Prior Likelihoods and Space-Group Preferences of Solvates

For a range of organic solvents, the likelihood of the solvent forming solvates has been estimated using the recrystallization solvent (RS) data in the Cambridge Structural Database (CSD). Although RS data are viewed with caution by some crystallographers, most of the likelihood estimates are shown to have good precision. Strong trends are apparent in the results. For example, high likelihoods are found for aromatic solvents with electron-withdrawing substituents and low likelihoods for acyclic aliphatic hydrocarbons. Results for different CSD subsets, such as organic and metalloorganic, are highly correlated. The likelihood that a solvent will form solvates is almost always higher when the solvent is part of a mixture than when it is pure. The likelihood of two solvents forming a heterosolvate (i.e., both solvents in the structure) can be well estimated by the product of the likelihoods of the solvents forming normal solvates (i.e., only one solvent in the structure). The space-group preferences of solvates vary significantly with the nature of the cocrystallized solvent. Those of nonsolvates vary significantly with the solvent(s) from which they were crystallized. Solvents with inversion centers favor solvate crystallization in centrosymmetric space groups, and solvents with 2-fold rotational symmetry promote crystallization in space groups with 2-fold proper rotational axes. The inclusion of cyclohexane and carbon tetrachloride in a lattice can facilitate crystallization in trigonal and tetragonal space groups, respectively. Our results can: (a) guide solvent selection when solvates are undesired; (b) assist in predicting solvate formation, e.g., using Bayesian algorithms; (c) assist in the choice of space groups for solvate crystal structure prediction; and (d) suggest ways in which solvent incorporation can be used to influence space groups.</p

CDASH: a cloud-enabled program for structure solution from powder diffraction data

The simulated annealing approach to crystal structure determination from powder diffraction data, as implemented in the DASH program, is readily amenable to parallelization at the individual run level. Very large scale increases in speed of execution can be achieved by distributing individual DASH runs over a network of computers. The CDASH program delivers this by using scalable on-demand computing clusters built on the Amazon Elastic Compute Cloud service. By way of example, a 360 vCPU cluster returned the crystal structure of racemic ornidazole (Z0 = 3, 30 degrees of freedom) ca 40 times faster than a typical modern quad-core desktop CPU. Whilst used here specifically for DASH, this approach is of general applicability to other packages that are amenable to coarse-grained parallelism strategies

HECT E3 Ubiquitin Ligase Itch Functions as a Novel Nega

The transcription factor Gli-similar 3 (Glis3) plays a critical role in the generation of pancreatic ß cells and the regulation insulin gene transcription and has been implicated in the development of several pathologies, including type 1 and 2 diabetes and polycystic kidney disease. However, little is known about the proteins and posttranslational modifications that regulate or mediate Glis3 transcriptional activity. In this study, we identify by mass-spectrometry and yeast 2-hybrid analyses several proteins that interact with the N-terminal region of Glis3. These include the WW-domain-containing HECT E3 ubiquitin ligases, Itch, Smurf2, and Nedd4. The interaction between Glis3 and the HECT E3 ubiquitin ligases was verified by co-immunoprecipitation assays and mutation analysis. All three proteins interact through their WW-domains with a PPxY motif located in the Glis3 N-terminus. However, only Itch significantly contributed to Glis3 polyubiquitination and reduced Glis3 stability by enhancing its proteasomal degradation. Itch-mediated degradation of Glis3 required the PPxY motif-dependent interaction between Glis3 and the WW-domains of Itch as well as the presence of the Glis3 zinc finger domains. Transcription analyses demonstrated that Itch dramatically inhibited Glis3-mediated transactivation and endogenous Ins2 expression by increasing Glis3 protein turnover. Taken together, our study identifies Itch as a critical negative regulator of Glis3-mediated transcriptional activity. This regulation provides a novel mechanism to modulate Glis3-driven gene expression and suggests that it may play a role in a number of physiological processes controlled by Glis3, such as insulin transcription, as well as in Glis3-associated diseases

Augmented Reality for Enhanced Visualization of MOF Adsorbents

Augmented reality (AR) is an emerging technique used to improve visualization and comprehension of complex 3D materials. This approach has been applied not only in the field of chemistry but also in real estate, physics, mechanical engineering, and many other areas. Here, we demonstrate the workflow for an app-free AR technique for visualization of metal–organic frameworks (MOFs) and other porous materials to investigate their crystal structures, topology, and gas adsorption sites. We think this workflow will serve as an additional tool for computational and experimental scientists working in the field for both research and educational purposes

Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins.

Funder: ExscientiaFunder: Diamond Light SourceFunder: Kungliga Tekniska HoegskolanFunder: Chinese Center for Disease Control and PreventionFunder: European Federation of Pharmaceutical Industries and AssociationsFunder: European CommissionFunder: Kennedy Trust for Rheumatology ResearchFunder: Ontario Institute for Cancer ResearchFunder: Royal Institution for the Advancement of Learning McGill UniversityFunder: UCBSelectivity is a crucial property in small molecule development. Binding site comparisons within a protein family are a key piece of information when aiming to modulate the selectivity profile of a compound. Binding site differences can be exploited to confer selectivity for a specific target, while shared areas can provide insights into polypharmacology. As the quantity of structural data grows, automated methods are needed to process, summarize, and present these data to users. We present a computational method that provides quantitative and data-driven summaries of the available binding site information from an ensemble of structures of the same protein. The resulting ensemble maps identify the key interactions important for ligand binding in the ensemble. The comparison of ensemble maps of related proteins enables the identification of selectivity-determining regions within a protein family. We applied the method to three examples from the well-researched human bromodomain and kinase families, demonstrating that the method is able to identify selectivity-determining regions that have been used to introduce selectivity in past drug discovery campaigns. We then illustrate how the resulting maps can be used to automate comparisons across a target protein family

Quasars Probing Quasars II: The Anisotropic Clustering of Optically Thick Absorbers around Quasars

With close pairs of quasars at different redshifts, a background quasar sightline can be used to study a foreground quasar's environment in absorption. We used a sample of 17 Lyman limit systems with column density N_HI > 10^19 cm^-2 selected from 149 projected quasar pair sightlines, to investigate the clustering pattern of optically thick absorbers around luminous quasars at z ~ 2.5. Specifically, we measured the quasar-absorber correlation function in the transverse direction, and found a comoving correlation length of r_0=9.2_{+1.5}_{-1.7} Mpc/h (comoving) assuming a power law correlation function, with gamma=1.6. Applying this transverse clustering strength to the line-of-sight, would predict that ~ 15-50% of all quasars should show a N_HI > 10^19 cm^-2 absorber within a velocity window of v < 3000 km/s. This overpredicts the number of absorbers along the line-of-sight by a large factor, providing compelling evidence that the clustering pattern of optically thick absorbers around quasars is highly anisotropic. The most plausible explanationfor the anisotropy is that the transverse direction is less likely to be illuminated by ionizing photons than the line-of-sight, and that absorbers along the line-of-sight are being photoevaporated. A simple model for the photoevaporation of absorbers subject to the ionizing flux of a quasar is presented, and it is shown that absorbers with volume densities n_H < 0.1 cm^-3 will be photoevaporated if they lie within ~ 1 Mpc (proper) of a luminous quasar. Using this simple model, we illustrate how comparisons of the transverse and line-of-sight clustering around quasars can ultimately be used to constrain the distribution of gas in optically thick absorption line systems.Comment: 14 pages of emulateapj, 7 figures, submitted to Ap

DigiMOF: A Database of Metal–Organic Framework Synthesis Information Generated via Text Mining

The vastness of materials space, particularly that which is concerned with metal–organic frameworks (MOFs), creates the critical problem of performing efficient identification of promising materials for specific applications. Although high-throughput computational approaches, including the use of machine learning, have been useful in rapid screening and rational design of MOFs, they tend to neglect descriptors related to their synthesis. One way to improve the efficiency of MOF discovery is to data-mine published MOF papers to extract the materials informatics knowledge contained within journal articles. Here, by adapting the chemistry-aware natural language processing tool, ChemDataExtractor (CDE), we generated an open-source database of MOFs focused on their synthetic properties: the DigiMOF database. Using the CDE web scraping package alongside the Cambridge Structural Database (CSD) MOF subset, we automatically downloaded 43,281 unique MOF journal articles, extracted 15,501 unique MOF materials, and text-mined over 52,680 associated properties including the synthesis method, solvent, organic linker, metal precursor, and topology. Additionally, we developed an alternative data extraction technique to obtain and transform the chemical names assigned to each CSD entry in order to determine linker types for each structure in the CSD MOF subset. This data enabled us to match MOFs to a list of known linkers provided by Tokyo Chemical Industry UK Ltd. (TCI) and analyze the cost of these important chemicals. This centralized, structured database reveals the MOF synthetic data embedded within thousands of MOF publications and contains further topology, metal type, accessible surface area, largest cavity diameter, pore limiting diameter, open metal sites, and density calculations for all 3D MOFs in the CSD MOF subset. The DigiMOF database and associated software are publicly available for other researchers to rapidly search for MOFs with specific properties, conduct further analysis of alternative MOF production pathways, and create additional parsers to search for additional desirable properties

Trigger for group A streptococcal M1T1 invasive disease

The globally disseminated Streptococcus pyogenes M1T1 clone causes a number of highly invasive human diseases. The transition from local to systemic infection occurs by an unknown mechanism; however invasive M1T1 clinical isolates are known to express significantly less cysteine protease SpeB than M1T1 isolates from local infections. Here, we show that in comparison to the M1T1 strain 5448, the isogenic mutant ΔspeB accumulated 75‐fold more human plasmin activity on the bacterial surface following incubation in human plasma. Human plasminogen was an absolute requirement for M1T1 strain 5448 virulence following subcutaneous (s.c.) infection of humanized plasminogen transgenic mice. S. pyogenes M1T1 isolates from the blood of infected humanized plasminogen transgenic mice expressed reduced levels of SpeB in comparison with the parental 5448 used as inoculum. We propose that the human plasminogen system plays a critical role in group A streptococcal M1T1 systemic disease initiation. SpeB is required for S. pyogenes M1T1 survival at the site of local infection, however, SpeB also disrupts the interaction of S. pyogenes M1T1 with the human plasminogen activation system. Loss of SpeB activity in a subpopulation of S. pyogenes M1T1 at the site of infection results in accumulation of surface plasmin activity thus triggering systemic spread.—Cole, J. N., McArthur, J. D., McKay, F. C., Sanderson‐Smith, M. L., Cork, A. J., Ranson, M., Rohde, M., Itzek, A., Sun, H., Ginsburg, D., Kotb, M., Nizet, V., Chhatwal, G. S., Walker, M. J. Trigger for group A streptococcal M1T1 invasive disease. FASEB J. 20, E1139–E1145 (2006)Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154248/1/fsb2fj065804fje.pd