Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites

NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, “closed” conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes

The JWST Early Release Science Program for Direct Observations of Exoplanetary Systems. IV. NIRISS Aperture Masking Interferometry Performance and Lessons Learned

This is the final version. Available on open access from IOP Publishing via the DOI in this recordWe present a performance analysis for the aperture masking interferometry (AMI) mode on board the James Webb Space Telescope Near Infrared Imager and Slitless Spectrograph (JWST/NIRISS). Thanks to self-calibrating observables, AMI accesses inner working angles down to and even within the classical diffraction limit. The scientific potential of this mode has recently been demonstrated by the Early Release Science (ERS) 1386 program with a deep search for close-in companions in the HIP 65426 exoplanetary system. As part of ERS 1386, we use the same data set to explore the random, static, and calibration errors of NIRISS AMI observables. We compare the observed noise properties and achievable contrast to theoretical predictions. We explore possible sources of calibration errors and show that differences in charge migration between the observations of HIP 65426 and point-spread function calibration stars can account for the achieved contrast curves. Lastly, we use self-calibration tests to demonstrate that with adequate calibration NIRISS F380M AMI can reach contrast levels of ~9-10 mag at ≥λ/D. These tests lead us to observation planning recommendations and strongly motivate future studies aimed at producing sophisticated calibration strategies taking these systematic effects into account. This will unlock the unprecedented capabilities of JWST/NIRISS AMI, with sensitivity to significantly colder, lower-mass exoplanets than lower-contrast ground-based AMI setups, at orbital separations inaccessible to JWST coronagraphy.National Science Foundation (NSF)NASAEuropean Union Horizon 2020Royal Societ

The JWST Early Release Science Program for Direct Observations of Exoplanetary Systems. V. Do Self-consistent Atmospheric Models Represent JWST Spectra? A Showcase with VHS 1256–1257 b

This is the final version. Available on open access from IOP Publishing via the DOI in this recordThe unprecedented medium-resolution (Rλ ∼ 1500–3500) near- and mid-infrared (1–18 μm) spectrum provided by JWST for the young (140 ± 20 Myr) low-mass (12–20 MJup) L–T transition (L7) companion VHS 1256 b gives access to a catalog of molecular absorptions. In this study, we present a comprehensive analysis of this data set utilizing a forward-modeling approach applying our Bayesian framework, ForMoSA. We explore five distinct atmospheric models to assess their performance in estimating key atmospheric parameters: Teff, log(g), [M/H], C/O, γ, fsed, and R. Our findings reveal that each parameter's estimate is significantly influenced by factors such as the wavelength range considered and the model chosen for the fit. This is attributed to systematic errors in the models and their challenges in accurately replicating the complex atmospheric structure of VHS 1256 b, notably the complexity of its clouds and dust distribution. To propagate the impact of these systematic uncertainties on our atmospheric property estimates, we introduce innovative fitting methodologies based on independent fits performed on different spectral windows. We finally derived a Teff consistent with the spectral type of the target, considering its young age, which is confirmed by our estimate of log(g). Despite the exceptional data quality, attaining robust estimates for chemical abundances [M/H] and C/O, often employed as indicators of formation history, remains challenging. Nevertheless, the pioneering case of JWST's data for VHS 1256 b has paved the way for future acquisitions of substellar spectra that will be systematically analyzed to directly compare the properties of these objects and correct the systematics in the models

Measurements of photo-nuclear jet production in Pb plus Pb collisions with ATLAS

Ultra-peripheral heavy ion collisions provide a unique opportunity to study the parton distributions in the colliding nuclei via the measurement of photo-nuclear jet production. An analysis of jet production in ultra-peripheral Pb+Pb collisions at √sNN = 5.02 TeV performed using data collected with the ATLAS detector in 2015 is described. The data set corresponds to a total Pb+Pb integrated luminosity of 0.38 nb−1. The ultra-peripheral collisions are selected using a combination of forward neutron and rapidity gap requirements. The cross-sections, not unfolded for detector response, are compared to results from Pythia Monte Carlo simulations re-weighted to match a photon spectrum obtained from the STARlight model. Qualitative agreement between data and these simulations is observed over a broad kinematic range suggesting that using these collisions to measure nuclear parton distributions is experimentally realisable

Measurements of photo-nuclear jet production in Pb + Pb collisions with ATLAS

Ultra-peripheral heavy ion collisions provide a unique opportunity to study the parton distributions in the colliding nuclei via the measurement of photo-nuclear jet production. An analysis of jet production in ultra-peripheral Pb+Pb collisions at √sNN = 5.02 TeV performed using data collected with the ATLAS detector in 2015 is described. The data set corresponds to a total Pb+Pb integrated luminosity of 0.38 nb⁻¹. The ultra-peripheral collisions are selected using a combination of forward neutron and rapidity gap requirements. The cross-sections, not unfolded for detector response, are compared to results from Pythia Monte Carlo simulations re-weighted to match a photon spectrum obtained from the STARlight model. Qualitative agreement between data and these simulations is observed over a broad kinematic range suggesting that using these collisions to measure nuclear parton distributions is experimentally realisable