Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing

Automated ligand fitting by core-fragment fitting and extension into density

An automated ligand-fitting procedure has been developed and tested on 9327 ligands and (F o − F c)exp(iϕc) difference density from macromolecular structures in the Protein Data Bank

How does iron interact with sporopollenin exine capsules? An X-ray absorption study including microfocus XANES and XRF imaging

Sporopollenin exine capsules (SECs) derived from plant spores and pollen grains have been proposed as adsorption, remediation and drug delivery agents. Despite many studies there is scant structural data available. This X-ray absorption investigation represents the first direct structural data on the interaction of metals with SECs and allows elucidation of their structure–property relationships. Fe K-edge XANES and EXAFS data have shown that the iron local environment in SECs (derived from Lycopodium clavatum) reacted with aqueous ferric chloride solutions is similar to that of ferrihydrite (FeOOH) and by implication ferritin. Fe Kα XRF micro-focus experiments show that there is a poor correlation between the iron distribution and the underlying SEC structure indicating that the SEC is coated in the FeOOH material. In contrast, the Fe Kα XRF micro-focus experiments on SECs reacted with aqueous ferrous chloride solutions show that there is a very high correlation between the iron distribution and the SEC structure, indicating a much more specific form of interaction of the iron with the SEC surface functional groups. Fe K-edge XANES and EXAFS data show that the FeII can be easily oxidised to give a structure similar to, but not identical to that in the FeIII case, and that even if anaerobic conditions are used there is still partial oxidation to FeIII

Correction of coarse-graining errors by a two-level method: Application to the Asakura-Oosawa model.

We present a method that exploits self-consistent simulation of coarse-grained and fine-grained models in order to analyze properties of physical systems. The method uses the coarse-grained model to obtain a first estimate of the quantity of interest, before computing a correction by analyzing properties of the fine system. We illustrate the method by applying it to the Asakura-Oosawa model of colloid-polymer mixtures. We show that the liquid-vapor critical point in that system is affected by three-body interactions which are neglected in the corresponding coarse-grained model. We analyze the size of this effect and the nature of the three-body interactions. We also analyze the accuracy of the method as a function of the associated computational effort.Leverhulme Trus

Search for B⁺_c→π⁺μ⁺μ⁻ decays and measurement of the branching fraction ratio <i>B</i>(B⁺_c→ψ(2<i>S</i>)π⁺)/<i>B</i>(B⁺_c→<i>J</i>/ψπ⁺)

The first search for nonresonant B+c→π+μ+μ− decays is reported. The analysis uses proton-proton collision data collected with the LHCb detector between 2011 and 2018, corresponding to an integrated luminosity of 9 fb−1. No evidence for an excess of signal events over background is observed and an upper limit is set on the branching fraction ratio B(B+c→π+μ+μ−)/B(B+c→J/ψπ+)&lt;2.1×10−4 at 90% confidence level. Additionally, an updated measurement of the ratio of the B+c→ψ(2S)π+ and B+c→J/ψπ+ branching fractions is reported. The ratio B(B+c→ψ(2S)π+)/B(B+c→J/ψπ+) is measured to be 0.254±0.018±0.003±0.005, where the first uncertainty is statistical, the second systematic, and the third is due to the uncertainties on the branching fractions of the leptonic J/ψ and ψ(2S) decays. This measurement is the most precise to date and is consistent with previous LHCb results

Endopolyploidy as a potential alternative adaptive strategy for Arabidopsis leaf size variation in response to UV-B

The extent of endoreduplication in leaf growth is group- or even species-specific, and its adaptive role is still unclear. A survey of Arabidopsis accessions for variation at the level of endopolyploidy, cell number, and cell size in leaves revealed extensive genetic variation in endopolyploidy level. High endopolyploidy is associated with increased leaf size, both in natural and in genetically unstructured (mapping) populations. The underlying genes were identified as quantitative trait loci that control endopolyploidy in nature by modulating the progression of successive endocycles during organ development. This complex genetic architecture indicates an adaptive mechanism that allows differential organ growth over a broad geographic range and under stressful environmental conditions. UV-B radiation was identified as a significant positive climatic predictor for high endopolyploidy. Arabidopsis accessions carrying the increasing alleles for endopolyploidy also have enhanced tolerance to UV-B radiation. UV-absorbing secondary metabolites provide an additional protective strategy in accessions that display low endopolyploidy. Taken together, these results demonstrate that high constitutive endopolyploidy is a significant predictor for organ size in natural populations and is likely to contribute to sustaining plant growth under high incident UV radiation. Endopolyploidy may therefore form part of the range of UV-B tolerance mechanisms that exist in natural populations

A comparative approach to understanding tissue-specific expression of uncoupling protein 1 expression in adipose tissue

Peer reviewedPublisher PD