Trajectory Analysis Research Articles

The three-sided right-handed 𝛽-helix is a versatile fold for glycan interactions.

Interactions between proteins and glycans are critical to various biological processes. With databases of carbohydrate-interacting proteins and increasing amounts of structural data, the three-sided right-handed 𝛽-helix (RHBH) has emerged as a significant structural fold for glycan interactions. In this review, we provide an overview of the sequence, mechanistic, and structural features that enable the RHBH to interact with glycans. The RHBH is a prevalent fold that exists in eukaryotes, prokaryotes, and viruses associated with adhesin and carbohydrate-active enzyme (CAZyme) functions. An evolutionary trajectory analysis on structurally characterized RHBH-containing proteins shows that they likely evolved from carbohydrate-binding proteins with their carbohydrate-degrading activities evolving later. By examining three polysaccharide lyase and three glycoside hydrolase structures, we provide a detailed view of the modes of glycan binding in RHBH proteins. The 3-dimensional shape of the RHBH creates an electrostatically and spatially favorable glycan binding surface that allows for extensive hydrogen bonding interactions, leading to favorable and stable glycan binding. The RHBH is observed to be an adaptable domain capable of being modified with loop insertions and charge inversions to accommodate heterogeneous and flexible glycans and diverse reaction mechanisms. Understanding this prevalent protein fold can advance our knowledge of glycan binding in biological systems and help guide the efficient design and utilization of RHBH-containing proteins in glycobiology research.

Molecular dynamics simulations of lipid-protein interactions in SLC4 proteins.

The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO3¯, CO32¯, Cl¯, Na+, K+, NH3 and H+ necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl¯/HCO3¯ exchanger) and NBCe1 (Na+-CO32¯cotransporter). Previous computational studies of the outward facing (OF) state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed coarse-grained and atomistic molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1 and NDCBE (a Na+-CO32¯/Cl¯ exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine (POPC), phosphatidylethanolamine (POPE), phosphatidylserine (POPS), and sphingomyelin (POSM). The recently resolved inward-facing (IF) state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, POPC, and POSM in the three studied proteins and their potential roles in the SLC4 transport function, conformational transition and protein dimerization were discussed.

Urban air PCDD/Fs: Atmospheric concentrations, temporal changes, gas/particle partitioning, possible sources and cancer risks.

Polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs) are pollutants of concern due to their toxic effects. No active sampling study on PCDD/Fs has been conducted in Bursa. This study aimed to fill this gap by measuring PCDD/F levels in the region. Accordingly, the samples were collected from an urban area in Bursa, covering four seasons between June 2022 and April 2023. The total (gas+particulate) ambient air concentrations were between 312.23 and 829.80 fg/m3 (mean: 555.05 ± 173.62 fg/m3). In terms of toxic equivalents (TEQ), the average concentration was 43.29 ± 9.18 fg WHOTEQ/m3. Based on the concentration values obtained, cancer and non-carcinogenic risk values of PCDD/Fs were calculated for three different age groups. The results indicated negligible health risks for all age groups. In addition, a seasonal assessment was also made and it was observed that PCDD/F concentration values varied with the ambient air temperatures. In general, higher values were measured in colder months compared to warmer months. This was probably due to the additional sources and adverse meteorological conditions. Moreover, the gas/particle partitioning of PCDD/Fs was investigated in detail. The average gas and particulate phase concentrations for PCDD/Fs were 101.81 ± 20.77 and 453.24 ± 172.50, respectively. It was found that an equilibrium state was not reached in the gas/particle partitioning. Two different gas/particle partition models based on adsorption and absorption mechanisms were compared, and the absorption model gave more consistent predictions. The Principal Component Analysis (PCA) was employed to identify the possible PCDD/F sources. The results indicated that the region was influenced by vehicle emissions, residential heating, organized industrial zones and metal recycling facilities. In addition, 72-hour backward air mass trajectory analyses were performed to understand the long-range transported air masses. However, it was found that the transported air masses did not significantly affect the concentration values measured in the sampling site.

Exploring the Evolution of GenAI in Music Composition

Exploring the Evolution of GenAI in Music Composition

SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories.

Research on ribonucleic acid (RNA) structures and functions benefits from easy-to-use tools for computational prediction and analyses of RNA three-dimensional (3D) structure. The SimRNAweb server version 2.0 offers an enhanced, user-friendly platform for RNA 3D structure prediction and analysis of RNA folding trajectories based on the SimRNA method. SimRNA employs a coarse-grained model, Monte Carlo sampling and statistical potentials to explore RNA conformational space, optionally guided by spatial restraints. Recognized for its accuracy in RNA 3D structure prediction in RNA-Puzzles and CASP competitions, SimRNA is particularly useful for incorporating restraints based on experimental data. The new server version introduces performance optimizations and extends user control over simulations and the processing of results. It allows the application of various hard and soft restraints, accommodating alternative structures involving canonical and noncanonical base pairs and unpaired residues, while also integrating data from chemical probing methods. Enhanced features include an improved analysis of folding trajectories, offering advanced clustering options and multiple analyses of the generated trajectories. These updates provide comprehensive tools for detailed RNA structure analysis. SimRNAweb v2.0 significantly broadens the scope of RNA modeling, emphasizing flexibility and user-defined parameter control. The web server is available at https://genesilico.pl/SimRNAweb.

Publication trends and research hotspots of the cardiorenal syndrome: A bibliometrics and visual analysis from 2003 to 2023.

Cardiorenal syndrome encompasses a range of disorders involving both the heart and kidneys, wherein dysfunction in one organ may induce dysfunction in the other, either acutely or chronically. This study conducted a literature search on cardiorenal syndrome from January 1, 2003, to September 8, 2023. Meanwhile, a quantitative analysis of the developmental trajectory, research hotspots and evolutionary trends in the field of cardiorenal syndrome through bibliometric analysis and knowledge mapping. The field of cardiorenal syndrome exhibits promising potential to grow and is emerging as a prominent research area. Future endeavours should prioritise a comprehensive understanding of the field and foster multi-centre co-operation among different countries and regions. The annual publication trend analysis revealed a consistent annual increase in cardiorenal syndrome literature over the last 20 years. The IL6, REN and INS genes were identified as the current research hotspots.

Single cells and TRUST4 reveal immunological features of the HFRS transcriptome

The etiology of hemorrhagic fever with renal syndrome (HFRS) is significantly impacted by a variety of immune cells. Nevertheless, the existing techniques for sequencing peripheral blood T cell receptor (TCR) or B cell receptor (BCR) libraries in HFRS are constrained by both limitations and high costs. In this investigation, we utilized the computational tool TRUST4 to generate TCR and BCR libraries utilizing comprehensive RNA-seq data from peripheral blood specimens of HFRS patients. This facilitated the examination of clonality and diversity within immune libraries linked to the condition. Despite previous research on immune cell function, the underlying mechanisms remain intricate, and differential gene expression across immune cell types and cell-to-cell interactions within immune cell clusters have not been thoroughly explored. To address this gap, we performed clustering analysis on 11 cell subsets derived from raw single-cell RNA-seq data, elucidating characteristic changes in cell subset proportions under disease conditions. Additionally, we utilized CellChat, a tool for cell–cell communication analysis, to investigate the impact of MIF family, CD70 family, and GALECTIN family cytokines—known to be involved in cell communication—on immune cell subsets. Furthermore, hdWGCNA analysis identified core genes implicated in HFRS pathogenesis within T cells and B cells. Trajectory analysis revealed that most cell subsets were in a developmental stage, with high expression of transcription factors such as NFKB and JUN in Effector CD8+ T cells, as well as in Naive CD4+ T cells and Naive B cells. Our findings provide a comprehensive understanding of the dynamic changes in immune cells during HFRS pathogenesis, identifying specific V genes and J genes in TCR and BCR that contribute to advancing our knowledge of HFRS. These insights offer potential implications for the diagnosis and treatment of this autoimmune disease.

Development and external validation of a multidimensional deep learning model to dynamically predict kidney outcomes in IgA nephropathy.

Accurately predicting kidney outcomes in IgA nephropathy is crucial for clinical decision making. Insufficient use of longitudinal data in previous studies has limited the accuracy and interpretability of prediction models for failing to reflect the chronic nature of IgA nephropathy. This study aimed at establishing a multivariable dynamic deep learning model using comprehensive longitudinal data for the prediction of kidney outcomes in IgA nephropathy. In this retrospective cohort study of 2,056 IgA nephropathy patients at 18 kidney centers, a total of 28,317 data points were collected by the sliding window method. Among them, 15,462 windows in a single center were randomly assigned to training (80%) and validation (20%) sets while 8797 windows in 18 kidney centers were assigned to an independently test set. Interpretable Multi-Variable Long Short-Term Memory (IMV-LSTM), a deep learning model, was implemented to predict kidney outcomes (kidney failure or 50% decline in kidney function) based on time-invariant variables measured at biopsy and time-variant variables measured during follow-up. Risk performance was evaluated using Kaplan-Meier analysis and the C statistic. Trajectory analysis was performed to assess the various trends of clinical variables during follow-up. The model achieved a higher C statistic (0.93; 95% CI, 0.92-0.95) on the test set than the XGBoost prediction model that we developed in a previous study using only baseline information (C statistic, 0.84; 95% CI, 0.80-0.88). Kaplan-Meier analysis showed that groups with lower predicted risks from the full model survived longer than groups with higher risks. Time-variant variables demonstrated higher importance scores than time-invariant variables. Within time-variant variables, more recent measurements showed higher importance scores. Further interpretation showed that certain trajectory groups of time-variant variables such as serum creatinine and urine protein were associated with elevated risks of adverse outcomes. In IgA nephropathy, a deep learning model can be used to accurately and dynamically predict kidney prognosis based on longitudinal data, and time-variant variables show strong ability to predict kidney outcome.

2-in-1 Phase Space Sampling for Calculating the Absorption Spectrum of the Hydrated Electron.

The investigation of vibrational effects on absorption spectrum calculations often employs Wigner sampling or thermal sampling. While Wigner sampling incorporates zero-point energy, it may not be suitable for flexible systems. Thermal sampling is applicable to anharmonic systems yet treats nuclei classically. The application of generalized smoothed trajectory analysis (GSTA) as a postprocessing method allows for the incorporation of nuclear quantum effects (NQEs), combining the advantages of both sampling methods. We demonstrate this approach in computing the absorption spectrum of a hydrated electron. Theoretical exploration of the hydrated electron and its embryonic forms, such as water cluster anions, poses a significant challenge due to the diffusivity of the excess electron and the continuous motion of water molecules. In many previous studies, the wave nature of atomic nuclei is often neglected, despite the substantial impact of NQEs on thermodynamic and spectroscopic properties, particularly for hydrogen atoms. In our studies, we examine these NQEs for the excess electrons in various water systems. We obtained structures from mixed classical-quantum simulations for water cluster anions and the hydrated electron by incorporating the quantum effects of atomic nuclei with the filtration of the classical trajectories. Absorption spectra were determined at different theoretical levels. Our results indicate significant NQEs, red shift, and broadening of the spectra for hydrated electron systems. This study demonstrates the applicability of GSTA to complex systems, providing insights into NQEs on energetic and structural properties.

Associations of Dietary Diversity Trajectories with Frailty among Chinese Older Adults: A Latent Class Trajectory Analysis Based on a CLHLS Cohort

Background: High dietary diversity has been found to be associated with frailty. However, the trajectory of dietary diversity intake in relation to frailty is unclear. Methods: Using the latent class trajectory modeling approach, we identified distinctive dietary variety trajectory groups among 2017 participants based on the Chinese Longitudinal Healthy Longevity Survey acquired at four time points within a 10-year period. Frailty status was assessed using a frailty index comprising 37 health deficits. Dietary diversity was quantified using the dietary variety score (DVS), based on food category consumption frequency. Logistic regression analyses were employed to explore the association between DVS change trajectories and frailty. Results: This study identified two distinct DVS trajectories: “Moderate-Slow decline-Slow growth”, encompassing 810 (40.16%) individuals, and “Moderate-Slow growth-Accelerated decline”, including 1207 (59.84%) individuals. After adjusting for covariates, the odds ratio for DVS in the “Moderate-Slow decline-Slow growth” group was 1.326 (95% confidence interval: 1.075–1.636) compared to the “Moderate-Slow growth-Accelerated decline” group. The “Moderate-Slow decline-Slow growth” trajectory continued to decrease and was maintained at a low level in the early stages of aging. Conclusion: Sustaining a high dietary diversity trajectory over time, particularly in the early stages of aging, could potentially decrease the risk of frailty among older Chinese adults.

Single-cell BCR and transcriptome analysis reveals peripheral immune signatures in patients with thyroid-associated ophthalmopathy.

Thyroid-associated ophthalmopathy (TAO) is the most prevalent orbital disease in adults caused by an autoimmune disorder, which can lead to disfigurement and vision impairment. Developing effective treatments for this condition presents challenges due to our limited understanding of its underlying immune aberrations. In this study, we profiled the immune components in the peripheral blood of patients with TAO as well as healthy individuals, utilizing single-cell RNA sequencing and B-cell receptor repertoires (BCR) analysis. We observed a significant reduction in the proportions of regulatory B cells (Bregs) and type 2 conventional dendritic cells (DCs) in patients with TAO during the active phase. Conversely, there was a significant increase in the proportion of type 1 DCs. Further analysis of cell differentiation trajectory revealed potential impairment in the transition of B cells towards Breg phenotype during the active phase of TAO. Besides, the activation process of TAO appeared to involve inflammation and immune dysfunction, as indicated by the dynamic changes in the activities of key regulators. The abnormalities in the peripheral immune system, such as the reduced capacity of Bregs to suppress inflammation, were primarily driven by the enhanced interaction among Breg, DCs, and monocytes (i.e., CD22-PTPRC and BTLA-TNFRSF14). Collectively, our findings offer a comprehensive insight into the molecular regulation and cellular reconfiguration during the active phase of TAO at the single-cell level, in order to explore the pathogenesis of TAO and provide new ideas for the future treatment of TAO.

Unraveling the Non‐Homogeneous Dispersion Processes in Ocean and Coastal Circulations Using a Clustering Approach

AbstractDispersion processes in environmental flows have been traditionally studied under the strong assumption of homogeneous, isotropic and stationary turbulence. To overcome this limitation, we propose a new approach that combines autocorrelation analysis of simulated Lagrangian trajectories together with unsupervised clustering. To test the approach, we consider several dynamic scenarios around a coastal gulf, subject to different forcing, in order to compare our method with other approaches. Lagrangian trajectories forced by the varying coastal circulation exhibited different behaviors, looping and non‐looping paths, and produced a variety of Lagrangian autocorrelation functions. Our approach proves to be able to reveal spatio‐temporal variations in ocean dispersion processes without any a priori knowledge of the character of the trajectories. Clusters based on the autocorrelation functions are associated to different inhomogeneous dispersion processes. Finally, we propose a new stochastic model capable of predicting the different forms of autocorrelations.

Knocking down of Xkr8 enhances chemotherapy efficacy through modulating tumor immune microenvironment

Scramblase Xk-related protein 8 (Xkr8) regulates the externalization of phosphatidylserine (PS) during apoptosis and holds a pivotal role in fostering tumor immunosuppression. Targeting Xkr8 in conjunction with chemotherapy demonstrated a novel avenue for amplifying antitumor immune response and overcoming chemo-immune resistance. Here we further evaluated this strategy by using a clinically relevant orthotopic model and elucidated the mechanism through in-depth single-cell RNA sequencing (scRNA-seq). We found that Xkr8 knockdown exhibited the potential to lead to immunogenic cell death (ICD) by impeding the normal clearance of apoptotic cells. Co-delivery of Xkr8 small interference RNA (siRNA) and a prodrug conjugate of 5-fluorouracil (5-Fu) and oxoplatin (FuOXP) showed remarkable therapeutic efficacy in an orthotopic pancreatic tumor model with increased infiltration of proliferative NK cells and activated macrophages in the tumor microenvironment (TME). Single-cell trajectory analysis further unveiled that tumor infiltrating CD8+ T cells are differentiated favorably to cytotoxic over exhausted phenotype after combination treatment. Our study sheds new light on the impact of Xkr8 knockdown on TME and solidifies the rationale of combining Xkr8 knockdown with chemotherapy to treat various types of cancers.

Cross-species single-cell analysis uncovers the immunopathological mechanisms associated with IgA nephropathy progression.

IgA nephropathy (IgAN) represents the main cause of renal failure, while the precise pathogenetic mechanisms have not been fully determined. Herein, we conducted a cross-species single-cell survey on human IgAN and mouse and rat IgAN models to explore the pathogenic programs. Cross-species single-cell RNA sequencing (scRNA-Seq) revealed that the IgAN mesangial cells (MCs) expressed high levels of inflammatory signatures CXCL12, CCL2, CSF1, and IL-34 and specifically interacted with IgAN macrophages via the CXCL12/CXCR4, CSF1/IL-34/CSF1 receptor, and integrin subunit alpha X/integrin subunit alpha M/complement C3 (C3) axes. IgAN macrophages expressed high levels of CXCR4, PDGFB, triggering receptor expressed on myeloid cells 2, TNF, and C3, and the trajectory analysis suggested that these cells derived from the differentiation of infiltrating blood monocytes. Additionally, protein profiling of 21 progression and 28 nonprogression IgAN samples revealed that proteins CXCL12, C3, mannose receptor C-type 1, and CD163 were negatively correlated with estimated glomerular filtration rate (eGFR) value and poor prognosis (30% eGFR as composite end point). Last, a functional experiment revealed that specific blockade of the Cxcl12/Cxcr4 pathway substantially attenuated the glomerulus and tubule inflammatory injury, fibrosis, and renal function decline in the mouse IgAN model. This study provides insights into IgAN progression and may aid in the refinement of IgAN diagnosis and the optimization of treatment strategies.

Association between serum albumin concentration change trajectory and risk of hypertension: a cohort study in China

BackgroundWe sought to assess the risk of hypertension based on the trajectory of changes in serum albumin concentrations.MethodsA total of 11,946 nonhypertension adults aged 30–60 years who underwent at least 3 medical examinations between 2009 and 2016 were included in this study. Group-based trajectory models were obtained for 4 category groups, and logistic regression models were used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for each category group of serum albumin concentration and the risk of hypertension.ResultsDuring a mean follow-up period of 4.30 years, 1,537 hypertension events occurred in 11,946 subjects without hypertension. A high stable trajectory of serum albumin concentrations (OR, 0.70, 95% CI, 0.51–0.96) was associated with a significantly lower risk of developing hypertension. The results of the sensitivity analysis of the high stable trajectory (OR, 0.64, 95% CI, 0.43–0.96) remained statistically significant. Subjects with normal weight and those ≥45 years of age had a significantly lower risk of hypertension at moderate increase (P = 0.053 or 0.026) and high stable trajectories (P = 0.011 or 0.016). In males and overweight subjects, the risk of hypertension was significantly lower in the high stable trajectory (P = 0.038 or 0.044).ConclusionIn this study, we found that moderate increase in serum albumin concentrations and a high stable trajectory were significantly associated with a reduced risk of hypertension in subjects aged ≥45 years and those with normal weight and that high stable serum albumin concentrations were significantly associated with a reduced risk of hypertension in males and overweight subjects.

Atmospheric gaseous mercury and associated health risk assessment in the economic capital of India.

Mercury cycling in coastal metropolitan areas on the west coast of India becomes complex due to the combined effects of both intensive domestic anthropogenic emissions and marine air masses. The present study is based on yearlong data of continuous measurements of gaseous elemental mercury (GEM) concentration concurrent with meteorological parameters and some air pollutants at a coastal urban site in Mumbai, on the west coast of India, for the first time. The concentration of GEM was found in a range between 2.2 and 12.3ng/m3, with a mean of 3.1 ± 1.1ng/m3, which was significantly higher than the continental background values in the Northern Hemisphere (~ 1.5ng/m3). Unlike particulates, GEM starts increasing post-winter to peak during the monsoon and decrease towards winter. July had the highest concentration of GEM followed by October, and a minimum in January. GEM exhibited a distinct diurnal cycle, mainly with a broad peak in the early morning, a narrow one by nightfall, and a minimum in the afternoon. The peaks and their timing suggest the origin of urban mobility and the start of local activities. A positive correlation between SO2, PM2.5, temperature, relative humidity, and GEM indicates that emissions from local industrial plants in the Mumbai coastal area. Principal component analysis (PCA) and cluster analysis (CA) confirm this fact. Monthly back trajectory analysis showed that air mass flows are predominantly from the Arabian Sea and local human activities. Assessment of human health risks by USEPA model reveals that the hazardous quotient, HQ < 1, implies negligible carcinogenic risk. GEM observations in Mumbai during the study period are below the World Health Organization's (WHO) safe limit (200ng/m3) for long-term inhalation.

Analysis of swimming trajectories in Daphnia similis as an environmental impact assessment tool

Analysis of swimming trajectories in <i>Daphnia similis</i> as an environmental impact assessment tool

Microplastics in remote region of the world: Insights from the glacier of Geladandong, China

Although microplastics have been detected in different remote areas, people are still short of knowledge for environmental background of microplastics in remote area. In this work, we collected air, snow, river and lake water samples from Geladandong region (the origin of the Yangtze River) of the Tibetan Plateau, along with microscopy and Micro-FTIR analyses. Microplastics abundance (0.13–19.8 items/L) was the low as compared with other remote areas worldwide, and the morphology of fiber and film, material of PP and PET, and size of <300 μm were the main microplastics features. Due to natural aging during the transport processes, microplastics were degrading to smaller particle in Geladandong. Air mass trajectory analysis shows microplastics in Geladandong is transferred by repeated atmospheric transport from no human activity place. All these results suggested that Geladandong is an ideal research area for environmental background value and characteristic of microplastics. In conjunction with data from other remote regions, we established the background values for microplastics in remote areas. This work provides quantitative evidence for establishing environmental quality standards, and monitoring environmental changes.

Dissecting microenvironment in cystadenomas and hepatic cysts based on single nucleus RNA-sequencing data

Hepatic cystadenoma is a rare disease, accounting for about 5% of all cystic lesions, with a high tendency of malignant transformation. The preoperative diagnosis of cystadenoma is difficult, and some cystadenomas are easily misdiagnosed as hepatic cysts at first. Hepatic cyst is a relatively common liver disease, most of which are benign, but large hepatic cysts can lead to pressure on the bile duct, resulting in abnormal liver function. To better understand the difference between the microenvironment of cystadenomas and hepatic cysts, we performed single-nuclei RNA-sequencing on cystadenoma and hepatic cysts samples. In addition, we performed spatial transcriptome sequencing of hepatic cysts. Based on nucleus RNA-sequencing data, a total of seven major cell types were identified. Here we described the tumor microenvironment of cystadenomas and hepatic cysts, particularly the transcriptome signatures and regulators of immune cells and stromal cells. By inferring copy number variation, it was found that the malignant degree of hepatic stellate cells in cystadenoma was higher. Pseudotime trajectory analysis demonstrated dynamic transformation of hepatocytes in hepatic cysts and cystadenomas. Cystadenomas had higher immune infiltration than hepatic cysts, and T cells had a more complex regulatory mechanism in cystadenomas than hepatic cysts. Immunohistochemistry confirms a cystadenoma-specific T-cell immunoregulatory mechanism. These results provided a single-cell atlas of cystadenomas and hepatic cyst, revealed a more complex microenvironment in cystadenomas than in hepatic cysts, and provided new perspective for the molecular mechanisms of cystadenomas and hepatic cyst.

Ionic Liquid Gating Induces Anomalous Permeation through Membrane Channel Proteins.

Membrane channel proteins (MCPs) play key roles in matter transport through cell membranes and act as major targets for vaccines and drugs. For emerging ionic liquid (IL) drugs, a rational understanding of how ILs affect the structure and transport function of MCP is crucial to their design. In this work, GPU-accelerated microsecond-long molecular dynamics simulations were employed to investigate the modulating mechanism of ILs on MCP. Interestingly, ILs prefer to insert into the lipid bilayer and channel of aquaporin-2 (AQP2) but adsorb on the entrance of voltage-gated sodium channels (Nav). Molecular trajectory and free energy analysis reflect that ILs have a minimal impact on the structure of MCPs but significantly influence MCP functions. It demonstrates that ILs can decrease the overall energy barrier for water through AQP2 by 1.88 kcal/mol, whereas that for Na+ through Nav is increased by 1.70 kcal/mol. Consequently, the permeation rates of water and Na+ can be enhanced and reduced by at least 1 order of magnitude, respectively. Furthermore, an abnormal IL gating mechanism was proposed by combining the hydrophobic nature of MCP and confined water/ion coordination effects. More importantly, we performed experiments to confirm the influence of ILs on AQP2 in human cells and found that treatment with ILs significantly accelerated the changes in cell volume in response to altered external osmotic pressure. Overall, these quantitative results will not only deepen the understanding of IL-cell interactions but may also shed light on the rational design of drugs and disease diagnosis.