Pore Size Gradient Effect in Monolithic Silica Mesopore Networks Revealed by In-Situ SAXS Physisorption.

In disordered mesopore networks, the size distribution and connection between adjacent pores control desorption. How network characteristics can be extracted from corresponding physisorption isotherms is still a matter of research. To elucidate this, we study krypton physisorption (117.8 K) in the mesopore networks of "Nakanishi"-type monolithic silica. Combining physisorption in scanning acquisition mode with synchrotron-based in-situ SAXS provides complementary information on pore-filling states. These data reveal a mean pore size gradient in which pores grow smaller towards the material's network center. This structural motif cannot be derived through conventional isotherm analysis, but it is clearly exposed through scanning desorption curves which do not quite converge but merge individually with the main desorption isotherm before the lower hysteresis closing point. Hence, our findings provide the basis to build advanced models for analyzing scanning isotherms and extracting network characteristics through new descriptors, such as pore size and connectivity distributions as a function of the distance from the network center.

Structure of a Therapeutic Full-Length Anti-NPRA IgG4 Antibody: Dissecting Conformational Diversity.

We report the x-ray crystal structure of intact, full-length human immunoglobulin (IgG4) at 1.8 Å resolution. The data for IgG4 (S228P), an antibody targeting the natriuretic peptide receptor A, show a previously unrecognized type of Fab-Fc orientation with a distorted λ-shape in which one Fab-arm is oriented toward the Fc portion. Detailed structural analysis by x-ray crystallography and molecular simulations suggest that this is one of several conformations coexisting in a dynamic equilibrium state. These results were confirmed by small angle x-ray scattering in solution. Furthermore, electron microscopy supported these findings by preserving molecule classes of different conformations. This study fosters our understanding of IgG4 in particular and our appreciation of antibody flexibility in general. Moreover, we give insights into potential biological implications, specifically for the interaction of human anti-natriuretic peptide receptor A IgG4 with the neonatal Fc receptor, Fcγ receptors, and complement-activating C1q by considering conformational flexibility.

Sub-Visible Particle Classification and Label Consistency Analysis for Flow-Imaging Microscopy Via Machine Learning Methods.

Sub-visible particles can be a quality concern in pharmaceutical products, especially parenteral preparations. To quantify and characterize these particles, liquid samples may be passed through a flow-imaging microscopy instrument that also generates images of each detected particle. Machine learning techniques have increasingly been applied to this kind of data to detect changes in experimental conditions or classify specific types of particles, primarily focusing on silicone oil. That technique generally requires manual labeling of particle images by subject matter experts, a time-consuming and complex task. In this study, we created artificial datasets of silicone oil, protein particles, and glass particles that mimicked complex datasets of particles found in biopharmaceutical products. We used unsupervised learning techniques to effectively describe particle composition by sample. We then trained independent one-class classifiers to detect specific particle populations: silicone oil and glass particles. We also studied the consistency of the particle labels used to evaluate these models. Our results show that one-class classifiers are a reasonable choice for handling heterogeneous flow-imaging microscopy data and that unsupervised learning can aid in the labeling process. However, we found agreement among experts to be rather low, especially for smaller particles (< 8 µm for our Micro-Flow Imaging data). Given the fact that particle label confidence is not usually reported in the literature, we recommend more careful assessment of this topic in the future.

Structure and function of the AAA+ nucleotide binding pocket.

Members of the diverse superfamily of AAA+ proteins are molecular machines responsible for a wide range of essential cellular processes. In this review we summarise structural and functional data surrounding the nucleotide binding pocket of these versatile complexes. Protein Data Bank (PDB) structures of closely related AAA+ ATPase are overlaid and biologically relevant motifs are displayed. Interactions between protomers are illustrated on the basis of oligomeric structures of each AAA+ subgroup. The possible role of conserved motifs in the nucleotide binding pocket is assessed with regard to ATP binding and hydrolysis, oligomerisation and inter-subunit communication. Our comparison indicates that in particular the roles of the arginine finger and sensor 2 residues differ subtly between AAA+ subgroups, potentially providing a means for functional diversification.

Size-dependent deformation behavior in nanosized amorphous metals suggesting transition from collective to individual atomic transport.

The underlying atomistic mechanism of deformation is a central problem in mechanics and materials science. Whereas deformation of crystalline metals is fundamentally understood, the understanding of deformation of amorphous metals lacks behind, particularly identifying the involved temporal and spatial scales. Here, we reveal that at small scales the size-dependent deformation behavior of amorphous metals significantly deviates from homogeneous flow, exhibiting increasing deformation rate with reducing size and gradually shifted composition. This transition suggests the deformation mechanism changes from collective atomic transport by viscous flow to individual atomic transport through interface diffusion. The critical length scale of the transition is temperature dependent, exhibiting a maximum at the glass transition. While viscous flow does not discriminate among alloy constituents, diffusion does and the constituent element with higher diffusivity deforms faster. Our findings yield insights into nano-mechanics and glass physics and may suggest alternative processing methods to epitaxially grow metallic glasses.

Compositional dependence of the fragility in metallic glass forming liquids.

The viscosity and its temperature dependence, the fragility, are key properties of a liquid. A low fragility is believed to promote the formation of metallic glasses. Yet, the fragility remains poorly understood, since experimental data of its compositional dependence are scarce. Here, we introduce the film inflation method (FIM), which measures the fragility of metallic glass forming liquids across wide ranges of composition and glass-forming ability. We determine the fragility for 170 alloys ranging over 25 at.% in Mg-Cu-Y. Within this alloy system, large fragility variations are observed. Contrary to the general understanding, a low fragility does not correlate with high glass-forming ability here. We introduce crystallization complexity as an additional contribution, which can potentially become significant when modeling glass forming ability over many orders of magnitude.

Combinatorial measurement of critical cooling rates in aluminum-base metallic glass forming alloys.

Direct measurement of critical cooling rates has been challenging and only determined for a minute fraction of the reported metallic glass forming alloys. Here, we report a method that directly measures critical cooling rate of thin film metallic glass forming alloys in a combinatorial fashion. Based on a universal heating architecture using indirect laser heating and a microstructure analysis this method offers itself as a rapid screening technique to quantify glass forming ability. We use this method to identify glass forming alloys and study the composition effect on the critical cooling rate in the Al-Ni-Ge system where we identified Al51Ge35Ni14 as the best glass forming composition with a critical cooling rate of 104 K/s.

Rational optimization of a monoclonal antibody improves the aggregation propensity and enhances the CMC properties along the entire pharmaceutical process chain.

The discovery of therapeutic monoclonal antibodies (mAbs) primarily focuses on their biological activity favoring the selection of highly potent drug candidates. These candidates, however, may have physical or chemical attributes that lead to unfavorable chemistry, manufacturing, and control (CMC) properties, such as low product titers, conformational and colloidal instabilities, or poor solubility, which can hamper or even prevent development and manufacturing. Hence, there is an urgent need to consider the developability of mAb candidates during lead identification and optimization. This work provides a comprehensive proof of concept study for the significantly improved developability of a mAb variant that was optimized with the help of sophisticated in silico tools relative to its difficult-to-develop parental counterpart. Interestingly, a single amino acid substitution in the variable domain of the light chain resulted in a three-fold increased product titer after stable expression in Chinese hamster ovary cells. Microscopic investigations revealed that wild type mAb-producing cells displayed potential antibody inclusions, while the in silico optimized variant-producing cells showed a rescued phenotype. Notably, the drug substance of the in silico optimized variant contained substantially reduced levels of aggregates and fragments after downstream process purification. Finally, formulation studies unraveled a significantly enhanced colloidal stability of the in silico optimized variant while its folding stability and potency were maintained. This study emphasizes that implementation of bioinformatics early in lead generation and optimization of biotherapeutics reduces failures during subsequent development activities and supports the reduction of project timelines and resources.

Atomic-Scale Imprinting by Sputter Deposition of Amorphous Metallic Films.

With its ease of implementation, low cost, high throughput, and excellent feature replication accuracy, nanoimprinting is used to fabricate structures for electrical, optical, and biological applications or to modify surface properties. If ultraprecise and/or subnanometer-sized patterns are desired, nanoimprinting has shown only limited success with polymers, silica glasses, or crystalline materials. In contrast, the absence of an intrinsic length scale that would interfere with imprinting resolution enables bulk metallic glasses (BMGs) to replicate structures down to the atomic scale through thermoplastic forming (TPF). However, only a small number of BMG-forming alloys can be used for TPF-based atomic-scale imprinting. Here, we demonstrate an alternative sputter deposition-based approach for the replication of atomic-scale features that is suited for a very broad range of amorphous alloys, thereby dramatically extending the available chemistries. Additional advantages are the method's scalability, its ability to replicate a wide range of molds, its low material consumption, and the fact that the films can readily be applied onto almost any workpiece, which together open up new avenues to atomically defined surface structuring and functionalization. Our method constitutes the advancement from proof of concept to a practical and highly versatile toolbox of atomic-scale imprinting to be explored for the science and technology of atomic-scale imprinting.

Janus electrocatalytic flow-through membrane enables highly selective singlet oxygen production.

The importance of singlet oxygen (1O2) in the environmental and biomedical fields has motivated research for effective 1O2 production. Electrocatalytic processes hold great potential for highly-automated and scalable 1O2 synthesis, but they are energy- and chemical-intensive. Herein, we present a Janus electrocatalytic membrane realizing ultra-efficient 1O2 production (6.9 mmol per m3 of permeate) and very low energy consumption (13.3 Wh per m3 of permeate) via a fast, flow-through electro-filtration process without the addition of chemical precursors. We confirm that a superoxide-mediated chain reaction, initiated by electrocatalytic oxygen reduction on the cathodic membrane side and subsequently terminated by H2O2 oxidation on the anodic membrane side, is crucial for 1O2 generation. We further demonstrate that the high 1O2 production efficiency is mainly attributable to the enhanced mass and charge transfer imparted by nano- and micro-confinement effects within the porous membrane structure. Our findings highlight a new electro-filtration strategy and an innovative reactive membrane design for synthesizing 1O2 for a broad range of potential applications including environmental remediation.

Semiconductor-to-conductor transition in 2D copper(ii) oxide nanosheets through surface sulfur-functionalization.

Functionalization is a widely-used strategy to modulate and optimize the properties of materials towards various applications, including sensing, catalysis, and energy generation. While the influence of sulfur-functionalization of carbon materials and oxides like ZnO and TiO2 has been studied, far less research has been devoted to analyzing sulfur-functionalization of CuO and other transition metal oxide nanomaterials. Here, we report sulfur-functionalization of copper(ii) oxide nanosheets synthesized by using a soft-templating procedure, with sulfur-addition based on hydrogen sulfide gas as a source. The resulting sulfur-functionalization does not change the overall crystal structure and morphology of the CuO nanosheets, but leads to a decrease in surface hydroxyl groups. Sulfur induces a semiconductor-to-conductor state transition of the CuO nanosheets, which is supported by computational modeling. The metallic transition results from shifting of the Fermi level into the valence band due to formation of Cu-S bonds on the surface of the CuO nanosheets.

Accelerated discovery and mechanical property characterization of bioresorbable amorphous alloys in the Mg-Zn-Ca and the Fe-Mg-Zn systems using high-throughput methods.

Ternary amorphous alloys in the magnesium (Mg)-zinc (Zn)-calcium (Ca) and the iron (Fe)-Mg-Zn systems are promising candidates for use in bioresorbable implants and devices. The optimal alloy compositions for biomedical applications should be chosen from a large variety of available alloys with best combination of mechanical properties (modulus, strength, hardness) and biological response (in situ degradation rates, cell adhesion and proliferation). As a first step towards establishing a database designed to enable such targeted material selection, amorphous alloy composition libraries were fabricated employing a combinatorial magnetron sputtering approach where Mg, Zn, and Ca/Fe are co-deposited from separate sources onto a silicon wafer substrate. Composition analysis using energy dispersive X-ray spectroscopy documented a composition range of ∼15-85 at% Mg, ∼6-55 at% Zn, and ∼5-60 at% Ca for the Mg-Zn-Ca library and ∼26-84 at% Mg, ∼10-61 at% Zn, and ∼7-55 at% Fe for the Fe-Mg-Zn library. X-ray diffraction measurements established that amorphous alloys (i.e., glasses) form in almost the entire range of composition at the high cooling rates during sputtering for both alloy libraries. Finally, the effective material modulus, the Oliver-Pharr hardness, and the yield strength values obtained using nanoindentation reveal a wide range of mechanical properties within both systems.

Adaption of human antibody λ and κ light chain architectures to CDR repertoires.

Monoclonal antibodies bind with high specificity to a wide range of diverse antigens, primarily mediated by their hypervariable complementarity determining regions (CDRs). The defined antigen binding loops are supported by the structurally conserved ß-sandwich framework of the light chain (LC) and heavy chain (HC) variable regions. The LC genes are encoded by two separate loci, subdividing the entity of antibodies into kappa (LCκ) and lambda (LCλ) isotypes that exhibit distinct sequence and conformational preferences. In this work, a diverse set of techniques were employed including machine learning, force field analysis, statistical coupling analysis and mutual information analysis of a non-redundant antibody structure collection. Thereby, it was revealed how subtle changes between the structures of LCκ and LCλ isotypes increase the diversity of antibodies, extending the predetermined restrictions of the general antibody fold and expanding the diversity of antigen binding. Interestingly, it was found that the characteristic framework scaffolds of κ and λ are stabilized by diverse amino acid clusters that determine the interplay between the respective fold and the embedded CDR loops. In conclusion, this work reveals how antibodies use the remarkable plasticity of the beta-sandwich Ig fold to incorporate a large diversity of CDR loops.

Formation and stability of complex metallic phases including quasicrystals explored through combinatorial methods.

Aluminum-based quasicrystals typically form across narrow composition ranges within binary to quaternary alloys, which makes their fabrication and characterization challenging. Here, we use combinatorial approaches together with fast characterization techniques to study a wide compositional range including known quasicrystal forming compositions. Specifically, we use magnetron co-sputtering to fabricate libraries of ~140 Al-Cu-Fe and ~300 Al-Cu-Fe-Cr alloys. The alloys compositions are measured through automated energy dispersive X-ray spectroscopy. Phase formation and thermal stability are investigated for different thermal processing conditions (as-sputtered and annealed at 400 °C, 520 °C and 600 °C for Al-Cu-Fe libraries; annealed at 600 °C for Al-Cu-Fe-Cr libraries) using automated X-ray diffraction and transmission electron microscopy. In both systems the compositional regions across which the quasicrystalline phase forms are identified. In particular, we demonstrate that the quasicrystalline phase forms across an unusually broad composition range in the Al-Cu-Fe-Cr system. Additionally, some of the considered alloys vitrify during sputtering, which also allows us to study their nucleation behavior. We find that phases with polytetrahedral symmetry, such as the icosahedral quasicrystal and the λ-Al13Fe4 phase, exhibit higher nucleation rates but lower growth rates, as compared to other phases with a lower degree of polytetrahedral order. Altogether, the here used combinatorial approach is powerful to identify compositional regions of quasicrystals.

Author Correction: Determination of critical cooling rates in metallic glass forming alloy libraries through laser spike annealing.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Improved Solution-State Properties of Monoclonal Antibodies by Targeted Mutations.

Monoclonal antibody (mAb)-based therapeutics often require high-concentration formulations. Unfortunately, highly concentrated antibody solutions often have biophysical properties that are disadvantageous for therapeutic development, such as high viscosity, solubility limitations, precipitation issues, or liquid-liquid phase separation. In this work, we present a computational rational design principle for improving the thermodynamic stability of mAb solutions through targeted point mutations. Two publicly available IgG1 monoclonal antibodies that exhibit high viscosity at high concentrations were used as model systems. Guided by a computationally efficient approach that combines molecular dynamics simulations with three-dimensional reference interaction site model theory, point mutations of charged residues were introduced in the variable Fv regions in such a manner that the hydration free energy was optimized. Two selected point mutants were then produced by transient expression and characterized experimentally. Both engineered mAbs have reduced viscosity at high concentration, less negative second virial coefficient, and improved solubility compared to the respective wild-types. The results obtained with the suggested straightforward design principle underline the relevance of solvation effects for understanding, and ultimately optimizing, the properties of highly concentrated mAb solutions, with possible implications also for other biomolecular systems.

Determination of critical cooling rates in metallic glass forming alloy libraries through laser spike annealing.

The glass forming ability (GFA) of metallic glasses (MGs) is quantified by the critical cooling rate (R C). Despite its key role in MG research, experimental challenges have limited measured R C to a minute fraction of known glass formers. We present a combinatorial approach to directly measure R C for large compositional ranges. This is realized through the use of compositionally-graded alloy libraries, which were photo-thermally heated by scanning laser spike annealing of an absorbing layer, then melted and cooled at various rates. Coupled with X-ray diffraction mapping, GFA is determined from direct R C measurements. We exemplify this technique for the Au-Cu-Si system, where we identify Au56Cu27Si17 as the alloy with the highest GFA. In general, this method enables measurements of R C over large compositional areas, which is powerful for materials discovery and, when correlating with chemistry and other properties, for a deeper understanding of MG formation.

Proteasome assembly from 15S precursors involves major conformational changes and recycling of the Pba1-Pba2 chaperone.

The chaperones Ump1 and Pba1-Pba2 promote efficient biogenesis of 20S proteasome core particles from its subunits via 15S intermediates containing alpha and beta subunits, except beta7. Here we elucidate the structural role of these chaperones in late steps of core particle biogenesis using biochemical, electron microscopy, cross-linking and mass spectrometry analyses. In 15S precursor complexes, Ump1 is largely unstructured, lining the inner cavity of the complex along the interface between alpha and beta subunits. The alpha and beta subunits form loosely packed rings with a wider alpha ring opening than in the 20S core particle, allowing for the Pba1-Pba2 heterodimer to be partially embedded in the central alpha ring cavity. During biogenesis, the heterodimer is expelled from the alpha ring by a restructuring event that organizes the beta ring and leads to tightening of the alpha ring opening. In this way, the Pba1-Pba2 chaperone is recycled for a new round of proteasome assembly.

Structure of the VipA/B type VI secretion complex suggests a contraction-state-specific recycling mechanism.

The bacterial type VI secretion system is a multicomponent molecular machine directed against eukaryotic host cells and competing bacteria. An intracellular contractile tubular structure that bears functional homology with bacteriophage tails is pivotal for ejection of pathogenic effectors. Here, we present the 6 Å cryoelectron microscopy structure of the contracted Vibrio cholerae tubule consisting of the proteins VipA and VipB. We localized VipA and VipB in the protomer and identified structural homology between the C-terminal segment of VipB and the tail-sheath protein of T4 phages. We propose that homologous segments in VipB and T4 phages mediate tubule contraction. We show that in type VI secretion, contraction leads to exposure of the ClpV recognition motif, which is embedded in the type VI-specific four-helix-bundle N-domain of VipB. Disaggregation of the tubules by the AAA+ protein ClpV and recycling of the VipA/B subunits are thereby limited to the contracted state.

Homotypic interaction and amino acid distribution of unilaterally conserved transmembrane helices.

Formation of non-covalent functional complexes of integral membrane proteins is frequently supported by sequence-specific interaction of their transmembrane helices. Here, we aligned human single-span membrane proteins with orthologs from other eukaryotes. We find that almost half of the human single-span membrane proteins contain a transmembrane helix that exhibits significant non-random unilateral conservation. Furthermore, unilateral conservation of transmembrane domains (TMDs) correlates well with their ability to self-interact. Glycine, polar non-ionizable, and aromatic amino acids are overrepresented in conserved versus non-conserved helix faces. Hence, our genome-wide analysis indicates that these amino acid types generally support interaction of single-span membrane protein TMDs.