Solution structure of a repeated unit of the ABA-1 nematode polyprotein allergen of ascaris reveals a novel fold and two discrete lipid-binding sites

Parasitic nematode worms cause serious health problems in humans and other animals. They can induce allergic-type immune responses, which can be harmful but may at the same time protect against the infections. Allergens are proteins that trigger allergic reactions and these parasites produce a type that is confined to nematodes, the nematode polyprotein allergens (NPAs). These are synthesized as large precursor proteins comprising repeating units of similar amino acid sequence that are subsequently cleaved into multiple copies of the allergen protein. NPAs bind small lipids such as fatty acids and retinol (Vitamin A) and probably transport these sensitive and insoluble compounds between the tissues of the worms. Nematodes cannot synthesize these lipids, so NPAs may also be crucial for extracting nutrients from their hosts. They may also be involved in altering immune responses by controlling the lipids by which the immune and inflammatory cells communicate. We describe the molecular structure of one unit of an NPA, the well-known ABA-1 allergen of Ascaris and find its structure to be of a type not previously found for lipid-binding proteins, and we describe the unusual sites where lipids bind within this structur

Binding, domain orientation, and dynamics of the Lck SH3-SH2 domain pair and comparison with other Src-family kinases

The catalytic activity of Src-family kinases is regulated by association with its SH3 and SH2 domains. Activation requires displacement of intermolecular contacts by SH3/SH2 binding ligands resulting in dissociation of the SH3 and SH2 domains from the kinase domain. To understand the contribution of the SH3-SH2 domain pair to this regulatory process, the binding of peptides derived from physiologically relevant SH2 and SH3 interaction partners was studied for Lck and its relative Fyn by NMR spectroscopy. In contrast to Fyn, activating ligands do not induce communication between SH2 and SH3 domains in Lck. This can be attributed to the particular properties of the Lck SH3-SH2 linker which is shown to be extremely flexible thus effectively decoupling the behavior of the SH3 and SH2 domains. Measurements on the SH32 tandem from Lck further revealed a relative domain orientation that is distinctly different from that found in the Lck SH32 crystal structure and in other Src kinases. These data suggest that flexibility between SH2 and SH3 domains contributes to the adaptation of Src-family kinases to specific environments and distinct functions

Development and Validation of the Short-LIMOS for the Acute Stroke Unit-A Short Version of the Lucerne ICF-Based Multidisciplinary Observation Scale.

Introduction At hospital stroke units, the time available to assess the patient's limitations in activities and participation is limited, although being essential for discharge planning. Till date, there is no quick-to-perform instrument available that captures the patient's actual performance during daily activities from a motor, cognitive, and communication perspective within the International Classification of Functioning, Disability and Health (ICF) framework. Therefore, the aim was to develop and validate a shortened version of the Lucerne ICF-Based Multidisciplinary Observation Scale (Short-LIMOS) that observes the patient's performance across ICF-domains and is applicable in the context of an acute stroke unit. Methods The Short-LIMOS was developed by reducing the original 45-item LIMOS to the ten most important items using a multivariable linear regression ANOVA with data of 836 stroke patients collected during inpatient neurorehabilitation. The Short-LIMOS's reliability, validity, and responsiveness were evaluated with data of 416 stroke patients in the acute stroke unit. Results A significant equation [F (10,825) = 232.083] with R 2 of 0.738 was found for the following ten items for the Short-LIMOS: maintaining a body position (d415), changing basic body position (d410), climbing stairs (d4551), eating (d550), dressing (d540), communicating with-receiving-written messages (reading) (d325), applying knowledge, remembering facts (d179), solving complex problems (d1751), making simple decisions (d177), and undertaking a simple task (d2100). Principal component analysis revealed a Short-LIMOS motor and a Short-LIMOS cognition/communication component. The Short-LIMOS had a high internal consistency and good test-retest reliability. A moderate construct validity was shown by the significant correlation with the Barthel Index. The Short-LIMOS had neither floor nor ceiling effects. Discussion and Conclusion The developed Short-LIMOS was found to be reliable and valid within a population of (hyper)acute and subacute stroke patients. The added value of this multidisciplinary assessment is its comprehensiveness by capturing the patient's actual performance on the motor, cognitive, and communication domain embedded in an ICF-framework in <10 mins

The anti-sigma factor RsrA responds to oxidative stress by reburying its hydrophobic core

Redox-regulated effector systems that counteract oxidative stress are essential for all forms of life. Here we uncover a new paradigm for sensing oxidative stress centred on the hydrophobic core of a sensor protein. RsrA is an archetypal zinc-binding anti-sigma factor that responds to disulfide stress in the cytoplasm of Actinobacteria. We show that RsrA utilizes its hydrophobic core to bind the sigma factor σ R preventing its association with RNA polymerase, and that zinc plays a central role in maintaining this high-affinity complex. Oxidation of RsrA is limited by the rate of zinc release, which weakens the RsrA-σ R complex by accelerating its dissociation. The subsequent trigger disulfide, formed between specific combinations of RsrA's three zinc-binding cysteines, precipitates structural collapse to a compact state where all σ R-binding residues are sequestered back into its hydrophobic core, releasing σ R to activate transcription of anti-oxidant genes

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Large Interferometer For Exoplanets (LIFE): VIII. Where is the phosphine? Observing exoplanetary PH3 with a space based MIR nulling interferometer

Phosphine could be a key molecule in the understanding of exotic chemistry happening in (exo)planetary atmospheres. While it has been detected in the Solar System's giant planets, it has not been observed in exoplanets yet. In the exoplanetary context however it has been theorized as a potential biosignature molecule. The goal of our study is to identify which illustrative science cases for PH3 chemistry are observable with a space-based mid-infrared nulling interferometric observatory like the LIFE (Large Interferometer For Exoplanets) concept. We identified a representative set of scenarios for PH3 detections in exoplanetary atmospheres varying over the whole dynamic range of the LIFE mission. We used chemical kinetics and radiative transfer calculations to produce forward models of these informative, prototypical observational cases for LIFEsim, our observation simulator software for LIFE. In a detailed, yet first order approximation it takes a mission like LIFE: (i) about 1h to find phosphine in a warm giant around a G star at 10 pc, (ii) about 10 h in H2 or CO2 dominated temperate super-Earths around M star hosts at 5 pc, (iii) and even in 100h it seems very unlikely that phosphine would be detectable in a Venus-Twin with extreme PH3 concentrations at 5 pc. Phosphine in concentrations previously discussed in the literature is detectable in 2 out of the 3 cases and about an order of magnitude faster than comparable cases with JWST. We show that there is a significant number of objects accessible for these classes of observations. These results will be used to prioritize the parameter range for the next steps with more detailed retrieval simulations. They will also inform timely questions in the early design phase of a mission like LIFE and guide the community by providing easy-to-scale first estimates for a large part of detection space of such a mission.Comment: In press. Accepted for publication in Astrobiology on 02 November 2022. 26 pages, 5 figures and 8 table

Watson–Crick and Sugar-Edge Base Pairing of Cytosine in the Gas Phase: UV and Infrared Spectra of Cytosine·2-Pyridone

While keto-amino cytosine is the dominant species in aqueous solution, spectroscopic studies in molecular beams and in noble gas matrices show that other cytosine tautomers prevail in apolar environments. Each of these offers two or three H-bonding sites (Watson–Crick, wobble, sugar-edge). The mass- and isomer-specific S1 ← S0 vibronic spectra of cytosine·2-pyridone (Cyt·2PY) and 1-methylcytosine·2PY are measured using UV laser resonant two-photon ionization (R2PI), UV/UV depletion, and IR depletion spectroscopy. The UV spectra of the Watson–Crick and sugar-edge isomers of Cyt·2PY are separated using UV/UV spectral hole-burning. Five different isomers of Cyt·2PY are observed in a supersonic beam. We show that the Watson–Crick and sugar-edge dimers of keto-amino cytosine with 2PY are the most abundant in the beam, although keto-amino-cytosine is only the third most abundant tautomer in the gas phase. We identify the different isomers by combining three different diagnostic tools: (1) methylation of the cytosine N1–H group prevents formation of both the sugar-edge and wobble isomers and gives the Watson–Crick isomer exclusively. (2) The calculated ground state binding and dissociation energies, relative gas-phase abundances, excitation and the ionization energies are in agreement with the assignment of the dominant Cyt·2PY isomers to the Watson–Crick and sugar-edge complexes of keto-amino cytosine. (3) The comparison of calculated ground state vibrational frequencies to the experimental IR spectra in the carbonyl stretch and NH/OH/CH stretch ranges strengthen this identification

Engineering a two-helix bundle protein for folding studies

The SAP domain from the Saccharomyces cerevisiae THO1 protein contains a hydrophobic core and just two α-helices. It could provide a system for studying protein folding that bridges the gap between studies on isolated helices and those on larger protein domains. We have engineered the SAP domain for protein folding studies by inserting a tryptophan residue into the hydrophobic core (L31W) and solved its structure. The helical regions had a backbone root mean-squared deviation of 0.9 Å from those of wild type. The mutation L31W destabilised wild type by 0.8 ± 0.1 kcal mol−1. The mutant folded in a reversible, apparent two-state manner with a microscopic folding rate constant of around 3700 s−1 and is suitable for extended studies of folding

Deuterium isotope effects on 15N backbone chemical shifts in proteins

Quantum mechanical calculations are presented that predict that one-bond deuterium isotope effects on the 15N chemical shift of backbone amides of proteins, 1Δ15N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for 1Δ15N(D) including the backbone dihedral angles, Φ and Ψ, and the hydrogen bonding geometry is presented for glycine and amino acid residues with aliphatic side chains. The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N–H bond length. Another contributing factor is the effect of increased anharmonicity of the N–H stretching vibrational state upon hydrogen bonding, which results in an altered N–H/N–D equilibrium bond length ratio. The N–H stretching anharmonicity contribution falls off with the cosine of the N–H···O bond angle. For residues with uncharged side chains a very good prediction of isotope effects can be made. Thus, for proteins with known secondary structures, 1Δ15N(D) can provide insights into hydrogen bonding geometries

Structural basis for the photoconversion of a phytochrome to the activated far-red light-absorbing form

Phytochromes are a collection of bilin-containing photoreceptors that regulate numerous photoresponses in plants and microorganisms through their ability to photointerconvert between a red light-absorbing, ground state Pr and a far-red light-absorbing, photoactivated state Pfr1,2. While the structures of several phytochromes as Pr have been determined3-7, little is known about the structure of Pfr and how it initiates signaling. Here, we describe the three-dimensional solution structure of the bilin-binding domain as Pfr using the cyanobacterial phytochrome from Synechococcus OSB’. Contrary to predictions, light-induced rotation of the A but not the D pyrrole ring is the primary motion of the chromophore during photoconversion. Subsequent rearrangements within the protein then affect intra- and interdomain contact sites within the phytochrome dimer. From our models, we propose that phytochromes act by propagating reversible light-driven conformational changes in the bilin to altered contacts between the adjacent output domains, which in most phytochromes direct differential phosphotransfer