Large Structural Changes Research Articles

Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion.

Antibody labeling has been conducted extensively for structure determination using both X-ray crystallography and electron microscopy (EM). However, establishing target-specific antibodies is a prerequisite for applying antibody-assisted structural analysis. To expand the applicability of this strategy, an alternative method has been developed to prepare an antibody complex by inserting an exogenous epitope into the target. It has already been demonstrated that the Fab of the NZ-1 monoclonal antibody can form a stable complex with a target containing a PA12 tag as an inserted epitope. Nevertheless, it was also found that complex formation through the inserted PA12 tag inevitably caused structural changes around the insertion site on the target. Here, an attempt was made to improve the tag-insertion method, and it was consequently discovered that an alternate tag (PA14) could replace various loops on the target without inducing large structural changes. Crystallographic analysis demonstrated that the inserted PA14 tag adopts a loop-like conformation with closed ends in the antigen-binding pocket of the NZ-1 Fab. Due to proximity of the termini in the bound conformation, the more optimal PA14 tag had only a minor impact on the target structure. In fact, the PA14 tag could also be inserted into a sterically hindered loop for labeling. Molecular-dynamics simulations also showed a rigid structure for the target regardless of PA14 insertion and complex formation with the NZ-1 Fab. Using this improved labeling technique, negative-stain EM was performed on a bacterial site-2 protease, which enabled an approximation of the domain arrangement based on the docking mode of the NZ-1 Fab.

Fluoro-bridged dimanganese(III) porphyrin dimer: Effect of intermacrocyclic interactions in modulating metal spin state

The synthesis, structure, and spectroscopic properties of a remarkably deformed dimanganese(III)-[Formula: see text]-fluoro porphyrin dimer in connection to its diiron(III) [Formula: see text]-fluoro and [Formula: see text]-hydroxo counterparts is reported. It is the most recent addition to the continued effort in understanding the effect of intermacrocyclic interaction on the molecular structure and properties of di-heme proteins. The dimanganese(III)-[Formula: see text]-fluoro porphyrin dimer, similar to its [Formula: see text]-hydroxo analogs, stabilizes two equivalent high-spin ([Formula: see text]= 2) manganese(III) centers. This is in contrast to the diiron(III) analogs where the [Formula: see text]-hydroxo complex stabilizes two inequivalent iron(III) centers with two different spin states of iron in the same molecule while the [Formula: see text]-fluoro complex stabilizes two equivalent metal centers with intermediate spin ([Formula: see text]= 3/2) state. The present results further establish the extreme interdependence of the energetically accessible spin states of the metal and the extent of porphyrin core deformation. It is very likely that nature utilizes the same powerful tool to modulate large change in the electronic structure and properties of the heme center needed for its function.

Azithromycin and the microbiota of cystic fibrosis sputum

BackgroundAzithromycin is commonly prescribed drug for individuals with cystic fibrosis (CF), with demonstrated benefits in reducing lung function decline, exacerbation occurrence and improving nutrition. As azithromycin has antimicrobial activity against components of the uncultured microbiome and increasingly the CF microbiome is implicated in disease pathogenesis – we postulated azithromycin may act through its manipulation. Herein we sought to determine if the CF microbiome changed following azithromycin use and if clinical benefit observed during azithromycin use associated with baseline community structure.ResultsDrawing from a prospectively collected biobank we identified patients with sputum samples prior to, during and after initiating azithromycin and determined the composition of the CF microbial community by sequencing the V3-V4 region of the 16S rRNA gene. We categorized patients as responders if their rate of lung function decline improved after azithromycin initiation. Thirty-eight adults comprised our cohort, nine who had not utilized azithromycin in at least 3 years, and 29 who were completely naïve. We did not observe a major impact in the microbial community structure of CF sputum in the 2 years following azithromycin usage in either alpha or beta-diversity metrics. Seventeen patients (45%) were classified as Responders – demonstrating reduced lung function decline after azithromycin. Responders who were naïve to azithromycin had a modest clustering effect distinguishing them from those who were non-Responders, and had communities enriched with several organisms including Stenotrophomonas, but not Pseudomonas.ConclusionsAzithromycin treatment did not associate with subsequent large changes in the CF microbiome structure. However, we found that baseline community structure associated with subsequent azithromycin response in CF adults.

Nanoconfined SnO2/SnSe2 heterostructures in N-doped carbon nanotubes for high-performance sodium-ion batteries

• The construction of heterostructures boosts the localized charge transfer kinetics. • N-doped carbon nanotubes improve both electronic and ionic conductivity. • The increased grain boundaries and CNTs enhance the electrode structural stability. • The reaction kinetics were analyzed to understand the superior performance. Tin-based compounds are promising anode materials for sodium-ion batteries (SIBs), owing to their high theoretical capacities and relatively low sodiation potential. However, their high-rate performance and cycle life-span are severely impeded by the inherent sluggish reaction kinetics and large structural change during charging and discharging. Herein, we report a composite anode consisting of SnO 2 /SnSe 2 heterostructure nanoparticles uniformly encapsulated in N-doped carbon nanotubes (SnO 2 /SnSe 2 @C) for high-performance SIBs. The hollow tube nano-architecture not only accommodates the volume expansion of SnO 2 /SnSe 2 , but also facilitates the electrolyte penetration and shortens Na + pathways. Meanwhile, the N-doped carbon shells provide highways for electron transport and contribute to the total capacity. More importantly, the construction of heterostructures boosts the charge transfer kinetics and further stabilizes the electrode structure by the additional confining effects of the increased crystalline boundaries. Benefiting from the synergistic effects between the elaborately-designed electrode architecture and the incorporation of heterostructures, the SnO 2 /SnSe 2 @C composite delivered a superior rate capability (322 mAh g −1 at 4 A g −1 ) and remarkable cycling stability with a capacity retention of 87.7% after 1000 cycles at 2 A g −1 .

Computational insight of ZrS2/graphene heterobilayer as an efficient anode material

A density functional theory-based study is carried out to examine the electrochemical performance of ZrS2 and graphene monolayers and ZrS2/graphene heterobilayer for anodic applications in rechargeable Li ion batteries (LIBs). The energetic and dynamic stabilities of the heterobilayer have been confirmed first. The low Li diffusion barrier (0.24 eV), low half-cell voltage (0.7 V) and high Li storage capacity (700 mAh/g) of ZrS2 monolayer makes it a prospective 2D anode material for the LIBs. However, the large energy gap of ZrS2 monolayer may reduce the reversibility, while large structural changes are on high Li load can lead to short cycle life. To handle these issues, the ZrS2 monolayer is capped with graphene. The graphene thus provides mechanical strength and conducting channels to the electron flow. It is well known that graphene is unable to store Li for LIBs applications. However, by making its interface with ZrS2 enables it to store Li ion reversibly. Furthermore, the graphene caping provides mechanical strength to the ZrS2 monolayer to insure long cycle life and high recyclability. Thus, the hybrid of ZrS2 and graphene makes a highly efficient 2D anode material for Li ion batteries.

Long-term ecosystem change in two highly degraded Lake Ontario (Canada) coastal wetlands

Coastal wetlands are essential to the ecosystem health of the Laurentian Great Lakes (North America) watershed. Multiple anthropogenic stressors have been impacting coastal wetlands since European settlement ca. 1850, and remain a concern for wetland health as watershed development intensifies. We used paleolimnological techniques to explore temporal ecosystem dynamics over the last ~ 100 years in two highly degraded Lake Ontario coastal wetlands located in southern Ontario, Canada, using Cladocera (Branchiopoda, Crustacea) subfossil remains as paleoecological indicators. In Cootes Paradise Marsh (Hamilton, Ontario), cladoceran assemblage changes exhibited a shift in dominance from Chydorus to Bosmina, at the turn of the twentieth century. That shift likely reflected the loss of aquatic macrophytes, and corresponds to the postulated timing of the arrival of invasive carp. Despite recent remediation efforts, including attempts to exclude carp from the wetland, little ecological recovery is evident from the subfossil Cladocera assemblage. No Daphnia remains were observed in our sediment core from Cootes Paradise, in contrast to previous studies on extant zooplankton communities, which reported a large Daphnia population in the west end of the marsh in the 1940s. This could indicate that our sediment core recorded ecological changes solely in the east end of Cootes Paradise Marsh. In Jordan Harbour (Lincoln, Ontario), Bosmina were dominant throughout the sediment record, and increases in littoral cladocerans were observed in the most recent sediments, in particular the appearance of periphytic Pleuroxus taxa after ~ 2008. This suggests that some recovery of aquatic macrophyte communities occurred in response to shoreline remediation efforts. Bosmina size structure exhibited only minimal changes in both wetlands, despite known large changes in historic fish community structure. Overall, our study provides perspectives on the benefits and limitations of paleolimnology for documenting ecological change in the Laurentian Great Lakes coastal wetlands.

Contrasting responses of DOM leachates to photodegradation observed in plant species collected along an estuarine salinity gradient

A series of abiotic processes affected by salinity changes involve light-mediated reactions and different degradation pathways of organic compounds, including altered photo-oxidation, photo-degradation, and photolysis of organic matter (OM). Sunlight is known to degrade, oxidize, or mineralize dissolved organic matter (DOM) in waterways, creating large changes in compositional structure of DOM near the water surface and ultimately in the mixed layer. DOM derived from various vegetation types has differing levels of susceptibility to photolytic degradation depending on initial chemical composition and in what matrix degradation takes place (e.g., salinity). The effect of sunlight and salinity on degradation of leached DOM derived from three dominant vegetative species, Avicennia germinans, Juncus romerianus, and Taxodium distichum, along a riverine continuum in northeast Florida was determined. Leachates from these three sources in a deionized or seawater matrix were irradiated in a continuous flow-through photolytic system over the course of 20 h. Avicennia germinans and Juncus roemerinaus DOM readily degraded as indicated by decreases in absorbance across all wavelengths during the irradiation period, while Taxodium distichum DOM was found to increase in absorbance across all wavelengths in the freshwater matrix, but not in seawater. PARAFAC analysis indicated differences in photochemical components and % change of absorbance and fluorescence over time indicate the importance and variability of individual contributions to the DOM pool across an estuarine continuum. This work characterizes the photochemical properties of three individual DOM sources, exhibits the need for further research on this topic, and explores the salinity effect on photo-degradation of DOM from unique plant-derived DOM.

Crop pangenomes.

Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identification and annotation. The published genomes of agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic selection. However, large structural genome changes, including gene copy number variations (CNVs) and gene presence/absence variations (PAVs), prevail in crops. These genomic variations play an important role in the functional set of genes and the gene composition in individuals of the same species and provide the genetic determination of the agronomically important crops properties. A high degree of genomic variation observed indicates that single reference genomes do not represent the diversity within a species, leading to the pangenome concept. The pangenome represents information about all genes in a taxon: those that are common to all taxon members and those that are variable and are partially or completely specific for particular individuals. Pangenome sequencing and analysis technologies provide a large-scale study of genomic variation and resources for an evolutionary research, functional genomics and crop breeding. This review provides an analysis of agricultural plants’ pangenome studies. Pangenome structural features, methods and programs for bioinformatic analysis of pangenomic data are described

The lithium ion storage performance of ZnSe particles with stable electrochemical reaction interfaces improved by carbon coating

Transition metal selenides have been extensively investigated in the field of energy storage and conversion, because of their unique physical and chemical properties. However, the large structural and volume change may lead to their poor electrochemical performance. In this work, the carbon coating design can effectively solve the above issues. The effect of carbon coating content on the electrochemical performance of zinc selenide is further studied. When composite has optimal ratio of ZnSe and carbon, it can present the superior cycling stability. The carbon modification not only provides three-dimensional conductive network for ZnSe particles, but also mitigates the inner stress and volume variation. More importantly, the active materials can be separated from the electrolyte by carbon coating, which can avoid side effects. This strategy might provide an effective route to address the issues of metal selenides.

Structural Changes in HPRT Gene of V79 Cells After Irradiation With Heavy Ions—Immediate and Delayed Effects

The radiobiological effects of accelerated ions with high charge and high energy (HZE) on mammalian cells and their propagation in time are still not sufficiently explained and attract great deal of attention. This work aims to compare the immediate and delayed effects with emphasis on the latter. As shown by our group, the dependence of mutant fraction on expression time after irradiation may have interesting, non-monotonic, character depending on LET (linear energy transfer) of the used heavy ions. We speculate that this phenomenon may occur due to the induced genomic instability. Another area of our research is the study of the DNA structural changes in these mutants induced at different expression times. Chinese hamster V79 cells were irradiated with accelerated ions 11B, 18O, 20Ne, and gamma radiation. The LET was ranging from 0.23 keV/μm of 60Co gamma rays up to 136 keV/μm of 20Ne ions. DNA of unique HPRT mutants was isolated, concentration measured, HPRT exons amplified, and analyzed at several different time points, up to about 40 days, after exposure. Over 1200 HPRT mutants were analyzed for deletions of exons and sorted into three main categories: partial deletion, PD—with deletion of one to eight exons; total deletions, TD—with all nine exons deleted; and no deletions—no change in the HPRT structure observed. In general, the number of samples with partial deletion was increasing with LET of the used radiation, suggesting that higher energy deposition to the cell nucleus is more likely to cause larger structural changes. In the case of total deletions, increase in their number with LET was observed up to LET ∼115 keV/μm followed by a sharp decrease. The samples were also analyzed for the distribution of deletions, in particular exons at various expression times, the so-called mutational patterns. Hypothesis of the mechanisms behind observed phenomena is given, and possible implications for further research are discussed.

Cognitive reappraisal and expressive suppression relate differentially to longitudinal structural brain development across adolescence

Emotional disorders commonly emerge in adolescence, a period characterized by changes in emotion-related processes. Thus, the ability to regulate emotions is crucial for well-being and adaptive social functioning during this period. Concurrently, the brain undergoes large structural and functional changes. We investigated relations between tendencies to use two emotion regulation strategies, cognitive reappraisal and expressive suppression, and structural development of the cerebral cortex and subcortical structures (specifically amygdala and nucleus accumbens given these structures are frequently associated with emotion regulation). A total of 112 participants (59 females) aged 8–26 were followed for up to 3 times over a 7-year period, providing 272 observations. Participants completed the Emotion Regulation Questionnaire (ERQ), yielding a measure of tendencies to use cognitive reappraisal and expressive suppression at the final time point. Linear mixed model analyses were performed to account for the longitudinal nature of the data. Contrary to expectations, volumetric growth of the amygdala and nucleus accumbens was not associated with either emotion regulation strategy. However, frequent use of expressive suppression was linked to greater regionally-specific apparent cortical thinning in both sexes, while tendency to use cognitive reappraisal was associated with greater regionally-specific apparent thinning in females and less thinning in males. Although cognitive reappraisal is traditionally associated with cognitive control regions of the brain, our results suggest it is also associated with regions involved in social cognition and semantics. The continued changes in cortical morphology and their associations with habitual use of different emotion regulation strategies indicate continued plasticity during this period, and represent an opportunity for interventions targeting emotion regulation for adolescents at risk.

Light-Responsive Proton Conductor: Record High Gain of Proton Conductivity Achieved by Photoinduced Electron-Transfer Strategy

Light-Responsive Proton Conductor: Record High Gain of Proton Conductivity Achieved by Photoinduced Electron-Transfer Strategy

Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations.

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations.OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models.METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations.RESULTS: The evolution of the domain opening angle clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation.CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

Light-induced difference FTIR spectroscopy of primate blue-sensitive visual pigment at 163 K.

Structural studies of color visual pigments lag far behind those of rhodopsin for scotopic vision. Using difference FTIR spectroscopy at 77 K, we report the first structural data of three primate color visual pig­ments, monkey red (MR), green (MG), and blue (MB), where the batho-intermediate (Batho) exhibits photo­equilibrium with the unphotolyzed state. This photo­chromic property is highly advantageous for limited samples since the signal-to-noise ratio is improved, but may not be applicable to late intermediates, because of large structural changes to proteins. Here we report the photochromic property of MB at 163 K, where the BL intermediate, formed by the relaxation of Batho, is in photoequilibrium with the initial MB state. A comparison of the difference FTIR spectra at 77 and 163 K provided information on what happens in the process of transition from Batho to BL in MB. The coupled C11=C12 HOOP vibration in the planer structure in MB is decoupled by distortion in Batho after retinal photoisomerization, but returns to the coupled C11=C12 HOOP vibration in the all-trans chromophore in BL. The Batho formation accompanies helical structural perturbation, which is relaxed in BL. Protein-bound water molecules that form an extended water cluster near the retinal chromophore change hydrogen bonds differently for Batho and BL, being stronger in the latter than in the initial state. In addition to structural dynamics, the present FTIR spectra show no signals of protonated carboxylic acids at 77 and 163 K, suggesting that E181 is deprotonated in MB, Batho and BL.

Graphene: A two dimensional super material for sensor applications

Abstract Sensor technology is the backbone of diverse engineering and biomedical applications that has attracted the attention of academicians and researchers. Design and development of an efficient sensor requires a material that can monitor large structural changes in response to a small applied input with high degree of precision and consistency. Graphene is a unique two-dimensional material with its spectacular structural and electronic properties that has appealed towards the emergence of sensors of new era. This paper presents the state-of-the-art review on scope and development of graphene based strain, gas, magnetic, piezoelectric, photoelectric and biosensors for chemical, mechanical, electrochemical and biomedical applications. A detailed survey of previously published studies has been conducted as a valuable tool for researchers to select the appropriate graphene based material(s) and substrates for further exploration in the field of sensors. Despite the exemplary performance of graphene based sensors, there is a dire need to exploit the high intrinsic mobilities of graphene with improved substrates for diverse applications.

Absorption Wavelength Along Chromophore Low-Barrier Hydrogen Bonds

In low-barrier hydrogen bonds (H-bonds), the pKa values for the H-bond donor and acceptor moieties are nearly equal, whereas the redox potential values depend on the H+ position. Spectroscopic details of low-barrier H-bonds remain unclear. Here, we report the absorption wavelength along low-barrier H-bonds in protein environments, using a quantum mechanical/molecular mechanical approach. Low-barrier H-bonds form-between Glu46 and p-coumaric acid (pCA) in the intermediate pRCW state of photoactive yellow protein and between Asp116 and the Schiff base in the intermediate M-state of the sodium-pumping rhodopsin KR2. The absorption wavelength remains constant at ~460 nm until H+ arrives at the pCA moiety. As H+ moves ~0.4 A and arrives at the pCA moiety, the absorption wavelength is discontinuously shortened to ~420 nm. The step-function-like switching mechanism may be advantageous in the adoption of the specific absorption wavelength of the signaling state prior to time-consuming large structural changes during the photoreceptor photocycle. This may be a basis of how photoreceptor proteins have evolved to proceed photocycles using abundant protons.

Characterization of CD8+ T-cell responses to non-anchor-type HLA class I neoantigens with single amino-acid substitutions

ABSTRACT CD8+ T cells are capable of recognizing mutation-derived neoantigens displayed by HLA class I molecules, thereby exhibiting the ability to distinguish between cancer and normal cells. However, accumulating evidence has shown that only a small fraction of nonsynonymous somatic mutations give rise to clinically relevant neoantigens. The properties of such neoantigens, which must be presented by HLA and immunogenic to induce a T-cell response, remain elusive. In this study, we explored the HLA class I ligandome of a human cancer cell line with microsatellite instability using a proteogenomic approach. The results demonstrated that neoantigens accounted for only 0.34% of the HLA class I ligandome, and most neoantigens were encoded by genes with abundant expression. Thereafter, T-cell responses were prioritized, and immunodominant neoantigens were defined using naive CD8+ T cells derived from healthy donors. AKF9, an immunogenic neoantigen with a mutation at a non-anchor position, formed a stable peptide-HLA complex. T-cell responses were analyzed against a panel of AKF9 variants with single amino-acid substitutions, in which mutations did not alter the high HLA-binding affinity and stability. The responses varied across individuals, demonstrating the impact of heterogeneous T-cell repertoires in this human cancer model. Moreover, responses were biased toward a variant group with large structural changes compared to the wild-type peptide. Thus, naive T-cell induction can be attributed to multiple determinants. Combining structural dissimilarity with gene-expression levels, HLA-binding affinity, and stability may further help prioritize the immunogenicity of non-anchor-type neoantigens.

Ensemble Learning Approach to Retinal Thickness Assessment in Optical Coherence Tomography

Manual assessment of the retinal thickness in optical coherence tomography images is a time-consuming task, prone to error and inter-observer variability. The wide variability of the retinal appearance makes the automation of retinal image processing a challenging problem to tackle. The difficulty is even more accentuated in practice when the retinal tissue exhibits large structural changes due to disruptive pathology. In this work, we propose an ensemble-learning-based method for the automated segmentation of retinal boundaries in optical coherence tomography images that is robust to retinal abnormalities. The segmentation accuracy of the proposed algorithm was evaluated on two publicly available datasets that included cases of severe retinal edema. Moreover, the performance of the proposed method was compared to two existing methods, widely referenced in the relevant literature. The proposed algorithm outperformed reference methods at segmenting the retinal boundaries in both normal and pathological images. Furthermore, a thorough reliability analysis showed a strong agreement between the retinal thickness measurements derived from the segmentation obtained with the proposed method and corresponding manual measurements computed with the manual annotations.

Redox-induced reversible [2 + 2] cycloaddition of an etheno-fused diporphyrin.

3,5-Ethenoporphyrin is a π-extended porphyrin containing a fused ethene unit between the meso- and β-positions, exhibiting unique contribution of macrocyclic antiaromaticity. We have recently reported that its analogue, etheno-fused diporphyrin, underwent thermal [2 + 2] cycloaddition to furnish X-shaped cyclobutane-linked tetraporphyrins. Here we demonstrate that the cyclobutane-ring formation is dynamically redox-active. Namely, the tetraporphyrin underwent two-step four-electron oxidation to afford two etheno-fused diporphyrin dications. The reduction of the resulting dication regenerated the cyclobutane-linked tetraporphyrin. The dication was sufficiently stable to allow its isolation under ambient conditions. The structure of the dication has been confirmed by 1H NMR spectroscopy and X-ray diffraction analysis. Importantly, the simultaneous double C–C bond cleavage in the cyclopropane ring in the tetraporphyrin is exceptional among dynamic redox (dyrex) systems to achieve large structural changes, thus offering new insights for the design of novel redox-active functional organic materials for electrochromic dyes, organic batteries, and organic memories.

CuSO4/[Cu(NH3)4]SO4-Composite Thermochemical Energy Storage Materials.

The thermochemical energy-storage material couple CuSO4/[Cu(NH3)4]SO4 combines full reversibility, application in a medium temperature interval (<350 °C), and fast liberation of stored heat. During reaction with ammonia, a large change in the sulfate solid-state structure occurs, resulting in a 2.6-fold expansion of the bulk material due to NH3 uptake. In order to limit this volume work, as well as enhance the thermal conductivity of the solid material, several composites of anhydrous CuSO4 with inorganic inert support materials were prepared and characterized with regard to their energy storage density, reversibility of the storage reaction, thermal conductivity, and particle morphology. The best thermochemical energy storage properties were obtained for a 10:1 CuSO4-sepiolite composite, combining an attractive energy storage density with slightly improved thermal conductivity and decreased bulk volume work compared to the pure salt.