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Our sensory adaptation to cold and chemically induced coolness is mediated by the intrinsic property of TRPM8 channels to desensitize. TRPM8 is also implicated in cold-evoked pain disorders and migraine, highlighting its inhibitors as an avenue for pain relief. Despite the importance, the mechanisms of TRPM8 desensitization and inhibition remained unclear. We found, using cryo-electron microscopy, electrophysiology, and molecular dynamics simulations, that TRPM8 inhibitors bind selectively to the desensitized state of the channel. These inhibitors were used to reveal the overlapping mechanisms of desensitization and inhibition and that cold and cooling agonists share a common desensitization pathway. Furthermore, we identified the structural determinants crucial for the conformational change in TRPM8 desensitization. Our study illustrates how receptor-level conformational changes alter cold sensation, providing insights into therapeutic development.
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Temperatura Baixa , Mentol , Canais de Cátion TRPM , Canais de Cátion TRPM/metabolismo , Canais de Cátion TRPM/antagonistas & inibidores , Humanos , Mentol/farmacologia , Simulação de Dinâmica Molecular , Adaptação Fisiológica , Microscopia Crioeletrônica , Células HEK293 , Conformação Proteica , AnimaisRESUMO
Cancer targeted therapy is essential to minimize damage to normal cells and improve treatment outcomes. The elevated activity of Cystathionine beta-synthase (CBS), an enzyme responsible for producing endogenous hydrogen sulfide (H2S), plays a significant role in promoting tumor growth, invasiveness, and metastatic potential. Consequently, the selective inhibition of CBS could represent a promising therapeutic strategy for cancer. Currently, there is much interest in combining paclitaxel with other drugs for cancer treatment. This study aimed to investigate the efficacy of combining benserazide, a CBS inhibitor, with paclitaxel in treating tumors. Firstly, we demonstrated CBS is indeed involved in the progression of multiple cancers. Then it was observed that the total binding free energy between the protein and the small molecule is -98.241 kJ/mol. The release of H2S in the group treated with 100 µM benserazide was reduced by approximately 90% compared to the negative control, and the thermal denaturation curve of the complex protein shifted to the right, suggesting that benserazide binds to and blocks the CBS protein. Next, it was found that compared to paclitaxel monotherapy, the combination of benserazide with paclitaxel demonstrated stronger antitumor activity in KYSE450, A549, and HCT8 cells, accompanied by reduced cell viability, cell migration and invasion, as well as diminished angiogenic and lymphangiogenic capabilities. In vivo studies showed that the combined administration of benserazide and paclitaxel significantly reduced the volume and weight of axillary lymph nodes in comparison to the control group and single administration group. Further mechanistic studies revealed that the combination of benserazide and paclitaxel significantly suppressed the S-sulfhydration of SIRT1 protein, thereby inhibiting the expression of SIRT1 protein and activating SIRT1 downstream Notch1/Hes1 signaling pathway in KYSE450, A549, and HCT8 cells. Meanwhile, we observed that benserazide combined with paclitaxel induced a more significant downregulation of HIF-1α, VEGF-A, VEGF-C, and VEGF-D proteins expression levels in KYSE450, A549, and HCT8 cells compared to paclitaxel alone. These findings indicated that benserazide enhances the anticancer effects of paclitaxel via inhibiting the S-sulfhydration of SIRT1 and down-regulating HIF-1α/VEGF signaling pathway. This study suggests that benserazide may have potential as a chemosensitizer in cancer treatment.
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A sandwich "signal-off" type photoelectrochemical (PEC) immunosensor was fabricated based on a composite heterojunction of tungsten oxide/titanium oxide microspheres (WO3/TiO2) acting as signal amplification platform and carbon microspheres loaded by gold nanoparticles (Cs@Au NPs) utilized as the label for detecting antibody. WO3/TiO2 had excellent photoelectric performance, and the results of Mott-Schottky plots, open-circuit voltage, and electron spin resonance spectroscopy indicated that it belonged to the Z-scheme heterojunction transfer mechanism of photogenerated carriers. To achieve the sensitization of PEC immunosensor, Cs@Au NP-labeled immunocomplex can effectively reduce the photocurrent signal. The PEC immunosensors were fabricated under the optimal conditions of 1:1 WO3/TiO2 (molar ratio), 2.0 mg mL-1 WO3/TiO2, and 1.5 mg mL-1 Cs@Au NPs. Through comparison of the detection results of label-free and sandwich-type PEC immunosensors for nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we found that the sensitivity of the sandwich type was 2.53 times the label-free type, and the limit of detection was 0.006 ng mL-1, i.e., 3.17 times lower than the label-free type. This demonstrates that the developed sandwich-type PEC immunosensor will have a brighter application prospect.
Assuntos
Técnicas Biossensoriais , COVID-19 , Nanopartículas Metálicas , Humanos , Ouro , Imunoensaio , SARS-CoV-2RESUMO
Crosstalk between ion channels and small GTPases is critical during homeostasis and disease, but little is known about the structural underpinnings of these interactions. TRPV4 is a polymodal, calcium-permeable cation channel that has emerged as a potential therapeutic target in multiple conditions. Gain-of-function mutations also cause hereditary neuromuscular disease. Here, we present cryo-EM structures of human TRPV4 in complex with RhoA in the ligand-free, antagonist-bound closed, and agonist-bound open states. These structures reveal the mechanism of ligand-dependent TRPV4 gating. Channel activation is associated with rigid-body rotation of the intracellular ankyrin repeat domain, but state-dependent interaction with membrane-anchored RhoA constrains this movement. Notably, many residues at the TRPV4-RhoA interface are mutated in disease and perturbing this interface by introducing mutations into either TRPV4 or RhoA increases TRPV4 channel activity. Together, these results suggest that RhoA serves as an auxiliary subunit for TRPV4, regulating TRPV4-mediated calcium homeostasis and disruption of TRPV4-RhoA interactions can lead to TRPV4-related neuromuscular disease. These insights will help facilitate TRPV4 therapeutics development.
Assuntos
Canais de Cátion TRPV , Proteína rhoA de Ligação ao GTP , Humanos , Repetição de Anquirina , Cálcio/metabolismo , Mutação , Canais de Cátion TRPV/química , Proteína rhoA de Ligação ao GTP/químicaRESUMO
G-protein coupled receptors (GPCRs) and ion channels serve as key molecular switches through which extracellular stimuli are transformed into intracellular effects, and it has long been postulated that ion channels are direct effector molecules of the alpha subunit of G-proteins (Gα). However, no complete structural evidence supporting the direct interaction between Gα and ion channels is available. Here, we present the cryo-electron microscopy structures of the human transient receptor potential canonical 5 (TRPC5)-Gαi3 complexes with a 4:4 stoichiometry in lipid nanodiscs. Remarkably, Gαi3 binds to the ankyrin repeat edge of TRPC5 ~ 50 Å away from the cell membrane. Electrophysiological analysis shows that Gαi3 increases the sensitivity of TRPC5 to phosphatidylinositol 4,5-bisphosphate (PIP2), thereby rendering TRPC5 more easily opened in the cell membrane, where the concentration of PIP2 is physiologically regulated. Our results demonstrate that ion channels are one of the direct effector molecules of Gα proteins triggered by GPCR activation-providing a structural framework for unraveling the crosstalk between two major classes of transmembrane proteins: GPCRs and ion channels.
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Canais de Potencial de Receptor Transitório , Humanos , Microscopia Crioeletrônica , Receptores Acoplados a Proteínas G/metabolismo , Membrana Celular/metabolismo , Canais de Cátion TRPC/metabolismoRESUMO
Since the global outbreak of coronavirus disease 2019 (COVID-19), it has spread rapidly around the world. The nucleocapsid (N) protein is one of the most abundant SARS-CoV-2 proteins. Therefore, a sensitive and effective detection method for SARS-CoV-2 N protein is the focus of research. Here, we developed a surface plasmon resonance (SPR) biosensor based on the dual signal-amplification strategy of Au@Ag@Au nanoparticles (NPs) and graphene oxide (GO). Additionally, a sandwich immunoassay was utilized to sensitively and efficiently detect SARS-CoV-2 N protein. On the one hand, Au@Ag@Au NPs have a high refractive index and the capability to electromagnetically couple with the plasma waves propagating on the surface of gold film, which are harnessed for amplifying the SPR response signal. On the other hand, GO, which has the large specific surface area and the abundant oxygen-containing functional groups, could provide unique light absorption bands that can enhance plasmonic coupling to further amplify the SPR response signal. The proposed biosensor could efficiently detect SARS-CoV-2 N protein for 15 min and the detection limit for SARS-CoV-2 N protein was 0.083 ng/mL, with a linear range of 0.1 ng/mL~1000 ng/mL. This novel method can meet the analytical requirements of artificial saliva simulated samples, and the developed biosensor had a good anti-interference capability.
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Técnicas Biossensoriais , COVID-19 , Nanopartículas Metálicas , Humanos , Ressonância de Plasmônio de Superfície/métodos , Técnicas Biossensoriais/métodos , SARS-CoV-2 , Ouro , Imunoensaio/métodos , COVID-19/diagnósticoRESUMO
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
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Proteínas de Membrana , Simulação de Dinâmica Molecular , Lipídeos/químicaRESUMO
Aiming for precise, real-time, and on-site analysis of proteins, an innovative binary-emission fluorescence imprinted polymer was designed by sol-gel method after mixing MIL-101(Cr), green CdTe (g-CdTe) and red CdTe (r-CdTe) for detection of protein. In this proposal, MIL-101(Cr), as a favorable supporter, provided high surface area and porosity for imprinting sites, which ameliorated the transfer rate and the sensitivity of the nanosensor. And g-CdTe and r-CdTe were served as signal transduction for dual-emission response. Based on strengthened recognition reaction between high-affinity imprinting sites and protein, the fluorescence intensities of g-CdTe and r-CdTe yielded conspicuous two responses at 528 nm and 634 nm for protein under the excitation of 350 nm. The cytochrome c (Cyt c) and trypsin were served as model proteins to verify the generality of strategy. Given prominent merits of MIL-101(Cr), g-CdTe/r-CdTe@MIL-101(Cr)@MIP exhibited good linear range of 1-30 µM for Cyt c and 0.15-4 µM for trypsin, and the limit of detection were 0.13 µM and 0.014 µM, respectively. Significantly, an unsophisticated smartphone-based sensing device was developed by integrating g-CdTe/r-CdTe@MIL-101(Cr)@MIP with a 3D printing portable device to obtain precise on-site results. As expected, this portable platform was successfully applied for monitoring Cyt c and trypsin with a detection limit of 0.71 µM and 0.026 µM, respectively. These results indicated this dual-response molecularly imprinted fluorescence senor based on smartphone provided promising perspectives on futural on-site protein analysis.
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Compostos de Cádmio , Impressão Molecular , Pontos Quânticos , Smartphone , Tripsina , Telúrio , Impressão Molecular/métodos , Limite de DetecçãoRESUMO
L-cysteine (L-Cys) capped ZnS fluorescent probe (L-ZnS) were synthesized by binding ZnS nanoparticles in situ with L-Cys, the fluorescence intensity of L-ZnS increased more than 3.5 times than that of ZnS due to the cleavage of S-H bonds and the formation of Zn-S bonds between the thiol group of L-Cys and ZnS. The addition of copper ions (Cu2+) can effectively quench the fluorescence of L-ZnS to realize the rapid detection of trace Cu2+. The L-ZnS showed high sensitivity and selectivity to Cu2+. The LOD (limit of detection) of Cu2+ was as low as 7.28 nM and linearity in the concentration range of 3.5-25.5 µM. Meanwhile, for the first time, electron localization function (ELF), bond order density (BOD), and natural adaptive orbital (NAdO) analysis in the Multiwfn wavefunction program based on density functional theory were carried out to probe the binding sites and binding mode of L-Cys with Cu2+, it indicated that the deprotonated carboxyl oxygen atoms of L-Cys had the lowest electrostatic potential (ESP) and provided lone pair electrons to coordinate with Cu2+ to form non-luminescent ground state complexes, which led to fluorescence quenching of L-ZnS. From the microscopic point of view of atoms, the mechanism of fluorescence enhancement of L-Cys capped ZnS and the mechanism of fluorescence quenching after adding Cu2+ were revealed in depth, the theoretical analysis results were accordance with the experiments.
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The novel CuMnS nanoflower fluorescent probe based on Mn-doped CuS was developed to achieve the fluorescence detection of oxytetracycline hydrochloride (OTC), the fluorescent sensor has good selectivity and stability. The doping of Mn significantly increased the fluorescence intensity of CuS, which was above 10 times that of CuS. When the predominant species of OTC molecule was zwitterionic OTC+/-at the solution pH of about 5.00, the fluorescence quenching efficiency of CuMnS by OTC reached the highest. Through fluorescence lifetime and UV absorption, the sensing mechanism between CuMnS and OTC was found to be static quenching. Moreover, Multiwfn wavefunction analysis program based on density function theory (DFT) calculation was applied to compare the interactions between different OTC species and CuMnS at different pH, to reveal the micromechanism of fluorescence quenching of CuMnS by OTC from the views of atoms. The molecular surface quantitative analysis and basin analysis of different OTC species demonstrated that the N atom and O atoms of tricarbonylamide moiety of zwitterionic OTC+/- can provide lone pair electrons to form a non-fluorescent ground state complex with CuMnS. Meanwhile, the electrostatic attraction of OTC+/- with negatively charged CuMnS was also beneficial to the interaction, resulting in the effective fluorescence quenching of CuMnS. This work offers a convenient method for sensitively detecting OTC and broadens the application of CuMnS in the field of fluorescence detection.
Assuntos
Oxitetraciclina , Cobre , Corantes Fluorescentes/química , Oxitetraciclina/análise , Oxitetraciclina/química , Espectrometria de Fluorescência/métodosRESUMO
Rapid, convenient and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is urgently needed to timely diagnosis of coronavirus pandemic (COVID-19) and control of the epidemic. In this study, a signal-off photoelectrochemical (PEC) immunosensor was constructed for SARS-CoV-2 nucleocapsid (N) protein detection based on a magnetic all-solid-state Z-scheme heterojunction (Fe3O4@SiO2@TiO2@CdS/Au, FSTCA). Integrating the advantages of magnetic materials and all-solid-state Z-scheme heterostructures, FSTCA was implemented to ligate the capture antibody to form magnetic capture probe (FSTCA/Ab1). It can simplify the separation and washing process to improve reproducibility and stability, while allowing immune recognition to be performed in the liquid phase instead of the traditional solid-liquid interface to improve anti-interference. Besides, the heterojunction inhibited the recombination of photogenerated electron/hole (e-/h+) and promoted the light absorption to provide superior photoelectric substrate signal. The mechanism of photogenerated e-/h+ transfer of FSTCA were investigated by the electron spin resonance (ESR) spectroscopy. SiO2 spheres loaded with Au NPs utilized as an efficient signal quencher. The steric hindrance effect of SiO2@Au labeled detection antibodies (SiO2@Au-Ab2) conjugates significantly diminished light absorption and hindered the transfer of photogenerated electrons, further amplifying the signal change value. Based on the above merits, the elaborated immunosensor had a wide linear range of 10 pg mL-1-100 ng mL-1 and a low detection limit down to 2.9 pg mL-1 (S/N = 3). The fabricated PEC immunosensor demonstrated strong anti-interference, easy operation, and high sensitivity, showing enormous potential in clinical diagnosis of SARS-CoV-2.
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Transient receptor potential vanilloid (TRPV) channels play various important roles in human physiology. As membrane proteins, these channels are modulated by their endogenous lipid environment as the recent wealth of structural studies has revealed functional and structural lipid binding sites. Additionally, it has been shown that exogenous ligands can exchange with some of these lipids to alter channel gating. Here, we used molecular dynamics simulations to examine how one member of the TRPV family, TRPV2, interacts with endogenous lipids and the pharmacological modulator cannabidiol (CBD). By computationally reconstituting TRPV2 into a typical plasma membrane environment, which includes phospholipids, cholesterol, and phosphatidylinositol (PIP) in the inner leaflet, we showed that most of the interacting surface lipids are phospholipids without strong specificity for headgroup types. Intriguingly, we observed that the C-terminal membrane proximal region of the channel binds preferentially to PIP lipids. We also modelled two structural lipids in the simulation: one in the vanilloid pocket and the other in the voltage sensor-like domain (VSLD) pocket. The simulation shows that the VSLD lipid dampens the fluctuation of the VSLD residues, while the vanilloid lipid exhibits heterogeneity both in its binding pose and in its influence on protein dynamics. Addition of CBD to our simulation system led to an open selectivity filter and a structural rearrangement that includes a clockwise rotation of the ankyrin repeat domains, TRP helix, and VSLD. Together, these results reveal the interplay between endogenous lipids and an exogenous ligand and their effect on TRPV2 stability and channel gating.
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Antineoplásicos , Canais de Cátion TRPV , Humanos , Canais de Cátion TRPV/química , Ligantes , Repetição de Anquirina , Sítios de Ligação , FosfolipídeosRESUMO
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seriously threatened global public health. Establishing a rapid and sensitive diagnostic test for early detection of the SARS-CoV-2 nucleocapsid protein is urgently required to defend against the pandemic. Herein, an enhanced lateral flow immunoassay (LFIA) was fabricated by trimetallic Au@Pd@Pt core-shell nanozymes for detection of the SARS-CoV-2 nucleocapsid protein. The Au@Pd@Pt nanozymes (Au@Pd@Pt NZs) synthesized via a one-pot method, with a dendrite morphology and uniform particle size, showed excellent peroxidase-like activity. Due to the perfect enzyme-like catalytic activity toward 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of hydrogen peroxide (H2O2), the catalytic signal could be generated even by a tiny amount of Au@Pd@Pt NZs accumulated on the test strip. Therefore, rapid detection with higher sensitivity was achieved. The Au@Pd@Pt NZs-based LFIA provided a quantitative range of 0.05-100 ng mL-1 with a limit of detection of 0.037 ng mL-1, which was 17-fold lower than the LFIA without enhancement. The average recoveries from spiked samples were in the range of 92.5-107.9% with relative standard deviations all less than 4%, indicating the reliability and repeatability of the proposed LFIA. Additionally, the proposed LFIA could report results within 30 min using a microplate reader. In conclusion, the Au@Pd@Pt NZs-LFIA is a rapid, simple, and sensitive method for detecting the SARS-CoV-2 nucleocapsid protein.
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COVID-19 , SARS-CoV-2 , Humanos , Peróxido de Hidrogênio , Reprodutibilidade dos Testes , COVID-19/diagnóstico , Imunoensaio/métodosRESUMO
A quantitative structure-activity relationship (QSAR) model for the structure and affinity of abrin aptamers was established. A higher affinity abrin aptamer based on the established QSAR model was screened by site-directed mutagenesis. The fluorescence quenching effect between magnetic microspheres and fluorescent molecules was studied for the first time. A new method for abrin detection based on the interaction between target molecules and fluorescently labeled aptamers on magnetic microspheres was developed, with the detection limit of 5 ng mL-1. This method can overcome the influence of complex environmental interferents in abrin detection and can meet the analysis requirements for simulated samples such as water, soil, and food.
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The SARS-CoV-2 pandemic has posed a huge challenge to rapid and accurate diagnosis of SARS-CoV-2 in the early stage of infection. In this work, we developed a novel magnetic/fluorescent dual-modal lateral flow immunoassay (LFIA) based on multifunctional nanobeads for rapid and accurate determination of SARS-CoV-2 nucleocapsid protein (NP). The multifunctional nanobeads were fabricated by using polyethyleneimine (PEI) as a mediate shell to combine superparamagnetic Fe3O4 core with dual quantum dot shells (MagDQD). The core-shell structure of MagDQD label with high loading density of quantum dots (QDs) and superior magnetic content realized LFIA with dual quantitative analysis modal from the assemblies of individual single nanoparticles. The LFIA integrated the advantages of magnetic signal and fluorescent signal, resulting excellent accuracy for quantitative analysis and high elasticity of the overall detection. In addition, magnetic signal and fluorescent signal both had high sensitivity with the limit of detection (LOD) as 0.235 ng mL-1 and 0.012 ng mL-1, respectively. The recovery rates of the methods in simulated saliva samples were 91.36%-103.60% (magnetic signal) and 94.39%-104.38% (fluorescent signal). The results indicate the method has a considerable potential to be an effective tool for diagnose SARS-CoV-2 in the early stage of infection.
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COVID-19 , SARS-CoV-2 , Humanos , Polietilenoimina , COVID-19/diagnóstico , Imunoensaio/métodos , Fenômenos MagnéticosRESUMO
A sensitive dual-readout immunosensor for fluorescence and electrochemiluminescence (ECL) detection of ricin was established, which was combined with a streptavidin-biotin signal amplification system. CdSe/ZnS quantum dots with fine fluorescence and ECL properties were used as the dual-signal function probes of the sandwich immunocomplex. Under the optimum experimental conditions, the dual signal intensity increased significantly with the rise in ricin concentration. The fluorescence intensity of the senor exhibited a good liner relationship toward the ricin concentrations with 0.1~100 ng/mL and the limit of detection (LOD) was 81.7 pg/mL; taking ECL as the detection signal, the sensor showed a linear relationship with the ricin concentrations ranging from 0.01 ng/mL to 100 ng/mL and the LOD was 5.5 pg/mL. The constructed sensor with high sensitivity had been successfully applied to the detection of ricin in complex matrices with satisfactory recoveries. The proposed immunosensor model can be extended to the analysis and detection of others target proteins.
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Técnicas Biossensoriais , Compostos de Cádmio , Pontos Quânticos , Ricina , Compostos de Selênio , Medições Luminescentes , Imunoensaio , Estreptavidina , Biotina , Eletrodos , Limite de Detecção , Técnicas EletroquímicasRESUMO
The transient receptor potential melastatin 8 (TRPM8) channel is the primary molecular transducer responsible for the cool sensation elicited by menthol and cold in mammals. TRPM8 activation is controlled by cooling compounds together with the membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP2). Our knowledge of cold sensation and the therapeutic potential of TRPM8 for neuroinflammatory diseases and pain will be enhanced by understanding the structural basis of cooling agonist- and PIP2-dependent TRPM8 activation. We present cryo-electron microscopy structures of mouse TRPM8 in closed, intermediate, and open states along the ligand- and PIP2-dependent gating pathway. Our results uncover two discrete agonist sites, state-dependent rearrangements in the gate positions, and a disordered-to-ordered transition of the gate-forming S6-elucidating the molecular basis of chemically induced cool sensation in mammals.
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Temperatura Baixa , Ativação do Canal Iônico , Fosfatidilinositol 4,5-Difosfato , Pirimidinonas , Canais de Cátion TRPM , Sensação Térmica , Animais , Camundongos , Microscopia Crioeletrônica , Ligantes , Mentol/química , Mentol/farmacologia , Canais de Cátion TRPM/agonistas , Canais de Cátion TRPM/química , Fosfatidilinositol 4,5-Difosfato/química , Fosfatidilinositol 4,5-Difosfato/farmacologia , Sensação Térmica/efeitos dos fármacos , Sensação Térmica/fisiologia , Ativação do Canal Iônico/efeitos dos fármacos , Ativação do Canal Iônico/fisiologia , Conformação Proteica , Pirimidinonas/química , Pirimidinonas/farmacologiaRESUMO
Enhanced sampling methodologies modifying underlying Hamiltonians can be used for the systems with a rugged potential energy surface that makes it hard to observe convergence using conventional unbiased molecular dynamics (MD) simulations. We present CHARMM-GUI Enhanced Sampler, a web-based tool to prepare various enhanced sampling simulations inputs with user-selected collective variables (CVs). Enhanced Sampler provides inputs for the following nine methods: accelerated MD, Gaussian accelerated MD, conformational flooding, metadynamics, adaptive biasing force, steered MD, temperature replica exchange MD, replica exchange solute tempering 2, and replica exchange umbrella sampling for the method-implemented MD packages including AMBER, CHARMM, GENESIS, GROMACS, NAMD, and OpenMM. Users only need to select a group of atoms via intuitive web-implementation in order to define commonly used nine CVs of interest: center of mass based distance, angle, dihedral, root-mean-square-distance, radius of gyration, distance projected on axis, two types of angles projected on axis, and coordination numbers. The enhanced sampling methods are tested with several biological systems to illustrate their efficiency over conventional MD. Enhanced Sampler with carefully optimized system-dependent parameters will help users to get meaningful results from their enhanced sampling simulations.
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Simulação de Dinâmica Molecular , Conformação Molecular , TemperaturaRESUMO
Dengue virus (DENV) has developed rapidly in the past few decades and has been becoming the most widespread arbovirus in the world. The vital role of NS2B-NS3 in virus replication and maturation of relevant proteins makes it the most promising target for anti-DENV drug discovery, although none of NS2B-NS3 inhibitors have been approved for the market so far. In this study, potent NS2B-NS3 covalent inhibitors were discovered via chemical modification of a published covalent inhibitor WSL-01 (IC50 = 129 nM), yielding promising analogs WSL-75 and WSL-84 (IC50 = 24.8 nM and IC50 = 32.89 nM, respectively) with more than 10-fold increased enzymatic activities compared to the lead compound, and no evident cellular toxicity was observed. Further comprehensive structure-activity relationship analysis through covalent docking and molecular dynamics simulation provides informative understanding of the binding modes of covalent inhibitors targeting NS2B-NS3, which would be beneficial for novel NS2B-NS3 inhibitory development.
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Vírus da Dengue , Antivirais/química , Antivirais/farmacologia , Vírus da Dengue/metabolismo , Simulação de Acoplamento Molecular , Inibidores de Proteases/farmacologia , Serina Endopeptidases/metabolismo , Proteínas não Estruturais Virais/químicaRESUMO
Airborne transmission of pathogens is the most probable cause for the spread of respiratory diseases, which can be intercepted by personal protective equipment such as masks. In this study, an efficient antiviral personal protective filter was fabricated by coupling the biocompatible curcumin (CCM) with nanofibrous polytetrafluoroethylene (PTFE) membrane. The CCM extracted from plants was first dissolved in acidified ethanol at a certain pH and temperature to optimize its loading concentration, antiviral activation, and binding forces on the polyethylene terephthalate (PET) support to form a pre-filtration layer at the front section of the filter. Ultrathin PTFE membrane was then fabricated on the antibacterial-antiviral PET support (A-A PET) by controllable heating lamination. This functional layer of the filter exhibits good gas permeance (3423.6 m3/(m2·h·kPa)) and ultrafine particles rejection rate (>98.79%). Moreover, the obtained A-A filter exhibit a high antibacterial rate against a variety of bacteria (E. coli, B. subtilis, A. niger, and Penicillium were 99.84%, 99.02%, 93.60%, 95.23%, respectively). Forthwith virucidal (SARS-CoV-2) efficiency of the A-A filter can reach 99.90% for 5 min. The filter shows good stability after 10 heating cycles, demonstrating its reusability.