament‐severing activities of the aplyronine, kabiramide, and reidispongiolide families of marine macrolides are located within the hydrophobic tail region of the molecule. Two synthetic tail analogues of aplyronine C (SF‐01 and GC‐04) are shown to bind to G‐actin with dissociation constants of (285±33) and (132±13) nM , respectively. The crystal structures of actin complexes with GC‐04, SF‐01, and kabiramide C reveal a conserved mode of tail binding within the cleft that forms between subdomains (SD) 1 and 3. Our studies support the view that filament severing is brought about by specific binding of the tail region to the SD1/SD3 cleft on the upper protomer, which displaces loop‐D from the lower protomer on the same half‐filament. With previous studies showing that the GC‐04 analogue can sever actin filaments, it is argued that the shorter complex lifetime of tail analogues with F‐actin would make them more effective at severing filaments compared with plasma gelsolin. Structure‐based analyses are used to suggest more reactive or targetable forms of GC‐04 and SF‐01, which may serve to boost the capacity of the serum actin scavenging system, to generate antibody conjugates against tumor cell antigens, and to decrease sputum viscosity in children with cystic fibrosis.     

MALDI-TOF MS and Morphology Studies of Thiacalixarene-Silsesquioxane Products of Oligo- and Polycondensation

For the first time condensed silsesquioxane derivatives of tetratrialkoxysilyl compounds have been characterized by MALDI-TOF mass spectrometry. Tetrasubstituted p-tert-butyl thiacalix[4]arene derivatives containing organosilicon fragments with variable stereochemistry were chosen as organosilicon compounds for polycondensation. Information obtained from mass spectra was used to deduce both the structures of oligomeric derivatives, as well as the structure of silsesquioxane framework. The morphology of formed polysilsesquioxanes was investigated by scanning and transmission electron microscopy.     

Design of a General‐Purpose European Compound Screening Library for EU‐OPENSCREEN

This work describes a collaborative effort to define and apply a protocol for the rational selection of a general‐purpose screening library, to be used by the screening platforms affiliated with the EU‐OPENSCREEN initiative. It is designed as a standard source of compounds for primary screening against novel biological targets, at the request of research partners. Given the general nature of the potential applications of this compound collection, the focus of the selection strategy lies on ensuring chemical stability, absence of reactive compounds, screening‐compliant physicochemical properties, loose compliance to drug‐likeness criteria (as drug design is a major, but not exclusive application), and maximal diversity/coverage of chemical space, aimed at providing hits for a wide spectrum of drugable targets. Finally, practical availability/cost issues cannot be avoided. The main goal of this publication is to inform potential future users of this library about its conception, sources, and characteristics. The outline of the selection procedure, notably of the filtering rules designed by a large committee of European medicinal chemists and chemoinformaticians, may be of general methodological interest for the screening/medicinal chemistry community. The selection task of 200K molecules out of a pre‐filtered set of 1.4M candidates was shared by five independent European research groups, each picking a subset of 40K compounds according to their own in‐house methodology and expertise. An in‐depth analysis of chemical space coverage of the library serves not only to characterize the collection, but also to compare the various chemoinformatics‐driven selection procedures of maximal diversity sets. Compound selections contributed by various participating groups were mapped onto general‐purpose self‐organizing maps (SOMs) built on the basis of marketed drugs and bioactive reference molecules. In this way, the occupancy of chemical space by the EU‐OPENSCREEN library could be directly compared with distributions of known bioactives of various classes. This mapping highlights the relevance of the selection and shows how the consensus reached by merging the five different 40K selections contributes to achieve this relevance. The approach also allows one to readily identify subsets of target‐ or target‐class‐oriented compounds from the EU‐OPENSCREEN library to suit the needs of the diverse range of potential users. The final EU‐OPENSCREEN library, assembled by merging five independent selections of 40K compounds from various expert groups, represents an excellent example of a Europe‐wide collaborative effort toward the common objective of building best‐in‐class European open screening platforms.     

Ecological resilience and resilient cities

The urban realm is changing rapidly and becoming increasingly interconnected across continents, and across contrasting types of land covers, while at the same time facing new environmental threats and experiencing new demographic and social pressures. The urban component of the global ecosystem can be made more sustainable by incorporating the ecological understanding of resilience into the discourse. Sustainability is seen as a social, normative goal, which can be promoted using the mechanisms of ecological resilience. Ecological resilience differs from engineering resilience. Ecological resilience emphasizes the capacity of a site to adjust to external shocks and changes in controlling interactions, while engineering resilience emphasizes its ability to return to a state that existed before perturbation. Ecological resilience is particularly appropriate to urban systems, given the extent and open-ended nature of the changes and challenges they face. Adaptive processes are explored as contributions to the achievement of a successful adaptive cycle in urban socio-ecological systems. Key tools for incorporating the ecological thinking about resilience into the social discourse include landscape or patch ecology, the novel idea of the metacity, an assessment of ecological and design models, and the use of designs as experiments.