scholarly journals Connecting chloride solvation with hydration in deep eutectic systems

2021 ◽  
Vol 23 (1) ◽  
pp. 107-111
Author(s):  
Maria Enrica Di Pietro ◽  
Oliver Hammond ◽  
Adriaan van den Bruinhorst ◽  
Alberto Mannu ◽  
Agilio Padua ◽  
...  
Keyword(s):  
Water Content ◽  
Deep Eutectic Solvents ◽  
Md Simulations ◽  
Eutectic Systems

The Deep Eutectic Solvents (DESs) choline chloride:urea (xChCl = 0.33) and choline chloride:glycolic acid (xChCl = 0.5) were studied using viscosity-corrected 35Cl NMR and MD simulations to probe the role of chloride as a function of water content.

The role of hydrogen bond donor and water content on the electrochemical reduction of Ni2+ from solvents – an experimental and modelling study

2020 ◽  
Vol 22 (28) ◽  
pp. 16125-16135 ◽  
Author(s):  
Monika Lukaczynska-Anderson ◽  
Mesfin Haile Mamme ◽  
Andrea Ceglia ◽  
Krista Van den Bergh ◽  
Joost De Strycker ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Water Content ◽  
Electrochemical Reduction ◽  
Water Concentration ◽  
Deep Eutectic Solvents ◽  
Hydrogen Bond Donor ◽  
Modelling Study

Water concentration and hydrogen bond donor have both a big influence in the coordination of Ni cations in deep eutectic solvents, and will therefore affect their electroreduction.

Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires

2019 ◽  
Author(s):  
Bella Grigorenko ◽  
Igor Polyakov ◽  
Alexander Nemukhin
Keyword(s):  
Adenylyl Cyclase ◽  
Bond Cleavage ◽  
Cyclic Adenosine Monophosphate ◽  
Adenosine Monophosphate ◽  
Md Simulations ◽  
Coordination Shell ◽  
Energy Profile ◽  
One Step ◽  
Type V

<p>We report a mechanism of adenosine triphosphate (ATP) to cyclic adenosine monophosphate (cAMP) conversion by the mammalian type V adenylyl cyclase revealed in molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) simulations. We characterize a set of computationally derived enzyme-substrate (ES) structures showing an important role of coordination shells of magnesium ions in the solvent accessible active site. Several stable six-fold coordination shells of Mg<sub>A</sub><sup>2+ </sup>are observed in MD simulations of ES complexes. In the lowest energy ES conformation, the coordination shell of Mg<sub>A</sub><sup>2+ </sup>does not include the O<sub>δ1</sub> atom of the conserved Asp440 residue. Starting from this conformation, a one-step reaction mechanism is characterized which includes proton transfer from the ribose O<sup>3'</sup>H<sup>3' </sup>group in ATP to Asp440 via a shuttling water molecule and P<sup>A</sup>-O<sup>3A</sup> bond cleavage and O<sup>3'</sup>-P<sup>A</sup> bond formation. The energy profile of this route is consistent with the observed reaction kinetics. In a higher energy ES conformation, Mg<sub>A</sub><sup>2+</sup> is bound to the O<sub>δ1</sub>(Asp440) atom as suggested in the relevant crystal structure of the protein with a substrate analog. The computed energy profile initiated by this ES is characterized by higher energy expenses to complete the reaction. Consistently with experimental data, we show that the Asp440Ala mutant of the enzyme should exhibit a reduced but retained activity. All considered reaction pathways include proton wires from the O<sup>3'</sup>H<sup>3' </sup>group via shuttling water molecules. </p>

scholarly journals Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Sensen Zhang ◽  
Baolei Yuan ◽  
Jordy Homing Lam ◽  
Jun Zhou ◽  
Xuan Zhou ◽  
...  
Keyword(s):  
Md Simulation ◽  
Potential Role ◽  
Md Simulations ◽  
Full Length ◽  
Inflammasome Activation ◽  
Simulation Studies ◽  
Cryo Electron Microscopy ◽  
Gating Mechanism ◽  
Atp Efflux

AbstractPannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses.

Eutectics: formation, properties, and applications

2021 ◽  
Author(s):  
Dongkun Yu ◽  
Zhimin Xue ◽  
Tiancheng Mu
Keyword(s):  
Deep Eutectic Solvents ◽  
Eutectic Systems

Various eutectic systems including eutectic metals, eutectic salts, and deep eutectic solvents have been proposed and applied in engineering, energy and environmental fields.

scholarly journals Tethering-induced destabilization and ATP-binding for tandem RRM domains of ALS-causing TDP-43 and hnRNPA1

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mei Dang ◽  
Yifan Li ◽  
Jianxing Song
Keyword(s):  
Conformational Dynamics ◽  
Md Simulations ◽  
Atp Binding ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Nucleic Acid Binding ◽  
General Role ◽  
Nmr Characterization ◽  
Lateral Sclerosis

AbstractTDP-43 and hnRNPA1 contain tandemly-tethered RNA-recognition-motif (RRM) domains, which not only functionally bind an array of nucleic acids, but also participate in aggregation/fibrillation, a pathological hallmark of various human diseases including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), alzheimer's disease (AD) and Multisystem proteinopathy (MSP). Here, by DSF, NMR and MD simulations we systematically characterized stability, ATP-binding and conformational dynamics of TDP-43 and hnRNPA1 RRM domains in both tethered and isolated forms. The results reveal three key findings: (1) upon tethering TDP-43 RRM domains become dramatically coupled and destabilized with Tm reduced to only 49 °C. (2) ATP specifically binds TDP-43 and hnRNPA1 RRM domains, in which ATP occupies the similar pockets within the conserved nucleic-acid-binding surfaces, with the affinity slightly higher to the tethered than isolated forms. (3) MD simulations indicate that the tethered RRM domains of TDP-43 and hnRNPA1 have higher conformational dynamics than the isolated forms. Two RRM domains become coupled as shown by NMR characterization and analysis of inter-domain correlation motions. The study explains the long-standing puzzle that the tethered TDP-43 RRM1–RRM2 is particularly prone to aggregation/fibrillation, and underscores the general role of ATP in inhibiting aggregation/fibrillation of RRM-containing proteins. The results also rationalize the observation that the risk of aggregation-causing diseases increases with aging.

Role of the hydrogen bond donor component for a proper development of novel hydrophobic deep eutectic solvents

2019 ◽  
Vol 281 ◽  
pp. 423-430 ◽  
Author(s):  
Matteo Tiecco ◽  
Federico Cappellini ◽  
Francesco Nicoletti ◽  
Tiziana Del Giacco ◽  
Raimondo Germani ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Deep Eutectic Solvents ◽  
Hydrogen Bond Donor

Crucial role of water content on the electrochemical performance of α-Ni(OH)2 as an anode material for lithium-ion batteries

Ionics ◽  
2020 ◽  
Vol 27 (1) ◽  
pp. 65-74
Author(s):  
Jinhuan Yao ◽  
Yanwei Li ◽  
Renshu Huang ◽  
Jiqiong Jiang ◽  
Shunhua Xiao ◽  
...  
Keyword(s):  
Electrochemical Performance ◽  
Lithium Ion Batteries ◽  
Water Content ◽  
Anode Material ◽  
Crucial Role ◽  
Lithium Ion

Bacteria Transport and Deposition under Unsaturated Flow Conditions: The Role of Water Content and Bacteria Surface Hydrophobicity

2008 ◽  
Vol 7 (2) ◽  
pp. 406-419 ◽  
Author(s):  
G. Gargiulo ◽  
S. A. Bradford ◽  
J. Simunek ◽  
P. Ustohal ◽  
H. Vereecken ◽  
...  
Keyword(s):  
Water Content ◽  
Unsaturated Flow ◽  
Surface Hydrophobicity ◽  
Flow Conditions ◽  
Bacteria Transport

How do mechanosensitive channels sense membrane tension?

2016 ◽  
Vol 44 (4) ◽  
pp. 1019-1025 ◽  
Author(s):  
Tim Rasmussen
Keyword(s):  
Membrane Lipids ◽  
Osmotic Shock ◽  
Md Simulations ◽  
Fatty Acyl ◽  
Membrane Bilayer ◽  
Cross Sectional ◽  
Conducting Path ◽  
Lipid Chain ◽  
Acyl Chains

Mechanosensitive (MS) channels provide protection against hypo-osmotic shock in bacteria whereas eukaryotic MS channels fulfil a multitude of important functions beside osmoregulation. Interactions with the membrane lipids are responsible for the sensing of mechanical force for most known MS channels. It emerged recently that not only prokaryotic, but also eukaryotic, MS channels are able to directly sense the tension in the membrane bilayer without any additional cofactor. If the membrane is solely viewed as a continuous medium with specific anisotropic physical properties, the sensitivity towards tension changes can be explained as result of the hydrophobic coupling between membrane and transmembrane (TM) regions of the channel. The increased cross-sectional area of the MS channel in the active conformation and elastic deformations of the membrane close to the channel have been described as important factors. However, recent studies suggest that molecular interactions of lipids with the channels could play an important role in mechanosensation. Pockets in between TM helices were identified in the MS channel of small conductance (MscS) and YnaI that are filled with lipids. Less lipids are present in the open state of MscS than the closed according to MD simulations. Thus it was suggested that exclusion of lipid fatty acyl chains from these pockets, as a consequence of increased tension, would trigger gating. Similarly, in the eukaryotic MS channel TRAAK it was found that a lipid chain blocks the conducting path in the closed state. The role of these specific lipid interactions in mechanosensation are highlighted in this review.

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