Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca\u3csup\u3e2+\u3c/sup\u3e-calmodulin

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca2+-CaM, but no assignment of these features has been made. In addition, Ca2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 A resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca2+-CaM. Density-modified electron-density maps enabled the accurate assignment of Ca2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using lowcontour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal

Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca\u3csup\u3e2+\u3c/sup\u3e-calmodulin

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca2+-CaM, but no assignment of these features has been made. In addition, Ca2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 A resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca2+-CaM. Density-modified electron-density maps enabled the accurate assignment of Ca2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using lowcontour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal

Elastic electron scattering from 3-hydroxytetrahydrofuran: experimental and theoretical studies

We report the results of measurements and calculations for elastic electron scattering from 3-hydroxytetrahydrofuran (C4H8O2). The measurements are performed with a crossed electron-target beam apparatus and the absolute cross-sections are determined using the relative flow technique. The calculations are carried out using the Schwinger multichannel method in the static-exchange plus polarization (SEP) approximation. A set of angular differential cross-sections (DCS) is provided at five incident energies (6.5, 8, 10, 15 and 20 eV) over an angular range of 20–130°, and the energy dependence of the elastic DCS at a scattering angle of 120° is also presented. Integral elastic and elastic momentum transfer cross-sections have also been derived and calculated. The results are compared with those of recent measurements and calculations for the structurally similar molecule tetrahydrofuran (C4H8O)

Delineation of functionally essential protein regions for 242 neurodevelopmental genes

Neurodevelopmental disorders (NDDs), including severe paediatric epilepsy, autism and intellectual disabilities are heterogeneous conditions in which clinical genetic testing can often identify a pathogenic variant. For many of them, genetic therapies will be tested in this or the coming years in clinical trials. In contrast to first-generation symptomatic treatments, the new disease-modifying precision medicines require a genetic test-informed diagnosis before a patient can be enrolled in a clinical trial. However, even in 2022, most identified genetic variants in NDD genes are "variants of uncertain significance'. To safely enrol patients in precision medicine clinical trials, it is important to increase our knowledge about which regions in NDD-associated proteins can "tolerate' missense variants and which ones are "essential' and will cause a NDD when mutated. In addition, knowledge about functionally indispensable regions in the 3D structure context of proteins can also provide insights into the molecular mechanisms of disease variants. We developed a novel consensus approach that overlays evolutionary, and population based genomic scores to identify 3D essential sites (Essential3D) on protein structures. After extensive benchmarking of AlphaFold predicted and experimentally solved protein structures, we generated the currently largest expert curated protein structure set for 242 NDDs and identified 14 377 Essential3D sites across 189 gene disorders associated proteins. We demonstrate that the consensus annotation of Essential3D sites improves prioritization of disease mutations over single annotations. The identified Essential3D sites were enriched for functional features such as intermembrane regions or active sites and discovered key inter-molecule interactions in protein complexes that were otherwise not annotated. Using the currently largest autism, developmental disorders, and epilepsies exome sequencing studies including > 360 000 NDD patients and population controls, we found that missense variants at Essential3D sites are 8-fold enriched in patients.In summary, we developed a comprehensive protein structure set for 242 NDDs and identified 14377 Essential3D sites in these. All data are available at https://es-ndd.broadinstitute.org for interactive visual inspection to enhance variant interpretation and development of mechanistic hypotheses for 242 NDDs genes. The provided resources will enhance clinical variant interpretation and in silico drug target development for NDD-associated genes and encoded proteins.Peer reviewe

Electron impact ionization of R-carvone: I. Mass spectra and appearance energies

The mass spectrum of R-carvone measured at 70 eV electron impact energy, in the mass region of 1-151 amu, is reported in this work. We observed in this spectrum 103 peaks associated with ionic fragmentation, 55 of them with abundances greater than 1%. The relative abundances, from this study, compare reasonably well with the corresponding values reported in the literature where such a comparison can be made. The R-carvone Ionization Energy (IE), as well as the ionic energy formation thresholds (Appearance Energy - AE) were experimentally determined for the 35 most intense cations registered in the mass spectrum, which provided values for 38 AEs and Wannier exponents (p) and the IE of this molecule. The values of the AEs and Wannier exponents produced in this work, to the best of our knowledge, are being presented for the first time to the scientific community, except for the masses of 135 amu and 150 amu. We also suggest some ionic fragmentation mechanisms and molecular structural ionic fragmentation mechanisms for R-carvone, based on the AE and p values found in this work. (C) 2020 Elsevier B.V. All rights reserved

Positron collisions with ethene

We present experimental and theoretical cross sections for positron collisions with ethene molecules. The experimental total cross sections (TCSs) were obtained with a linear transmission technique, for energies from 0.1 eV up to 70 eV. The calculations employed the Schwinger multichannel method and were performed in the static plus polarization approximation for energies up to 10 eV. Our calculated elastic cross sections indicate a Ramsauer-Townsend minimum around 2.8 eV and a virtual state, in agreement with previous calculations by da Silva et al. [ Phys. Rev. Lett. 77 1028 (1996)]. We found reasonable agreement between the calculated elastic integral cross section and the measured total cross section below the positronium formation threshold. The present results are also in quite good agreement with available theoretical and experimental data, although for the experiments this is only true for TCSs above about 7 eV