Dissection of the structure-function relationship of Nav channels.

Voltage-gated sodium channels (Nav) undergo conformational shifts in response to membrane potential changes, a mechanism known as the electromechanical coupling. To delineate the structure-function relationship of human Nav channels, we have performed systematic structural analysis using human Nav1.7 as a prototype. Guided by the structural differences between wild-type (WT) Nav1.7 and an eleven mutation-containing variant, designated Nav1.7-M11, we generated three additional intermediate mutants and solved their structures at overall resolutions of 2.9-3.4 Å. The mutant with nine-point mutations in the pore domain (PD), named Nav1.7-M9, has a reduced cavity volume and a sealed gate, with all voltage-sensing domains (VSDs) remaining up. Structural comparison of WT and Nav1.7-M9 pinpoints two residues that may be critical to the tightening of the PD. However, the variant containing these two mutations, Nav1.7-M2, or even in combination with two additional mutations in the VSDs, named Nav1.7-M4, failed to tighten the PD. Our structural analysis reveals a tendency of PD contraction correlated with the right shift of the static inactivation I-V curves. We predict that the channel in the resting state should have a "tight" PD with down VSDs.

Hemodynamic transient and functional connectivity follow structural connectivity and cell type over the brain hierarchy.

The neural circuit of the brain is organized as a hierarchy of functional units with wide-ranging connections that support information flow and functional connectivity. Studies using MRI indicate a moderate coupling between structural and functional connectivity at the system level. However, how do connections of different directions (feedforward and feedback) and regions with different excitatory and inhibitory (E/I) neurons shape the hemodynamic activity and functional connectivity over the hierarchy are unknown. Here, we used functional MRI to detect optogenetic-evoked and resting-state activities over a somatosensory pathway in the mouse brain in relation to axonal projection and E/I distribution. Using a highly sensitive ultrafast imaging, we identified extensive activation in regions up to the third order of axonal projections following optogenetic excitation of the ventral posteriomedial nucleus of the thalamus. The evoked response and functional connectivity correlated with feedforward projections more than feedback projections and weakened with the hierarchy. The hemodynamic response exhibited regional and hierarchical differences, with slower and more variable responses in high-order areas and bipolar response predominantly in the contralateral cortex. Electrophysiological recordings suggest that these reflect differences in neural activity rather than neurovascular coupling. Importantly, the positive and negative parts of the hemodynamic response correlated with E/I neuronal densities, respectively. Furthermore, resting-state functional connectivity was more associated with E/I distribution, whereas stimulus-evoked effective connectivity followed structural wiring. These findings indicate that the structure-function relationship is projection-, cell-type- and hierarchy-dependent. Hemodynamic transients could reflect E/I activity and the increased complexity of hierarchical processing.

Linker Domains: Why ABC Transporters 'Live in Fragments no Longer'.

ATP-binding cassette (ABC) transporters are membrane proteins present in all kingdoms of life. We have considered the disordered region that connects the N- and C-terminal halves in many eukaryotic ABC transporters, allowing all four consensus functional domains to be linked. The recent availability of structures of ABC transporters containing linker regions has allowed us to identify the start and end points of the connectors as well as hinting at their localisation. We address questions such as: Where did the linker regions come from? Why do some ABC transporters have connectors and others not? What are the rules and roles of the linker regions? What are the consequences of mutations in these connector regions for disease in humans?

What makes functional amyloids work?

Although first described in the context of disease, cross-ß (amyloid) fibrils have also been found as functional entities in all kingdoms of life. However, what are the specific properties of the cross-ß fibril motif that convey biological function, make them especially suited for their particular purpose, and distinguish them from other fibrils found in biology? This review approaches these questions by arguing that cross-ß fibrils are highly periodic, stable, and self-templating structures whose formation is accompanied by substantial conformational change that leads to a multimerization of their core and framing sequences. A discussion of each of these properties is followed by selected examples of functional cross-ß fibrils that show how function is usually achieved by leveraging many of these properties.

Bioactive atropisomers: Unraveling design strategies and synthetic routes for drug discovery.

Atropisomerism, an expression of axial chirality caused by limited bond rotation, is a prominent aspect within the field of medicinal chemistry. It has been shown that atropisomers of a wide range of compounds, including established FDA-approved drugs and experimental molecules, display markedly different biological activities. The time-dependent reversal of chirality in atropisomers poses complexity and obstacles in the process of drug discovery and development. Nonetheless, recent progress in understanding atropisomerism and enhanced characterization methods have greatly assisted medicinal chemists in the effective development of atropisomeric drug molecules. This article provides a comprehensive review of their special design thoughts, synthetic routes, and biological activities, serving as a reference for the synthesis and biological evaluation of bioactive atropisomers in the future.

Genetic code expansion, an emerging tool in the Ca2+ ion channel field.

Various methods for characterizing binding forces as well as for monitoring and remote control of ion channels are still emerging. A recent innovation is the direct incorporation of unnatural amino acids (UAAs) with corresponding biophysical or biochemical properties, which are integrated using genetic code expansion technology. Minimal changes to natural amino acids, which are achieved by chemical synthesis of corresponding UAAs, are valuable tools to provide insight into the contributions of physicochemical properties of side chains in binding events. To gain unique control over the conformational changes or function of ion channels, a series of light-sensitive, chemically reactive and posttranslationally modified UAAs have been developed and utilized. Here, we present the existing UAA tools, their mode of action, their potential and limitations as well as their previous applications to Ca2+-permeable ion channels.

Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data.

Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure-function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient-weighted Class Activation Mapping for graphs (Graph Grad-CAM) to automatically identify structurally important residues and residue-residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad-CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well-known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad-CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub-classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high-throughput identification of protein structure-function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.

Understanding the role of negative charge in the scaffold of an artificial enzyme for CO2 hydrogenation on catalysis.

We have approached the construction of an artificial enzyme by employing a robust protein scaffold, lactococcal multidrug resistance regulator, LmrR, providing a structured secondary and outer coordination spheres around a molecular rhodium complex, [RhI(PEt2NglyPEt2)2]-. Previously, we demonstrated a 2-3 fold increase in activity for one Rh-LmrR construct by introducing positive charge in the secondary coordination sphere. In this study, a series of variants was made through site-directed mutagenesis where the negative charge is located in the secondary sphere or outer coordination sphere, with additional variants made with increasingly negative charge in the outer coordination sphere while keeping a positive charge in the secondary sphere. Placing a negative charge in the secondary or outer coordination sphere demonstrates decreased activity by a factor of two compared to the wild-type Rh-LmrR. Interestingly, addition of positive charge in the secondary sphere, with the negatively charged outer coordination sphere restores activity. Vibrational and NMR spectroscopy suggest minimal changes to the electronic density at the rhodium center, regardless of inclusion of a negative or positive charge in the secondary sphere, suggesting another mechanism is impacting catalytic activity, explored in the discussion.

Understanding Flexdispersion: Structure-Function Relationship Studies of Organic Amphiphilic Ligands.

Since inorganic nanoparticles have unique properties that differ from those of bulk materials, their material applications have attracted attention in various fields. In order to utilize inorganic nanoparticles for functional materials, they must be dispersed without agglomeration. Therefore, the surfaces of inorganic nanoparticles are typically modified with organic ligands to improve their dispersibility. Nevertheless, the relationship between the tail group structure in organic ligands and the dispersibility of inorganic nanoparticles in organic solvents remains poorly understood. We previously developed amphiphilic ligands that consist of ethylene glycol chains and alkyl chains to disperse inorganic nanoparticles in a variety of organic solvents. However, the structural requirements for amphiphilic ligands to "flexibly" disperse nanoparticles in less polar to polar solvents are still unclear. Here, we designed and synthesized several phosphonic acid ligands for structure-function relationship studies of flexdispersion. Dynamic light scattering analysis and visible light transmittance measurements revealed that the ratio of alkyl/ethylene glycol chains in organic ligands alone does not determine the dispersibility of the nanoparticles in organic solvents, but the arrangement of the individual chains also has an effect. From a practical application standpoint, it is preferable to design ligands with ethylene glycol chains on the outside relative to the particle surface.

Robust Red-Absorbing Donor-Acceptor Stenhouse Adduct Photoswitches.

Donor-Acceptor Stenhouse Adduct (DASA), a class of push-pull negative photochrome, has received large interest lately owing to its versatile synthesis, modularity and excellent photoswitching in solutions. From a technological perspective, it is imperative for this class of photoswitches to work robustly in solid state, e. g. thin films. We feature a molecular framework for the optimized design of DASAs by introducing a new thioindoline donor (D3) and assessing its performance against known 2nd generation indoline-based donors. The systematic structure-function investigations suggest that to achieve robust reversible photoswitching, a ground state with low charge separation is desired. DASAs with stronger electron donors and a larger charge separation in the ground state result in a low population of the photothermalstationary state (PTSS) and reduced photostability. The DASA with thioindoline donor (D3A3) seems to be a special case among the donor series as it causes a red shift (ca. 15 nm), however with less polarization of the ground state and marginally better photostability as compared to the unsubstituted 2-methyl indoline (D1A3). We also emphasize the consideration of the key additional factors that can modulate the red-light photoswitching properties of DASA chromophores in polymer thin films, which might not be dominant in homogenous solution state.

Roles of Oxygen-Containing Functional Groups in Carbon for Electrocatalytic Two-Electron Oxygen Reduction Reaction.

Recent years have witnessed great research interests in developing high-performance electrocatalysts for the two-electron (2e-) oxygen reduction reaction (ORR) that enables the sustainable and flexible synthesis of H2O2. Carbon-based electrocatalysts exhibit attractive catalytic performance for the 2e- ORR, where oxygen-containing functional groups (OFGs) play a decisive role. However, current understanding is far from adequate, and the contribution of OFGs to the catalytic performance remains controversial. Therefore, a critical overview on OFGs in carbon-based electrocatalysts toward the 2e- ORR is highly desirable. Herein, we go over the methods for constructing OFGs in carbon including chemical oxidation, electrochemical oxidation, and precursor inheritance. Then we review the roles of OFGs in activating carbon toward the 2e- ORR, focusing on the intrinsic activity of different OFGs and the interplay between OFGs and metal species or defects. At last, we discuss the reasons for inconsistencies among different studies, and personal perspectives on the future development in this field are provided. The results provide insights into the origin of high catalytic activity and selectivity of carbon-based electrocatalysts toward the 2e- ORR and would provide theoretical foundations for the future development in this field.

The art and science of porous starch: understanding the preparation method and structure-function relationship.

Porous starch (PS), a modified form of starch with unique properties, is attracting substantial attention for its diverse advantages and applications. Its intricate porous structure, crystalline and amorphous characteristics, and hydrophilic-hydrophobic properties stem from pore formation via physical, chemical, enzymatic, and combined synergistic methods. Porous starch offers benefits like improved gelatinization temperature, water absorption, increased surface area, tunable crystallinity, and enhanced functional properties, making it appealing for diverse food industry applications. To optimize its properties, determining the parameters governing porous structure formation is crucial. Factors such as processing conditions, starch source, and modification methods substantially impact porosity and the overall characteristics of the material. Understanding and controlling these parameters allows customization for specific applications, from pharmaceutical drug delivery systems to enhancing texture and moisture retention in food products. To date, studies shedding light on how porosity formation can be fine-tuned for specific applications are fewer. This review critically assesses the existing reports on porous starch, focusing on how preparation methods affect porosity formation, thereby influencing the product's crystallinity/hydrophilic-hydrophobic nature and overall applicability.

From Software to Hardware: A Case Series of Functional Neurological Symptoms and Cerebrovascular Disease.

OBJECTIVE: Neuroimaging studies have identified alterations in both brain structure and functional connectivity in patients with functional neurological disorder (FND). For many patients, FND emerges from physical precipitating events. Nevertheless, there are a limited number of case series in the literature that describe the clinical presentation and neuroimaging correlates of FND following cerebrovascular disease. METHODS: The authors collected data from two clinics in the United Kingdom on 14 cases of acute, improving, or delayed functional neurological symptoms following cerebrovascular events. RESULTS: Most patients had functional neurological symptoms that were localized to cerebrovascular lesions, and the lesions mapped onto regions known to be part of functional networks disrupted in FND, including the thalamus, anterior cingulate gyrus, insula, and temporoparietal junction. CONCLUSIONS: The findings demonstrate that structural lesions can lead to FND symptoms, possibly explained through changes in relevant mechanistic functional networks.

Temperature Dependent Activity of the Voltage-Gated Proton Channel.

Voltage-gated proton channel (Hv) has activity of proton transport following electrochemical gradient of proton. Hv is expressed in neutrophils and macrophages of which functions are physiologically temperature-sensitive. Hv is also expressed in human sperm cells and regulates their locomotion. H+ transport through Hv is both regulated by membrane potential and pH difference across biological membrane. It is also reported that properties of Hv such as proton conductance and gating are highly temperature-dependent. Hv consists of the N-terminal cytoplasmic domain, the voltage sensor domain (VSD), and the C-terminal coiled-coil domain, and H+ permeates through VSD voltage-dependently. The functional unit of Hv is a dimer via the interaction between C-terminal coiled-coils assembly domain. We have reported that the coiled-coil domain of Hv has the nature of dissociation around our bodily temperature and mutational change of the coiled-coil affected temperature-sensitive gating, especially its temperature threshold. The temperature-sensitive gating is assessed from two separate points: temperature threshold and temperature dependence. In this chapter, I describe physiological roles and molecular structure mechanisms of Hv by mainly focusing on thermosensitive properties.

Structure of human Nav1.5 reveals the fast inactivation-related segments as a mutational hotspot for the long QT syndrome.

Nav1.5 is the primary voltage-gated Na+ (Nav) channel in the heart. Mutations of Nav1.5 are associated with various cardiac disorders exemplified by the type 3 long QT syndrome (LQT3) and Brugada syndrome (BrS). E1784K is a common mutation that has been found in both LQT3 and BrS patients. Here we present the cryo-EM structure of the human Nav1.5-E1784K variant at an overall resolution of 3.3 Å. The structure is nearly identical to that of the wild-type human Nav1.5 bound to quinidine. Structural mapping of 91- and 178-point mutations that are respectively associated with LQT3 and BrS reveals a unique distribution pattern for LQT3 mutations. Whereas the BrS mutations spread evenly on the structure, LQT3 mutations are clustered mainly to the segments in repeats III and IV that are involved in gating, voltage-sensing, and particularly inactivation. A mutational hotspot involving the fast inactivation segments is identified and can be mechanistically interpreted by our "door wedge" model for fast inactivation. The structural analysis presented here, with a focus on the impact of mutations on inactivation and late sodium current, establishes a structure-function relationship for the mechanistic understanding of Nav1.5 channelopathies.

Synthesis, and Insecticidal Activities of Propargyloxy-Diphenyl Oxide-Sulfonamide Derivatives.

Agricultural pests are the primary contributing factor to crop yield reduction, particularly in underdeveloped regions. Despite the significant efficacy of pesticides in pest control, their extensive use has led to the drug-fast of insecticide resistance. Developing of new environmentally friendly plant-based pesticides is an urgent necessity. In this study, a series of diaryl ether compounds containing propargyloxy and sulfonamide groups were designed. The synthesis of these 36 compounds primarily relied on nuclear magnetic resonance for structure determination, while single-crystal X-ray diffraction was employed for certain compounds. Meanwhile, the insecticidal activities against Mythimna separata were also assessed. Some of the compounds exhibited significantly enhanced activity, the LC50 value of the highest activity compound TD8 (0.231 mg/mL) demonstrating respective increases by 100-fold compared to the plant pesticide celangulin V (23.9 mg/mL), and a 5-fold increase with the positive control L-1 (1.261 mg/mL). The interaction between the target compound and the target, as well as the consistency of the target, were verified through symptomological analysis and molecular docking. The structure-activity relationships were also conducted. This study offered a novel trajectory for the advancement and formulation of future pesticides.

Hollow CoZnSe@CN nanocage with enzymatic activity for determination of tetracycline using smartphone platforms and virtual reality revealing.

Antibiotic residues in the environment pose a serious threat to ecosystems and human health. Therefore, it is important to develop sensitive and rapid in situ detection methods. In this work, the designed nanozymes, with excellent four enzyme activities, were proved to be constituted of unique hollow nanocage structures (CoZnSe@CN HCs). Based on the peroxidase-like enzymes, a portable colorimetric sensor was constructed for the on-site determination of tetracycline (TC) in real samples. The linear range of TC detection was 0.1-100 µM, and the detection limit was 0.02 µM. At the same time, colorimetric detection and smartphones have also been combined for on-site colorimetric detection of TC. In-depth exploration of the detection mechanism showed that TC could be bound with the material, inhibiting the production of oxidized 3,3',5,5'-tetramethylbenzidine. The sensor was also used for the detection of TC in environmental soil and water samples. This study can provide an intelligent detection method for environmental monitoring.

Exploring the Structurally Conserved Regions and Functional Significance in Bacterial N-Terminal Nucleophile (Ntn) Amide-Hydrolases.

The initial adoption of penicillin as an antibiotic marked the start of exploring other compounds essential for pharmaceuticals, yet resistance to penicillins and their side effects has compromised their efficacy. The N-terminal nucleophile (Ntn) amide-hydrolases S45 family plays a key role in catalyzing amide bond hydrolysis in various compounds, including antibiotics like penicillin and cephalosporin. This study comprehensively analyzes the structural and functional traits of the bacterial N-terminal nucleophile (Ntn) amide-hydrolases S45 family, covering penicillin G acylases, cephalosporin acylases, and D-succinylase. Utilizing structural bioinformatics tools and sequence analysis, the investigation delineates structurally conserved regions (SCRs) and substrate binding site variations among these enzymes. Notably, sixteen SCRs crucial for substrate interaction are identified solely through sequence analysis, emphasizing the significance of sequence data in characterizing functionally relevant regions. These findings introduce a novel approach for identifying targets to enhance the biocatalytic properties of N-terminal nucleophile (Ntn) amide-hydrolases, while facilitating the development of more accurate three-dimensional models, particularly for enzymes lacking structural data. Overall, this research advances our understanding of structure-function relationships in bacterial N-terminal nucleophile (Ntn) amide-hydrolases, providing insights into strategies for optimizing their enzymatic capabilities.

Self-Assembly Behavior, Aggregation Structure, and the Charge Carrier Transport Properties of S-Heterocyclic Annulated Perylene Diimide Derivatives.

The construction of high-performance n-type semiconductors is crucial for the advancement of organic electronics. As an attractive n-type semiconductor, molecular systems based on perylene diimide derivatives (PDIs) have been extensively investigated over recent years. Owing to the fascinating aggregated structure and high performance, S-heterocyclic annulated PDIs (SPDIs) are receiving increasing attention. However, the relationship between the structure and the electrical properties of SPDIs has not been deeply revealed, restricting the progress of PDI-based organic electronics. Here, we developed two novel SPDIs with linear and dendronized substituents in the imide position, named linear SPDI and dendronized SPDI, respectively. A series of structural and property characterizations indicated that linear SPDI formed a long-range-ordered crystalline structure based on helical supramolecular columns, while dendronized SPDI, with longer alkyl side chains, formed a 3D-ordered crystalline structure at a low temperature, which transformed into a hexagonal columnar liquid crystal structure at a high temperature. Moreover, no significant charge carrier transport signal was examined for linear SPDI, while dendronized SPDI had a charge carrier mobility of 3.5 × 10-3 cm2 V-1 s-1 and 2.1 × 10-3 cm2 V-1 s-1 in the crystalline and liquid crystalline state, respectively. These findings highlight the importance of the structure-function relationship in PDIs, and also offer useful roadmaps for the design of high-performance organic electronics for down-to-earth applications.

Decoding coffee cardiometabolic potential: Chemical composition, nutritional, and health relationships.

Coffee is one of the most consumed beverages worldwide, recognized for its unique taste and aroma and for its social and health impacts. Coffee contains a plethora of nutritional and bioactive components, whose content can vary depending on their origin, processing, and extraction methods. Gathered evidence in literature shows that the regular coffee consumption containing functional compounds (e.g., polysaccharides, phenolic compounds, and melanoidins) can have potential beneficial effects on cardiometabolic risk factors such as abdominal adiposity, hyperglycemia, and lipogenesis. On the other hand, coffee compounds, such as caffeine, diterpenes, and advanced glycation end products, may be considered a risk for cardiometabolic health. The present comprehensive review provides up-to-date knowledge on the structure-function relationships between different chemical compounds present in coffee, one of the most prevalent beverages present in human diet, and cardiometabolic health.