Selectivity 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.
Immobilisation of organocatalysts onto solid supports represents a very promising solution to tackle their low productivity by enabling their reuse. Herein, the use of NMR relaxation measurements, coupled with reaction screening, was used to investigate the effect of solvent interactions with the immobilised catalyst matrix on reactivity in an asymmetric organocatalysed aldol reaction. Important insights for the further development of such complex, yet promising catalytic systems are provided.
Many soft tissues, such as the intervertebral disc (IVD), have a hierarchical fibrous composite structure which suffers from regional damage. We hypothesise that these tissue regions have distinct, inherent fibre structure and structural response upon loading. Here we used synchrotron computed tomography (sCT) to resolve collagen fibre bundles (∼5μm width) in 3D throughout an intact native rat lumbar IVD under increasing compressive load. Using intact samples meant that tissue boundaries (such as endplate-disc or nucleus-annulus) and residual strain were preserved; this is vital for characterising both the inherent structure and structural changes upon loading in tissue regions functioning in a near-native environment. Nano-scale displacement measurements along >10,000 individual fibres were tracked, and fibre orientation, curvature and strain changes were compared between the posterior-lateral region and the anterior region. These methods can be widely applied to other soft tissues, to identify fibre structures which cause tissue regions to be more susceptible to injury and degeneration. Our results demonstrate for the first time that highly-localised changes in fibre orientation, curvature and strain indicate differences in regional strain transfer and mechanical function (e.g. tissue compliance). This included decreased fibre reorientation at higher loads, specific tissue morphology which reduced capacity for flexibility and high strain at the disc-endplate boundary.
Ordered mesoporous silicas are widely used in separation science and catalysis, however, their slow batch synthesis is a barrier to scale-up and new applications. SBA-15 is one of the most extensively studied and commercially available mesoporous silicas, whose textural properties can be readily tuned through judicious choice of synthesis conditions. Here we demonstrate the continuous flow synthesis of SBA-15 in high yield at 80 °C using a simple tube reactor without any mixing device. The resulting SBA-15 exhibits excellent textural properties, with a BET surface area of 566 m2 g−1 and ordered 5.1 nm mesopore channels in a p6mm arrangement, akin to those from conventional batch synthesis, but with far higher productivity than previously reported in batch or flow (5.3 g L−1 h−1 versus 0.4 and 0.6 g L−1 h−1 respectively).
Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome.
The existence of asymmetry in X-ray photoelectron spectroscopy (XPS) photoemission lines is widely accepted, but line shapes designed to accommodate asymmetry are generally lacking in theoretical justification. In this work, we present a new line shape for describing asymmetry in XPS signals that is based on two facts. First, the most widely known line shape for fitting asymmetric XPS signals that has a theoretical basis, referred to as the Doniach-Sunjic (DS) line shape, suffers from a mathematical inconvenience, which is that for asymmetric shapes the area beneath the curve (above the x-axis) is infinite. Second, it is common practice in XPS to remove the inelastically scattered background response of a peak in question with the Shirley algorithm. The new line shape described herein attempts to retain the theoretical virtues of the DS line shape, while allowing the use of a Shirley background, with the consequence that the resulting line shape has a finite area. To illustrate the use of this Doniach-Sunjic-Shirley (DSS) line shape, a set of spectra obtained from varying amounts of graphene oxide (GO) and reduced GO on a patterned, heterogeneous surface are fit and discussed.
Although experimental protein-structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or appear as a contaminant. Regardless of the source of the problem, the unknown protein always requires characterization. Here, an automated pipeline is presented for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. The method’s application to characterize the crystal structure of an unknown protein purified from a snake venom is presented. It is also shown that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.
In this study, we aim to contribute an understanding of the pathway of formation of Fe species during top-down synthesis of dispersed Fe on N-functionalized few layer graphene, widely used in electrocatalysis. We use X-ray absorption spectroscopy to determine the electronic structure and coordination geometry of the Fe species and in situ high angle annular dark field scanning transmission electron microscopy combined with atomic resolved electron energy loss spectroscopy to localize these, identify their chemical configuration and monitor their dynamics during thermal annealing. We show the high mobility of peripheral Fe atoms, first diffusing rapidly at the trims of the graphene layers and at temperatures as high as 573 K, diffusing from the edge planes towards in-plane locations of the graphene layers forming three-, four-coordinated metal sites and more complexes polynuclear Fe species. This process occurs via bond C-C breaking which partially reduces the extension of the graphene domains. However, the vast majority of Fe is segregated as a metal phase. This dynamic interconversion depends on the structural details of the surrounding graphitic environment in which these are formed as well as the Fe loading. N species appear stabilizing isolated and polynuclear Fe species even at temperatures as high as 873 K. The significance of our results lies on the fact that single Fe atoms in graphene are highly mobile and therefore a structural description of the electroactive sites as such is insufficient and more complex species might be more relevant, especially in the case of multielectron transfer reactions. Here we provide the experimental evidence of the formation of these polynuclear Fe–N sites and their structural characteristics.
In specialised solidification processing techniques such as High Pressure Die Casting, Twin-Roll Casting and others, an additional external deformation load is applied to achieve the required shape, leading to the formation of microstructural features such as shear bands. The mechanism for forming these features is believed to be dependent on dynamically evolving strain fields, which are dependent on the local solid fraction, applied strain rates and casting geometry. To investigate this, a semisolid ( 50 % solid fraction) Al-10 wt.% Cu alloy is isothermally injected into a bespoke die using a custom-designed thermo-mechanical rig. The semisolid deformation, formation of Cu-rich dilatant bands and subsequent pore nucleation and growth are captured using fast synchrotron X-ray radiography. The local normal and shear strains acting on the mush are quantified using digital image correlation to identify the dilatant shear bands and the dominant local strain component. Correlating the radiographs with strain maps reveals that gas pores within the dilated interstices grow, while those in compressed regions are squeezed out. A linear correlation between accumulated volumetric strain and porosity volume fraction demonstrates that higher dilations give rise to a local increase in both gas and shrinkage porosity.