Photon Upconversion in TTA-Inducing Ionic Liquids: Pinpointing the Role of IL Nanostructured Media Using MD Simulations

2020 ◽  
Vol 124 (15) ◽  
pp. 3137-3144
Author(s):  
Karina Shimizu ◽  
Shota Hisamitsu ◽  
Nobuhiro Yanai ◽  
Nobuo Kimizuka ◽  
José N. Canongia Lopes
Keyword(s):  
Ionic Liquids ◽  
Md Simulations ◽  
Nanostructured Media

Isolating the role of hydrogen bonding in hydroxyl-functionalized ionic liquids by means of vaporization enthalpies, infrared spectroscopy and molecular dynamics simulations

2019 ◽  
Vol 21 (36) ◽  
pp. 20308-20314 ◽  
Author(s):  
Dzmitry H. Zaitsau ◽  
Jan Neumann ◽  
Thomas Niemann ◽  
Anne Strate ◽  
Dietmar Paschek ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Infrared Spectroscopy ◽  
Ir Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Dispersion Interaction ◽  
Dynamics Simulations

Hydrogen bonding in hydroxyl-functionalized ionic liquids (right) prevents favourable dispersion interaction between cation and anion (left). We analyze this subtle balance of interactions by combining calorimetry, IR spectroscopy and MD simulations.

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.

scholarly journals Current trends in leather science

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Anthony D. Covington ◽  
William R. Wise
Keyword(s):  
Ionic Liquids ◽  
Potential Role ◽  
Solid Medium ◽  
Leather Industry ◽  
Chromium Vi ◽  
Current Trends ◽  
New Findings ◽  
Vegetable Tanning ◽  
Sulfide Species

Abstract In preparing the second edition of ‘Tanning Chemistry. The Science of Leather.’, the literature was updated and the content was revised and reviewed. Here, the new findings are presented and discussed. Notable developments include the necessary rethinking of the mechanism of sulfide unhairing because of new understanding of the aqueous chemistry of sulfide species. Revision upwards of the value of the second pKa for sulfide species ionisation means that S2− cannot exist in an aqueous medium, so the unhairing species in hair burn reactions is HS−. Although the technology remains the same, this means the mechanisms of associated reactions such as immunisation must be revised. Rawstock preservation has benefitted from studies of the potential role of materials from plants which accumulate salt, but which also contribute terpene compounds. There is also further discussion on the continuing issue of chromium (VI) in the leather industry. The application to processing of new solvents, ionic liquids and deep eutectics, is the coming technology, which offers transforming options for new chemistries and products. Renewed interest in vegetable tanning and methods of wet white processing are current trends. Also, within the topic of reagent delivery is processing in a solid medium of plastic beads. Graphical abstract

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.

scholarly journals Protic Ionic Liquids as Reagent, Catalyst, and Solvent: Triple Role of 1‐Methylimidazolium Thiocyanate

2021 ◽  
Author(s):  
Daniel B. Werz ◽  
Ivan A. Andreev ◽  
Nina K. Ratmanova ◽  
André U. Augustin ◽  
Olga A. Ivanova ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Protic Ionic Liquids

Copper ionic liquids: Examining the role of the anion in determining physical and electrochemical properties

2013 ◽  
Vol 396 ◽  
pp. 78-83 ◽  
Author(s):  
Harry D. Pratt ◽  
Jonathan C. Leonard ◽  
Leigh Anna M. Steele ◽  
Chad L. Staiger ◽  
Travis M. Anderson
Keyword(s):  
Ionic Liquids ◽  
Electrochemical Properties

Ionic liquids: Solvation ability and polarity

2009 ◽  
Vol 81 (4) ◽  
pp. 767-776 ◽  
Author(s):  
Cinzia Chiappe ◽  
Marco Malvaldi ◽  
Christian Silvio Pomelli
Keyword(s):  
Ionic Liquids ◽  
Kinetic Data ◽  
Classification Criteria ◽  
Experimental Measurements ◽  
Molecular Liquids ◽  
The Poor ◽  
Poor Understanding ◽  
The Many ◽  
Molecular Solvents

The role of ionic liquids (ILs) as solvents in chemistry is limited by the poor understanding of the solvation phenomenon in these media. The usual classification criteria used for molecular solvents through various experimental measurements fail to insert ILs into a univocal classification for ILs. Here, we first discuss the unsuitability of the usual interpretative scheme for molecular liquids and elucidate schematically the mechanism of solvation in ILs, pointing out the peculiarities that differentiate them with respect to molecular liquids. Second, we focus on reactivity and reaction kinetics in ILs, underlining the many problems that the complexity of these media reflects on the interpretation of kinetic data and some possible approaches to understand qualitatively the (often not trivial) kinetic problems for reactions performed in ILs.

Sign in / Sign up

Export Citation Format

Share Document