Separate Entrance and Exit Portals for Ligand Traffic in Mycobacterium tuberculosis FabH

SummaryMycobacterium tuberculosis FabH initiates type II fatty acid synthase-catalyzed formation of the long chain (C16–C22) acyl-coenzyme A (CoA) precursors of mycolic acids, which are major constituents of the bacterial cell envelope. Crystal structures of M. tuberculosis FabH (mtFabH) show the substrate binding site to be a buried, extended L-shaped channel with only a single solvent access portal. Entrance of an acyl-CoA substrate through the solvent portal would require energetically unfavorable reptational threading of the substrate to its reactive position. Using a class of FabH inhibitors, we have tested an alternative hypothesis that FabH exists in an “open” form during substrate binding and product release, and a “closed” form in which catalysis and intermediate steps occur. This hypothesis is supported by mass spectrometric analysis of the product profile and crystal structures of complexes of mtFabH with these inhibitors

Applying an Empirical Hydropathic Forcefield in Refinement May Improve Low-Resolution Protein X-Ray Crystal Structures

BACKGROUND: The quality of X-ray crystallographic models for biomacromolecules refined from data obtained at high-resolution is assured by the data itself. However, at low-resolution, >3.0 Å, additional information is supplied by a forcefield coupled with an associated refinement protocol. These resulting structures are often of lower quality and thus unsuitable for downstream activities like structure-based drug discovery. METHODOLOGY: An X-ray crystallography refinement protocol that enhances standard methodology by incorporating energy terms from the HINT (Hydropathic INTeractions) empirical forcefield is described. This protocol was tested by refining synthetic low-resolution structural data derived from 25 diverse high-resolution structures, and referencing the resulting models to these structures. The models were also evaluated with global structural quality metrics, e.g., Ramachandran score and MolProbity clashscore. Three additional structures, for which only low-resolution data are available, were also re-refined with this methodology. RESULTS: The enhanced refinement protocol is most beneficial for reflection data at resolutions of 3.0 Å or worse. At the low-resolution limit, ≥4.0 Å, the new protocol generated models with Cα positions that have RMSDs that are 0.18 Å more similar to the reference high-resolution structure, Ramachandran scores improved by 13%, and clashscores improved by 51%, all in comparison to models generated with the standard refinement protocol. The hydropathic forcefield terms are at least as effective as Coulombic electrostatic terms in maintaining polar interaction networks, and significantly more effective in maintaining hydrophobic networks, as synthetic resolution is decremented. Even at resolutions ≥4.0 Å, these latter networks are generally native-like, as measured with a hydropathic interactions scoring tool

Identification of carbon dioxide in an exoplanet atmosphere

Carbon dioxide (CO2) is a key chemical species that is found in a wide range of planetary atmospheres. In the context of exoplanets, CO2 is an indicator of the metal enrichment (that is, elements heavier than helium, also called 'metallicity')1-3, and thus the formation processes of the primary atmospheres of hot gas giants4-6. It is also one of the most promising species to detect in the secondary atmospheres of terrestrial exoplanets7-9. Previous photometric measurements of transiting planets with the Spitzer Space Telescope have given hints of the presence of CO2, but have not yielded definitive detections owing to the lack of unambiguous spectroscopic identification10-12. Here we present the detection of CO2 in the atmosphere of the gas giant exoplanet WASP-39b from transmission spectroscopy observations obtained with JWST as part of the Early Release Science programme13,14. The data used in this study span 3.0-5.5 micrometres in wavelength and show a prominent CO2 absorption feature at 4.3 micrometres (26-sigma significance). The overall spectrum is well matched by one-dimensional, ten-times solar metallicity models that assume radiative-convective-thermochemical equilibrium and have moderate cloud opacity. These models predict that the atmosphere should have water, carbon monoxide and hydrogen sulfide in addition to CO2, but little methane. Furthermore, we also tentatively detect a small absorption feature near 4.0 micrometres that is not reproduced by these models

The TESS-Keck Survey. III. A Stellar Obliquity Measurement of TOI-1726 c

We report the measurement of a spectroscopic transit of TOI-1726c, one of two planets transiting a G-type star with V = 6.9 in the Ursa Major Moving Group (~400 Myr). With a precise age constraint from cluster membership, TOI-1726 provides a great opportunity to test various obliquity excitation scenarios that operate on different timescales. By modeling the Rossiter–McLaughlin (RM) effect, we derived a sky-projected obliquity of −1^(+35)_(−32)∘. This result rules out a polar/retrograde orbit and is consistent with an aligned orbit for planet c. Considering the previously reported, similarly prograde RM measurement of planet b and the transiting nature of both planets, TOI-1726 tentatively conforms to the overall picture that compact multitransiting planetary systems tend to have coplanar, likely aligned orbits. TOI-1726 is also a great atmospheric target for understanding differential atmospheric loss of sub-Neptune planets (planet b 2.2 R⊕ and c 2.7 R⊕ both likely underwent photoevaporation). The coplanar geometry points to a dynamically cold history of the system that simplifies any future modeling of atmospheric escape

Awesome SOSS: transmission spectroscopy of WASP-96b with NIRISS/SOSS

This is the final version. Available from Oxford University Press via the DOI in this recordData availability: All data used in this study is publicly available from the Barbara A. Mikulski Archive for Space Telescopes: https://mast.stsci.edu/portal/Mashup/Clients/Mast/Portal.htmlThe future is now - after its long-awaited launch in 2021 December, JWST began science operations in 2022 July and is already revolutionizing exoplanet astronomy. The Early Release Observations (ERO) programme was designed to provide the first images and spectra from JWST, covering a multitude of science cases and using multiple modes of each on-board instrument. Here, we present transmission spectroscopy observations of the hot-Saturn WASP-96 b with the Single Object Slitless Spectroscopy (SOSS) mode of the Near Infrared Imager and Slitless Spectrograph, observed as part of the ERO programme. As the SOSS mode presents some unique data reduction challenges, we provide an in-depth walk-through of the major steps necessary for the reduction of SOSS data: including background subtraction, correction of 1/f noise, and treatment of the trace order overlap. We furthermore offer potential routes to correct for field star contamination, which can occur due to the SOSS mode's slitless nature. By comparing our extracted transmission spectrum with grids of atmosphere models, we find an atmosphere metallicity between 1× and 5× solar, and a solar carbon-to-oxygen ratio. Moreover, our models indicate that no grey cloud deck is required to fit WASP-96 b's transmission spectrum, but find evidence for a slope shortward of 0.9 μm, which could either be caused by enhanced Rayleigh scattering or the red wing of a pressure-broadened Na feature. Our work demonstrates the unique capabilities of the SOSS mode for exoplanet transmission spectroscopy and presents a step-by-step reduction guide for this new and exciting instrument

A second planet transiting LTT 1445A and a determination of the masses of both worlds

K.H. acknowledges support from STFC grant ST/R000824/1.LTT 1445 is a hierarchical triple M-dwarf star system located at a distance of 6.86 pc. The primary star LTT 1445A (0.257 M⊙) is known to host the transiting planet LTT 1445Ab with an orbital period of 5.36 days, making it the second-closest known transiting exoplanet system, and the closest one for which the host is an M dwarf. Using Transiting Exoplanet Survey Satellite data, we present the discovery of a second planet in the LTT 1445 system, with an orbital period of 3.12 days. We combine radial-velocity measurements obtained from the five spectrographs, Echelle Spectrograph for Rocky Exoplanets and Stable Spectroscopic Observations, High Accuracy Radial Velocity Planet Searcher, High-Resolution Echelle Spectrometer, MAROON-X, and Planet Finder Spectrograph to establish that the new world also orbits LTT 1445A. We determine the mass and radius of LTT 1445Ab to be 2.87 ± 0.25 M⊕ and 1.304-0.060+0.067 R⊕, consistent with an Earth-like composition. For the newly discovered LTT 1445Ac, we measure a mass of 1.54-0.19+0.20 M⊕ and a minimum radius of 1.15 R⊕, but we cannot determine the radius directly as the signal-to-noise ratio of our light curve permits both grazing and nongrazing configurations. Using MEarth photometry and ground-based spectroscopy, we establish that star C (0.161 M⊙) is likely the source of the 1.4 day rotation period, and star B (0.215 M⊙) has a likely rotation period of 6.7 days. We estimate a probable rotation period of 85 days for LTT 1445A. Thus, this triple M-dwarf system appears to be in a special evolutionary stage where the most massive M dwarf has spun down, the intermediate mass M dwarf is in the process of spinning down, while the least massive stellar component has not yet begun to spin down.Publisher PDFPeer reviewe

The TESS-Keck Survey. XI. Mass Measurements for Four Transiting Sub-Neptunes Orbiting K Dwarf TOI-1246

Multiplanet systems are valuable arenas for investigating exoplanet architectures and comparing planetary siblings. TOI-1246 is one such system, with a moderately bright K dwarf (V = 11.6, K = 9.9) and four transiting sub-Neptunes identified by TESS with orbital periods of 4.31, 5.90, 18.66, and 37.92 days. We collected 130 radial velocity observations with Keck/HIRES and TNG/HARPS-N to measure planet masses. We refit the 14 sectors of TESS photometry to refine planet radii (2.97 +/- 0.06 R (circle plus), 2.47 +/- 0.08 R (circle plus), 3.46 +/- 0.09 R (circle plus), and 3.72 +/- 0.16 R (circle plus)) and confirm the four planets. We find that TOI-1246 e is substantially more massive than the three inner planets (8.1 +/- 1.1 M (circle plus), 8.8 +/- 1.2 M (circle plus), 5.3 +/- 1.7 M (circle plus), and 14.8 +/- 2.3 M (circle plus)). The two outer planets, TOI-1246 d and TOI-1246 e, lie near to the 2:1 resonance (P (e)/P ( d ) = 2.03) and exhibit transit-timing variations. TOI-1246 is one of the brightest four-planet systems, making it amenable for continued observations. It is one of only five systems with measured masses and radii for all four transiting planets. The planet densities range from 0.70 +/- 0.24 to 3.21 +/- 0.44 g cm(-3), implying a range of bulk and atmospheric compositions. We also report a fifth planet candidate found in the RV data with a minimum mass of 25.6 +/- 3.6 M (circle plus). This planet candidate is exterior to TOI-1246 e, with a candidate period of 93.8 days, and we discuss the implications if it is confirmed to be planetary in nature

The TESS-Keck Survey. XI. Mass Measurements for Four Transiting sub-Neptunes orbiting K dwarf TOI-1246

Multi-planet systems are valuable arenas for investigating exoplanet architectures and comparing planetary siblings. TOI-1246 is one such system, with a moderately bright K dwarf (V=11.6, K=9.9) and four transiting sub-Neptunes identified by TESS with orbital periods of 4.31 d, 5.90 d, 18.66 d, and 37.92 d. We collected 130 radial velocity observations with Keck/HIRES and TNG/HARPS-N to measure planet masses. We refit the 14 sectors of TESS photometry to refine planet radii (2.97±0.06 R⊕,2.47±0.08 R⊕,3.46±0.09 R⊕, 3.72±0.16 R⊕), and confirm the four planets. We find that TOI-1246 e is substantially more massive than the three inner planets (8.1±1.1M⊕, 8.8±1.2M⊕, 5.3±1.7M⊕, 14.8±2.3M⊕). The two outer planets, TOI-1246 d and TOI-1246 e, lie near to the 2:1 resonance (Pe/Pd=2.03) and exhibit transit timing variations. TOI-1246 is one of the brightest four-planet systems, making it amenable for continued observations. It is one of only six systems with measured masses and radii for all four transiting planets. The planet densities range from 0.70±0.24 to 3.21±0.44g/cm3, implying a range of bulk and atmospheric compositions. We also report a fifth planet candidate found in the RV data with a minimum mass of 25.6 ± 3.6 M⊕. This planet candidate is exterior to TOI-1246 e with a candidate period of 93.8 d, and we discuss the implications if it is confirmed to be planetary in nature

HD 207897 b : a dense sub-Neptune transiting a nearby and bright K-type star

We present the discovery and characterization of a transiting sub-Neptune that orbits the nearby (28 pc) and bright (V = 8.37) K0V star HD 207897 (TOI-1611) with a 16.20-day period. This discovery is based on photometric measurements from the Transiting Exoplanet Survey Satellite mission and radial velocity (RV) observations from the SOPHIE, Automated Planet Finder, and HIRES high-precision spectrographs. We used EXOFASTv2 to model the parameters of the planet and its host star simultaneously, combining photometric and RV data to determine the planetary system parameters. We show that the planet has a radius of 2.50 ± 0.08 RE and a mass of either 14.4 ± 1.6 ME or 15.9 ± 1.6 ME with nearly equal probability. The two solutions correspond to two possibilities for the stellar activity period. The density accordingly is either 5.1 ± 0.7 g cm−3 or 5.5−0.7+0.8 g cm−3, making it one of the relatively rare dense sub-Neptunes. The existence of this dense planet at only 0.12 AU from its host star is unusual in the currently observed sub-Neptune (2 < RE < 4) population. The most likely scenario is that this planet has migrated to its current position

The TESS-keck survey. III. A stellar obliquity measurement of TOI-1726 c

We report the measurement of a spectroscopic transit of TOI-1726c, one of two planets transiting a G-type star with V = 6.9 in the Ursa Major Moving Group (∼400 Myr). With a precise age constraint from cluster membership, TOI-1726 provides a great opportunity to test various obliquity excitation scenarios that operate on different timescales. By modeling the Rossiter-McLaughlin (RM) effect, we derived a sky-projected obliquity of -1-+3235∘. This result rules out a polar/retrograde orbit and is consistent with an aligned orbit for planet c. Considering the previously reported, similarly prograde RM measurement of planet b and the transiting nature of both planets, TOI-1726 tentatively conforms to the overall picture that compact multitransiting planetary systems tend to have coplanar, likely aligned orbits. TOI-1726 is also a great atmospheric target for understanding differential atmospheric loss of sub-Neptune planets (planet b 2.2 R☉ and c 2.7 R☉ both likely underwent photoevaporation). The coplanar geometry points to a dynamically cold history of the system that simplifies any future modeling of atmospheric escape