Structure-function Relationships Research Articles

Amine-Terminated Silver Nanoparticles Exhibit Potential for Selective Targeting of Triple-Negative Breast Cancer

Silver nanoparticles (AgNPs) demonstrate potential in treating aggressive cancers such as triple-negative breast cancer (TNBC) in preclinical models. To further the development of AgNP-based therapeutics for clinical use, it is essential to clearly define the specific physicochemical characteristics of the nanoparticles and connect these properties to biological outcomes. This study addresses this knowledge gap through detailed investigations into the structural and surface functional relationships, exploring the mechanisms, safety, and efficacy of AgNPs in targeting TNBC. The surface functionality of nanoparticles is crucial not only for their internalization into cancer cells but also for enhancing their toxicity toward tumor cells. Although the nanoparticles internalized into cancer cells, they failed to exhibit their full toxicity against the cancer. Herein we report a solvent-assisted synthesis amine, mercaptohexanol and bifunctional silver nanoparticles and performing comparative study to understand their selectivity and toxicity toward TNBC cells. The nanoparticles are fully characterized by UV–visible absorption spectroscopy, Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and dynamic light scattering measurement (DLS). The synthesis method achieves an extremely high yield and surface coating ratio of synthesized colloidal AgNPs. Our findings reveal that the amine-capped AgNPs exhibit significant selective toxicity against TNBC cell lines MCF7 and MDA-MB-231 at a concentration of 40 µg/mL without affecting normal breast cell lines MCF10A. This study underscores the potential of functionalized AgNPs in developing safe and targeted therapeutic approaches for treating aggressive cancers like TNBC, laying the groundwork for future clinical advancements.

Immobilization of Membrane-Associated Protein Complexes on SERS-Active Nanomaterials for Structural and Dynamic Characterization.

Exploring the structural basis of membrane proteins is significant for a deeper understanding of protein functions. In situ analysis of membrane proteins and their dynamics, however, still challenges conventional techniques. Here we report the first attempt to immobilize membrane protein complexes on surface-enhanced Raman scattering (SERS)-active supports, titanium dioxide-coated silver (Ag@TiO2) nanoparticles. Biocompatible immobilization of microsomal monooxygenase complexes is achieved through lipid fission and fusion. SERS activity of the Ag@TiO2 nanoparticles enables in situ monitoring of protein-protein electron transfer and enzyme catalysis in real time. Through SERS fingerprints of the monooxygenase redox centers, the correlations between these protein-ligand interactions and reactive oxygen species generation are revealed, providing novel insights into the molecular mechanisms underlying monooxygenase-mediated apoptotic regulation. This study offers a novel strategy to explore structure-function relationships of membrane protein complexes and has the potential to advance the development of novel reactive oxygen species-inducing drugs for cancer therapy.

Relieving the transfusion tissue traffic jam: a network model of radial transport in conifer needles.

Characteristic of all conifer needles, the transfusion tissue mediates the radial transport of water and sugar between the endodermis and axial vasculature. Physical constraints imposed by the needle's linear geometry introduce two potential extravascular bottlenecks where the opposition of sugar and water flows may frustrate sugar export: one at the vascular access point and the other at the endodermis. We developed a network model of the transfusion tissue to explore how its structure and composition affect the delivery of sugars to the axial phloem. To describe extravascular transport with cellular resolution, we construct networks from images of Pinus pinea needles obtained through tomographic microscopy, as well as fluorescence and electron microscopy. The transfusion tissue provides physically distinct pathways for sugar and water, reducing resistance between the vasculature and endodermis and mitigating flow constriction at the vascular flank. Dissipation of flow velocities through the transfusion tissue's branched structure allows for bidirectional transport of an inbound diffusive sugar flux against an outbound advective water flux across the endodermis. Our results clarify the structure-function relationships of the transfusion tissue under conditions free of physiological stress. The presented model framework is also applicable to different transfusion tissue morphologies in other gymnosperms.

SUPREM: an engineered non-site-specific m6A RNA methyltransferase with highly improved efficiency.

N 6-Methyladenine(m6A) RNA methylation plays a key role in RNA processing and translational regulation, influencing both normal physiological and pathological processes. Yet, current techniques for studying RNA methylation struggle to isolate the effects of individual m6A modifications. Engineering of RNA methyltransferases (RNA MTases) could enable development of improved synthetic biology tools to manipulate RNA methylation, but it is challenging due to limited understanding of structure-function relationships in RNA MTases. Herein, using ancestral sequence reconstruction, we explore the sequence space of the bacterial DNA methyltransferase EcoGII (M.EcoGII), a promising target for protein engineering due to its lack of sequence specificity and its residual activity on RNA. We thereby created an efficient non-specific RNA MTase termed SUPer RNA EcoGII Methyltransferase (SUPREM), which exhibits 8-fold higher expression levels, 7°C higher thermostability and 12-fold greater m6A RNA methylation activity compared with M.EcoGII. Immunofluorescent staining and quantitativeliquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis confirmed SUPREM's higher RNA methylation activity compared with M.EcoGII in mammalian cells. Additionally, Nanopore direct RNA sequencing highlighted that SUPREM is capable of methylating a larger number of RNA methylation sites than M.EcoGII. Through phylogenetic and mutational analysis, we identified a critical residue for the enhanced RNA methylation activity of SUPREM. Collectively, our findings indicate that SUPREM holds promise as a versatile tool for in vivo RNA methylation and labeling.

Use of a portable MRI to evaluate root structure-function relationships in water-use for several herbaceous species

Use of a portable MRI to evaluate root structure-function relationships in water-use for several herbaceous species

Proteome-scale structural prediction of the giant Marseillevirus reveals conserved folds and putative homologs of the hypothetical proteins.

A significant proportion of the highly divergent and novel proteins of giant viruses are termed "hypothetical" due to the absence of detectable homologous sequences in the existing databases. The quality of genome and proteome annotations often relies on the identification of signature sequences and motifs in order to assign putative functions to the gene products. These annotations serve as the first set of information for researchers to develop workable hypotheses for further experimental research. The structure-function relationship of proteins suggests that proteins with similar functions may also exhibit similar folding patterns. Here, we report the first proteome-wide structure prediction of the giant Marseillevirus. We use AlphaFold-predicted structures and their comparative analysis with the experimental structures in the PDB database to preliminarily annotate the viral proteins. Our work highlights the conservation of structural folds in proteins with highly divergent sequences and reveals potentially paralogous relationships among them. We also provide evidence for gene duplication and fusion as contributing factors to giant viral genome expansion and evolution. With the easily accessible AlphaFold and other advanced bioinformatics tools for high-confidence de novo structure prediction, we propose a combined sequence and predicted-structure-based proteome annotation approach for the initial characterization of novel and complex organisms or viruses.

Mechanistic insights on stabilization and destabilization effect of ionic liquids on type I collagen fibrils

Tuned assembly of collagen has tremendous applications in the field of biomedical and tissue engineering owing to its targeted biological functionalities. In this study, ionic liquids choline dihydrogen citrate (CDHC) and diethyl methyl ammonium methane sulfonate (AMS) have been used to regulate the self-assembly of collagen at its physiological pH by probing the assembled systems at certain concentration ratios of ionic liquids and the systems were studied using various characterization methods. Due to interaction with collagen, choline dihydrogen citrate causes delay in the collagen fibrillisation process showing no binding interactions with collagen. In contrast, diethyl methyl ammonium methane sulfonate shows crosslinking effect on collagen fibrillisation due to the electrostatic interaction with the tetrahedral hydration shell of collagen moieties. From rheological studies it was observed that the AMS treated collagen fibril at 1:1 % (w/v) has highest linear viscoelastic range, this can bear the stress under high strain compare to native collagen fibril as well as all CDHC composites. For a sustainable biomaterial or bio-scaffold, mechanical property plays pivotal role on it and from our experimental analysis we found certain composites of ionic liquid treated collagen fibrillar assembly which may act as a sustainable biomaterial or bio-scaffold. It was also evolved that, how the structure-function relationship of ionic force modulated fibrillar assembly controlling the mechanical properties of the tuned system. This self-assembled, ionic-liquid treated collagen-fibrillar system would accelerate various force modulated fibrillar network study, for mimicking the ECM and tissue engineering application.

Structural dynamics of the intrinsically disordered linker region of cardiac troponin T.

Troponin plays a central role in regulating heart contraction, and mutations in troponin can cause human cardiomyopathies. There are several functionally-significant regions of troponin that have not been structurally resolved, including the troponin T linker region that contains multiple cardiomyopathy mutations. In these unresolved regions, it is not possible to understand how changes in sequence affect function. We used computational and experimental techniques to demonstrate that this linker is dynamic and intrinsically disordered both in isolation and in the fully regulated thin filament. Moreover, we show how a cardiomyopathy mutation in this region affects function via allosteric disruption of intermolecular interactions. Our results highlight the need to consider how key mutations affect troponin disorder rather than the structure-function relationship.

Understanding fungal and plant active urea transport systems: Keys from Aspergillus nidulans and beyond

Urea is present in all ecosystems, as a result of the metabolism of different organisms and also of human activity, being the world's most common form of nitrogen fertilizer. Fungi and plants can use urea as a nitrogen source, taking it up from the environment through specialized active transport proteins. These proteins belong to a subfamily of urea/H+ symporters included in the Solute:Sodium Symporter (SSS) family of transporters. In this review we summarize the current knowledge on this group of transporters, based on our previous studies on Aspergillus nidulans UreA. We delve into its transcriptional and post-translational regulation, structure-function relationships, transport mechanism, and certain aspects of its biogenesis. Recent findings suggest that this urea transporter subfamily is more expanded than originally thought, with representatives found in organisms as diverse as Archaea and mollusks, which raises questions on evolutionary aspects. A. nidulans ureA knockout strains provide a valuable platform for expressing urea transporters from diverse sources, facilitating their characterization and functional analysis. In this context, given the close relationship between plant and fungal active urea transporters, this knowledge could serve to develop strategies to improve the efficiency of applied urea as fertilizer.

ExoSloNano: Multi-Modal Nanogold Tags for identification of Macromolecules in Live Cells & Cryo-Electron Tomograms.

In situ cryo-Electron Microscopy (cryo-EM) enables the direct interrogation of structure-function relationships by resolving macromolecular structures in their native cellular environment. Tremendous progress in sample preparation, imaging and data processing over the past decade has contributed to the identification and determination of large biomolecular complexes. However, the majority of proteins are of a size that still eludes identification in cellular cryo-EM data, and most proteins exist in low copy numbers. Therefore, novel tools are needed for cryo-EM to identify the vast majority of macromolecules across multiple size scales (from microns to nanometers). Here, we introduce and validate novel nanogold probes that enable the detection of specific proteins using cryo-ET (cryo-Electron Tomography) and resin-embedded correlated light and electron microscopy (CLEM). We demonstrate that these nanogold probes can be introduced into live cells, in a manner that preserves intact molecular networks and cell viability. We use this system to identify both cytoplasmic and nuclear proteins by room temperature EM, and resolve associated structures by cryo-ET. We further employ gold particles of different sizes to enable future multiplexed labeling and structural analysis. By providing high efficiency protein labeling in live cells and molecular specificity within cryo-ET tomograms, we establish a broadly enabling tool that significantly expands the proteome available to electron microscopy.

Insight into the Coordination Environment of Ru Single-Atom for Dry Reforming of Methane.

Dry reforming of methane (DRM), a pivotal process for converting greenhouse gases into syngas is demanding rationally designed catalysts with high stability and ideal catalytic performance for industrial applications due to its stability of reactant molecules and characteristic of carbon deposition. However, the mechanistic understanding of how the coordination environment of the metal in a single-atom catalytic system may influence the catalytic performance remains limited. In this work, high- and low-coordinating Ru-based (RuHC and RuLC) catalysts with distinct Ru-O coordination numbers are prepared using one-pot and two-step methods. The difference in the stability (12.3% and negligible deactivation during 20 h test for RuLC and RuHC catalysts respectively) and selectivity (0.57 and 0.37 of H2/CO ratio) brought by the coordination environment signified the structure-function relationship of single-atom catalysts in DRM. The impact of the structure on the properties is systematically investigated by thorough structural and operando characterization as well as density functional theory (DFT) calculation. The findings contribute to the optimal design of single-atom catalysts for DRM, offering a theoretical basis for industrial catalyst development and the potential to improve the process's environmental impact.

Zwitterionic Peptides: From Mechanism, Design Strategies to Applications.

Zwitterionic peptides, as a type of peptide composed of charged residues, are electrically neutral, which combine the advantages of zwitterionic materials and biological peptides, exhibiting hydrophilicity and programmable properties. As attractive candidates for resisting nonspecific adsorption of biomacromolecules and microorganisms, zwitterionic peptides have been applied in materials science, biomedicine, and biochemistry over the past decade. In this review, the development of zwitterionic peptides has been systematically outlined and analyzed, including their mechanisms, structure-function relationships, and design strategies. Furthermore, this review emphasizes and discusses their recent applications for developing functional coatings, biosensors, drug delivery systems, and engineering proteins. Finally, future research perspectives and challenges of zwitterionic peptides are also prospected and discussed. This review is intended to provide clarity and insight into the design and applications of zwitterionic peptides.

Synergistic Coordination Effect and Metal-Support Interaction Engineering of Single-Atom Mn-N2 Sites for Boosting Sensitive and Selective Dopamine Biosensing in Human Serum.

Coordination environment of metal atoms is core for designing high-performance single-atom catalysts (SACs), while metal-support interaction also has an important effect on structure-function relationship. Nevertheless, the interaction effect of metal-support is mostly ignored. Through synergistic regulation of coordination environment and metal-support interaction, Mn SAC with atom-dispersed Mn-N2 sites on dopamine (DA) support is synthesized for sensitive and selective DA oxidation based on theoretical calculations and experimental explorations. MnN2 presents the more optimal catalytic site for DA oxidation than other coordination conditions, enhancing sensitivity including a wide range, a low limit of detection, and particularly a very low catalytic potential. The construction of Mn-N2 active sites on DA carbon promotes the coupling between Mn metal atoms and DA support, decreasing work function, facilitating electron exchange, shortening response time, and boosting selectivity. Both the catalytic mechanism of Mn SAC toward DA and the relation construction of catalyst's structure and catalytic function are established.

Multimodal evidence for cerebellar influence on cortical development in autism: structural growth amidst functional disruption.

Despite perinatal damage to the cerebellum being one of the highest risk factors for later being diagnosed with autism spectrum disorder (ASD), it is not yet clear how the cerebellum might influence the development of cerebral cortex and whether this co-developmental process is distinct between neurotypical and ASD children. Leveraging a large structural brain MRI dataset of neurotypical children and those diagnosed with ASD, we examined whether structural variation in cerebellar tissue across individuals was correlated with neocortical variation during development, including the thalamus as a coupling factor. We found that the thalamus plays a distinct role in moderating cerebro-cerebellar structural coordination in ASD. Notably, structural coupling between cerebellum, thalamus, and neocortex was strongest in younger childhood and waned by early adolescence, mirroring a previously undescribed trajectory of behavioral development between ASD and neurotypical children. Complementary functional connectivity analyses likewise revealed atypical connectivity between cerebellum and neocortex in ASD. This relationship was particularly prominent in a model of cerebellar structure predicting functional connectivity, where ASD and neurotypical children showed divergent patterns. Interestingly, these functional-structural relationships became more prominent with age, while structural effects were most prominent earlier in childhood, and showed significant lateralization. This pattern may suggest a developmental sequence where early uncoordinated structural growth amongst regions is followed by increasingly atypical functional synchronization. These findings provide multimodal evidence in the living brain for a cerebellar diaschisis model of autism, where both increased cerebellar-cerebral structural coupling and altered functional connectivity in cerebro-cerebellar pathways contribute to the ontogeny of this neurodevelopmental disorder.

Bayesian inference of frequency-specific functional connectivity in MEG imaging using a spectral graph model

Abstract Understanding the relationship between structural connectivity (SC) and functional connectivity (FC) of the human brain is an important goal of neuroscience. Highly detailed mathematical models of neural masses exist that can simulate the interactions between functional activity and structural wiring. These models are often complex and require intensive computation. Most importantly, they do not provide a direct or intuitive interpretation of this structure–function relationship. In this study, we employ the emerging concepts of spectral graph theory to obtain this mapping in terms of graph harmonics, which are eigenvectors of the structural graph’s Laplacian matrix. In order to imbue these harmonics with biophysical underpinnings, we leverage recent advances in parsimonious spectral graph modeling (SGM) of brain activity. Here, we show that such a model can indeed be cast in terms of graph harmonics, and can provide a closed-form prediction of FC in an arbitrary frequency band. The model requires only three global, spatially invariant parameters, yet is capable of generating rich FC patterns in different frequency bands. Only a few harmonics are sufficient to reproduce realistic FC patterns. We applied the method to predict FC obtained from pairwise magnitude coherence of source-reconstructed resting-state magnetoencephalography (MEG) recordings of 36 healthy subjects. To enable efficient model inference, we adopted a deep neural network-based Bayesian procedure called simulation-based inference. Using this tool, we were able to speedily infer not only the single most likely model parameters, but also their full posterior distributions. We also implemented several other benchmark methods relating SC to FC, including graph diffusion and coupled neural mass models. The present method was shown to give the best performance overall. Notably, we discovered that a single biophysical parameterization is capable of fitting FCs from all relevant frequency bands simultaneously, an aspect that did not receive adequate attention in prior computational studies.

Long-Time Scale Simulations Reveal Key Dynamics That Drive the Onset of the N State in the Proteorhodopsin Photocycle.

Proteorhodopsin (PR) is a microbial proton pump that plays a significant role in phototrophy of bacteria in marine environments. Fundamental understanding of the structure-function relationship that drives proton pumping in PR has largely been elusive due to a lack of high-resolution structures of the photointermediates in the PR photocycle. Extending upon previous work, we used long-time scale molecular dynamics (MD) simulations to characterize the M state of the blue variant of PR, which represents the first proton transfer that takes place in the photocycle. Several notable structural changes occur in the M state that are hallmarks of subsequent steps in the PR photocycle, indicating that although this protein is often compared to the canonical microbial rhodopsins, such as bacteriorhodopsin, PR possesses characteristics that make it distinct among the rapidly increasing and widely variable catalog of microbial rhodopsins.

Strain-dependent glutathionylation of fibronectin fibers impacts mechano-chemical behavior and primes an integrin switch

The extracellular matrix (ECM) is a protein polymer network that physically supports cells within a tissue. It acts as an important physical and biochemical stimulus directing cell behaviors. For fibronectin (Fn), a predominant component of the ECM, these physical and biochemical activities are inextricably linked as physical forces trigger conformational changes that impact its biochemical activity. Here, we analyze whether oxidative post-translational modifications, specifically glutathionylation, alter Fn’s mechano-chemical characteristics through stretch-dependent protein modification. ECM post-translational modifications represent a potential for time- or stimulus-dependent changes in ECM structure-function relationships that could persist over time with potentially significant impacts on cell and tissue behaviors. In this study, we show evidence that glutathionylation of Fn ECM fibers is stretch-dependent and alters Fn fiber mechanical properties with implications on the selectivity of engaging integrin receptors. These data demonstrate the existence of multimodal post-translational modification mechanisms within the ECM with high relevance to the microenvironmental regulation of downstream cell behaviors.

Upcycling of polyethylene waste to biodegradable adhesive and coating via Baeyer-Villiger reaction: A new view on oxidation-fracture mechanism and structure-function relationship

Non-biodegradable polyethylene waste accumulates in large quantities in the environment posing a serious threat to the survival of creatures. Meanwhile, polyethylene suffers from inherent polarity limitations that curtails its application scope. Oxidation is an efficient approach of upcycling waste polyethylene through introduction of hydrophilic functional groups (such as –COOH, –OH), yet often at the expense of their original hydrophobicity. Herein, the hydrophobic ester groups, were introduced via Baeyer-Villiger oxidation to ingeniously balance the contradiction among hydrophobicity, interfacial forces and sustainability of polyethylene oxidation products. A tandem conversion mechanism among the oxidative groups was proposed while the decrease in molecular weight and branching degree was clarified to be a result of β-scissions occurring the branches during the oxidation. Meanwhile, the effect of oxidation degree and molecular weight on interfacial forces was revealed. The excellent hydrophobicity and corrosion resistance of the oxidized polyethylene coating can be attributed to the low content of carboxyl/hydroxyl groups, rich hydrophobic ester groups and the retained long carbon chain structure. Besides, the introduced ester groups and lower molecular weight also provided the oxidation products with potential biodegradability. This work provided a new insight on the Baeyer-Villiger oxidation of polyethylene and the potential for upcycling of polyethylene waste into sustainable materials.

Exploration and Design of Carbon Dot-Based Long Afterglow Materials Using Active Machine Learning and Quantum Chemical Simulations.

Long afterglow materials based on carbon dots (CDs) have attracted extensive attention in the field of optics due to their low cost and nontoxic properties. However, the targeted synthesis of specific properties of complex and unknown structures such as CDs remains a daunting challenge. In this study, the powerful nonlinear fitting ability of machine learning was used to explore the afterglow properties of CDs. The XGBoost algorithm demonstrates high prediction accuracy in determining the optimal excitation wavelength, optimal emission wavelength, and afterglow lifetime. Using Bayesian optimization, we screened and synthesized the CDs-based long afterglow materials with the longest lifetime reported so far by a one-step microwave method. By combining quantum chemical calculations with experimental data, we revealed the structure-function relationship between CDs and their precursors through electron-hole analysis. These results show that machine learning can establish nonlinear correlations between precursors and materials with unknown structures, clarify their intrinsic relationships, simplify the material design process, and thus accelerate the development of advanced materials.

Establishing a Robust Nonlinear Targeted Switch for C1 Electroproduction in Atomic Alloy Cox/Pd Bimetallenes.

Establishing a targeted switch for CO2 conversion under electric drive is essential for achieving carbon-balance by enabling selective chemicals. However, engineering the topological assembly of active sites to precisely regulate the competing pathways for various intermediates has been plagued by unclear structure-function relationships. To tailor the CO/formate pathways, herein we established a robust nonlinear targeted switch with tunable active Cox sites integrated into Pd metallene, which involves Co1/Pd single-atom alloy (favoring CO) and Co2/Pd diatomic alloy (favoring formate). Transitioning from Co1/Pd to Co2/Pd atomic alloy bimetallenes resulted in a nonlinear, high-contrast flip in selectivity, surpassing 94% for CO and formate productions in both H-cell and flow cell. Furthermore, the superior selectivity and current efficiency for CO (> 80 %) and formate (> 88%) were consistently maintained at -150 mA cm-2 over continuous 200 h. Theoretical simulations and in-situ spectroscopy analyses unveiled that appropriate adjacent metal site combinations (Pd-Pd, Pd-Co and Co-Co) lead to tunable dz2 band center and a nonlinear shift in preferred adsorption configurations of intermediates, dictating the C1 pathways. Our finding reveals a desired switch in C1 selectivity and robust stability within Cox/Pd system, providing a new perspective for fine-tuning energy conversion processes through specific topological assembly.