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1.
Q Rev Biophys ; 57: e9, 2024 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-39225237

RESUMO

Structure-switching aptamers have become ubiquitous in several applications, notably in analytical devices such as biosensors, due to their ease of supporting strong signaling. Aside from their ability to bind specifically with their respective target, this class of aptamers also undergoes a conformational rearrangement upon target recognition. While several well-studied and early-developed aptamers (e.g., cocaine, ATP, and thrombin) have been found to have this structure-switching property, the vast majority do not. As a result, it is common to try to engineer aptamers into switches. This proves challenging in part because of the difficulty in obtaining structural and functional information about aptamers. In response, we review various readily available biophysical characterization tools that are capable of assessing structure switching of aptamers. In doing so, we delve into the fundamentals of these different techniques and detail how they have been utilized in characterizing structure-switching aptamers. While each of these biophysical techniques alone has utility, their real power to demonstrate the occurrence of structural change with ligand binding is when multiple techniques are used. We hope that through a deeper understanding of these techniques, researchers will be better able to acquire biophysical information about their aptamer-ligand systems and accelerate the translation of aptamers into biosensors.


Assuntos
Aptâmeros de Nucleotídeos , Conformação de Ácido Nucleico , Aptâmeros de Nucleotídeos/química , Aptâmeros de Nucleotídeos/metabolismo , Soluções , Humanos , Fenômenos Biofísicos , Técnicas Biossensoriais
2.
Nat Commun ; 15(1): 7763, 2024 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-39237564

RESUMO

The challenge of transforming organized DNA structures into their metallized counterparts persists in the scientific field. In this context, utilizing DNA molecules modified with 7-deazapurine, provides a transformative solution. In this study, we present the solution structure of a DNA duplex that can be transformed into its metallized equivalent while retaining the natural base pairing arrangement through the creation of silver-modified Watson-Crick base pairs. Unlike previously documented X-ray structures, our research demonstrates the feasibility of preserving the intrinsic DNA self-assembly while incorporating AgI into the double helix, illustrating that the binding of silver does not disrupt the canonical base-pairing organization. Moreover, in our case, the uninterrupted AgI chain deviates from forming conventional straight linear chains; instead, it adheres to a helical arrangement dictated by the underlying DNA structure. This research challenges conventional assumptions and opens the door to precisely design structures based on the organization of highly stable Ag-DNA assemblies.


Assuntos
Pareamento de Bases , DNA , Conformação de Ácido Nucleico , Prata , Prata/química , DNA/química , Modelos Moleculares , Soluções
3.
Carbohydr Polym ; 345: 122567, 2024 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-39227104

RESUMO

Solution blowing process was used to prepare cellulose nonwovens, by using N-methyl morpholine-N-oxide (NMMO) as solvent, and salicylic acid (SA) microcapsules as antibacterial additives. The structure and properties of cellulose nonwovens modified with different SA microcapsules contents were compared and evaluated. The results showed that more uniform and denser web structure was formed with the increase of SA microcapsules content, the average fiber diameter of cellulose nonwoven increased from 1.99 µm to 2.65 µm. The air flow resistance and filtration efficiency of cellulose nonwovens increased with addition of SA microcapsules, whereas the mechanical properties, and wearing comfort including air permeability, moisture vapor transfer rate, and softness of cellulose nonwovens decreased slightly, under the same basis weight. SA microcapsules modified cellulose nonwovens exhibited good sustained-release behavior and antimicrobial activity against Escherichia coli. The higher SA microcapsules content in cellulose nonwovens, the faster release rate and the higher antimicrobial activity. The cellulose solution-blown nonwovens modified with SA microcapsules are expected to find applications in medical and healthcare fields due to its antibacterial activity and biodegradability.


Assuntos
Antibacterianos , Cápsulas , Celulose , Escherichia coli , Ácido Salicílico , Solventes , Celulose/química , Ácido Salicílico/química , Ácido Salicílico/farmacologia , Antibacterianos/farmacologia , Antibacterianos/química , Escherichia coli/efeitos dos fármacos , Solventes/química , Liberação Controlada de Fármacos , Óxidos N-Cíclicos/química , Soluções , Testes de Sensibilidade Microbiana
4.
J Chem Phys ; 161(9)2024 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-39225532

RESUMO

The diffusion of proteins is significantly affected by macromolecular crowding. Molecular simulations accounting for protein interactions at atomic resolution are useful for characterizing the diffusion patterns in crowded environments. We present a comprehensive analysis of protein diffusion under different crowding conditions based on our recent docking-based approach simulating an intracellular crowded environment by sampling the intermolecular energy landscape using the Markov Chain Monte Carlo protocol. The procedure was extensively benchmarked, and the results are in very good agreement with the available experimental and theoretical data. The translational and rotational diffusion rates were determined for different types of proteins under crowding conditions in a broad range of concentrations. A protein system representing most abundant protein types in the E. coli cytoplasm was simulated, as well as large systems of other proteins of varying sizes in heterogeneous and self-crowding solutions. Dynamics of individual proteins was analyzed as a function of concentration and different diffusion rates in homogeneous and heterogeneous crowding. Smaller proteins diffused faster in heterogeneous crowding of larger molecules, compared to their diffusion in the self-crowded solution. Larger proteins displayed the opposite behavior, diffusing faster in the self-crowded solution. The results show the predictive power of our structure-based simulation approach for long timescales of cell-size systems at atomic resolution.


Assuntos
Método de Monte Carlo , Difusão , Proteínas/química , Soluções , Simulação de Acoplamento Molecular , Escherichia coli/química , Simulação de Dinâmica Molecular , Cadeias de Markov
5.
PLoS One ; 19(9): e0309544, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39231150

RESUMO

This study examines the corrosion characteristics of weakly cemented sandstone under alkaline conditions, evaluating the effects of varying pH levels on its macroscopic degradation, micro-porosity, and mechanical properties, notably uniaxial compressive strength. Findings reveal that heightened alkalinity exacerbates rock damage, although a temporary alleviation in mass loss occurs between pH 9 and 11 due to pore clogging by complexes formed from cations like Ca2+ and Mg2+.Increased alkalinity induces marked changes in pore features, with an observed rise in pore numbers, transformation of pore shapes from elongated to more spherical, and adjustments in porosity, pore size, and roundness. Furthermore, the study confirms a decline in both the rock's compressive strength and elastic modulus as pH rises. These revelations shed light on the role of pH in the corrosion behavior of weakly cemented sandstone under alkaline conditions, providing a fresh perspective for understanding its corrosion mechanisms in such environments.


Assuntos
Força Compressiva , Corrosão , Concentração de Íons de Hidrogênio , Porosidade , Soluções , Álcalis/química , Módulo de Elasticidade
6.
Nat Commun ; 15(1): 7740, 2024 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-39231922

RESUMO

The physical characterization of proteins in terms of their sizes, interactions, and assembly states is key to understanding their biological function and dysfunction. However, this has remained a difficult task because proteins are often highly polydisperse and present as multicomponent mixtures. Here, we address this challenge by introducing single-molecule microfluidic diffusional sizing (smMDS). This approach measures the hydrodynamic radius of single proteins and protein assemblies in microchannels using single-molecule fluorescence detection. smMDS allows for ultrasensitive sizing of proteins down to femtomolar concentrations and enables affinity profiling of protein interactions at the single-molecule level. We show that smMDS is effective in resolving the assembly states of protein oligomers and in characterizing the size of protein species within complex mixtures, including fibrillar protein aggregates and nanoscale condensate clusters. Overall, smMDS is a highly sensitive method for the analysis of proteins in solution, with wide-ranging applications in drug discovery, diagnostics, and nanobiotechnology.


Assuntos
Proteínas , Imagem Individual de Molécula , Imagem Individual de Molécula/métodos , Proteínas/química , Proteínas/análise , Soluções , Difusão , Microfluídica/métodos , Hidrodinâmica , Técnicas Analíticas Microfluídicas/métodos
7.
Biophys Chem ; 314: 107318, 2024 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-39226875

RESUMO

The Ebola delta peptide is an amphipathic, 40-residue peptide encoded by the Ebola virus, referred to as E40. The membrane-permeabilising activity of the E40 delta peptide has been demonstrated in cells and lipid vesicles suggesting the E40 delta peptide likely acts as a viroporin. The lytic activity of the peptide increases in the presence of anionic lipids and a disulphide bond in the C-terminal part of the peptide. Previous in silico work predicts the peptide to show a partially helical structure, but there is no experimental information on the structure of E40. Here, we use circular dichroism spectroscopy to report the secondary structure propensities of the reduced and oxidised forms of the E40 peptide in water, detergent micelles, and lipid vesicles composed of neutral and anionic lipids (POPC and POPG, respectively). Results indicate that the peptide is predominately a random coil in solution, and the disulphide bond has a small but measurable effect on peptide conformation. Secondary structure analysis shows large uncertainties and dependence on the reference data set and, in our system, cannot be used to accurately determine the secondary structure motifs of the peptide in membrane environments. Nevertheless, the spectra can be used to assess the relative changes in secondary structure propensities of the peptide depending on the solvent environment and disulphide bond. In POPC-POPG vesicles, the peptide transitions from a random coil towards a more structured conformation, which is even more pronounced in negatively charged SDS micelles. In vesicles, the effect depends on the peptide-lipid ratio, likely resulting from vesicle surface saturation. Further experiments with zwitterionic POPC vesicles and DPC micelles show that both curvature and negatively charged lipids can induce a change in conformation, with the two effects being cumulative. Electrostatic screening from Na+ ions reduced this effect. The oxidised form of the peptide shows a slightly lower propensity for secondary structure and retains a more random coil conformation even in the presence of PG-PC vesicles.


Assuntos
Dicroísmo Circular , Ebolavirus , Micelas , Estrutura Secundária de Proteína , Ebolavirus/química , Fosfatidilcolinas/química , Soluções , Fosfatidilgliceróis/química , Peptídeos/química , Água/química , Proteínas Virais/química , Sequência de Aminoácidos
8.
Int J Mol Sci ; 25(17)2024 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-39273676

RESUMO

Microwaves have been successfully employed in the Lewis acid titanium tetrachloride-assisted synthesis of peptide systems. Dipeptide systems with their amino function differently protected with urethane protecting groups have been synthesized in short periods of time and with high yields. The formation of the peptide bond between the two reacting amino acids was achieved in pyridine by using titanium tetrachloride as a condensing agent and heating the reaction mixture with a microwave reactor. The reaction conditions are compatible with amino acids featuring various side chains and different protecting groups on both the amino function and side chains. Additionally, the substrates retain their chiral integrity after reaction.


Assuntos
Dipeptídeos , Micro-Ondas , Titânio , Dipeptídeos/química , Dipeptídeos/síntese química , Titânio/química , Aminoácidos/química , Soluções
9.
Sensors (Basel) ; 24(17)2024 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-39275661

RESUMO

The accurate determination of the post-dilution concentration of biological buffers is essential for retaining the necessary properties and effectiveness of the buffer to maintain stable cellular environments and optimal conditions for biochemical reactions. In this work, we introduce a silicon-based impedance chip, which offers a rapid and reagent-free approach for monitoring the buffer concentrations after dilution with deionized (DI) water. The impedance of the impedance chip is measured, and the impedance data are modeled using a multiparameter equivalent circuit model. We investigated six aqueous biological buffers with pH values above and below the physiological pH for most tissues (pH ~ 7.2-7.4) following dilution with DI water by factors of 2.0, 10.0, 20.0, 100.0, and 200.0. The impedance measurement is then performed for the frequency spectrum of 40 Hz to 1 MHz. From the interpretation of the impedance measurement using the multiparameter equivalent circuit model, we report a buffer-sensitive equivalent circuit parameter RAu/Si of the silicon-based impedance chip showing a linear trend on a logarithmic scale with the buffer concentration change after dilution. The parameter RAu/Si is independent of the buffer pH and the added volume. The results demonstrate the efficacy of the silicon-based impedance chip as a versatile tool for precise post-dilution concentration determination of diverse biologically relevant buffers. The presented impedance chip offers rapid, accurate, and reliable monitoring, making it highly suitable for integration into automated liquid-handling systems to enhance the efficiency and precision of biological and chemical processes.


Assuntos
Impedância Elétrica , Concentração de Íons de Hidrogênio , Soluções Tampão , Silício/química , Soluções/química , Técnicas Biossensoriais/métodos , Água/química
10.
Medicine (Baltimore) ; 103(36): e39453, 2024 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-39252294

RESUMO

BACKGROUND: Del Nido cardioplegia (DNC) has extensively been used for pediatric population undergoing cardiac surgery. However, its use in adult cardiac surgeries have been limited thus, its benefits are not yet fully known. This analysis was performed to evaluate the impact of DNC versus any other type of cardioplegia in adult patients who are undergoing cardiac surgery. METHODS: We systematically searched PubMed, Cochrane Library, and Scopus from database inception till March 2023, and moderate to high-quality randomized controlled trials were included which compared DNC to other cardioplegia. The primary outcome was postoperative stroke and/or transient ischemic attack (TIA). Secondary outcomes included spontaneous rhythm return, postoperative myocardial infarction, all-cause mortality, postoperative atrial fibrillation, defibrillation after coronary reperfusion, postoperative intra-aortic balloon pump, postoperative kidney injury, postoperative low cardiac output syndrome, inotropic support, cardiopulmonary bypass time, cross-clamp time, blood transfusion, cardioplegia volume, hospital stay, intensive care unit stay, mechanical ventilation stay, postoperative left ventricular ejection fraction, and cardiac markers. RESULTS: In this meta-analysis, 13 studies were included with a patient population of 2207. Stroke and/or TIA studies (risk ratio [RR]: 0.54, 95% CI [0.29, 1.00]) and all-cause mortality studies (RR: 1.30, 95% CI [0.66, 2.56]) were insignificant. From the secondary outcomes, spontaneous rhythm return (RR: 1.58, 95% CI [1.02, 2.45]), defibrillation after coronary reperfusion (RR: 0.49, 95% CI [0.30, 0.79]), inotropic support (RR: 0.70, 95% CI [0.57, 0.85]), composite risk of stroke and/or TIA and/or acute kidney injury and mortality (RR: 0.72, 95% CI [0.53, 0.99]), cross-clamp time (mean difference [MD]: -6.01, 95% CI [-11.14, -0.89]), blood transfusion (RR: 0.73, 95% CI [0.60, 0.90]), cardioplegia volume (MD: -537.17, 95% CI [-758.89, -315.45]), troponin T (MD: -1.71, 95% CI [-2.11, -1.32]), creatine phosphokinase-MB (MD: -2.96, 95% CI [-5.84, -0.07]) were significant. Whereas all other secondary outcomes were found to be insignificant. CONCLUSION: No significant difference was observed between patients undergoing Del Nido administration in comparison to other cardioplegia solutions for the primary outcome, stroke or/and TIA.


Assuntos
Procedimentos Cirúrgicos Cardíacos , Parada Cardíaca Induzida , Complicações Pós-Operatórias , Ensaios Clínicos Controlados Aleatórios como Assunto , Humanos , Parada Cardíaca Induzida/métodos , Procedimentos Cirúrgicos Cardíacos/métodos , Adulto , Complicações Pós-Operatórias/epidemiologia , Complicações Pós-Operatórias/prevenção & controle , Soluções Cardioplégicas/uso terapêutico , Cloreto de Potássio , Manitol , Lidocaína , Soluções , Eletrólitos , Sulfato de Magnésio , Bicarbonato de Sódio
11.
Int J Mol Sci ; 25(16)2024 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-39201432

RESUMO

To realize the potential for the use of N-chlorotaurine (NCT) in healthcare, a better understanding of the long-term stability of the compound in water is needed. An array of analytical procedures is required that can measure changes in NCT concentration over time and allow for the detection and identification of contaminants and likely degradation end products. We used UV-Vis and NMR spectroscopy, HPLC, and LCMS to establish the stability of NCT in solutions subjected to prolonged ambient and elevated temperatures. Stability proved to be dependent on concentration with half-lives of ~120 days and ~236 days for 1% and 0.5% solutions of NCT at ~20 °C. Regardless of initial pH, all solutions shifted toward and maintained a pH of ~8.3 at 20 °C and 40 °C. NCT at 500 µg/mL and 250 µg /mL inhibited biofilm formation by Pseudomonas aeruginosa and Staphylococcus aureus but did not disperse established biofilms. NCT exposure to the biofilms had profound effects on the viability of both bacteria, reducing live organisms by >90%. Exposure of Interleukin-6 (IL-6) to 11 µM NCT reduced the binding of IL-6 to an immobilized specific antibody by ~48%, which is 5× the amount required for HOCl to bring about the same effect in this test system. Our data demonstrate the potency of the compound as an antimicrobial agent with potential benefits in the management of infected chronic wounds and suggest that NCT may contribute to anti-inflammatory processes in vivo by direct modification of cytokine mediators.


Assuntos
Biofilmes , Pseudomonas aeruginosa , Staphylococcus aureus , Taurina , Pseudomonas aeruginosa/efeitos dos fármacos , Staphylococcus aureus/efeitos dos fármacos , Taurina/farmacologia , Taurina/química , Biofilmes/efeitos dos fármacos , Estabilidade de Medicamentos , Interleucina-6/metabolismo , Concentração de Íons de Hidrogênio , Antibacterianos/farmacologia , Antibacterianos/química , Soluções , Humanos
12.
Int J Mol Sci ; 25(15)2024 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-39125824

RESUMO

The study presents a thorough and detailed analysis of bicalutamide's structural and conformational properties. Quantum chemical calculations were employed to explore the conformational properties of the molecule, identifying significant energy differences between conformers. Analysis revealed that hydrogen bonds stabilise the conformers, with notable variations in torsion angles. Conformers were classified into 'closed' and 'open' types based on the relative orientation of the cyclic fragments. NOE spectroscopy in different solvents (CDCl3 and DMSO-d6) was used to study the conformational preferences of the molecule. NOESY experiments provided the predominance of 'closed' conformers in non-polar solvents and a significant presence of 'open' conformers in polar solvents. The proportions of open conformers were 22.7 ± 3.7% in CDCl3 and 59.8 ± 6.2% in DMSO-d6, while closed conformers accounted for 77.3 ± 3.7% and 40.2 ± 6.2%, respectively. This comprehensive study underscores the solvent environment's impact on its structural behaviour. The findings significantly contribute to a deeper understanding of conformational dynamics, stimulating further exploration in drug development.


Assuntos
Anilidas , Ligação de Hidrogênio , Espectroscopia de Ressonância Magnética , Conformação Molecular , Nitrilas , Solventes , Compostos de Tosil , Anilidas/química , Compostos de Tosil/química , Solventes/química , Nitrilas/química , Espectroscopia de Ressonância Magnética/métodos , Teoria Quântica , Modelos Moleculares , Soluções
13.
Int J Mol Sci ; 25(15)2024 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-39125837

RESUMO

In this work, the conformational behaviors of ring polyelectrolyte in tetravalent salt solutions are discussed in detail through molecular dynamics simulation. For simplification, here we have neglected the effect of the twisting interaction, although it has been well known that both bending and twisting interactions play a deterministic in the steric conformation of a semiflexible ring polymer. The salt concentration CS and the bending energy b take a decisive role in the conformation of the ring polyelectrolyte (PE). Throughout our calculations, the b varies from b = 0 (freely joint chain) to b = 120. The salt concentration CS changes in the range of 3.56 × 10-4 M ≤ CS ≤ 2.49 × 10-1 M. Upon the addition of salt, ring PE contracts at first, subsequently re-expands. More abundant conformations are observed for a semiflexible ring PE. For b = 10, the conformation of semiflexible ring PE shifts from the loop to two-racquet-head spindle, then it condenses into toroid, finally arranges into coil with the increase of CS. As b increases further, four phase transitions are observed. The latter two phase transitions are different. The semiflexible ring PE experiences transformation from toroid to two racquet head spindle, finally to loop in the latter two phase transitions. Its conformation is determined by the competition among the bending energy, cation-bridge, and entropy. Combined, our findings indicate that the conformations of semiflexible ring PE can be controlled by changing the salt concentration and chain stiffness.


Assuntos
Conformação Molecular , Simulação de Dinâmica Molecular , Polieletrólitos , Sais , Polieletrólitos/química , Sais/química , Soluções
14.
Luminescence ; 39(8): e4856, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39129424

RESUMO

Most nonconventional luminogens enjoy good water solubility and biocompatibility, showing unique application prospects in fields like biological imaging. Although clustering-triggered emission (CTE) mechanisms have been proposed to explain such emissions, the have not been thoroughly elucidated, which limits their development and application. Here, the photoluminescence properties of carboxymethyl ß-cyclodextrin (CM-ß-CD) aqueous solution are utilized to further investigate the effects of changes in concentration, in order to elucidate the emission mechanism through cryo-transmission electron microscopy (cryo-TEM), small-angle X-ray scattering (SAXS), molecular interaction analysis, and theoretical calculation. The results showed that the size distribution, morphology, and distance between water aggregates were successfully correlated with the cluster emission centers. The emission mechanism of nonconventional luminogen solutions was more clearly and intuitively elucidated, which has a promoting effect on the emission and application of this field. It is interesting that temperature-dependent emission spectra show the blue-shift phenomenon of PL with increasing excitation wavelengths. Moreover, due to its strong static quenching effect for Fe3+, CM-ß-CD can efficiently detect Fe3+ in mixed-ion aqueous solutions. It provides a strategy to clarify the CTE mechanism of nonconventional luminogen solutions more clearly and its application of mixed-ion detection.


Assuntos
Água , beta-Ciclodextrinas , beta-Ciclodextrinas/química , Água/química , Luminescência , Íons/química , Soluções , Difração de Raios X , Espalhamento a Baixo Ângulo , Estrutura Molecular , Compostos Férricos/química
15.
Nat Commun ; 15(1): 6645, 2024 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-39103332

RESUMO

Multidomain proteins with flexible linkers and disordered regions play important roles in many cellular processes, but characterizing their conformational ensembles is difficult. We have previously shown that the coarse-grained model, Martini 3, produces too compact ensembles in solution, that may in part be remedied by strengthening protein-water interactions. Here, we show that decreasing the strength of protein-protein interactions leads to improved agreement with experimental data on a wide set of systems. We show that the 'symmetry' between rescaling protein-water and protein-protein interactions breaks down when studying interactions with or within membranes; rescaling protein-protein interactions better preserves the binding specificity of proteins with lipid membranes, whereas rescaling protein-water interactions preserves oligomerization of transmembrane helices. We conclude that decreasing the strength of protein-protein interactions improves the accuracy of Martini 3 for IDPs and multidomain proteins, both in solution and in the presence of a lipid membrane.


Assuntos
Ligação Proteica , Soluções , Água/química , Água/metabolismo , Simulação de Dinâmica Molecular , Proteínas/química , Proteínas/metabolismo , Conformação Proteica , Proteínas de Membrana/metabolismo , Proteínas de Membrana/química , Bicamadas Lipídicas/metabolismo , Bicamadas Lipídicas/química
16.
ACS Appl Mater Interfaces ; 16(32): 43016-43025, 2024 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-39088740

RESUMO

Motile droplets using Marangoni convection are attracting attention for their potential as cell-mimicking small robots. However, the motion of droplets relative to the internal and external environments that generate Marangoni convection has not been quantitatively described. In this study, we used an aqueous two-phase system [poly(ethylene glycol) (PEG) and dextran] in an elongated chamber to generate motile dextran droplets in a constant PEG concentration gradient. We demonstrated that dextran droplets move by Marangoni convection, resulting from the PEG concentration gradient and the active transport of PEG and dextran into and out of the motile dextran droplet. Furthermore, by spontaneously incorporating long DNA into the dextran droplets, we achieved cell-like motility changes controlled by coexisting environment-sensing molecules. The DNA changes its position within the droplet and motile speed in response to external conditions. In the presence of Mg2+, the coil-globule transition of DNA inside the droplet accelerates the motile speed due to the decrease in the droplet's dynamic viscosity. Globule DNA condenses at the rear part of the droplet along the convection, while coil DNA moves away from the droplet's central axis, separating the dipole convections. These results provide a blueprint for designing autonomous small robots using phase-separated droplets, which change the mobility and molecular distribution within the droplet in reaction with the environment. It will also open unexplored areas of self-assembly mechanisms through phase separation under convections, such as intracellular phase separation.


Assuntos
DNA , Dextranos , Polietilenoglicóis , Dextranos/química , Polietilenoglicóis/química , DNA/química , Viscosidade , Soluções
17.
Water Res ; 265: 122221, 2024 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-39128334

RESUMO

Low molecular weight organic acids (LMWOA) are commonly present in natural water and play a pivotal role in the reduction of Cr(VI). In frozen solutions, the efficiency of Cr(VI) reduction is significantly enhanced due to the freezing concentration effect. However, this facilitation is found to be contingent upon the functional groups of LMWOA in this study. To be specific, LMWOA and Cr(VI) can form five-membered ring complexes, which greatly enhance electron transfer efficiency through Ligand-to-Metal Charge Transfer (LMCT). DFT calculations indicate that oxygen-containing groups located on carbon atoms at α positions play a crucial role in forming these complexes, ultimately determining the kinetics of Cr(VI) reduction. Moreover, freezing not only increases proton concentrations but also reduces free water molecule content in the liquid-like layer (LLL), thereby affecting LMWOA species through regulation of protonation and hydrolysis, and subsequently impacting reaction mechanisms. The stoichiometric ratios between LMWOA and Cr(VI) exceed theoretical values due to complexation with Cr(III). The reduction of Cr(VI) by LMWOA in frozen solutions is inhibited by soil solution, while the degree of inhibition varies among different types of LMWOA.


Assuntos
Cromo , Cromo/química , Cinética , Congelamento , Peso Molecular , Oxirredução , Teoria da Densidade Funcional , Soluções
18.
Langmuir ; 40(33): 17613-17621, 2024 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-39120008

RESUMO

Dopamine (DA), a neurotransmitter, plays a crucial role in regulating motor functions and emotions and can serve as a marker for several diseases. In this study, we report a highly sensitive polydiacetylenes (PDA)-based dual-output sensor for dopamine detection in both solution and solid phases that was developed by modifying PDA liposomes with boronic acid groups at the termini. This sensor exploits the high affinity between the catechol residue of dopamine and the -B(OH)2 group of the PDA-based probe (PDA-PhBA) to form boronate ester bonds, causing a stress-induced blue-to-red color change along with a steady increase in fluorescence response at λmax 622 nm. The PDA-PhBA-based sensor displays high sensitivity toward dopamine with low limit of detection of 6.2 ppb in colorimetric analysis and 0.6 ppb in fluorimetric measurements, demonstrating its dual optical output ability. The sensor works well for adrenaline, another catecholamine, with similar efficacy. Its practical applicability was validated by the successful recovery of trace level dopamine in blood serum and real water samples. Additionally, immobilizing PDA-PhBA liposomes in sodium alginate produced PDA beads for the solid-phase detection of dopamine with an limit of detection (LOD) of 59 nM (9.0 ppb) in colorimetric detection using a smartphone for capturing images and ImageJ software for analysis.


Assuntos
Dopamina , Lipossomos , Polímero Poliacetilênico , Lipossomos/química , Dopamina/análise , Dopamina/sangue , Polímero Poliacetilênico/química , Limite de Detecção , Colorimetria/métodos , Polímeros/química , Poli-Inos/química , Soluções
19.
Anal Chem ; 96(37): 14963-14970, 2024 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-39214608

RESUMO

Solution-phase hydrogen/deuterium exchange (HDX) coupled to native ion mobility spectrometry mass spectrometry (IMS-MS) can provide complementary structural information about the conformational dynamics of biological molecules. In the present work, the solution-stable isotope labeling (SIL) combined with trapped ion mobility spectrometry (TIMS) in tandem with top-down electron capture dissociation (ECD) is illustrated for the structural characterization of the solution native states of ubiquitin. Four different ubiquitin electrospray solution conditions: (i) single-tip nondeuterated, (ii) theta tip for online SIL HDX, (iii) single-tip SIL-deuterated, and (iv) theta tip for online SIL H/D back exchange (HDbX), were investigated to assess the H/D exchange reactivities of native ubiquitin. The combination of TIMS and ECD in a q-ToF MS instrument allowed for additional inspection of gas-phase HDbX added by top-down fragmentation, revealing the exposed and protected residues with limited scrambling effects (e.g., intramolecular H/D migration). A native charge state distribution (5+ to 7+) and TIMS profiles were observed under the single-tip nondeuterated solution conditions. Mass shift distributions of ∼40, ∼104, and ∼87D were observed when incorporating deuterium for online SIL HDX, SIL HDX, and online SIL HDbX, respectively, while retaining similar conformational states. ECD fragmentation allowed for the localization of the deuterated labeled residues of the peptide fragments, with a sequence coverage of ∼90%, for each of the ubiquitin solution condition. Changes in the TIMS trapping time settings (∼70 to ∼795 ms) were used to determine the H/D back exchange dynamics of native ubiquitin. HDbX-TIMS-q-ECD-MS/MS exhibited H/D back exchanges in the six-residue C-terminal tail as well as around Lys6, Lys11, Lys33, Lys48, and Lys63 residues, indicating that these regions are the most exposed area (less protected hydrogens) of ubiquitin as compared to the rest of the core residues that adopt a compact ß-grasp fold (protected hydrogens), which was consistent with the accessible surface area of ubiquitin. The present data highlight for the first time consistency between the solution HDX and gas-phase HDbX-TIMS data for native studies.


Assuntos
Espectrometria de Mobilidade Iônica , Marcação por Isótopo , Ubiquitina , Ubiquitina/química , Medição da Troca de Deutério , Espectrometria de Massas em Tandem/métodos , Soluções , Conformação Proteica , Modelos Moleculares , Sequência de Aminoácidos
20.
Int J Biol Macromol ; 278(Pt 3): 134847, 2024 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-39168190

RESUMO

Ciprofloxacin (CIP) is one of the most widely used antibiotics to treat bacterial infections. Consequently, there is concern that it may contaminate water resources due to its high usage level. It is therefore necessary to monitor, trace, and reduce exposure to these antibiotic residues. In the current study, the extraction of CIP from water was performed using a green adsorbent material based on cellulose/polyvinyl alcohol (PVA) decorated with mixed metal oxides (MMO). This cellulose/MMO/PVA adsorbent was synthesized using a simple sol-gel method. The prepared adsorbent materials were then characterized using a range of methods, including scanning electron microscopy, energy-dispersive X-ray spectroscopy, gas adsorption analysis, X-ray diffraction, and Fourier Transform infrared. The impact of pH, adsorbent dose, contact time, and CIP concentration on ciprofloxacin extraction were examined. The equilibrium and kinetic adsorption data were well described using the Freundlich model (R2 = 0.965). The optimum conditions for CIP adsorption were: pH = 4.5; adsorbent dosage = 0.55 g·L-1; contact time = 83 min; and initial CIP concentration = 2 mg·L-1. The adsorption capacity of the cellulose/MMO/PVA adsorbent for CIP removal was ∼19 mg·g-1 (CIP removal = 86.48 %). This study shows that cellulose/MMO/PVA adsorbents have potential for removing contaminants from aqueous environments.


Assuntos
Celulose , Ciprofloxacina , Poluentes Químicos da Água , Purificação da Água , Ciprofloxacina/química , Ciprofloxacina/isolamento & purificação , Celulose/química , Adsorção , Poluentes Químicos da Água/química , Poluentes Químicos da Água/isolamento & purificação , Purificação da Água/métodos , Cinética , Concentração de Íons de Hidrogênio , Água/química , Álcool de Polivinil/química , Transição de Fase , Soluções , Espectroscopia de Infravermelho com Transformada de Fourier
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