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1.
J Colloid Interface Sci ; 675: 451-460, 2024 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-38981254

RESUMEN

HYPOTHESIS: Ice friction plays a crucial role in both basic study and practical use. Various strategies for controlling ice friction have been developed. However, one unsolved puzzle regarding ice friction is the effect of ion-ice interplay on its tribological properties. EXPERIMENTS AND SIMULATIONS: Here, we conducted ice friction experiments and summarized the specific effects of hydrated ions on ice friction. By selecting cations and anions, the coefficient of ice friction can be reduced by more than 70 percent. Experimental spectra, low-field nuclear magnetic resonance (LF-NMR), density functional theory (DFT) calculations, and Molecular dynamics (MD) simulations demonstrated that the addition of ions could break the H-bonds in water. FINDINGS: The link between the charge density of ions and the coefficients of ice friction was revealed. A part of the ice structure was changed from an ice-like to a liquid-like interfacial water structure with the addition of ions. Lower charge density ions led to weaker ionic forces with the water molecules in the immobilized water layer, resulting in free water molecules increasing in the lubricating layer. This study provides guidance for preparing ice-making solutions with low friction coefficients and a fuller understanding of the interfacial water structure at low temperatures.

2.
Angew Chem Int Ed Engl ; : e202406888, 2024 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-39007540

RESUMEN

Transition metal/p-block compounds are regarded as the most essential materials for electrochemical energy converting systems involving various electrocatalysis. Understanding the role of p-block element on the interaction of key intermediates and interfacial water molecule orientation at the polarized catalyst-electrolyte interface during the electrocatalysis is important for rational designing advanced p-block modified metal electrocatalysts. Herein, taking a sequence of ruthenium phosphides (including Ru2P, RuP and RuP2) as model catalysts, we establish a volcanic-relation between P-proportion and alkaline hydrogen oxidation reaction (HOR) activity. The dominant role of P for regulating hydroxyl binding energy is validated by active sites poisoning experiments, pH-dependent infection-point behavior, in situ surface enhanced absorption spectroscopy, and density functional theory calculations, in which P could tailor the d-band structure of Ru, optimize the hydroxyl adsorption sites across the Ru-P moieties, thereby leading to improved proportion of strongly hydrogen-bonded water and facilitated proton-coupled electron transfer process, which are responsible for the enhanced alkaline HOR performance.

3.
Spectrochim Acta A Mol Biomol Spectrosc ; 322: 124790, 2024 Dec 05.
Artículo en Inglés | MEDLINE | ID: mdl-38981286

RESUMEN

Interactions of water and chemical or bio-compound have a universal concern and have been extensively studied. For spectroscopic analysis, the complexity and the low resolution of the spectra make it difficult to obtain the spectral features showing the interactions. In this work, the structures and interactions in gaseous water and water-alcohol mixtures were studied using high-resolution infrared (HR-IR) spectroscopy. The spectral features of water clusters of different sizes, including dimer, trimer, tetramer and pentamer, were observed from the measured spectra of the samples in different volume concentrations, and the interactions of water and methanol/ethanol in the mixtures were obtained. In the analysis, a method based on principal component analysis was used to separate the overlapping spectra. In water-alcohol mixtures, when water is less, water molecules tend to interact with the OH groups on the exterior of the alcohol aggregate, and with the increase of water, a water cage forms around the aggregates. Furthermore, the ratio of the molecule number of methanol in the aggregate to that of water in the cage is around 1:2.3, and the ratio for ethanol is about 1:3.2.

4.
Appl Spectrosc ; : 37028241261097, 2024 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-38881287

RESUMEN

This paper describes an approach based on the method of terahertz time-domain spectroscopy, which allows the analysis of dynamical hydration shells of proteins with a thickness of 1-2 nm. Using the example of bovine serum albumin in three conformations, it is shown that the hydration shells of the protein are characterized by increased binding of water molecules in the primary hydration layers, and in more distant areas of hydration, on the contrary, the water structure is somewhat destroyed. The fraction of free or weakly bound molecules, usually observed in the structure of liquid water in hydration shells, become more numerous but its average binding is greater than in undisturbed water. The energy distribution of hydrogen bonds in hydration shells is narrowed compared to undisturbed water. All these manifestations of hydration are most pronounced for the native conformation of the protein. Also, the hydration shells of the native protein are characterized by a smaller number of hydrogen bonds and a tendency to decrease their average energy compared to non-native conformations. The fact of a pronounced peculiarity of the hydration shells of the protein in the native conformation has been noted for different proteins before. However, the methodological approach used in this work for the first time allowed this peculiarity to be described by specific parameters of the intermolecular structure and dynamics of water.

5.
Chemphyschem ; 25(12): e202400077, 2024 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-38709643

RESUMEN

The UV/Vis absorption energies νmax of Reichardt's dye B30 with respect to ET(30) and 4-nitroaniline (NA) are investigated as a function of the solvent composition Nav,z. in co-solvent/water mixtures. Nav,z. is the average molar concentration of the solvent mixture at a given solvent fraction z. The z can be the mole, the volume or the mass fraction. The co-solvents considered were acetonitrile, acetone, tetrahydrofuran, pyridine, piperidine and 2-(diethylamino)-ethanol. Acetone and acetonitrile can be expected to slightly enhance the water structure at low co-solvent concentrations. This interpretation is supported by the analysis of the refractive index as a function of the solvent composition. In general, it can be stated that the structural complexity of the binary solvent mixtures is mainly responsible for the evolution of the absorption energies ET(30) or νmax(NA) as a function of the mixture composition. In particular, the endothermic solvation of NA in co-solvent/water mixtures and its effect on the νmax(NA) is highlighted.

6.
Biosystems ; 240: 105213, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38616011

RESUMEN

The central problem in transduction is to explain how the energy caught from sunlight by chloroplasts becomes biological work. Or to express it in different terms: how does the energy remain trapped in the biological network and not get lost through thermalization into the environment? The pathway consists of an immensely large number of steps crossing hierarchical levels - some upwards, to larger assemblies, others downwards into energy rich molecules - before fuelling an action potential or a contracting cell. Accepting the assumption that steps are executed by protein domains, we expect that transduction mechanisms are the result of conformational changes, which in turn involve rearrangements of the bonds responsible for the protein fold. But why are these essential changes so difficult to detect? In this presentation, the metabolic pathway is viewed as equivalent to an energy conduit composed of equally sized units - the protein domains - rather than a row of catalysts. The flow of energy through them occurs by the same mechanism as through the cytoplasmic medium (water). This mechanism is based on the cluster-wave model of water structure, which successfully explains the transfer of energy through the liquid medium responsible for the build up of osmotic pressure. The analogy to the line of balls called "Newton's cradle" provides a useful comparison, since there the transfer is also invisible to us because the intermediate balls are motionless. It is further proposed that the spatial arrangements of the H-bonds of the α and ß secondary structures support wave motion, with the linear and lateral forms of the groups of bonds belonging to the helices and sheets executing the longitudinal and transverse modes, respectively.


Asunto(s)
Transferencia de Energía , Transferencia de Energía/fisiología , Modelos Biológicos , Metabolismo Energético/fisiología , Humanos , Agua/metabolismo
7.
J Biomater Sci Polym Ed ; 35(8): 1258-1272, 2024 06.
Artículo en Inglés | MEDLINE | ID: mdl-38457333

RESUMEN

Recently, we applied solution 2H-nuclear magnetic resonance spectroscopy (2H NMR) to analyze the water (deuterium oxide, D2O) structure in several biopolymers at ambient temperature. We established that polymers with good blood compatibility (i.e. poly(2-methoxyethyl acrylate) (PMEA)) have water observed at high magnetic fields (upfield) compared with bulk water. Polymers containing poly(propylene glycol) (PPG) or poly(propylene oxide) (PPO) exhibit good compatibility; however, the reason for this remains unclear. In addition, reports on the blood compatibility of PPO/PPG are limited. Therefore, PPG diester (PPGest) was prepared as a model polymer, and its blood compatibility and water structure were investigated. PPGest exhibited excellent blood compatibility. The water in PPGest was observed upfield by 2H NMR, and it was defined as non-freezing water via differential scanning calorimetry. Based on these observations, the relationship between the blood compatibility and water structure of PPGest is discussed by comparing with those of PMEA, and the reason for the good performance of PPG/PPO-based polymers is discussed.


Asunto(s)
Rastreo Diferencial de Calorimetría , Espectroscopía de Resonancia Magnética , Glicoles de Propileno , Agua , Glicoles de Propileno/química , Agua/química , Humanos , Materiales Biocompatibles/química , Ensayo de Materiales , Polímeros/química , Animales
8.
ACS Appl Mater Interfaces ; 16(1): 1416-1427, 2024 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-38149814

RESUMEN

Preventing metal corrosion has usually been associated with water-repellent coatings that inhibit the penetration of aggressive chloride ions. Contrary to this conventional wisdom, we engineered ultrathin superhydrophilic zwitterionic hydrogel brushes rooted in a nanoporous anodic aluminum oxide (AAO) substrate that effectively hampered the adsorption of hydrated chloride ions (Cl-·H2O) on the Al alloy surface. The hydrogel brush coating enhanced corrosion resistance by 3 orders of magnitude, with corrosion current density declining from 1.518 to 1.567 × 10-3 µA cm-2. Despite suffering from long-term salt-spaying tests, zwitterionic hydrogel brush coating retained 2 orders of magnitude of corrosion resistance. Direct Raman spectroscopic evidence manifested that interfacial water comprised both highly ordered hydrogen-bonded water and disordered water containing hydrated Cl- ions. Under the hydration effect of zwitterionic hydrogel brushes, an interfacial disordered water structure dynamically transformed into a hydrogen-bonded water film. We correlated the structure and quantities of interfacial water with the corrosion current density and chloride adsorption. Hydrogen-bonded water improved by zwitterionic hydrogel brushes weakened the affinity and adsorption of hydrated Cl- ion water on the oxide film, resulting in excellent corrosion protection. Therefore, employing localized hydration tuning strategies, these findings are anticipated to generally empower ordered interfacial water to enhance metal corrosion resistance through precise interfacial engineering.

9.
J Phys Condens Matter ; 36(10)2023 Dec 04.
Artículo en Inglés | MEDLINE | ID: mdl-37988750

RESUMEN

The change induced in the physicochemical properties of polymer while hosting ions provides a platform for studying its potential applications in electrochemical devices, water treatment plants, and materials engineering science. The ability to host ions is limited in very few polymers, which lack a detailed molecular-level understanding for showcasing the polymer-ion linkage behavior at the interfacial region. In the present manuscript, we have employed sum frequency generation (SFG) vibrational spectroscopy to investigate the interfacial structure of a new class phosphazene-based methoxyethoxyethoxyphosphazene (MEEP) polymer in the presence of lithium chloride salt at the air-aqueous interface. The interfacial aspects of the molecular system collected through SFG spectral signatures reveal enhanced water ordering and relative hydrogen bonding strength at the air-aqueous interface. The careful observation of the study finds a synchronous contribution of van der Waals and electrostatic forces in facilitating changes in the interfacial water structure that are susceptible to MEEP concentration in the presence of ions. The observation indicates that dilute MEEP concentrations support the role of electrostatic interaction, leading to an ordered water structure in proximity to diffused ions at the interfacial region. Conversely, higher MEEP concentrations promote the dominance of van der Waals interactions at the air-aqueous interface. Our study highlights the establishment of polymer electrolyte (PE) characteristics mediated by intermolecular interactions, as observed through the spectral signatures witnessed at the air-aqueous interface. The investigation illustrates the polymer-ion linkage adsorption effects at the interfacial region, which explains the macroscopic changes observed from the cyclic voltammetry studies. The fundamental findings from our studies can be helpful in the design and fine-tuning of better PE systems that can offer improved hydrophobic membranes and interface stability for use in electrochemical-based power sources.

10.
Biophys Rev ; 15(5): 833-849, 2023 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-37974994

RESUMEN

The hydration of biomolecules is one of the fundamental processes underlying the construction of living matter. The formation of the native conformation of most biomolecules is possible only in an aqueous environment. At the same time, not only water affects the structure of biomolecules, but also biomolecules affect the structure of water, forming hydration shells. However, the study of the structure of biomolecules is given much more attention than their hydration shells. A real breakthrough in the study of hydration occurred with the development of the THz spectroscopy method, which showed that the hydration shell of biomolecules is not limited to 1-2 layers of strongly bound water, but also includes more distant areas of hydration with altered molecular dynamics. This review examines the fundamental features of the THz frequency range as a source of information about the structural and dynamic characteristics of water that change during hydration. The applied approaches to the study of hydration shells of biomolecules based on THz spectroscopy are described. The data on the hydration of biomolecules of all main types obtained from the beginning of the application of THz spectroscopy to the present are summarized. The emphasis is placed on the possible participation of extended hydration shells in the realization of the biological functions of biomolecules and at the same time on the insufficient knowledge of their structural and dynamic characteristics.

11.
Biophys Rev ; 15(4): 639-660, 2023 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-37681097

RESUMEN

Under macromolecular crowding (MC) conditions such as cellular, extracellular, food and other environments of biotechnological interest, the thermodynamic activity of the different macromolecules present in the system is several orders of magnitude higher than in dilute solutions. In this state, the diffusion rates are affected by the volume exclusion induced by the crowders. Immiscible liquid phases, which may arise in MC by liquid-liquid phase separation, may induce a dynamic confinement of reactants, products and/or enzymes, tuning reaction rates. In cellular environments and other crowding conditions, membranes and macromolecules provide, on the whole, large surfaces that can perturb the solvent, causing its immobilisation by adsorption in the short range and also affecting the solvent viscosity in the long range. The latter phenomenon can affect the conformation of a protein and/or the degree of association of its protomers and, consequently, its activity. Changes in the water structure can also alter the enzyme-substrate interaction, and, in the case of hydrolytic enzymes, where water is one of the substrates, it also affects the reaction mechanism. Here, we review the evidence for how macromolecular crowding affects the catalysis induced by hydrolytic enzymes, focusing on the structure and dynamics of water.

12.
Biology (Basel) ; 12(9)2023 Sep 18.
Artículo en Inglés | MEDLINE | ID: mdl-37759649

RESUMEN

Living bodies comprise approximately 55-75% water to maintain homeostasis. However, little is known about the comprehensive differences in in vivo water molecule dynamics (water structure dynamics; WSD) between physiological and pathophysiological statuses. Here, we examined the WSD of ex vivo tumor tissues and organs from tumor-bearing mice with engrafted mouse malignant melanoma cells (B16-F10) in the right flanks to compare with those in healthy mice, using time domain reflectometry of dielectric spectroscopy at days 9, 11, and 14 after engrafting. The relaxation parameters of relaxation time (τ), relaxation time distribution parameter (ß), and relaxation strength (∆ε) were measured on tumor tissues and lung, liver, kidney, and skin tissues. Immediately afterward, the water contents (%) in the tumor and the other organs were calculated by measuring their weights before and after freeze-drying. Each parameter of the tumor was compared to that of pooled values of other organs in tumor-bearing (TO) and healthy mice (HO). The tumor water content temporarily increased compared to that of HO at day 11; the tumor volume was also prone to increase. In contrast, tumor tissues exhibited significantly higher values of ß close to 1 of ultrapure water and ∆ε compared to TO and HO at all times. Moreover, ß in the viscera of TO was prone to increase compared to that of HO with significantly higher levels at day 11. Conclusively, tumor-bearing mice exhibited systemically aberrant WSD, unlike healthy mice. Thus, dielectric spectroscopy in terms of WSD may provide novel pathophysiological perspectives in tumor-bearing living bodies.

13.
Appl Spectrosc ; 77(9): 1087-1094, 2023 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-37415528

RESUMEN

In this study, we evaluated the state of water by performing infrared (IR) spectroscopic analysis in the 4000-100 cm-1 region. The effects of ions on the structure of water molecules were investigated by analyzing specific IR bands of salt solutions in the 1000-100 cm-1 region. Chloride solutions of Li, Na, K, Cs, Ba, and Ca were prepared at different concentrations, and their IR spectra were recorded by the attenuated total reflection method. The isosbestic point was observed in the 1000-100 cm-1 region, and the position was related to the ratio of the Stokes radius and effective ionic radius of each ion. Two bands were identified at around 660 and 400 cm-1 by curve fitting, and the intensity ratio increased linearly with a decrease in water activity. Thus, this demonstrates the potential of the 1000-100 cm-1 region as a marker for the evaluation of water structure subjected to ions. Moreover, it is possible to evaluate different states of water simultaneously by combining this with the band in the 4000-3000 cm-1 region. These results successfully demonstrate the effectiveness of the spectra in the 1000-100 cm-1 region to evaluate the state of water in ionic solutions.

14.
Angew Chem Int Ed Engl ; 62(34): e202307303, 2023 Aug 21.
Artículo en Inglés | MEDLINE | ID: mdl-37329231

RESUMEN

In the past, the design of efficient electrocatalyst materials for alkaline hydrogen evolution reaction (HER) was mostly focused on tuning the adsorption properties of reaction intermediates. A recent breakthrough shows that the performance can be improved by manipulating water structure at the electrode-electrolyte interface using atomically localized electric fields. The new approach was realized by using IrRu dizygotic single-atom sites and led to a significantly accelerated water dissociation and an overall improved alkaline HER performance. Supported by extensive data from advanced modeling, characterization, and electrochemical measurements, the work delivers an intricate examination of the interaction between water molecules and the catalyst surface, thereby enriching our understanding of water dissociation kinetics and offering new insights to boost overall alkaline HER efficiency.

15.
J Phys Condens Matter ; 35(39)2023 Jun 29.
Artículo en Inglés | MEDLINE | ID: mdl-37339659

RESUMEN

An in-depth understanding of liquid-liquid phase transition (LLPT) in condensed water will gain insight into anomalous behaviors of dual-amorphous condensed water. Despite numerous experimental, molecular simulation, and theoretical studies, it is yet to achieve a widely accepted consensus with convinced evidence in the condensed matter physics for two-state liquid-liquid transition of water. In this work, a theoretical model is proposed based on the Avrami equation, commonly used to describe first-order phase transitions, to elucidate complex homogeneous and inhomogeneous condensation from high-density liquid (HDL) water to low-density liquid (LDL) water for both pure and ionic dual-amorphous condensed water. This model unifies the coupling effects of temperature and electrolyte concentration based on the new theoretical framework. The Adam-Gibbs theory is then introduced to characterize the synergistic motion and relaxation behavior of condensed water. Variations in the configurational entropy under electrostatic forces are further explored, and an analytical 2D cloud chart is developed to visualize the synergistic effect of temperature and electrolyte concentration on the configurational entropy of ionic water. The constitutive relationships among viscosity, temperature, and electrolyte concentration are derived to analyze their synergistic effects under different condensation fractions of LDL and HDL. The Stokes-Einstein relation and free volume theory are further used to analyze diffusion coefficients and densities (or apparent density) during both pure and ionic LLPT. Finally, theoretical results obtained from these models are compared with experimental results reported in literature to validate the accuracy and applicability of the proposed models, which offer significant benefits and advancements in effectively predicting physical property changes of dual-amorphous condensed water.

16.
Gels ; 9(4)2023 Apr 14.
Artículo en Inglés | MEDLINE | ID: mdl-37102945

RESUMEN

This study investigated the performance of novel hydrogels based on poly (N-vinylformamide) (PNVF), copolymers of NVF with N-hydroxyethyl acrylamide (HEA) (P(NVF-co-HEA)), and 2-carboxyethyl acrylate (CEA) (P(NVF-co-CEA)), which were synthesized by photopolymerization using a UVLED light source. The hydrogels were analyzed for important properties such as equilibrium water content (%EWC), contact angle, freezing and non-freezing water, and diffusion-based in vitro release. The results showed that PNVF had an extremely high %EWC of 94.57%, while a decreasing NVF content in the copolymer hydrogels led to a decrease in water content with a linear relationship with HEA or CEA content. Water structuring in the hydrogels showed appreciably more variance, with ratios of free to bound water differing from 16.7:1 (NVF) to 1.3:1 (CEA), corresponding to PNVF having ~67 water molecules per repeat unit. The release studies of different dye molecules followed Higuchi's model, with the amount of dye released from the hydrogels depending on the amount of free water and the structural interactions between the polymer and the molecule being released. The results suggest that PNVF copolymer hydrogels have potential for controlled drug delivery by altering the polymer composition to govern the amount and ratio of free to bound water contained in the hydrogels.

17.
Spectrochim Acta A Mol Biomol Spectrosc ; 296: 122605, 2023 Aug 05.
Artículo en Inglés | MEDLINE | ID: mdl-37004424

RESUMEN

Insights into the solute-induced water structural transformations are essential to understand the role of water in biological and chemical reaction processes. Herein, the structural changes in water induced by amphiphilic organic molecules were investigated using concentration-dependent derivative Raman spectroscopy (DRS) combined with two-dimensional Raman correlation spectroscopy (2D Raman-COS). We shall restrict our attention in this work to binary mixtures of water with dimethyl sulfoxide (DMSO), acetone, and isopropanol (IPA), all of which have similar chemical structures. The spectral changes in O:H and OH stretching modes illustrate that the solute molecules induce an enhancement of the water structure in dilute solutions, where the enhanced degree of water structure is closely related to the size of the dipole moment of organic molecules. In addition, the transformations of solute-induced water-specific structures were evaluated by 2D Raman-COS, which shows that the strong hydrogen bond (H-bond) structure of water is more sensitive to organic molecules and induces a transition to the weak H-bond structure of water.

18.
ACS Appl Mater Interfaces ; 15(6): 8676-8690, 2023 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-36734329

RESUMEN

Novel brush coatings were fabricated with glass surface-grafted chains copolymerized using surface-initiated atom transfer radical polymerization (SI-ATRP) from 2-(2-methoxyethoxy)ethyl methacrylate (OEGMA188) and acrylamide (AAm), taken in different proportions. P(OEGMA188-co-AAm) brushes with AAm mole fraction >44% (determined with XPS and TOF-SIMS spectroscopy) and nearly constant with the depth copolymer composition (TOF-SIMS profiling) exhibit unusual temperature-induced transformations: The contact angle of water droplets on P(OEGMA188-co-AAm) coatings increases by ∼45° with temperature, compared to 17-18° for POEGMA188 and PAAm. The thickness of coatings immersed in water and the morphology of coatings imaged in air show a temperature response for POEGMA188 (using reflectance spectroscopy and AFM, respectively), but this response is weak for P(OEGMA188-co-AAm) and absent for PAAm. This suggests mechanisms more complex than a simple transition between hydrated loose coils and hydrophobic collapsed chains. For POEGMA188, the hydrogen bonds between the ether oxygens of poly(ethylene glycol) and water hydrogens are formed below the transition temperature Tc and disrupted above Tc when polymer-polymer interactions are favored. Different hydrogen bond structures of PAAm include free amide groups, cis-trans-multimers, and trans-multimers of amide groups. Here, hydrogen bonds between free amide groups and water dominate at T < Tc but structures favored at T > Tc, such as cis-trans-multimers and trans-multimers of amide groups, can still be hydrated. The enhanced temperature-dependent response of wettability for P(OEGMA188-co-AAm) with a high mole fraction of AAm suggests the formation at Tc of more hydrophobic structures, realized by hydrogen bonding between the ether oxygens of OEGMA188 and the amide fragments of AAm, where water molecules are caged. Furthermore, P(OEGMA188-co-AAm) coatings immersed in pH buffer solutions exhibit a 'schizophrenic' behavior in wettability, with transitions that mimic LCST and UCST for pH = 3, LCST for pH = 5 and 7, and any transition blocked for pH = 9.

19.
Angew Chem Int Ed Engl ; 62(14): e202218669, 2023 Mar 27.
Artículo en Inglés | MEDLINE | ID: mdl-36762956

RESUMEN

Proton transfer is crucial for electrocatalysis. Accumulating cations at electrochemical interfaces can alter the proton transfer rate and then tune electrocatalytic performance. However, the mechanism for regulating proton transfer remains ambiguous. Here, we quantify the cation effect on proton diffusion in solution by hydrogen evolution on microelectrodes, revealing the rate can be suppressed by more than 10 times. Different from the prevalent opinions that proton transport is slowed down by modified electric field, we found water structure imposes a more evident effect on kinetics. FTIR test and path integral molecular dynamics simulation indicate that proton prefers to wander within the hydration shell of cations rather than to hop rapidly along water wires. Low connectivity of water networks disrupted by cations corrupts the fast-moving path in bulk water. This study highlights the promising way for regulating proton kinetics via a modified water structure.

20.
Acta Crystallogr D Struct Biol ; 79(Pt 1): 50-65, 2023 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-36601807

RESUMEN

It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain multiple structures. Methods for building such models can fail, however, in regions where the crystallographic density is difficult to interpret, for example at the protein-solvent interface. To address this limitation, a set of MD-MX methods that combine MD simulations of protein crystals with conventional modeling and refinement tools have been developed. In an application to a cyclic adenosine monophosphate-dependent protein kinase at room temperature, the procedure improved the interpretation of ambiguous density, yielding an alternative water model and a revised protein model including multiple conformations. The revised model provides mechanistic insights into the catalytic and regulatory interactions of the enzyme. The same methods may be used in other MX studies to seek mechanistic insights.


Asunto(s)
Simulación de Dinámica Molecular , Proteínas , Conformación Proteica , Proteínas/química , Solventes/química , Cristalografía por Rayos X
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