The Molecular Mechanism of Transport by the Mitochondrial ADP/ATP Carrier.

Mitochondrial ADP/ATP carriers transport ADP into the mitochondrial matrix for ATP synthesis, and ATP out to fuel the cell, by cycling between cytoplasmic-open and matrix-open states. The structure of the cytoplasmic-open state is known, but it has proved difficult to understand the transport mechanism in the absence of a structure in the matrix-open state. Here, we describe the structure of the matrix-open state locked by bongkrekic acid bound in the ADP/ATP-binding site at the bottom of the central cavity. The cytoplasmic side of the carrier is closed by conserved hydrophobic residues, and a salt bridge network, braced by tyrosines. Glycine and small amino acid residues allow close-packing of helices on the matrix side. Uniquely, the carrier switches between states by rotation of its three domains about a fulcrum provided by the substrate-binding site. Because these features are highly conserved, this mechanism is likely to apply to the whole mitochondrial carrier family. VIDEO ABSTRACT.

TRAPs: the 'elevator-with-an-operator' mechanism.

Tripartite ATP-independent periplasmic (TRAP) transporters are nutrient-uptake systems found in bacteria and archaea. These evolutionary divergent transporter systems couple a substrate-binding protein (SBP) to an elevator-type secondary transporter, which is a first-of-its-kind mechanism of transport. Here, we highlight breakthrough TRAP transporter structures and recent functional data that probe the mechanism of transport. Furthermore, we discuss recent structural and biophysical studies of the ion transporter superfamily (ITS) members and highlight mechanistic principles that are relevant for further exploration of the TRAP transporter system.

Substrate recognition and transport mechanism of the PIN-FORMED auxin exporters.

Auxins are pivotal plant hormones that regulate plant growth and transmembrane polar auxin transport (PAT) direct patterns of development. The PIN-FORMED (PIN) family of membrane transporters mediate auxin export from the plant cell and play crucial roles in PAT. Here we describe the recently solved structures of PIN transporters, PIN1, PIN3, and PIN8, and also their mechanisms of substrate recognition and transport of auxin. We compare structures of PINs in both inward- and outward-facing conformations, as well as PINs with different binding configurations for auxin. By this comparative analysis, a model emerges for an elevator transport mechanism. Central structural elements necessary for function are identified, and we show that these are shared with other distantly related protein families.

Alternating access of a bacterial homolog of neurotransmitter: sodium symporters determined from AlphaFold2 ensembles and DEER spectroscopy.

Neurotransmitter:sodium symporters (NSSs) play critical roles in neural signaling by regulating neurotransmitter uptake into cells powered by sodium electrochemical gradients. Bacterial NSSs orthologs, including MhsT from Bacillus halodurans, have emerged as model systems to understand the structural motifs of alternating access in NSSs and the extent of conservation of these motifs across the family. Here, we apply a computational/experimental methodology to illuminate the conformational landscape of MhsT alternating access. Capitalizing on our recently developed method, Sampling Protein Ensembles and Conformational Heterogeneity with AlphaFold2 (SPEACH_AF), we derived clusters of MhsT models spanning the transition from inward-facing to outward-facing conformations. Systematic application of double electron-electron resonance (DEER) spectroscopy revealed ligand-dependent movements of multiple structural motifs that underpin MhsT's conformational cycle. Remarkably, comparative DEER analysis in detergent micelles and lipid nanodiscs highlights the profound effect of the environment on the energetics of conformational changes. Through experimentally derived selection of collective variables, we present a model of ion and substrate-powered transport by MhsT consistent with the conformational cycle derived from DEER. Our findings not only advance the understanding of MhsT's function but also uncover motifs of conformational dynamics conserved within the broader context of the NSS family and within the LeuT-fold class of transporters. Importantly, our methodological blueprint introduces an approach that can be applied across a diverse spectrum of transporters to describe their conformational landscapes.

The SLC25 Mitochondrial Carrier Family: Structure and Mechanism.

Members of the mitochondrial carrier family (SLC25) provide the transport steps for amino acids, carboxylic acids, fatty acids, cofactors, inorganic ions, and nucleotides across the mitochondrial inner membrane and are crucial for many cellular processes. Here, we use new insights into the transport mechanism of the mitochondrial ADP/ATP carrier to examine the structure and function of other mitochondrial carriers. They all have a single substrate-binding site and two gates, which are present on either side of the membrane and involve salt-bridge networks. Transport is likely to occur by a common mechanism, in which the coordinated movement of six structural elements leads to the alternating opening and closing of the matrix or cytoplasmic side of the carriers.

Physics, Structures, and Applications of Fluorite-Structured Ferroelectric Tunnel Junctions.

The interest in ferroelectric tunnel junctions (FTJ) has been revitalized by the discovery of ferroelectricity in fluorite-structured oxides such as HfO2 and ZrO2 . In terms of thickness scaling, CMOS compatibility, and 3D integration, these fluorite-structured FTJs provide a number of benefits over conventional perovskite-based FTJs. Here, recent developments involving all FTJ devices with fluorite structures are examined. The transport mechanism of fluorite-structured FTJs is explored and contrasted with perovskite-based FTJs and other 2-terminal resistive switching devices starting with the operation principle and essential parameters of the tunneling electroresistance effect. The applications of FTJs, such as neuromorphic devices, logic-in-memory, and physically unclonable function, are then discussed, along with several structural approaches to fluorite-structure FTJs. Finally, the materials and device integration difficulties related to fluorite-structure FTJ devices are reviewed. The purpose of this review is to outline the theories, physics, fabrication processes, applications, and current difficulties associated with fluorite-structure FTJs while also describing potential future possibilities for optimization.

Electrostatic Repulsion Facilitated Ion Transport in Covalent-Organic Framework Membranes.

Covalent-organic framework (COF) membranes are increasingly used for many potential applications including ion separation, fuel cells, and ion batteries. It is of central importance to fundamentally and quantitatively understand ion transport in COF membranes. In this study, a series of COF membranes is designed with different densities and arrangements of functional groups and subsequently utilize molecular simulation to provide microscopic insights into ion transport in these membranes. The membrane with a single-sided layer exhibits the highest chloride ion (Cl-) conductivity of 77.2 mS cm-1 at 30 °C. Replacing the single-sided layer with a double-sided layer or changing layer arrangement leads to a decrease in Cl- conductivity up to 33% or 53%, respectively. It is revealed that the electrostatic repulsion between ions serves as a driving force to facilitate ion transport and the positions of functional groups determine the direction of electrostatic repulsion. Furthermore, the ordered pores generate concentrated ions and allow rapid ion transport. This study offers bottom-up inspiration on the design of new COF membranes with moderate density and proper arrangement of functional groups to achieve high ion conductivity.

Photo-Thermal Mediated Li-ion Transport for Solid-State Lithium Metal Batteries.

The development of lithium-based solid-state batteries (SSBs) has to date been hindered by the limited ionic conductivity of solid polymer electrolytes (SPEs), where nonsolvated Li-ions are difficult to migrate in a polymer framework at room temperature. Despite the improved cationic migration by traditional heating systems, they are far from practical applications of SSBs. Here, an innovative strategy of light-mediated energy conversion is reported to build photothermal-based SPEs (PT-SPEs). The results suggest that the nanostructured photothermal materials acting as a powerful light-to-heat converter enable heating within a submicron space, leading to a decreased Li+ migration barrier and a stronger solid electrolyte interface. Via in situ X-ray diffraction analysis and molecular dynamics simulation, it is shown that the generated heating effectively triggers the structural transition of SPEs from a highly crystalline to an amorphous state, that helps mediate lithium-ion transport. Using the assembled SSBs for exemplification, PT-SPEs function as efficient ion-transport media, providing outstanding capacity retention (96% after 150 cycles) and a stable charge/discharge capacity (140 mA g-1 at 1.0 C). Overall, the work provides a comprehensive picture of the Li-ion transport in solid polymer electrolytes and suggests that free volume may be critical to achieving high-performance solid-state batteries.

SLC26 Anion Transporters.

Solute carrier family 26 (SLC26) is a family of functionally diverse anion transporters found in all kingdoms of life. Anions transported by SLC26 proteins include chloride, bicarbonate, and sulfate, but also small organic dicarboxylates such as fumarate and oxalate. The human genome encodes ten functional homologs, several of which are causally associated with severe human diseases, highlighting their physiological importance. Here, we review novel insights into the structure and function of SLC26 proteins and summarize the physiological relevance of human members.

Magnetism-Induced Band-Edge Shift as the Mechanism for Magnetoconductance in CrPS4 Transistors.

Transistors realized on the 2D antiferromagnetic semiconductor CrPS4 exhibit large magnetoconductance due to magnetic-field-induced changes in the magnetic state. The microscopic mechanism coupling the conductance and magnetic state is not understood. We identify it by analyzing the evolution of the parameters determining the transistor behavior─carrier mobility and threshold voltage─with temperature and magnetic field. For temperatures T near the Néel temperature TN, the magnetoconductance originates from a mobility increase due to the applied magnetic field that reduces spin fluctuation induced disorder. For T ≪ TN, instead, what changes is the threshold voltage, so that increasing the field at fixed gate voltage increases the density of accumulated electrons. The phenomenon is explained by a conduction band-edge shift correctly predicted by the ab initio calculations. Our results demonstrate that the band structure of CrPS4 depends on its magnetic state and reveal a mechanism for magnetoconductance that had not been identified earlier.

Enhanced Sampling Molecular Dynamics Simulations Reveal Transport Mechanism of Glycoconjugate Drugs through GLUT1.

Glucose transporters GLUT1 belong to the major facilitator superfamily and are essential to human glucose uptake. The overexpression of GLUT1 in tumor cells designates it as a pivotal target for glycoconjugate anticancer drugs. However, the interaction mechanism of glycoconjugate drugs with GLUT1 remains largely unknown. Here, we employed all-atom molecular dynamics simulations, coupled to steered and umbrella sampling techniques, to examine the thermodynamics governing the transport of glucose and two glycoconjugate drugs (i.e., 6-D-glucose-conjugated methane sulfonate and 6-D-glucose chlorambucil) by GLUT1. We characterized the specific interactions between GLUT1 and substrates at different transport stages, including substrate recognition, transport, and releasing, and identified the key residues involved in these procedures. Importantly, our results described, for the first time, the free energy profiles of GLUT1-transporting glycoconjugate drugs, and demonstrated that H160 and W388 served as important gates to regulate their transport via GLUT1. These findings provide novel atomic-scale insights for understanding the transport mechanism of GLUT1, facilitating the discovery and rational design of GLUT1-targeted anticancer drugs.

A Conserved Intramolecular Ion-Pair Plays a Critical but Divergent Role in Regulation of Dimerization and Transport Function among the Monoamine Transporters.

The monoamine transporters, including the serotonin transporter (SERT), dopamine transporter (DAT), and norepinephrine transporter (NET), are the therapeutic targets for the treatment of many neuropsychiatric disorders. Despite significant progress in characterizing the structures and transport mechanisms of these transporters, the regulation of their transport functions through dimerization or oligomerization remains to be understood. In the present study, we identified a conserved intramolecular ion-pair at the third extracellular loop (EL3) connecting TM5 and TM6 that plays a critical but divergent role in the modulation of dimerization and transport functions among the monoamine transporters. The disruption of the ion-pair interactions by mutations induced a significant spontaneous cross-linking of a cysteine mutant of SERT and an increase in cell surface expression but with an impaired specific transport activity. On the other hand, similar mutations of the corresponding ion-pair residues in both DAT and NET resulted in an opposite effect on their oxidation-induced dimerization, cell surface expression, and transport function. Reversible biotinylation experiments indicated that the ion-pair mutations slowed down the internalization of SERT but stimulated the internalization of DAT. In addition, cysteine accessibility measurements for monitoring SERT conformational changes indicated that substitution of the ion-pair residues resulted in profound effects on the rate constants for cysteine modification in both the extracellular and cytoplasmatic substrate permeation pathways. Furthermore, molecular dynamics simulations showed that the ion-pair mutations increased the interfacial interactions in a SERT dimer but decreased it in a DAT dimer. Taken together, we propose that the transport function is modulated by the equilibrium between monomers and dimers on the cell surface, which is regulated by a potential compensatory mechanism but with different molecular solutions among the monoamine transporters. The present study provided new insights into the structural elements regulating the transport function of the monoamine transporters through their dimerization.

Soil type regulates the divergent loss characteristics of sediment associated carbon and nitrogen in different size classes during rainfall erosion on cultivated lands.

Sediment associated carbon and nitrogen loss under rainfall, an important cause of soil quality degradation and water eutrophication, strongly depends on the intrinsic properties of original soil types. Relative to total loss, the transport behaviors of organic carbon and nitrogen among sediment size classes and response to soil types remain poorly understood. The concentrations of organic carbon (OC) and total nitrogen (TN) in different sediment size classes (>1, 0.25-1, 0.10-0.25, and <0.10 mm) and their contributions to total sediment load during rainfall erosion were determined under field plot rainfall simulation (at 90 mm h-1) on three contrasting soil types (Luvisol, Alisol and Ferralsol) with increased aggregate stability. During rainfall erosion, the concentrations of OC and TN in total and different sized sediments decreased first and then reached a steady state. The variability of OC and TN concentrations (coefficient of variations in 4.2-53.1% and 6.6-41.9%) among sediment size classes decreased from Luvisol to Ferralsol. Compared to original soils, sediments exhibited larger C/N ratios for Luvisol, and smaller values for Alisol, indicating the more selective transport of labile organic matter for weaker aggregated soils. Among sediment size classes, fine particles (<0.10 mm) accounted 69-88% of total OC and TN losses for Luvisol, and decreased to 30-39% for Ferralsol; and the main transport mechanisms of sediment associated OC and TN shifting from suspension-saltation (<0.10 mm) to rolling (>0.25 mm) with increased aggregate stability. Among original soil properties, inorganic cementing agents (including amorphous iron oxides and clay minerals) showed closer relationships with sediment OC and TN losses (|r| = 0.61-0.89, p < 0.001) than organic matter properties (|r| = 0.55-0.87, p < 0.001), further implying the important role of soil aggregate stability across soil types. This study provides an in-depth understanding on soil carbon and nitrogen losses and their divergent characteristics among soil types deserves consideration in the development of erosion model and land management in agricultural systems.

Transport of glycinin, the major soybean allergen, across intestinal epithelial IPEC-J2 cell monolayers.

Soybean allergen entering the body is the initial step to trigger intestinal allergic response. However, it remains unclear how glycinin, the major soybean allergen, is transported through the intestinal mucosal barrier. The objective of this study was to elucidate the pathway and mechanism of glycinin hydrolysate transport through the intestinal epithelial barrier using IPEC-J2 cell model. Purified glycinin was digested by in vitro static digestion model. The pathway and mechanism of glycinin hydrolysates transport through intestinal epithelial cells were investigated by cellular transcytosis assay, cellular uptake assay, immunoelectron microscopy and endocytosis inhibition assay. The glycinin hydrolysates were transported across IPEC-J2 cell monolayers in a time/dose-dependent manner following the Michaelis equation. Immunoelectron microscopy showed a number of glycinin hydrolysates appeared in the cytoplasm, but no glycinin hydrolysates were observed in the intercellular space of IPEC-J2 cells. The inhibitors, colchicine, chlorpromazine and methyl-ß-cyclodextrin, significantly inhibited the cellular uptake of glycinin hydrolysates. The glycinin hydrolysates crossed IPEC-J2 cell monolayers through the transcellular pathway. Both clathrin- and caveolae-dependent endocytosis were involved in the epithelial uptake of the hydrolysates. These findings provided potential targets for the prevention and treatment of soybean allergy.

Prokaryotic ammonium transporters: what has three decades of research revealed?

The exchange of ammonium across cellular membranes is a fundamental process in all domains of life. In plants, bacteria and fungi, ammonium represents a vital source of nitrogen, which is scavenged from the external environment. In contrast, in animal cells ammonium is a cytotoxic metabolic waste product and must be excreted to prevent cell death. Transport of ammonium is facilitated by the ubiquitous Amt/Mep/Rh transporter superfamily. In addition to their function as transporters, Amt/Mep/Rh proteins play roles in a diverse array of biological processes and human physiopathology. Despite this clear physiological importance and medical relevance, the molecular mechanism of Amt/Mep/Rh proteins has remained elusive. Crystal structures of bacterial Amt/Rh proteins suggest electroneutral transport, whilst functional evidence supports an electrogenic mechanism. Here, focusing on bacterial members of the family, we summarize the structure of Amt/Rh proteins and what three decades of research tells us concerning the general mechanisms of ammonium translocation, in particular the possibility that the transport mechanism might differ in various members of the Amt/Mep/Rh superfamily.

Study on the transport and internalisation mechanism of dietary supplement nattokinase in the small intestine using animal and Caco-2 cell monolayer models.

Maintaining proper blood flow is critical to promoting good health. Nattokinase is a serine protease from Bacillus subtilis that has significant in vitro thrombolytic activity, but its mechanism as a dietary supplement to prevent thrombosis through intestinal absorption and transport is still unclear.The purpose of this study is to study the transport and internalisation mechanism of NK in the small intestine using animal models and Caco-2 cell monolayer models.This study first evaluated the preventive effect of supplementing low dose (4000 FU (Fibrin Unit)/kg, n = 6), medium dose (8000 FU/kg, n = 6), and high dose (12000 FU/kg, n = 6) of nattokinase on carrageenan induced thrombosis in mice. Subsequently, we used the rat gut sac model, ligated intestinal loop model, and Caco-2 cell uptake model to study the intestinal transport mechanism of NK.Results indicate that NK is a moderately absorbed biomolecule whose transport through enterocytes is energy- and time-dependent. Chlorpromazine, nystatin and EIPA all inhibited the endocytosis of NK to varying degrees, indicating that the endocytosis of NK in Caco-2 cells involves macropinocytosis, clathrin-mediated and caveolae-mediated pathway. These findings offer a theoretical basis for investigating the mechanism of oral NK supplementation in greater depth.

Sequence and structural determinants of ligand-dependent alternating access of a MATE transporter.

Multidrug and toxic compound extrusion (MATE) transporters are ubiquitous ion-coupled antiporters that extrude structurally and chemically dissimilar cytotoxic compounds and have been implicated in conferring multidrug resistance. Here, we integrate double electron-electron resonance (DEER) with functional assays and site-directed mutagenesis of conserved residues to illuminate principles of ligand-dependent alternating access of PfMATE, a proton-coupled MATE from the hyperthermophilic archaeon Pyrococcus furiosus Pairs of spin labels monitoring the two sides of the transporter reconstituted into nanodiscs reveal large-amplitude movement of helices that alter the orientation of a putative substrate binding cavity. We found that acidic pH favors formation of an inward-facing (IF) conformation, whereas elevated pH (>7) and the substrate rhodamine 6G stabilizes an outward-facing (OF) conformation. The lipid-dependent PfMATE isomerization between OF and IF conformation is driven by protonation of a previously unidentified intracellular glutamate residue that is critical for drug resistance. Our results can be framed in a mechanistic model of transport that addresses central aspects of ligand coupling and alternating access.

SLC22A11 Inserts the Uremic Toxins Indoxyl Sulfate and P-Cresol Sulfate into the Plasma Membrane.

Chronic kidney disease (CKD) is a global health concern affecting millions worldwide. One of the critical challenges in CKD is the accumulation of uremic toxins such as p-cresol sulfate (pCS) and indoxyl sulfate (IS), which contribute to systemic damage and CKD progression. Understanding the transport mechanisms of these prominent toxins is essential for developing effective treatments. Here, we investigated whether pCS and IS are routed to the plasma membrane or to the cytosol by two key transporters, SLC22A11 and OAT1. To distinguish between cytosolic transport and plasma membrane insertion, we used a hyperosmolarity assay in which the accumulation of substrates into HEK-293 cells in isotonic and hypertonic buffers was measured in parallel using LC-MS/MS. Judging from the efficiency of transport (TE), pCS is a relevant substrate of SLC22A11 at 7.8 ± 1.4 µL min-1 mg protein-1 but not as good as estrone-3-sulfate; OAT1 translocates pCS less efficiently. The TE of SLC22A11 for IS was similar to pCS. For OAT1, however, IS is an excellent substrate. With OAT1 and p-aminohippuric acid, our study revealed an influence of transporter abundance on the outcomes of the hyperosmolarity assay; very high transport activity confounded results. SLC22A11 was found to insert both pCS and IS into the plasma membrane, whereas OAT1 conveys these toxins to the cytosol. These disparate transport mechanisms bear profound ramifications for toxicity. Membrane insertion might promote membrane damage and microvesicle release. Our results underscore the imperative for detailed structural inquiries into the translocation of small molecules.

Low-gradient magnetic separation of magnetic nanoparticles under continuous flow: Experimental study, transport mechanism and mathematical modelling.

Low-gradient magnetic separation (LGMS) of magnetic nanoparticles (MNPs) has been proven as one of the techniques with great potential for biomedical and environmental applications. Recently, the underlying principle of particle capture by LGMS, through a process known as magnetophoresis, under the influence of hydrodynamic effect has been widely studied and illustrated. Even though the hydrodynamic effect is very substantial for batch processes, its impact on LGMS operated at continuous flow (CF) condition remained largely unknown. Hence, in this study, the dynamical behaviour of LGMS process operated under CF was being studied. First, the LGMS experiments using poly(sodium 4-styrenesulfonate)-functionalized-MNP as modelled particle system were performed through batchwise (BW) and CF modes at different operating conditions. Here BW operation was used as a comparative study to elucidate the transport mechanism of MNP under the similar environment of CF-LGMS process, and it was found out that the convection induced by magnetophoresis (timescale effective is ∼1200 s) is only significant at far-from-magnet region. Hence, it can be deduced that forced convection is more dominant on influencing the transport behaviour of CF-LGMS (with resident time ≤240 s). Moreover, we found that the separation efficiency of CF-LGMS process can be boosted by the higher number of magnets, the higher MNP concentration and the lower flowrate of MNP solution. To better illustrate the underlying dynamical behaviour of LGMS process, a mathematical model was developed to predict its kinetic profile and separation efficiency (with average error of ∼2.6% compared to the experimental results).

Superhydrophobic Carbon Nanotube Network Membranes for Membrane Distillation: High-Throughput Performance and Transport Mechanism.

Despite increasing sustainable water purification, current desalination membranes still suffer from insufficient permeability and treatment efficiency, greatly hindering extensive practical applications. In this work, we provide a new membrane design protocol and molecule-level mechanistic understanding of vapor transport for the treatment of hypersaline waters via a membrane distillation process by rationally fabricating more robust metal-based carbon nanotube (CNT) network membranes, featuring a superhydrophobic superporous surface (80.0 ± 2.3% surface porosity). With highly permeable ductile metal hollow fibers as substrates, the construction of a superhydrophobic (water contact angle ∼170°) CNT network layer endows the membranes with not only almost perfect salt rejection (over 99.9%) but a promising water flux (43.6 L·m-2·h-1), which outperforms most existing inorganic distillation membranes. Both experimental and molecular dynamics simulation results indicate that such an enhanced water flux can be ascribed to an ultra-low liquid-solid contact interface (∼3.23%), allowing water vapor to rapidly transport across the membrane structure via a combined mechanism of Knudsen diffusion (more dominant) and viscous flow while efficiently repelling high-salinity feed via forming a Cassie-Baxter state. A more hydrophobic surface is more in favor of not only water desorption from the CNT outer surface but superfast and frictionless water vapor transport. By constructing a new superhydrophobic triple-phase interface, the conceptional design strategy proposed in this work can be expected to be extended to other membrane material systems as well as more water treatment applications.