Multidimensional NMR identifies the conformational shift essential for catalytic competence in the 60-kDa Drosophila melanogaster dUTPase trimer

The catalytic mechanism of dUTP pyrophosphatase (dUTPase), responsible for the prevention of uracil incorporation into DNA, involves ordering of the flexible C terminus of the enzyme. This conformational shift is investigated by multidimensional NMR on the Drosophila enzyme. Flexible segments of the homotrimer give rise to sharp resonances in the H-1-N-15 heteronuclear single-quantum coherence (HSQC) spectra, which are clearly distinguishable from the background resonances of the well folded protein globule. Binding of the product dUMP or the analogues dUDP and alpha,beta-imino-dUTP to the enzyme induces a conformational change reflected in the disappearance of eight sharp resonances. This phenomenon is interpreted as nucleotide binding-induced ordering of some residues upon the folded protein globule. Three-dimensional N-15-edited H-1-N-15 HSQC total correlation spectroscopy (TOCSY) and H-1-N-15 HSQC nuclear Overhauser effect spectroscopy measurements allowed clear assignment of these eight specific resonance peaks. The residues identified correspond to the conserved C-terminal sequence motif, indicating that (i) this conformational shift is amenable to NMR studies in solution even in the large trimeric molecule and (ii) formation of the closed enzyme conformer in the case of the Drosophila enzyme does not require the complete triphosphate chain of the substrate. NMR titration of the enzyme with the nucleotide ligands as well as kinetic data indicated significant deviation from the model of independent active sites within the homotrimer. The results suggest allosterism in the eukaryotic dUTPase

The Legacy of Sycamore Gap: The Potential of Photogrammetric AI for Reverse Engineering Lost Heritage with Crowdsourced Data

\ua9 Author(s) 2024.The orientation of crowdsourced and multi-temporal image datasets presents a challenging task for traditional photogrammetry. Indeed, traditional image matching approaches often struggle to find accurate and reliable tie points in images that appear significantly different from one another. In this paper, in order to preserve the memory of the Sycamore Gap tree, a symbol of Hadrian\u27s Wall that was felled in an act of vandalism in September 2023, deep-learning-based features trained specifically on challenging image datasets were employed to overcome limitations of traditional matching approaches. We demonstrate how unordered crowdsourced images and UAV videos can be oriented and used for 3D reconstruction purposes, together with a recently acquired terrestrial laser scanner point cloud for scaling and referencing. This allows the memory of the Sycamore Gap tree to live on and exhibits the potential of photogrammetric AI (Artificial Intelligence) for reverse engineering lost heritage

Directly Tracing Cool Filamentary Accretion over >100 kpc into the Interstellar Medium of a Quasar Host at z = 1

We report the discovery of giant (50−100 kpc) [O ii] emitting nebulae with MUSE in the field of TXS 0206−048, a luminous quasar at z = 1.13. “Down-the-barrel” UV spectra of the quasar show absorption at velocities coincident with those of the extended nebulae, enabling new insights into inflows and outflows around the quasar host. One nebula exhibits a filamentary morphology extending over 120 kpc from the halo toward the quasar and intersecting with another nebula surrounding the quasar host with a radius of 50 kpc. This is the longest cool filament observed to date and arises at higher redshift and in a less massive system than those in cool-core clusters. The filamentary nebula has line-of-sight velocities >300 km s−1 from nearby galaxies but matches that of the nebula surrounding the quasar host where they intersect, consistent with accretion of cool intergalactic or circumgalactic medium or cooling hot halo gas. The kinematics of the nebulae surrounding the quasar host are unusual and complex, with redshifted and blueshifted spiral-like structures. The emission velocities at 5−10 kpc from the quasar match those of inflowing absorbing gas observed in UV spectra of the quasar. Together, the extended nebulae and associated redshifted absorption represent a compelling case of cool, filamentary gas accretion from halo scales into the extended interstellar medium and toward the nucleus of a massive quasar host. The inflow rate implied by the combined emission and absorption constraints is well below levels required to sustain the quasar’s radiative luminosity, suggesting anisotropic or variable accretion

Infrastructure for Detector Research and Development towards the International Linear Collider

The EUDET-project was launched to create an infrastructure for developing and testing new and advanced detector technologies to be used at a future linear collider. The aim was to make possible experimentation and analysis of data for institutes, which otherwise could not be realized due to lack of resources. The infrastructure comprised an analysis and software network, and instrumentation infrastructures for tracking detectors as well as for calorimetry.Comment: 54 pages, 48 picture

Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability

Naturally-occurring single α-helices (SAHs), are rich in Arg (R), Glu (E) and Lys (K) residues, and stabilized by multiple salt bridges. Understanding how salt bridges promote their stability is challenging as SAHs are long and their sequences highly variable. Thus, we designed and tested simple de novo 98-residue polypeptides containing 7-residue repeats (AEEEXXX, where X is K or R) expected to promote salt-bridge formation between Glu and Lys/Arg. Lys-rich sequences (EK3 (AEEEKKK) and EK2R1 (AEEEKRK)) both form SAHs, of which EK2R1 is more helical and thermo-stable suggesting Arg increases stability. Substituting Lys with Arg (or vice versa) in the naturally-occurring myosin-6 SAH similarly increased (or decreased) its stability. However, Arg-rich de novo sequences (ER3 (AEEERRR) and EK1R2 (AEEEKRR)) aggregated. Combining a PDB analysis with molecular modelling provides a rational explanation, demonstrating that Glu and Arg form salt bridges more commonly, utilize a wider range of rotamer conformations, and are more dynamic than Glu–Lys. This promiscuous nature of Arg helps explain the increased propensity of de novo Arg-rich SAHs to aggregate. Importantly, the specific K:R ratio is likely to be important in determining helical stability in de-novo and naturally-occurring polypeptides, giving new insight into how single α-helices are stabilized

Astrophysics with the Laser Interferometer Space Antenna

The Laser Interferometer Space Antenna (LISA) will be a transformative experiment for gravitational wave astronomy, and, as such, it will offer unique opportunities to address many key astrophysical questions in a completely novel way. The synergy with ground-based and space-born instruments in the electromagnetic domain, by enabling multi-messenger observations, will add further to the discovery potential of LISA. The next decade is crucial to prepare the astrophysical community for LISA’s first observations. This review outlines the extensive landscape of astrophysical theory, numerical simulations, and astronomical observations that are instrumental for modeling and interpreting the upcoming LISA datastream. To this aim, the current knowledge in three main source classes for LISA is reviewed; ultra-compact stellar-mass binaries, massive black hole binaries, and extreme or interme-diate mass ratio inspirals. The relevant astrophysical processes and the established modeling techniques are summarized. Likewise, open issues and gaps in our understanding of these sources are highlighted, along with an indication of how LISA could help making progress in the different areas. New research avenues that LISA itself, or its joint exploitation with upcoming studies in the electromagnetic domain, will enable, are also illustrated. Improvements in modeling and analysis approaches, such as the combination of numerical simulations and modern data science techniques, are discussed. This review is intended to be a starting point for using LISA as a new discovery tool for understanding our Universe

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

We review the role conformational ensembles can play in the analysis of biomolecular dynamics, molecular recognition, and allostery. We introduce currently available methods for generating ensembles of biomolecules and illustrate their application with relevant examples from the literature. We show how, for binding, conformational ensembles provide a way of distinguishing the competing models of induced fit and conformational selection. For allostery we review the classic models and show how conformational ensembles can play a role in unravelling the intricate pathways of communication that enable allostery to occur. Finally, we discuss the limitations of conformational ensembles and highlight some potential applications for the future