scholarly journals Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics

2021 ◽  
Vol 22 (22) ◽  
pp. 12360
Author(s):  
Piotr Bełdowski ◽  
Maciej Przybyłek ◽  
Przemysław Raczyński ◽  
Andra Dedinaite ◽  
Krzysztof Górny ◽  
...  

The lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin is one of the major components in synovial fluid. Its electrostatic properties, including the ability to form molecular complexes, are closely related to pH, solvation, and the presence of ions. In the context of synovial fluid, it is relevant to describe the possible interactions between albumin and hyaluronate, taking into account solution composition effects. In this study, the influence of Na+, Mg2+, and Ca2+ ions on human serum albumin–hyaluronan interactions were examined using molecular dynamics tools. It was established that the presence of divalent cations, and especially Ca2+, contributes mostly to the increase of the affinity between hyaluronan and albumin, which is associated with charge compensation in negatively charged hyaluronan and albumin. Furthermore, the most probable binding sites were structurally and energetically characterized. The indicated moieties exhibit a locally positive charge which enables hyaluronate binding (direct and water mediated).

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>


1977 ◽  
Vol 12 (1) ◽  
pp. 191-212
Author(s):  
B. Volesky ◽  
Q. Samak ◽  
P. Waller

Abstract Review of the available results appearing in the recent literature is presented focusing particularly upon the effects of metallic ions such as Cr, Cu, Zn, Cd, Hg, V, Zn, Ni and Co. Some original data involving the effects of Na are presented and discussed. Development of parameters used in evaluating the influence of toxic or inhibitory species on the mixed microbial population of an activated sludge system is of crucial importance and different techniques employed such as BOD-COD-TOC-removal rates, Oxygen Uptake Rate, and others are discussed, showing relative inadequacy of currently applied assays. From the data available, certain trends can be discerned. There is a definite threshold concentration for each metallic ion, depending on the organic load of the feed. In the order of increasing toxicity to activated sludge systems reflected in lower BOD removals the following metals have been listed as inhibiting factors at concentrations starting from 1 ppm applied on a continuous basis: hexavalent chromium, cobalt, zinc, cadmium, trivalent chromium, copper and nickel. Metals in combination have not been reported to exhibit any significantly different effects as compared to those observed with individually introduced metallic ions. Tolerance of some activated sludge systems to shock loadings by various inorganic ions and metals is reviewed. The conclusions are of particular importance for estimating the performance of biox systems handling industrial effluents which are likely to contain toxic components of inorganic or metallic nature.


Nanomaterials ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 64 ◽  
Author(s):  
Qin Wang ◽  
Hui Xie ◽  
Zhiming Hu ◽  
Chao Liu

In this study, molecular dynamics simulations were carried out to study the coupling effect of electric field strength and surface wettability on the condensation process of water vapor. Our results show that an electric field can rotate water molecules upward and restrict condensation. Formed clusters are stretched to become columns above the threshold strength of the field, causing the condensation rate to drop quickly. The enhancement of surface attraction force boosts the rearrangement of water molecules adjacent to the surface and exaggerates the threshold value for shape transformation. In addition, the contact area between clusters and the surface increases with increasing amounts of surface attraction force, which raises the condensation efficiency. Thus, the condensation rate of water vapor on a surface under an electric field is determined by competition between intermolecular forces from the electric field and the surface.


1982 ◽  
Vol 99 (1) ◽  
pp. 447-467
Author(s):  
MICHÈLE G. WHEATLY ◽  
B. R. MCMAHON

The effect of 48 h of hypersaline exposure (25, 50 and 75% SW) on haemocyanin oxygenation properties in the euryhaline crayfish Pacifastacus leniusculus was investigated in vitro and in vivo. In vitro significant increases in affinity and cooperativity were measured, although the magnitude of the Bohr shift was unaffected. In vitro dialysis of haemolymph against physiological salines of variable ionic composition proved that these changes were only partly attributable to altered levels of haemolymph ions, implicating the existence of modulators other than H+ and inorganic ions, the possible identities of which are discussed. Significant depressions of both pre- and postbranchial oxygen tensions (Pv, Ov, O2 and Pa, Oa, O2) were observed, but O2 delivery was maintained by utilization of the venous reserve and by an increase in haemocyanin O2 affinity. This occurred despite a concomitant acidosis whose effect on O2 affinity was directly opposed by the ‘salt’ effect. Under hypersaline conditions, haemocyanin played an increasingly important role in O2 delivery in vivo. Despite a reduction in the concentration of combined O2 at complete saturation of the pigment (CmaxHCyOHCyO2). indicating lowered haemocyanin concentration, compensatory changes in O2-binding and cardiac output precluded an impairment to O2 transfer. Equilibration at the tissues (Et,Ot,O2) in FW was less effective than at the gills (Eb,Ob,O2 but progressively improved with hypersaline exposure reversing this trend. Although effects of increased salinity on O2 equilibrium characteristics were qualitatively similar in vivo and in vitro, some interesting quantitative differences are discussed.


Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2349 ◽  
Author(s):  
Wei-Hua Wang ◽  
Wen-Ling Feng ◽  
Wen-Liang Wang ◽  
Ping Li

Both sulfuric acid (H2SO4) and nitrous oxide (N2O) play a central role in the atmospheric chemistry in regulating the global environment and climate changes. In this study, the interaction behavior between H2SO4 and N2O before and after electron capture has been explored using the density functional theory (DFT) method as well as molecular dynamics simulation. The intermolecular interactions have been characterized by atoms in molecules (AIM), natural bond orbital (NBO), and reduced density gradient (RDG) analyses, respectively. It was found that H2SO4 and N2O can form two transient molecular complexes via intermolecular H-bonds within a certain timescale. However, two molecular complexes can be transformed into OH radical, N2, and HSO4− species upon electron capture, providing an alternative formation source of OH radical in the atmosphere. Expectedly, the present findings not only can provide new insights into the transformation behavior of H2SO4 and N2O, but also can enable us to better understand the potential role of the free electron in driving the proceeding of the relevant reactions in the atmosphere.


2021 ◽  
Author(s):  
David Carrasco-Busturia ◽  
Steen Lysgaard ◽  
Piotr Jankowski ◽  
Tejs Vegge ◽  
Arghya Bhowmik ◽  
...  

Deep eutectic solvents (DES) have emerged as an alternative for conventional ionic<br>liquids in aluminum batteries. Elucidating DES composition is fundamental to<br>understand aluminum electrodeposition in the battery anode. Despite numerous<br>experiemental efforts, the speciation of these DES remains elusive. This work shows<br>how \textit{Ab initio} molecular dynamics (AIMD) simulations can shed light on the<br>molecular composition of DES. For the particular example of AlCl$_{3}$:urea, one of<br>the most popular DES, we carried out a systematic AIMD study, showing how an<br>excess of AlCl$_{3}$ in the AlCl$_{3}$:urea mixture promotes the stability of ionic<br>species vs neutral ones and also favors the reactivity in the system. These two facts<br>explain the experimentally observed enhanced electrochemical activity in salt-rich<br>DES. We also observe the transfer of simple $[$AlCl$_{x}$(urea)$_{y}]$ clusters<br>between different species in the liquid, giving rise to free $[$AlCl$_{4}]^{-}$ units. The<br>small size of these $[$AlCl$_{4}]^{-}$ units favors the transport of ionic species towards<br>the anode, facilitating the electrodeposition of aluminum.


Coatings ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1303
Author(s):  
Pinhui Zhao ◽  
Mingliang Dong ◽  
Yansheng Yang ◽  
Jingtao Shi ◽  
Junjie Wang ◽  
...  

Warm mix asphalt (WMA) technology can bring certain environmental and technical benefits through reducing the temperature of production, paving, and compaction of mixture asphalt. Recent studies have shown that some WMA additives are able to reduce the temperature by increasing the lubricating properties of asphalt binder.-based on the tribological theory, this paper studied the mechanism of adsorbing and lubricating film of base asphalt and WMA on the surface of stone by molecular dynamics (MD) simulation method, and the effect of surfactant WMA additive on the lubrication performance of the shear friction system of “stone–asphalt–stone”. The model of base asphalt lubricating film, including saturates, aromatics, resin and asphaltene, as well as the model of warm mix asphalt lubricating film containing imidazoline-type surfactant WMA (IMDL WMA) additive molecule, were established. The shear friction system of “stone–asphalt–stone” of base asphalt and warm mix asphalt was built on the basis of an asphalt lubrication film model and representative calcite model. The results show that the addition of IMDL WMA additive can effectively improve the lubricity of asphalt, reduce the shear stress of asphalt lubricating film, and increase the stability of asphalt film. The temperature in the WMA lubricating film rises, while the adsorption energy on the stone surface decreases with the increase of shear rate, indicating that the higher the shear rate is, the more unfavorable it is for the WMA lubricating film to wrap on the stone surface. In addition, the shear stress of the WMA lubricating film decreased with increasing temperature, while the shear stress of the base asphalt lubricating film increased first and then decreased, demonstrating that the compactability of the asphalt mixture did not improve linearly with the increase of temperature.


Sign in / Sign up

Export Citation Format

Share Document