Near-physiological Conditions Research Articles

Attenuation of alcohol-induced hepatocyte damage by ginsenoside Rg1 evaluated using atomic force microscopy.

Alcoholic liver disease is an important cause of death worldwide. Hepatocyte apoptosis is commonly observed in alcoholic liver disease. In this study, we investigated the effect of ginsenoside Rg1 (G-Rg1), an organic component of ginseng, on the alcohol-induced morphological and biophysical properties of hepatocytes. Human hepatocytes (HL-7702) were treated in vitro with alcohol and G-Rg1. The cell morphology was observed using scanning electron microscopy. Cell height, roughness, adhesion, and elastic modulus were detected using atomic force microscopy. We found that alcohol significantly induced hepatocyte apoptosis, whereas G-Rg1 attenuated the alcohol-induced hepatocyte damage. Scanning electron microscopy revealed that alcohol-induced significant morphological changes in hepatocytes, including decreased cell contraction, roundness, and pseudopods, whereas G-Rg1 inhibited these negative changes. Atomic force microscopy revealed that alcohol increased the cell height and decreased the adhesion and elastic modulus of hepatocytes. Following treatment with G-Rg1, the cell height, adhesion, and elastic modulus of alcohol-injured hepatocytes were all similar to those of normal cells. Thus, G-Rg1 can attenuate the alcohol-induced damage to hepatocytes by modulating the morphology and biomechanics of the cells. RESEARCH HIGHLIGHTS: In this study, the morphological characteristics of hepatocytes were observed using SEM. The changes in hepatocyte three-dimensional images and biomechanical action caused by alcohol and G-Rg1 were examined at the nanoscale using AFM under near-physiological conditions. Alcohol-induced hepatocytes showed abnormal morphology and biophysical properties. G-Rg1 attenuated the alcohol-induced damage to hepatocytes by modulating the morphology and biomechanics of the cells.

Sensing a CO-Releasing Molecule (CORM) Does Not Equate to Sensing CO: The Case of DPHP and CORM-3.

Carbon monoxide (CO) is an endogenous signaling molecule with demonstrated pharmacological effects. For studying CO biology, there is a need for sensitive and selective fluorescent probes for CO as research tools. In developing such probes, CO gas and/or commercially available metal-carbonyl-based "CO-releasing molecules" (CORMs) have been used as CO sources. However, new findings are steadily emerging that some of these commonly used CORMs do not release CO reliably in buffers commonly used for studying such CO probes and have very pronounced chemical reactivities of their own, which could lead to the erroneous identification of "CO probes" that merely detect the CORM used, not CO. This is especially true when the CO-sensing mechanism relies on chemistry that is not firmly established otherwise. Cu2+ can quench the fluorescence of an imine-based fluorophore, DPHP, presumably through complexation. The Cu2+-quenched fluorescence was restored through the addition of CORM-3, a Ru-based CORM. This approach was reported as a new "strategy for detecting carbon monoxide" with the proposed mechanism being dependent on CO reduction of Cu2+ to Cu1+ under near-physiological conditions ( Anal. Chem. 2022, 94, 11298-11306). The study only used CORM-3 as the source of CO. CORM-3 has been reported to have very pronounced redox reactivity and is known not to release CO in an aqueous solution unless in the presence of a strong nucleophile. To assess whether the fluorescent response of the DPHP-Cu(II) cocktail to CORM-3 was truly through detecting CO, we report experiments using both pure CO and CORM-3. We confirm the reported DPHP-Cu(II) response to CORM-3 but not pure CO gas. Further, we did not observe the stated selectivity of DPHP for CO over sulfide species. Along this line, we also found that a reducing agent such as ascorbate was able to induce the same fluorescent turn-on as CORM-3 did. As such, the DPHP-Cu(II) system is not a CO probe and cannot be used to study CO biology. Corollary to this finding, it is critical that future work in developing CO probes uses more than a chemically reactive "CO donor" as the CO source. Especially important will be to confirm the ability of the "CO probe" to detect CO using pure CO gas or another source of CO.

Normothermic machine perfusion versus static cold storage in donation after circulatory death kidney transplantation: a randomized controlled trial

Kidney transplantation is the optimal treatment for end-stage renal disease, but it is still severely limited by a lack of suitable organ donors. Kidneys from donation after circulatory death (DCD) donors have been used to increase transplant rates, but these organs are susceptible to cold ischemic injury in the storage period before transplantation, the clinical consequence of which is high rates of delayed graft function (DGF). Normothermic machine perfusion (NMP) is an emerging technique that circulates a warmed, oxygenated red-cell-based perfusate through the kidney to maintain near-physiological conditions. We conducted a randomized controlled trial to compare the outcome of DCD kidney transplants after conventional static cold storage (SCS) alone or SCS plus 1-h NMP. A total of 338 kidneys were randomly allocated to SCS (n = 168) or NMP (n = 170), and 277 kidneys were included in the final intention-to-treat analysis. The primary endpoint was DGF, defined as the requirement for dialysis in the first 7 d after transplant. The rate of DGF was 82 of 135 (60.7%) in NMP kidneys versus 83 of 142 (58.5%) in SCS kidneys (adjusted odds ratio (95% confidence interval) 1.13 (0.69–1.84); P = 0.624). NMP was not associated with any increase in transplant thrombosis, infectious complications or any other adverse events. A 1-h period of NMP at the end of SCS did not reduce the rate of DGF in DCD kidneys. NMP was demonstrated to be feasible, safe and suitable for clinical application. Trial registration number: ISRCTN15821205.

Activation of skeletal muscle is controlled by a dual-filament mechano-sensing mechanism

Contraction of skeletal muscle is triggered by a transient rise in intracellular calcium concentration leading to a structural change in the actin-containing thin filaments that allows binding of myosin motors from the thick filaments. Most myosin motors are unavailable for actin binding in resting muscle because they are folded back against the thick filament backbone. Release of the folded motors is triggered by thick filament stress, implying a positive feedback loop in the thick filaments. However, it was unclear how thin and thick filament activation mechanisms are coordinated, partly because most previous studies of the thin filament regulation were conducted at low temperatures where the thick filament mechanisms are inhibited. Here, we use probes on both troponin in the thin filaments and myosin in the thick filaments to monitor the activation states of both filaments in near-physiological conditions. We characterize those activation states both in the steady state, using conventional titrations with calcium buffers, and during activation on the physiological timescale, using calcium jumps produced by photolysis of caged calcium. The results reveal three activation states of the thin filament in the intact filament lattice of a muscle cell that are analogous to those proposed previously from studies on isolated proteins. We characterize the rates of the transitions between these states in relation to thick filament mechano-sensing and show how thin- and thick-filament-based mechanisms are coupled by two positive feedback loops that switch on both filaments to achieve rapid cooperative activation of skeletal muscle.

Automated Solid-Phase Oligo(disulfide) Synthesis.

A method for automated solid-phase synthesis of oligo(disulfide)s was developed. It is based on a synthetic cycle comprising removal of a protecting group from a resin-bound thiol followed by treatment with monomers containing a thiosulfonate as an activated precursor. For ease of purification and characterization, the disulfide oligomers were synthesized as extensions of oligonucleotides on an automated oligonucleotide synthesizer. Six different dithiol monomer building blocks were synthesized. Sequence-defined oligomers of up to seven disulfide units were synthesized and purified. The sequence of the oligomer was confirmed by tandem MS/MS analysis. One of the monomers contains a coumarin cargo that can be released by a thiol-mediated release mechanism. When the monomer was incorporated into an oligo(disulfide) and subjected to reducing conditions, the cargo was released under near-physiological conditions, which underlines the potential use of these molecules in drug delivery systems.

Particle Smoother to Assimilate Asynchronous Movie Data of High-Speed AFM with MD Simulations.

High-speed (HS) atomic force microscopy (AFM) can be used to observe structural dynamics of biomolecules under near-physiological conditions. In the AFM measurement, the probe tip scans an area of interest and acquires height data pixel by pixel so that the obtained AFM image contains a measurement time difference. In this study, to integrate molecular dynamics simulations with asynchronous HS-AFM movie data, we developed a particle smoother (PS) method for Bayesian data assimilation, one of the machine learning approaches, by extending the previous particle filter method. With a twin experiment with an asynchronous pseudo HS-AFM movie of a nucleosome, we found that the PS method with the pixel-by-pixel data acquisition reproduced the dynamic behavior of a nucleosome better than the previous particle filter method that ignored the data asynchronicity. We examined several frequencies of particle resampling in the PS method, and found that resampling once per one frame was optimal for reproducing the dynamic behavior. Thus, we found that the PS method with an appropriate resampling frequency is a powerful method for estimating the dynamic behavior of a target molecule from HS-AFM data with low spatiotemporal resolution.

Visualizing RNA conformational and architectural heterogeneity in solution

RNA flexibility is reflected in its heterogeneous conformation. Through direct visualization using atomic force microscopy (AFM) and the adenosylcobalamin riboswitch aptamer domain as an example, we show that a single RNA sequence folds into conformationally and architecturally heterogeneous structures under near-physiological solution conditions. Recapitulated 3D topological structures from AFM molecular surfaces reveal that all conformers share the same secondary structural elements. Only a population-weighted cohort, not any single conformer, including the crystal structure, can account for the ensemble behaviors observed by small-angle X-ray scattering (SAXS). All conformers except one are functionally active in terms of ligand binding. Our findings provide direct visual evidence that the sequence-structure relationship of RNA under physiologically relevant solution conditions is more complex than the one-to-one relationship for well-structured proteins. The direct visualization of conformational and architectural ensembles at the single-molecule level in solution may suggest new approaches to RNA structural analyses.

Investigating the structural mechanism of gamma-D crystallin aggregation.

Human γD-crystallin (γDC) is a monomeric protein abundant in the eye lens nucleus. In order to avoid aggregation and cataract formation, γDC must remain stably folded for an individual's entire lifetime. γDC has two homologous domains containing two Greek key motifs, the N-terminal domain (NTD) and the C-terminal domain (CTD). V75D is an NTD-destabilizing mutation linked to early-onset cataract. V75D γDC unfolds in vitro through a three-state mechanism, populating an intermediate with the NTD completely unfolded and the CTD native-like, but it is not clear whether this intermediate is populated under non-denaturing conditions, or what relevance this intermediate has to its mechanism of aggregation. We employed hydrogen deuterium exchange mass spectrometry (HDX-MS) on V75D γDC under both native and denaturing conditions, as well as on the individual isolated domains of γDC. We observe that V75D γDC populates a “hidden” intermediate under native conditions that, unlike the intermediate observed via urea denaturation, does not correspond to a fully unfolded NTD. It is possible that this intermediate could be relevant to V75D γDC aggregation, given that it is the most populated intermediate under near-physiological conditions. This result provides a demonstration of how intermediates characterized under denaturing conditions are not always the ones relevant to native conditions.

Interpreting equatorial X-ray diffraction patterns from striated muscle with multiscale modeling.

Small-angle X-ray diffraction is the tool of choice to obtain nm-scale structural information from striated muscle under near-physiological conditions. A critical barrier to progress has been the lack of generally applicable computational tools for modeling these X-ray diffraction patterns, limiting our ability to extract all the structural information potentially available. We addressed this need by extending the spatially explicit simulation platform MUSICO to predict equatorial fiber X-ray diffraction patterns from skeletal muscle. Electron densities for thin filaments with bound crossbridges were calculated using PDB structures of myosin S1, actin, tropomyosin, troponin and analogous nebulin structure derived from tropomyosin PDB. Thick filament backbone densities were constructed based on the Squire 1973 model incorporating “ribbon motifs” from a high-resolution cryo-EM structure of the Lethocerus thick filament. Titin and myosin S2 regions were constructed as cylindrical rings of density shells. Myosin heads in an ordered “parked state” were positioned in a shell close to the thick filament backbone with any disordered myosin heads distributed in a shell extending out to actin. X-ray diffraction patterns were calculated from sub-system motifs consisting of 1 thick filament and two thin filaments by evaluating the Fourier transform of this object at the reciprocal hexagonal lattice positions. Intensities were averaged over the 500 thick filaments and 1000 thin filaments used in simulation. Using this approach, we found that we could recapitulate 7 independent experimental intensities (out to the 4,0 reflection) from relaxed rat soleus and EDL muscle by varying only the proportion of heads in the parked state and a temperature factor type disorder term. Fits to contracting data could be achieved by adjusting only the temperature factor term and the number of force-producing crossbridges predicted by MUSICO to match the force levels observed experimentally.

Nonspecific Amyloid Aggregation of Chicken Smooth-Muscle Titin: In Vitro Investigations.

A giant multidomain protein of striated and smooth vertebrate muscles, titin, consists of tandems of immunoglobulin (Ig)- and fibronectin type III (FnIII)-like domains representing β-sandwiches, as well as of disordered segments. Chicken smooth muscles express several titin isoforms of ~500-1500 kDa. Using various structural-analysis methods, we investigated in vitro nonspecific amyloid aggregation of the high-molecular-weight isoform of chicken smooth-muscle titin (SMTHMW, ~1500 kDa). As confirmed by X-ray diffraction analysis, under near-physiological conditions, the protein formed amorphous amyloid aggregates with a quaternary cross-β structure within a relatively short time (~60 min). As shown by circular dichroism and Fourier-transform infrared spectroscopy, the quaternary cross-β structure-unlike other amyloidogenic proteins-formed without changes in the SMTHMW secondary structure. SMTHMW aggregates partially disaggregated upon increasing the ionic strength above the physiological level. Based on the data obtained, it is not the complete protein but its particular domains/segments that are likely involved in the formation of intermolecular interactions during SMTHMW amyloid aggregation. The discovered properties of titin position this protein as an object of interest for studying amyloid aggregation in vitro and expanding our views of the fundamentals of amyloidogenesis.

Integrative Metallomics Studies of Toxic Metal(loid) Substances at the Blood Plasma–Red Blood Cell–Organ/Tumor Nexus

Globally, an estimated 9 million deaths per year are caused by human exposure to environmental pollutants, including toxic metal(loid) species. Since pollution is underestimated in calculations of the global burden of disease, the actual number of pollution-related deaths per year is likely to be substantially greater. Conversely, anticancer metallodrugs are deliberately administered to cancer patients, but their often dose-limiting severe adverse side-effects necessitate the urgent development of more effective metallodrugs that offer fewer off-target effects. What these seemingly unrelated events have in common is our limited understanding of what happens when each of these toxic metal(loid) substances enter the human bloodstream. However, the bioinorganic chemistry that unfolds at the plasma/red blood cell interface is directly implicated in mediating organ/tumor damage and, therefore, is of immediate toxicological and pharmacological relevance. This perspective will provide a brief synopsis of the bioinorganic chemistry of AsIII, Cd2+, Hg2+, CH3Hg+ and the anticancer metallodrug cisplatin in the bloodstream. Probing these processes at near-physiological conditions and integrating the results with biochemical events within organs and/or tumors has the potential to causally link chronic human exposure to toxic metal(loid) species with disease etiology and to translate more novel anticancer metal complexes to clinical studies, which will significantly improve human health in the 21st century.

Species-specific acid-base characterization of carnosine and homocarnosine using nuclear magnetic resonance

Carnosine and homocarnosine have long been known to be important constituents of the human metabolome, performing pH- and redox homeostasis-related roles. These are the most important imidazole-containing ‘small’ chemical entities in biological media. In this work these dipeptides were studied by 1H NMR-pH titration under near-physiological conditions. The resulting acid-base properties are quantified in terms of 6 macroscopic and 24 microscopic protonation constants, which show good agreement with previous results. A deeper knowledge in the physicochemical properties of the studied dipeptides may give further insight into the molecular level interpretation of their biosynthesis pathways, and biochemical reactions.

Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide.

Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein (IDP) whose abnormal aggregation into toxic soluble oligomers and insoluble amyloid fibrils is a pathological feature in type-2 diabetes. Rat IAPP (rIAPP) differs from hIAPP by only six amino acids yet has a reduced tendency to aggregate or form fibrils. The structures of the monomeric forms of IAPP are difficult to characterize due to their intrinsically disordered nature. Molecular dynamics simulations can provide a detailed characterization of the monomeric forms of rIAPP and hIAPP in near-physiological conditions. In this work, the conformational landscapes of rIAPP and hIAPP as a function of secondary structure content were predicted using well-tempered bias exchange metadynamics simulations. Several combinations of commonly used biomolecular force fields and water models were tested. The predicted conformational preferences of both rIAPP and hIAPP are typical of IDPs, exhibiting dominant random coil structures but showing a low propensity for transient α-helical conformations. Predicted nuclear magnetic resonance Cα chemical shifts reveal different preferences with each force field towards certain conformations, with AMBERff99SBnmr2/TIP4Pd showing the best agreement with the experiment. Comparisons of secondary structure content demonstrate residue-specific differences between hIAPP and rIAPP that may reflect their different aggregation propensities.

Mutual leveraging of proximity effects and click chemistry in chemical biology.

Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.

Determination of the nanoscale electrical properties of olfactory receptor hOR1A1 and their dependence on ligand binding: Towards the development of capacitance-operated odorant biosensors

The transduction of odorant binding into cellular signaling by olfactory receptors (ORs) is not understood and knowing its mechanism would enable developing new pharmacology and biohybrid electronic detectors of volatile organic compounds bearing high sensitivity and selectivity. The electrical characterization of ORs in bulk experiments is subject to microscopic models and assumptions. We have directly determined the nanoscale electrical properties of ORs immobilized in a fixed orientation, and their change upon odorant binding, using electrochemical scanning tunneling microscopy (EC-STM) in near-physiological conditions. Recordings of current versus time, distance, and electrochemical potential allows determining the OR impedance parameters and their dependence with odorant binding. Our results allow validating OR structural-electrostatic models and their functional activation processes, and anticipating a novel macroscopic biosensor based on ORs.

Flow cytometric kinetic assay of calcium mobilization in whole blood platelets of bottlenose dolphins (Tursiops truncatus).

Marine mammals may suffer alterations in platelet function and hemostasia due to multiple pathologies, environmental conditions (including stress) or exposure to different contaminants that induce platelet activation. Detecting early alterations in platelet function in these animals could be an especially relevant diagnostic tool in these species because they typically do not show signs of weakness or disease until the pathology is in advanced state, in order to avoid attracting predators in natural conditions. The study of early markers of platelet activation is relevant for the detection, monitoring and therapy of inflammation and hemostasis disorders. Flow cytometry provides a convenient method to evaluate platelet activation by following the kinetics of intracellular Ca2+ , using sensitive fluorescent indicators that can be loaded into intact cells. In order to study intraplatelet Ca2+ mobilization in marine mammals, we have adapted a kinetic assay of human platelet activation to study platelet activation in whole-blood samples of bottlenose dolphins (Tursiops truncatus) using the Ca2+ -sensitive dye Fluo-4AM and a clone of the platelet-specific antibody CD41-PE that recognizes dolphin platelets. This no-wash, no-lyse protocol provides a simple and sensitive tool to assess in vitro the time course and intensity of signal-transduction responses to platelet agonists under near-physiological conditions. The adaptation of this technique to marine mammals represents a methodological advance for basic and clinical veterinary applications but also for general environmental studies on these species.

Recent progress in structural study of DNA and its protein and small molecule complexes through NMR spectroscopy

<p indent="0mm"><b/>As the main genetic material, DNA tends to form complexes with other molecules both in its resting state, where it is packaged as heterochromatin, and in its active state during replication, recombination, and transcription. These complexes are closely associated with DNA protection, amplification and utilization. On the other hand, due to the high variability of DNA sequence and structure, aptamers are increasingly developed to recognize other molecules. The elucidation of the complex structure formed by DNA and other molecules in these systems can facilitate the understanding of basic principles of life, and provide key information for the DNA application in genetic modification, disease treatment and biosafety analysis. NMR is one of the main methods for determining molecular structure. Its advantage is that it can obtain the information of structure, intermolecular interaction sites and kinetics under near-physiological conditions. In this paper, we focus on the complex structure of DNA and other molecules, introduce the representative work recently carried out by Chinese scholars using NMR methods, and discuss the application value and development direction of NMR method in this field.

Three-dimensional structure determination of gold nanotriangles in solution using X-ray free-electron laser single-particle analysis

X-ray free-electron lasers (XFELs) have allowed the imaging of nanoscale samples in near-physiological conditions. To achieve three-dimensional (3D) nanostructural reconstruction, many challenges need to be addressed, such as sample delivery for data collection and data processing of noisy diffraction patterns. Here, we provided a demonstration of the 3D structure reconstruction of a gold nanoparticle from XFEL diffraction data measured at the SPring-8 Angstrom Compact Free-Electron Laser using microliquid enclosure arrays (MLEAs) sample holders. MLEAs enable in-solution measurements, however, they induce a significant amount of background noise. Thus, we performed a series of data analyses to identify the diffraction patterns suitable for 3D reconstruction as well as nonhit patterns to estimate the background noise. The background subtraction from the data significantly improved the quality of the restored structure, with the resolution estimated to be 5 nm using Fourier shell correlation. Our paper has revealed the notable potential of XFEL imaging using MLEAs in combination with the developed data-analysis protocol.

Acid-etched Halloysite nanotubes as superior carriers for ciprofloxacin

Clay minerals have opened new avenues in drug delivery, including antimicrobials, greatly enhancing the stability and efficacy of the active payloads. Among these clay mineral hosts, Halloysite nanotubes (HNT) have emerged as a prominent carrier owing to their intrinsic mesoporous tubular nanostructure and high adsorption capacity. The acidic etching of HNT increases their specific surface area and porosity, consequently enhancing their loading potential. In this work, we show for the first time, that etched HNT (E-HNT) are superior carriers of the potent antibiotic ciprofloxacin (CIP) compared to pristine HNT in terms of loading capacity and antibacterial effect. The loading conditions are optimized within near-physiological conditions to enable future combinations with biomolecules; where CIP loading and release are characterized by UV–Vis measurements and thermogravimetry. Solid-state characterization suggests an adsorptive loading mechanism, involving electrostatic attraction and possible tautomerism. Release experiments show that the loaded CIP exhibits a sustained release profile and maintains its antibacterial potency as confirmed by the broth microdilution (BMD) and zone of inhibition methods. Thus, the facile etching of HNT enhances the nanoclay properties rendering it suitable for future application in drug delivery formulations.

High-throughput single cell metabolomics and cellular heterogeneity exploration by inertial microfluidics coupled with pulsed electric field-induced electrospray ionization-high resolution mass spectrometry

Single cell metabolomics can obtain the metabolic profiles of individual cells and reveal cellular heterogeneity. However, high-throughput single-cell mass spectrometry (MS) analysis under physiological conditions remains a great challenge due to the presence of complex matrix and extremely small cell volumes. Herein, a serpentine channel microfluidic device which was designed to achieve continuous cell separation and inertial focusing, was coupled with a pulsed electric field-induced electrospray ionization-high resolution MS (PEF-ESI-HRMS) to achieve high-throughput single cell analysis. The pulsed square wave electric field was applied to realize on-line cell disruption and induce electrospray ionization. Single cells were analyzed under near-physiological conditions at a throughput of up to 80 cells min−1. More than 900 features were detected and approximately 120 metabolites were tentatively identified from a single cell. Further, by continually analyzing more than 3000 MCF7 and HepG2 cells, discrimination of different cancer cells based on their individual metabolic profiles was achieved by using the principal component analysis. The PEF-ESI-HRMS method was also applied for the analysis of single yeast cells, and more than 40 metabolites were annotated. This method is versatile and has good robustness, which is promising for high-throughput single cell metabolomics analysis.