Conformational Disorder Analysis of the Conditionally Disordered Protein CP12 from Arabidopsis thaliana in Its Different Redox States

CP12 is a redox-dependent conditionally disordered protein universally distributed in oxygenic photosynthetic organisms. It is primarily known as a light-dependent redox switch regulating the reductive step of the metabolic phase of photosynthesis. In the present study, a small angle X-ray scattering (SAXS) analysis of recombinant Arabidopsis CP12 (AtCP12) in a reduced and oxidized form confirmed the highly disordered nature of this regulatory protein. However, it clearly pointed out a decrease in the average size and a lower level of conformational disorder upon oxidation. We compared the experimental data with the theoretical profiles of pools of conformers generated with different assumptions and show that the reduced form is fully disordered, whereas the oxidized form is better described by conformers comprising both the circular motif around the C-terminal disulfide bond detected in previous structural analysis and the N-terminal disulfide bond. Despite the fact that disulfide bridges are usually thought to confer rigidity to protein structures, in the oxidized AtCP12, their presence coexists with a disordered nature. Our results rule out the existence of significant amounts of structured and compact conformations of free AtCP12 in a solution, even in its oxidized form, thereby highlighting the importance of recruiting partner proteins to complete its structured final folding.

Impact of non-ionizable lipids and phase mixing methods on structural properties of lipid nanoparticle formulations

Lipid nanoparticles (LNPs) have been widely investigated for nucleic acid therapeutic delivery, and demonstrated their potential in enabling new mRNA vaccines. LNPs are usually formulated with multi-lipid components and the composition variables may impact their structural properties. Here, we investigated the impact of helper lipids on physicochemical properties of LNPs using a Design of Experiments (DoE) definitive screening design. Phospholipid head group, degree of unsaturation, ratio to cholesterol as well as PEG-lipid content were varied and a series of 14 LNPs were prepared by microfluidic- and solvent-injection mixing. Solvent-injection mixing by a robotic liquid handler yielded 50-225 nm nanoparticles with highly ordered, ∼5 nm inter-lamellar spacing as measured by small angle X-ray scattering (SAXS) and confirmed by cryo-transmission electron microscopy (cryo-EM). In contrast, microfluidic mixing resulted in less ordered, notably smaller (50-75 nm) and more homogenous nanoparticles. Significant impacts of the stealth-lipid DSPE-PEG2000 on nanoparticle size, polydispersity and encapsulation efficiency of an oligonucleotide cargo were observed in LNPs produced by both methods, while varying the phospholipid type and content had only marginal effect on these physicochemical properties. These findings suggest that from a physicochemical perspective, the design space for combinations of helper lipids in LNPs may be considerably larger than anticipated based on the conservative formulation composition of the currently FDA-approved LNPs, thereby opening opportunities for screening and optimization of novel LNP formulations.

Analysis of Stress Relaxation in Bulk and Porous Ultra-High Molecular Weight Polyethylene (UHMWPE)

The reported study was devoted to the investigation of viscoelastic behavior for solid and porous ultra-high molecular weight polyethylene (UHMWPE) under compression. The obtained experimental stress curves were interpreted using a two-term Prony series to represent the superposition of two coexisting activation processes corresponding to long molecular (~160 s) and short structural (~20 s) time scales, respectively, leading to good statistical correlation with the observations. In the case of porous polymer, the internal strain redistribution during relaxation was quantified using digital image correlation (DIC) analysis. The strongly inhomogeneous deformation of the porous polymer was found not to affect the relaxation times. To illustrate the possibility of generalizing the results to three dimensions, X-ray tomography was used to examine the porous structure relaxation at the macro- and micro-scale levels. DIC analysis revealed positive correlation between the applied force and relative density. The apparent stiffness variation for UHMWPE foams with mixed open and closed cells was described using a newly proposed three-term expression. Furthermore, in situ tensile loading and X-ray scattering study was applied for isotropic solid UHMWPE specimens to investigate the evolution of internal structure and orientation during drawing and stress relaxation in another loading mode.

Novel interaction interfaces mediate the interaction between the NEIL1 DNA glycosylase and mitochondrial transcription factor A

The maintenance of human mitochondrial DNA (mtDNA) is critical for proper cellular function as damage to mtDNA, if left unrepaired, can lead to a diverse array of pathologies. Of the pathways identified to participate in DNA repair within the mitochondria, base excision repair (BER) is the most extensively studied. Protein-protein interactions drive the step-by-step coordination required for the successful completion of this pathway and are important for crosstalk with other mitochondrial factors involved in genome maintenance. Human NEIL1 is one of seven DNA glycosylases that initiates BER in both the nuclear and mitochondrial compartments. In the current work, we scrutinized the interaction between NEIL1 and mitochondrial transcription factor A (TFAM), a protein that is essential for various aspects of mtDNA metabolism. We note, for the first time, that both the N- and C- terminal domains of NEIL1 interact with TFAM revealing a unique NEIL1 protein-binding interface. The interaction between the two proteins, as observed biochemically, appears to be transient and is most apparent at concentrations of low salt. The presence of DNA (or RNA) also positively influences the interaction between the two proteins, and molar mass estimates indicate that duplex DNA is required for complex formation at higher salt concentrations. Hydrogen deuterium exchange mass spectrometry data reveal that both proteins exchange less deuterium upon DNA binding, indicative of an interaction, and the addition of NEIL1 to the TFAM-DNA complex alters the interaction landscape. The transcriptional activity of TFAM appears to be independent of NEIL1 expression under normal cellular conditions, however, in the presence of DNA damage, we observe a significant reduction in the mRNA expression of TFAM-transcribed mitochondrial genes in the absence of NEIL1. Overall, our data indicate that the interaction between NEIL1 and TFAM can be modulated by local environment such as salt concentrations, protein availability, the presence of nucleic acids, as well as the presence of DNA damage.

Understanding the self-assembly of the polymeric drug solubilizer Soluplus®

HYPOTHESIS

Soluplus® is one of the most widely used amphiphilic copolymers in drug delivery and has been reported to strongly enhance the adsorption of model drugs. However, there is still a limited understanding of its micellar behavior as it responds to the different routes of administration, which involve important changes in concentration.

EXPERIMENTS

The microstructure of Soluplus aqueous solutions has been investigated at a wide range of polymer concentrations (2 × 10^-6 - 0.2 g/mL) by a combination of diffusion NMR (dNMR), small angle X-ray scattering (SAXS), static (SLS) dynamic (DLS) light scattering and viscosity measurements. These techniques have been coupled with surface tension measurements to frame the polymer's critical micellar concentration (cmc).

FINDINGS

We demonstrate the presence at all tested concentrations of two forms of Soluplus, with hydrodynamic radii of 3 and 26 nm, where the fraction of smaller objects accounts for as much as 60-70%. dNMR, SAXS, DLS and SLS indicate that Soluplus spontaneously self-assembles into large spherical particles with a core-shell structure. However, self-assembly takes place three orders of magnitude above the cmc evaluated via surface tension measurements. Instead of the traditional cooperative micellization process, we propose a thermal-activated isodesmic self-assembly of the small aggregates into core-shell micelles.

Dependence of the Nanoscale Composite Morphology of Fe3O4 Nanoparticle-Infused Lysozyme Amyloid Fibrils on Timing of Infusion: A Combined SAXS and AFM Study

Understanding the formation process and the spatial distribution of nanoparticle (NP) clusters on amyloid fibrils is an essential step for the development of NP-based methods to inhibit aggregation of amyloidal proteins or reverse the assembling trend of the proto-fibrillary complexes that prompts pathogenesis of neuro degeneration. For this, a detailed structural determination of the diverse hybrid assemblies that are forming is needed, which can be achieved by advanced X-ray scattering techniques. Using a combined solution small angle X-ray scattering (SAXS) and atomic force microscopy (AFM) approach, this study investigates the intrinsic trends of the interaction between lysozyme amyloid fibrils (LAFs) and Fe₃O₄ NPs before and after fibrillization at nanometer resolution. AFM images reveal that the number of NP clusters interacting with the lysozyme fibers does not increase significantly with NP volume concentration, suggesting a saturation in NP aggregation on the fibrillary surface. The data indicate that the number of non-adsorbed Fe₃O₄ NPs is highly dependent on the timing of NP infusion within the synthesis process. SAXS data yield access to the spatial distribution, aggregation manner and density of NP clusters on the fibrillary surfaces. Employing modern data analysis approaches, the shape and internal structural morphology of the so formed nanocomposites are revealed. The combined experimental approach suggests that while Fe₃O₄ NPs infusion does not prevent the fibril-formation, the variation of NP concentration and size at different stages of the fibrillization process can impose a pronounced impact on the superficial and internal structural morphologies of these nanocomposites. These findings may be applicable in devising advanced therapeutic treatments for neurodegenerative diseases and designing novel bio-inorganic magnetic devices. Our results further demonstrate that modern X-ray methods give access to the structure of—and insight into the formation process of—biological–inorganic hybrid structures in solution.

Structural Analysis of a Genetically Encoded FRET Biosensor by SAXS and MD Simulations

Inspired by the modular architecture of natural signaling proteins, ligand binding proteins are equipped with two fluorescent proteins (FPs) in order to obtain Förster resonance energy transfer (FRET)-based biosensors. Here, we investigated a glucose sensor where the donor and acceptor FPs were attached to a glucose binding protein using a variety of different linker sequences. For three resulting sensor constructs the corresponding glucose induced conformational changes were measured by small angle X-ray scattering (SAXS) and compared to recently published single molecule FRET results (Höfig et al., ACS Sensors, 2018). For one construct which exhibits a high change in energy transfer and a large change of the radius of gyration upon ligand binding, we performed coarse-grained molecular dynamics simulations for the ligand-free and the ligand-bound state. Our analysis indicates that a carefully designed attachment of the donor FP is crucial for the proper transfer of the glucose induced conformational change of the glucose binding protein into a well pronounced FRET signal change as measured in this sensor construct. Since the other FP (acceptor) does not experience such a glucose induced alteration, it becomes apparent that only one of the FPs needs to have a well-adjusted attachment to the glucose binding protein.

Electronics of Anion Hot Injection-Synthesized Te-Functionalized Kesterite Nanomaterial

Metal chalcogenides such as copper zinc tin sulfide (CZTS) have been intensively studied as potential photovoltaic cell materials, but their viability have been marred by crystal defects and low open circuit potential (V_oc) deficit, which affected their energy conversion efficiency. Strategies to improve on the properties of this material such as alloying with other elements have been explored and have yielded promising results. Here, we report the synthesis of CZTS and the partial substitution of S with Te via anion hot injection synthesis method to form a solid solution of a novel kesterite nanomaterial, namely, copper zinc tin sulfide telluride (CZTSTe). Particle-size analyzed via small angle X-ray scattering spectroscopy (SAXS) confirmed that CZTS and CZTSTe materials are nanostructured. Crystal planes values of 112, 200, 220 and 312 corresponding to the kesterite phase with tetragonal modification were revealed by the X-ray diffraction (XRD) spectroscopic analysis of CZTS and CZTSTe. The Raman spectroscopy confirmed the shifts at 281 cm⁻¹ and 347 cm⁻¹ for CZTS, and 124 cm⁻¹, 149 cm⁻¹ and 318 cm⁻¹ for CZTSTe. High degradation rate and the production of hot electrons are very detrimental to the lifespan of photovoltaic cell (PVC) devices, and thus it is important to have PVC absorber layer materials that are thermally stable. Thermogravimetric analysis (TGA) analysis indicated a 10% improvement in the thermal stability of CZTSTe compared to CZTS at 650 °C. With improved electrical conductivity, low charge transfer resistance (R_ct) and absorption in the visible region with a low bandgap energy (E_g) of 1.54 eV, the novel CZTSTe nanomaterials displayed favorable properties for photovoltaics application.

Probing Protein Folding with Sequence-Reversed α-Helical Bundles

Recurrent protein folding motifs include various types of helical bundles formed by α-helices that supercoil around each other. While specific patterns of amino acid residues (heptad repeats) characterize the highly versatile folding motif of four-α-helical bundles, the significance of the polypeptide chain directionality is not sufficiently understood, although it determines sequence patterns, helical dipoles, and other parameters for the folding and oligomerization processes of bundles. To investigate directionality aspects in sequence-structure relationships, we reversed the amino acid sequences of two well-characterized, highly regular four-α-helical bundle proteins and studied the folding, oligomerization, and structural properties of the retro-proteins, using Circular Dichroism Spectroscopy (CD), Size Exclusion Chromatography combined with Multi-Angle Laser Light Scattering (SEC-MALS), and Small Angle X-ray Scattering (SAXS). The comparison of the parent proteins with their retro-counterparts reveals that while the α-helical character of the parents is affected to varying degrees by sequence reversal, the folding states, oligomerization propensities, structural stabilities, and shapes of the new molecules strongly depend on the characteristics of the heptad repeat patterns. The highest similarities between parent and retro-proteins are associated with the presence of uninterrupted heptad patterns in helical bundles sequences.

Study of the Segmental Dynamics and Ion Transport of Solid Polymer Electrolytes in the Semi-crystalline State

Solid polymer electrolytes are promising in fulfilling the requirements for a stable lithium metal anode toward higher energy and power densities. In this work, we investigate the segmental dynamics, ionic conductivity, and crystallinity of a polymer electrolyte consisting of poly(ethylene oxide) (PEO) and lithium triflate salt, in the semi-crystalline state. Using quasi-elastic neutron scattering, the segmental dynamics of PEO chains confined between the crystalline lamellae is quantified, using Cole-Cole analysis. We show that the structural relaxation time, τ0, of PEO equilibrated near room temperature is six-fold longer than the same sample that had just cooled down to room temperature. This corresponds to a three-fold smaller ionic conductivity in the equilibrated condition. This work reveals that the segmental dynamics of semi-crystalline polymer electrolytes is very sensitive to thermal history. We demonstrate that quasi-elastic neutron scattering can be used to characterize the ion transport and segmental dynamics in the semi-crystalline state.

Structural Study of (Hydroxypropyl)Methyl Cellulose Microemulsion-Based Gels Used for Biocompatible Encapsulations

(Hydroxypropyl)methyl cellulose (HPMC) can be used to form gels integrating a w/o microemulsion. The formulation in which a microemulsion is mixed with a hydrated HPMC matrix has been successfully used as a carrier of biocompatible ingredients. However, little is known about the structure of these systems. To elucidate this, scanning electron microscopy was used to examine the morphology and the bulk of the microemulsion-based gels (MBGs) and small-angle X-ray scattering to clarify the structure and detect any residual reverse micelles after microemulsion incorporation in the gel. Electron paramagnetic resonance spectroscopy was applied using spin probes to investigate the polar and non-polar areas of the gel. Furthermore, the enzyme-labelling technique was followed to investigate the location of an enzyme in the matrix. A structural model for HPMC matrix is proposed according to which, although a w/o microemulsion is essential to form the final gel, no microemulsion droplets can be detected after incorporation in the gel. Channels are formed by the organic solvent (oil), which are coated by surfactant molecules and a water layer in which the enzyme can be hosted.

Ex Vivo Conjunctival Retention and Transconjunctival Transport of Poorly Soluble Drugs Using Polymeric Micelles

This paper addresses the problem of ocular delivery of lipophilic drugs. The aim of the paper is the evaluation of polymeric micelles, prepared using TPGS (d-α-Tocopheryl polyethylene glycol 1000 succinate), a water-soluble derivative of Vitamin E and/or poloxamer 407, as a vehicle for the ocular delivery of dexamethasone, cyclosporine, and econazole nitrate. The research steps were: (1) characterize polymeric micelles by dynamic light scattering (DLS) and X-ray scattering; (2) evaluate the solubility increase of the three drugs; (3) measure the in vitro transport and conjunctiva retention, in comparison to conventional vehicles; (4) investigate the mechanisms of enhancement, by studying drug release from the micelles and transconjunctival permeation of TPGS; and (5) study the effect of micelles application on the histology of conjunctiva. The data obtained demonstrate the application potential of polymeric micelles in ocular delivery, due to their ability to increase the solubility of lipophilic drugs and enhance transport in and across the conjunctival epithelium. The best-performing formulation was the one made of TPGS alone (micelles size ≈ 12 nm), probably because of the higher mobility of these micelles, an enhanced interaction with the conjunctival epithelium, and, possibly, the penetration of intact micelles.

Solution Processing Dependent Bulk Heterojunction Nanomorphology of P3HT/PCBM Thin Films

Mixtures of poly(3-hexyl-thiophene) (P3HT) and phenyl-C61-butyric acid methyl ester (PCBM) have been widely employed as donor and acceptor materials, respectively, for the active layer of the bulk heterojunction (BHJ) organic solar cells. Experiments are able to provide only limited insights on the dynamics of blend morphology of these organic materials because of the challenges in extracting microstructural characterization amidst the poor contrast in electron microscopy. We present results from coarse-grained molecular dynamics simulations (CGMD) describing the morphological evolution of P3HT/PCBM active layer under solution processing in chlorobenzene (CB). We examine the impact of various processing parameters such as weight ratio, degree of polymerization (DOP), thermal annealing, and preheating on the BHJ active layers using morphological characterizations from atomic trajectories. Simulated diffraction patterns are compared with experimental results of X-ray diffraction and Small Angle X-ray Scattering (SAXS). Both simulated scattering and experimental X-ray diffraction and X-ray scattering measurements reveal increase in crystallinity for P3HT upon annealing until PCBM weight fraction ∼50%. The solubility of PCBM being greater in CB than that of P3HT facilitates the phase separation of the polymer during early stages of solvent evaporation. An increase in the average size of the P3HT domain relative to the preannealed morphology, is due to phase segregation and crystallization of the polymer upon annealing. Percolation for PCBM remains unchanged until PCBM constitutes at least one-half of the composition. Although 1.0:2.0 weight ratio is predicted to be ideal for balanced charge transport, 1.0:1.0 weight ratio is the most beneficial of overall power conversion based on exciton generation and charge separation at the interface. DOP of P3HT molecules is another important design variable as larger P3HT molecules tend to entangle more often deteriorating molecular order of P3HT phase in the active layer. Preheating the ternary mixture of P3HT, PCBM, and CB modifies the structural order and morphology of the BHJ due to changes in PCBM diffusion into the P3HT phase.

A Mechanism of Calmodulin Modulation of the Human Cardiac Sodium Channel

The function of the human cardiac sodium channel (Na_V1.5) is modulated by the Ca²⁺ sensor calmodulin (CaM), but the underlying mechanism(s) are controversial and poorly defined. CaM has been reported to bind in a Ca²⁺-dependent manner to two sites in the intracellular loop that is critical for inactivation of Na_V1.5 (inactivation gate [IG]). The affinity of CaM for the complete IG was significantly stronger than that of fragments that lacked both complete binding sites. Structural analysis by nuclear magnetic resonance, crystallographic, and scattering approaches revealed that CaM simultaneously engages both IG sites using an extended configuration. Patch-clamp recordings for wild-type and mutant channels with an impaired CaM-IG interaction revealed CaM binding to the IG promotes recovery from inactivation while impeding the kinetics of inactivation. Models of full-length Na_V1.5 suggest that CaM binding to the IG directly modulates channel function by destabilizing the inactivated state, which would promote resetting of the IG after channels close.

Small Angle X-ray Scattering and Electron Spin Resonance Spectroscopy Study on Fragrance Infused Cationic Vesicles Modeling Scent-Releasing Fabric Softeners

Industrially relevant systems for household and personal-care products often involve a large number of components. Such multiple component formulations are indispensable and effective for functionalization of the products, but may simultaneously provide more complex structural features compared to those in ideal systems comprising a smaller number of highly pure substances. Using cryogenic transmission electron microscopy (cryo-TEM), small angle X-ray scattering (SAXS), and electron spin resonance (ESR) spectroscopy, we have investigated effects of fragrance-incorporation into cationic vesicles on their bilayer structures and membrane-membrane interactions. Cationic vesicles were prepared from TEQ surfactant, whose major component was di(alkyl fatty ester) quaternary ammonium methosulfate, and fragrance components, l-menthol, linalool, and d-limonene, were infused into the vesicle membranes to model scent-releasing fabric softeners. The cryo-TEM images confirm formation of multilamellar vesicles (MLVs). Generalized indirect Fourier transformation (GIFT) analysis of the SAXS intensities based on the modified Caillé structure factor model reveals that incorporation of a more hydrophobic fragrance component leads to a more pronounced increase of the surface separation (water layer thickness). Furthermore, the fragrance-infused systems show longer-range order of the bilayer correlations and enhanced undulation fluctuation of the membranes than those in the TEQ alone system. The spin-label ESR results indicate different restricted molecular motions in the TEQ bilayers depending on the labeled position and their marked changes upon addition of the fragrance components, suggesting different mixing schemes and solubilization positions of the fragrance molecules in the TEQ bilayers. The present data have demonstrated how the infused fragrance molecules having different hydrophobicity and molecular architectures into the cationic vesicles affect the membrane structures and the intermembrane interactions, which may provide useful information for precisely controlling a fragrance-releasing property.

Towards understanding the microstructural and structural changes in natural hierarchical materials for energy recovery: In-operando multi-scale X-ray scattering characterization of Na- and Ca-montmorillonite on heating to 1150 °C

Understanding the changes in the microstructures and structures of clays with varying intercalated metal ions at elevated temperatures is of importance for many applications ranging from the recovery of shale gas from unconventional formations to developing effective nuclear waste containment technologies, and engineering materials such as ceramics for fuel cell applications. In this study, synchrotron-based in-operando multi-scale X-ray scattering analyses are used to determine dynamic microstructural and crystal structural changes in Na- and Ca-montmorillonite on heating from 30 °C to 1150 °C. Larger cations such as Ca²⁺ confer more defined morphological regimes compared to Na⁺ ions in compacted clays, as evident from the ultra-small-angle X-ray scattering results. The hierarchical morphology of clays is characterized to distinguish between nano-scale interlayer swelling porosity, meso-scale porosity, and intergranular pore spaces between powdered clay grains. On heating from ambient temperature to 200 °C, the removal of interlayer water reduced the basal distances to 9.6 Å. On further heating to 800 °C, gradual dehydroxylation of the clay sheets is evident from the structural changes. The effects of sintering at temperatures greater than 800 °C are evident from significant reductions in the intrinsic porosities of the clay sheets, and the formation of newer phases such as mullite. By connecting the in-operando microstructural and structural changes across spatial scales ranging from micrometers to Angstroms, the possibility of engineering high temperature processes for achieving morphologies and chemical compositions of interest is presented.

On the effect of alkaline pH and cofactor availability in the conformational and oligomeric state of Escherichia coli glutamate decarboxylase

Escherichia coli glutamate decarboxylase (EcGad) is a homohexameric pyridoxal 5'-phosphate (PLP)-dependent enzyme. It is the structural component of the major acid resistance system that protects E. coli from strong acid stress (pH < 3), typically encountered in the mammalian gastrointestinal tract. In fact EcGad consumes one proton/catalytic cycle while yielding γ-aminobutyrate and carbon dioxide from the decarboxylation of l-glutamate. Two isoforms of Gad occur in E. coli (GadA and GadB) that are 99% identical in sequence. GadB is the most intensively investigated. Prompted by the observation that some transcriptomic and proteomic studies show EcGad to be expressed in conditions far from acidic, we investigated the structural organization of EcGadB in solution in the pH range 7.5-8.6. Small angle X-ray scattering, combined with size exclusion chromatography, and analytical ultracentrifugation analysis show that the compact and entangled EcGadB hexameric structure undergoes dissociation into dimers as pH alkalinizes. When PLP is not present, the dimeric species is the most abundant in solution, though evidence for the occurrence of a likely tetrameric species was also obtained. Trp fluorescence emission spectra as well as limited proteolysis studies suggest that PLP plays a key role in the acquisition of a folding necessary for the canonical catalytic activity.

Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase

The highly mutagenic A:8-oxoguanine (oxoG) base pair is generated mainly by misreplication of the C:oxoG base pair, the oxidation product of the C:G base pair. The A:oxoG base pair is particularly insidious because neither base in it carries faithful information to direct the repair of the other. The bacterial MutY (MUTYH in humans) adenine DNA glycosylase is able to initiate the repair of A:oxoG by selectively cleaving the A base from the A:oxoG base pair. The difference between faithful repair and wreaking mutagenic havoc on the genome lies in the accurate discrimination between two structurally similar base pairs: A:oxoG and A:T. Here we present two crystal structures of the MutY N-terminal domain in complex with either undamaged DNA or DNA containing an intrahelical lesion. These structures have captured for the first time a DNA glycosylase scanning the genome for a damaged base in the very first stage of lesion recognition and the base extrusion pathway. The mode of interaction observed here has suggested a common lesion-scanning mechanism across the entire helix-hairpin-helix superfamily to which MutY belongs. In addition, small angle X-ray scattering studies together with accompanying biochemical assays have suggested a possible role played by the C-terminal oxoG-recognition domain of MutY in lesion scanning.

The Human RecQ4 Helicase Contains a Functional RecQ C-terminal Region (RQC) That Is Essential for Activity

RecQ helicases are essential in the maintenance of genome stability. Five paralogues (RecQ1, Bloom, Werner, RecQ4, and RecQ5) are found in human cells, with distinct but overlapping roles. Mutations in human RecQ4 give rise to three distinct genetic disorders (Rothmund-Thomson, RAPADILINO, and Baller-Gerold syndromes), characterized by genetic instability, growth deficiency, and predisposition to cancer. Previous studies suggested that RecQ4 was unique because it did not seem to contain a RecQ C-terminal region (RQC) found in the other RecQ paralogues; such a region consists of a zinc domain and a winged helix domain and plays an important role in enzyme activity. However, our recent bioinformatic analysis identified in RecQ4 a putative RQC. To experimentally confirm this hypothesis, we report the purification and characterization of the catalytic core of human RecQ4. Inductively coupled plasma-atomic emission spectrometry detected the unusual presence of two zinc clusters within the zinc domain, consistent with the bioinformatic prediction. Analysis of site-directed mutants, targeting key RQC residues (putative zinc ligands and the aromatic residue predicted to be at the tip of the winged helix β-hairpin), showed a decrease in DNA binding, unwinding, and annealing, as expected for a functional RQC domain. Low resolution structural information obtained by small angle X-ray scattering data suggests that RecQ4 interacts with DNA in a manner similar to RecQ1, whereas the winged helix domain may assume alternative conformations, as seen in the bacterial enzymes. These combined results experimentally confirm the presence of a functional RQC domain in human RecQ4.

Biophysical Evidence for Intrinsic Disorder in the C-terminal Tails of the Epidermal Growth Factor Receptor (EGFR) and HER3 Receptor Tyrosine Kinases

The epidermal growth factor receptor (EGFR)/ErbB family of receptor tyrosine kinases includes oncogenes important in the progression of breast and other cancers, and they are targets for many drug development strategies. Each member of the ErbB family possesses a unique, structurally uncharacterized C-terminal tail that plays an important role in autophosphorylation and signal propagation. To determine whether these C-terminal tails are intrinsically disordered regions, we conducted a battery of biophysical experiments on the EGFR and HER3 tails. Using hydrogen/deuterium exchange mass spectrometry, we measured the conformational dynamics of intracellular half constructs and compared the tails with the ordered kinase domains. The C-terminal tails demonstrate more rapid deuterium exchange behavior when compared with the kinase domains. Next, we expressed and purified EGFR and HER3 tail-only constructs. Results from circular dichroism spectroscopy, size exclusion chromatography with multiangle light scattering, dynamic light scattering, analytical ultracentrifugation, and small angle X-ray scattering each provide evidence that the EGFR and HER3 C-terminal tails are intrinsically disordered with extended, non-globular structure in solution. The intrinsic disorder and extended conformation of these tails may be important for their function by increasing the capture radius and reducing the thermodynamic barriers for binding of downstream signaling proteins.

Thermo-Responsive Polyurethane Hydrogels Based on Poly(ε-caprolactone) Diol and Amphiphilic Polylactide-Poly(Ethylene Glycol) Block Copolymers

Waterborne polyurethane (PU) based on poly(ε-caprolactone) (PCL) diol and an amphiphilic polylactide-poly(ethylene glycol) (PLA-PEG) diblock copolymer was synthesized. The molar ratio of PCL/PLA-PEG was 9:1 with different PLA chain lengths. The PU nanoparticles were characterized by dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and rheological analysis. The water contact angle measurement, infrared spectroscopy, wide angle X-ray scattering (WAXS), thermal and mechanical analyses were conducted on PU films. Significant changes in physio-chemical properties were observed for PUs containing 10 mol % of amphiphilic blocks. The water contact angle was reduced to 12°⁻13°, and the degree of crystallinity was 5%⁻10%. The PU dispersions underwent sol-gel transition upon the temperature rise to 37 °C. The gelation time increased as the PLA chain length increased. In addition, the fractal dimension of each gel was close to that of a percolation cluster. Moreover, PU4 with a solid content of 26% could support the proliferation of human mesenchymal stem cells (hMSCs). Therefore, thermo-responsive hydrogels with tunable properties are promising injectable materials for cell or drug delivery.

The Borrelia afzelii outer membrane protein BAPKO_0422 binds human factor-H and is predicted to form a membrane-spanning β-barrel

The deep evolutionary history of the Spirochetes places their branch point early in the evolution of the diderms, before the divergence of the present day Proteobacteria. As a spirochete, the morphology of the Borrelia cell envelope shares characteristics of both Gram-positive and Gram-negative bacteria. A thin layer of peptidoglycan, tightly associated with the cytoplasmic membrane, is surrounded by a more labile outer membrane (OM). This OM is rich in lipoproteins but with few known integral membrane proteins. The outer membrane protein A (OmpA) domain is an eight-stranded membrane-spanning β-barrel, highly conserved among the Proteobacteria but so far unknown in the Spirochetes. In the present work, we describe the identification of four novel OmpA-like β-barrels from Borrelia afzelii, the most common cause of erythema migrans (EM) rash in Europe. Structural characterization of one these proteins (BAPKO_0422) by SAXS and CD indicate a compact globular structure rich in β-strand consistent with a monomeric β-barrel. Ab initio molecular envelopes calculated from the scattering profile are consistent with homology models and demonstrate that BAPKO_0422 adopts a peanut shape with dimensions 25×45 Å (1 Å=0.1 nm). Deviations from the standard C-terminal signature sequence are apparent; in particular the C-terminal phenylalanine residue commonly found in Proteobacterial OM proteins is replaced by isoleucine/leucine or asparagine. BAPKO_0422 is demonstrated to bind human factor H (fH) and therefore may contribute to immune evasion by inhibition of the complement response. Encoded by chromosomal genes, these proteins are highly conserved between Borrelia subspecies and may be of diagnostic or therapeutic value.

Conformal SiO2 coating of sub-100 nm diameter channels of polycarbonate etched ion-track channels by atomic layer deposition

Polycarbonate etched ion-track membranes with about 30 µm long and 50 nm wide cylindrical channels were conformally coated with SiO2 by atomic layer deposition (ALD). The process was performed at 50 °C to avoid thermal damage to the polymer membrane. Analysis of the coated membranes by small angle X-ray scattering (SAXS) reveals a homogeneous, conformal layer of SiO2 in the channels at a deposition rate of 1.7-1.8 Å per ALD cycle. Characterization by infrared and X-ray photoelectron spectroscopy (XPS) confirms the stoichiometric composition of the SiO2 films. Detailed XPS analysis reveals that the mechanism of SiO2 formation is based on subsurface crystal growth. By dissolving the polymer, the silica nanotubes are released from the ion-track membrane. The thickness of the tube wall is well controlled by the ALD process. Because the track-etched channels exhibited diameters in the range of nanometres and lengths in the range of micrometres, cylindrical tubes with an aspect ratio as large as 3000 have been produced.

SAXS Studies of the Endoglucanase Cel12A from Gloeophyllum trabeum Show Its Monomeric Structure and Reveal the Influence of Temperature on the Structural Stability of the Enzyme

Endoglucanases are key enzymes applied to the conversion of biomass aiming for second generation biofuel production. In the present study we obtained the small angle X-ray scattering (SAXS) structure of the G. trabeumendo-1,4-β-glucanase Cel12A and investigated the influence of an important parameter, temperature, on both secondary and tertiary structure of the enzyme and its activity. The CD analysis for GtCel12A revealed that changes in the CD spectra starts at 55 °C and the T_m calculated from the experimental CD sigmoid curve using the Boltzmann function was 60.2 ± 0.6 °C. SAXS data showed that GtCel12A forms monomers in solution and has an elongated form with a maximum diameter of 60 ± 5 Å and a gyration radius of 19.4 ± 0.1 Å as calculated from the distance distribution function. Kratky analysis revealed that 60 °C is the critical temperature above which we observed clear indications of denaturation. Our results showed the influence of temperature on the stability and activity of enzymes and revealed novel structural features of GtCel12A.