Grotthuss Molecular Dynamics Simulations for Modeling Proton Hopping in Electrosprayed Water Droplets

Structural, Functional and Molecular Dynamics Examination of a de novo cloned Otopetrin-like Proton Channel in crayfish

Proton channels play a crucial role in many biological functions, as they are responsible for the selective transport of protons across cell membranes. Recently, Otopetrins, a family of eukaryotic proton-selective ion channels, have attracted significant attention due to their diverse physiological roles. Despite the importance of Otopetrins, their structural and functional properties remain relatively unexplored. As a model organism, crayfish have been extensively studied to gain insights into the functioning of the nervous system. These studies cover a wide range of aspects, including the properties of individual neurons and behavioral science. However, studying the physiological systems of crayfish poses challenges for molecular research due to limited molecular sequence information available for these organisms. In the present work was identified an originally cloned mRNA, coding an Otopetrin like proton channel in the crayfish. The coded protein was modeled in silico and possible conduction mechanisms and pathways were revealed. A plasmid of the cloned mRNA was heterologously expressed in HEK293T cells. Functional experiments on transfected cells indicated that the expressed mRNA was coupled to proton conduction across the cell membrane.

Flexible Humidity Sensor Based on a Graphene Oxide-Carbon Nanotube-Modified Co3O4 Nanoparticle-Embedded Laser-Induced Graphene Electrode

To meet evolving humidity monitoring needs, the development of flexible, high-performance humidity sensors is crucial. This study introduces an innovative flexible humidity sensor using a single-step laser scribing technique to fabricate a flexible in situ Co3O4 nanoparticle-embedded laser-induced graphene (Co3O4-LIG) composite electrode. Compared to conventional LIG electrodes, the Co3O4-LIG electrode exhibits improved conductivity and hydrophilicity, enhancing charge transfer and water molecule affinity. The unique two-dimensional structure and exceptional water permeability of graphene oxide (GO) combine with the rapid water response and high specific surface area of carboxylated multiwalled carbon nanotubes (MWCNTs), thereby assuming a crucial function in the modification and optimization of the performance of humidity sensors. Through the application of a homogenously blended aqueous solution comprising GO and MWCNTs in precise proportions onto the Co3O4-LIG composite electrode, an excellent humidity-responsive layer is established, culminating in the realization of a cutting-edge GO-MWCNTs@Co3O4-LIG flexible humidity sensor. Noteworthy attributes of this sensor include a heightened sensitivity [959.1% (ΔR/R0)], rapid response and recovery times (within 5 and 26 s, respectively), and a noteworthy linearity (R2 = 0.994) across a relative humidity range of 14 to 95%. The findings presented herein offer valuable insights and a practical blueprint for the design and production of flexible humidity sensors.

MD Simulations of Peptide-Containing Electrospray Droplets: Effects of Parameter Settings on the Predicted Mechanisms of Gas Phase Ion Formation

Electrospray ionization (ESI) mass spectrometry is widely used for interrogating peptides, proteins, and other biomolecular analytes. A growing number of laboratories use molecular dynamics (MD) simulations for uncovering ESI mechanisms by modeling the behavior of highly charged nanodroplets. The outcome of any MD simulation depends on certain assumptions and parameter settings, and it is desirable to optimize these factors by benchmarking computational data against experiments. Unfortunately, benchmarking of ESI simulations is difficult because experimentally generated gaseous ions do not generally retain any features that would reveal their formation pathway [e.g., the charged residue mechanism (CRM) or the ion evaporation mechanism (IEM)]. Here, we tackle this problem by examining the effects of various MD settings on the ESI behavior of the 9-residue peptide bradykinin in acidic aqueous droplets. Several parameters were found to significantly affect the kinetic competition between peptide IEM and CRM. By systematically probing the droplet behavior, we uncovered problems associated with certain settings, including peptide/solvent temperature imbalances, unexpected peptide deceleration during IEM, and a dependence of the ESI mechanism on the water model. We also noted different simulation outcomes for different force fields. On the basis of comprehensive tests, we propose a set of "best practice" parameter settings for MD simulations of ESI droplets. The strategies used here should be transferable to other types of droplet simulations, paving the way toward a more solid understanding of ESI mechanisms.

Molecular Dynamics Simulations of Native Protein Charging via Proton Transfer during Electrospray Ionization with Grotthuss Diffuse H3O. Anal Chem 2024;96:4146-4153. [PMID: 38427846 PMCID: PMC11337394 DOI: 10.1021/acs.analchem.3c05089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Unraveling the mechanism by which native proteins are charged through electrospray ionization (ESI) has been the focus of considerable research because observable charge states can be correlated to biophysical characteristics, such as protein folding and, thus, solution conformation. Difficulties in characterizing electrosprayed droplets have catalyzed the use of molecular dynamics (MD) to provide insights into the mechanisms by which proteins are charged and transferred to the gas phase. However, prior MD studies have utilized metal ions, primarily Na+, as charge carriers, even though proteins are primarily detected as protonated ions in the mass spectra. Here, we propose a modified MD protocol for simulating discrete Grotthuss diffuse H3O+ that is capable of dynamically altering amino-acid protonation states to model electrospray charging and gaseous ion formation of model proteins, ubiquitin, and myoglobin. Application of the protocol to the evaporation of acidic droplets enables a molecular perspective of H3O+ coordination and proton transfer to/from proteins, which is unfeasible with the metal charge carriers used in previous MD studies of ESI. Our protocol recreates experimentally observed charge-state distributions and supports the charge residue model (CRM) as the dominant mechanism of native protein ionization during ESI. Additionally, our results suggest that protonation is highly specific to individual residues and is correlated to the formation of localized hydrated regions on the protein surface as droplets desolvate. Considering the use of discrete H3O+ instead of Na+, the developed protocol is a necessary step toward developing a more comprehensive model of protein ionization during ESI.

Mechanism for Generating H2 O2 at Water-Solid Interface by Contact-Electrification

The recent intensification of the study of contact-electrification at water-solid interfaces and its role in physicochemical processes lead to the realization that electron transfers during water-solid contact-electrification can drive chemical reactions. This mechanism, named contact-electro-catalysis (CEC), allows chemically inert fluorinated polymers to act like single electrode electrochemical systems. This study shows hydrogen peroxide (H2 O2 ) is generated from air and deionized water, by ultrasound driven CEC, using fluorinated ethylene propylene (FEP) as the catalyst. For a mass ratio of catalyst to solution of 1:10000, at 20 °C, the kinetic rate of H2 O2 evolution reaches 58.87 mmol L-1  gcat -1  h-1 . Electron paramagnetic resonance (EPR) shows electrons are emitted in the solution by the charged FEP, during ultrasonication. EPR and isotope labelling experiments show H2 O2 is formed from hydroxyl radicals (HO• ) or two superoxide radicals (O2 •- ) generated by CEC. Finally, it is traditionally believed such radicals migrate in the solution by Brownian diffusion prior to reactions. However, ab-initio molecular dynamic calculations reveal the radicals can react by exchanging protons and electrons through the hydrogen bonds network of water, i.e., owing to the Grotthuss mechanism. This mechanism can be relevant to other systems, artificial or natural, generating H2 O2 from air and water.

On the Rich Chemistry of Pseudo-Protic Ionic Liquid Electrolytes

Mixing weak acids and bases can produce highly complicated binary mixtures, called pseudo-protic ionic liquids, in which a complex network of effects determines the physicochemical properties that are currently impossible to predict. In this joint computational-experimental study, we investigated 1-methylimidazole-acetic acid mixtures through the whole concentration range. Effects of the varying ionization and excess of either components on the properties, such as density, diffusion coefficients, and overall hydrogen bonding structure were uncovered. A special emphasis was put on understanding the multiple factors that govern the conductivity of the system. In the presence of an excess of acetic acid, the 1-methylimidazolium acetate ion pairs dissociate more efficiently, resulting in a higher concentration of independently moving, conducting ions. However, the conductivity measurements showed that higher concentrations of acetic acid improve the conductivity beyond this effect, suggesting in addition to standard dilution effects the occurrence of Grotthuss diffusion in high acid-to-base ratios. The results here will potentially help designing novel electrolytes and proton conducting systems, which can be exploited in a variety of applications.

Comparison of classical and ab initio simulations of hydronium and aqueous proton transfer

Proton transport in aqueous systems occurs by making and breaking covalent bonds, a process that classical force fields cannot reproduce. Various attempts have been made to remedy this deficiency, by valence bond theory or instantaneous proton transfers, but the ability of such methods to provide a realistic picture of this fundamental process has not been fully evaluated. Here we compare an ab initio molecular dynamics (AIMD) simulation of an excess proton in water to a simulation of a classical H3O+ in TIP3P water. The energy gap upon instantaneous proton transfer from H3O+ to an acceptor water molecule is much higher in the classical simulation than in the AIMD configurations evaluated with the same classical potential. The origins of this discrepancy are identified by comparing the solvent structures around the excess proton in the two systems. One major structural difference is in the tilt angle of the water molecules that accept an hydrogen bond from H3O+. The lack of lone pairs in TIP3P produces a tilt angle that is too large and generates an unfavorable geometry after instantaneous proton transfer. This problem can be alleviated by the use of TIP5P, which gives a tilt angle much closer to the AIMD result. Another important factor that raises the energy gap is the different optimal distance in water-water vs H3O+-water H-bonds. In AIMD the acceptor is gradually polarized and takes a hydronium-like configuration even before proton transfer actually happens. Ways to remedy some of these problems in classical simulations are discussed.

On the Chemistry of Aqueous Ammonium Acetate Droplets during Native Electrospray Ionization Mass Spectrometry

Ammonium acetate (NH4Ac) is a widely used solvent additive in native electrospray ionization (ESI) mass spectrometry. NH4Ac can undergo proton transfer to form ammonia and acetic acid (NH4+ + Ac- → NH3 + HAc). The volatility of these products ensures that electrosprayed ions are free of undesired adducts. NH4Ac dissolution in water yields pH 7, providing "physiological" conditions. However, NH4Ac is not a buffer at pH 7 because NH4+ and Ac- are not a conjugate acid/base pair (Konermann, L. J. Am. Soc. Mass Spectrom. 2017, 28, 1827-1835.). In native ESI, it is desirable that analytes experience physiological conditions not only in bulk solution but also while they reside in ESI droplets. Little is known about the internal milieu of NH4Ac-containing ESI droplets. The current work explored the acid/base chemistry of such droplets, starting from a pH 7 analyte solution. We used a two-pronged approach involving evaporation experiments on bulk solutions under ESI-mimicking conditions, as well as molecular dynamics simulations using a newly developed algorithm that allows for proton transfer. Our results reveal that during droplet formation at the tip of the Taylor cone, electrolytically generated protons get neutralized by Ac-, making NH4+ the net charge carriers in the weakly acidic nascent droplets. During the subsequent evaporation, the droplets lose water as well as NH3 and HAc that were generated by proton transfer. NH3 departs more quickly because of its greater volatility, causing the accumulation of HAc. Together with residual Ac-, these HAc molecules form an acetate buffer that stabilizes the average droplet pH at 5.4 ± 0.1, as governed by the Henderson-Hasselbalch equation. The remarkable success of native ESI investigations in the literature implies that this pH drop by ∼1.6 units relative to the initially neutral analyte solution can be tolerated by most biomolecular analytes on the short time scale of the ESI process.

Inter-Domain Repulsion of Dumbbell-Shaped Calmodulin during Electrospray Ionization Revealed by Molecular Dynamics Simulations

The mechanisms whereby protein ions are released from nanodroplets at the liquid-gas interface have continued to be controversial since electrospray ionization (ESI) mass spectrometry was widely applied in biomolecular structure analysis in solution. Several viable pathways have been proposed and verified for single-domain proteins. However, the ESI mechanism of multi-domain proteins with more complicated and flexible structures remains unclear. Herein, dumbbell-shaped calmodulin was chosen as a multi-domain protein model to perform molecular dynamics simulations to investigate the structural evolution during the ESI process. For [Ca₄CAM], the protein followed the classical charge residue model. As the inter-domain electrostatic repulsion increased, the droplet was found to split into two sub-droplets, while stronger-repulsive apo-calmodulin unfolded during the early evaporation stage. We designated this novel ESI mechanism as the domain repulsion model, which provides new mechanistic insights into further exploration of proteins containing more domains. Our results suggest that greater attention should be paid to the effect of domain-domain interactions on structure retention during liquid-gas interface transfer when mass spectrometry is used as the developing technique in gas phase structural biology.

An Approach for the Optimization of Thermal Conductivity and Viscosity of Hybrid (Graphene Nanoplatelets, GNPs: Cellulose Nanocrystal, CNC) Nanofluids Using Response Surface Methodology (RSM)

Response surface methodology (RSM) is used in this study to optimize the thermal characteristics of single graphene nanoplatelets and hybrid nanofluids utilizing the miscellaneous design model. The nanofluids comprise graphene nanoplatelets and graphene nanoplatelets/cellulose nanocrystal nanoparticles in the base fluid of ethylene glycol and water (60:40). Using response surface methodology (RSM) based on central composite design (CCD) and mini tab 20 standard statistical software, the impact of temperature, volume concentration, and type of nanofluid is used to construct an empirical mathematical formula. Analysis of variance (ANOVA) is applied to determine that the developed empirical mathematical analysis is relevant. For the purpose of developing the equations, 32 experiments are conducted for second-order polynomial to the specified outputs such as thermal conductivity and viscosity. Predicted estimates and the experimental data are found to be in reasonable arrangement. In additional words, the models could expect more than 85% of thermal conductivity and viscosity fluctuations of the nanofluid, indicating that the model is accurate. Optimal thermal conductivity and viscosity values are 0.4962 W/m-K and 2.6191 cP, respectively, from the results of the optimization plot. The critical parameters are 50 °C, 0.0254%, and the category factorial is GNP/CNC, and the relevant parameters are volume concentration, temperature, and kind of nanofluid. From the results plot, the composite is 0.8371. The validation results of the model during testing indicate the capability of predicting the optimal experimental conditions.

Structural Characterization of Dendriplexes In Vacuo: A Joint Ion Mobility/Molecular Dynamics Investigation

The combination between ion mobility mass spectrometry and molecular dynamics simulations is demonstrated for the first time to afford valuable information on structural changes undergone by dendriplexes containing ds-DNA and low-generation dendrimers when transferred from the solution to the gas phase. Dendriplex ions presenting 1:1 and 2:1 stoichiometries are identified using mass spectrometry experiments, and the collision cross sections (CCS) of the 1:1 ions are measured using drift time ion mobility experiments. Structural predictions using Molecular Dynamics (MD) simulations showed that gas-phase relevant structures, i.e., with a good match between the experimental and theoretical CCS, are generated when the global electrospray process is simulated, including the solvent molecule evaporation, rather than abruptly transferring the ions from the solution to the gas phase. The progressive migration of ammonium groups (either NH₄⁺ from the buffer or protonated amines of the dendrimer) into the minor and major grooves of DNA all along the evaporation processes is shown to compact the DNA structure by electrostatic and hydrogen-bond interactions. The subsequent proton transfer from the ammonium (NH₄⁺ or protonated amino groups) to the DNA phosphate groups allows creation of protonated phosphate/phosphate hydrogen bonds within the compact structures. MD simulations showed major structural differences between the dendriplexes in solution and in the gas phase, not only due to the loss of the solvent but also due to the proton transfers and the huge difference between the solution and gas-phase charge states.