Explicit correlation and intermolecular interactions: Investigating carbon dioxide complexes with the CCSD(T)-F12 method

We have optimized the lowest energy structures and calculated interaction energies for the CO₂–Ar, CO₂–N₂, CO₂–CO, CO₂–H₂O, and CO₂–NH₃ dimers with the recently developed explicitly correlated coupled cluster singles doubles and perturbative triples [CCSD(T)]-F12 methods and the associated VXZ-F12 (where X = D,T,Q) basis sets. For a given cardinal number, we find that results obtained with the CCSD(T)-F12 methods are much closer to the CCSD(T) complete basis set limit than the conventional CCSD(T) results. The relatively modest increase in the computational cost between explicit and conventional CCSD(T) is more than compensated for by the impressive accuracy of the CCSD(T)-F12 method. We recommend use of the CCSD(T)-F12 methods in combination with the VXZ-F12 basis sets for the accurate determination of equilibrium geometries and interaction energies of weakly bound electron donor acceptor complexes

Quantifying cooperative intermolecular interactions for improved carbon dioxide capture materials

We have optimized the geometry and calculated interaction energies for over 100 different complexes of CO₂ with various combinations of electron accepting (Lewis acid) and electron donating (Lewis base) molecules. We have used the recently developed explicitly correlated coupled cluster singles doubles and perturbative triples [CCSD(T)-F12] methods and the associated VXZ-F12 (where X = D,T,Q) basis sets. We observe only modest changes in the geometric parameters of CO₂ upon complexation, which suggests that the geometry of CO₂ adsorbed in a nanoporous material should be similar to that of CO₂ in gas phase. When CO₂ forms a complex with two Lewis acids via the two electron rich terminal oxygen atoms, the interaction energy is less than twice what would be expected for the same complex involving a single Lewis acid. We consider a series of complexes that exhibit simultaneous CO₂-Lewis acid and CO₂-Lewis base intermolecular interactions, with total interaction energies spanning 14.1–105.9 kJ mol⁻¹. For these cooperative complexes, we find that the total interaction energy is greater than the sum of the interaction energies of the constituent complexes. Furthermore, the intermolecular distances of the cooperative complexes are contracted as compared to the constituent complexes. We suggest that metal-organic-framework or similar nanoporous materials could be designed with adsorption sites specifically tailored for CO₂ to allow cooperative intermolecular interactions, facilitating enhanced CO₂ adsorption

Exome sequencing and genotyping identify a rare variant in NLRP7 gene associated with ulcerative colitis.

Background and Aims Although genome-wide association studies [GWAS] in inflammatory bowel disease [IBD] have identified a large number of common disease susceptibility alleles for both Crohn’s disease [CD] and ulcerative colitis [UC], a substantial fraction of IBD heritability remains unexplained, suggesting that rare coding genetic variants may also have a role in pathogenesis. We used high-throughput sequencing in families with multiple cases of IBD, followed by genotyping of cases and controls, to investigate whether rare protein-altering genetic variants are associated with susceptibility to IBD. Methods Whole-exome sequencing was carried out in 10 families in whom three or more individuals were affected with IBD. A stepwise filtering approach was applied to exome variants, to identify potential causal variants. Follow-up genotyping was performed in 6025 IBD cases [2948 CD; 3077 UC] and 7238 controls. Results Our exome variant analysis revealed coding variants in the NLRP7 gene that were present in affected individuals in two distinct families. Genotyping of the two variants, p.S361L and p.R801H, in IBD cases and controls showed that the p.S361L variant was significantly associated with an increased risk of ulcerative colitis [odds ratio 4.79, p = 0.0039] and IBD [odds ratio 3.17, p = 0.037]. A combined analysis of both variants showed suggestive association with an increased risk of IBD [odds ratio 2.77, p = 0.018]. Conclusions The results suggest that NLRP7 signalling and inflammasome formation may be a significant component in the pathogenesis of IBD

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

Genetic association studies have identified 215 risk loci for inflammatory bowel disease, thereby uncovering fundamental aspects of its molecular biology. We performed a genome-wide association study of 25,305 individuals and conducted a meta-analysis with published summary statistics, yielding a total sample size of 59,957 subjects. We identified 25 new susceptibility loci, 3 of which contain integrin genes that encode proteins in pathways that have been identified as important therapeutic targets in inflammatory bowel disease. The associated variants are correlated with expression changes in response to immune stimulus at two of these genes ($\textit{ITGA4 }$ and $\textit{ITGB8}$) and at previously implicated loci ($\textit{ITGAL }$and $\textit{ICAM1}$). In all four cases, the expression-increasing allele also increases disease risk. We also identified likely causal missense variants in a gene implicated in primary immune deficiency, $\textit{PLCG2}$, and a negative regulator of inflammation, $\textit{SLAMF8}$. Our results demonstrate that new associations at common variants continue to identify genes relevant to therapeutic target identification and prioritization.This work was co-funded by the Wellcome Trust [098051] and the Medical Research Council, UK [MR/J00314X/1]. Case collections were supported by Crohn’s and Colitis UK. KMdL, LM, CAL, YL, DR, JG-A, NJP, CAA and JCB are supported by the Wellcome Trust [098051; 093885/Z/10/Z; 094491/Z/10/Z]. KMdL is supported by a Woolf Fisher Trust scholarship. CAL is a clinical lecturer funded by the NIHR. We thank Anna Stanton for co-ordinating the Guy’s and St Thomas’ patient recruitment. We acknowledge support from the Department of Health via the NIHR comprehensive Biomedical Research Centre awards to Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London and to Addenbrooke’s Hospital, Cambridge in partnership with the University of Cambridge. This research was also supported by the NIHR Newcastle Biomedical Research Centre. The UK Household Longitudinal Study is led by the Institute for Social and Economic Research at the University of Essex and funded by the Economic and Social Research Council

Datasets, processing and refinement details for Mtb-AnPRT: inhibitor structures with various space groups

There are twenty-five published structures of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (Mtb-AnPRT) that use the same crystallization protocol. The structures include protein complexed with natural and alternative substrates, protein:inhibitor complexes, and variants with mutations of substrate-binding residues. Amongst these are varying space groups (i.e. P21, C2, P21212, P212121). This article outlines experimental details for 3 additional Mtb-AnPRT:inhibitor structures. For one protein:inhibitor complex, two datasets are presented â one generated by crystallization of protein in the presence of the inhibitor and another where a protein crystal was soaked with the inhibitor. Automatic and manual processing of these datasets indicated the same space group for both datasets and thus indicate that the space group differences between structures of Mtb-AnPRT:ligand complexes are not related to the method used to introduce the ligand. Keywords: Crystallography, Macromolecules, X-ray diffraction, Ligand binding, Structure-based inhibitor desig

Amphotericin forms an extramembranous and fungicidal sterol sponge

Amphotericin has remained the powerful but highly toxic last line of defense in treating life-threatening fungal infections in humans for over 50 years with minimal development of microbial resistance. Understanding how this small molecule kills yeast is thus critical for guiding development of derivatives with an improved therapeutic index and other resistance-refractory antimicrobial agents. In the widely accepted ion channel model for its mechanism of cytocidal action, amphotericin forms aggregates inside lipid bilayers that permeabilize and kill cells. In contrast, we report that amphotericin exists primarily in the form of large, extramembranous aggregates that kill yeast by extracting ergosterol from lipid bilayers. These findings reveal that extraction of a polyfunctional lipid underlies the resistance-refractory antimicrobial action of amphotericin and suggests a roadmap for separating its cytocidal and membrane-permeabilizing activities. This new mechanistic understanding is also guiding development of the first derivatives of amphotericin that kill yeast but not human cells