Engagement of CF3 Group in N–H···F–C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies

2013 ◽  
Vol 117 (4) ◽  
pp. 1123-1129 ◽  
Author(s):  
Sachin Rama Chaudhari ◽  
Santosh Mogurampelly ◽  
N. Suryaprakash
Keyword(s):  
Hydrogen Bond ◽  
Nmr Spectroscopy ◽  
Md Simulation ◽  
Simulation Studies ◽  
Solution State

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.

Carbon-dot organic surface modifier analysis by solution-state NMR spectroscopy

2013 ◽  
Vol 15 (7) ◽  
Author(s):  
Aggelos Philippidis ◽  
Apostolos Spyros ◽  
Demetrios Anglos ◽  
Athanasios B. Bourlinos ◽  
Radek Zbořil ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Carbon Dot ◽  
Surface Modifier ◽  
Solution State

Influence of a Combined Low Dosage Gas Hydrate Inhibitor on Methane Hydrate Surface

2014 ◽  
Vol 1008-1009 ◽  
pp. 300-306
Author(s):  
Cui Ping Tang ◽  
Dong Liang Li ◽  
De Qing Liang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Gas Hydrate ◽  
Methane Hydrate ◽  
Md Simulation ◽  
Side Group ◽  
Large Space ◽  
Surface Molecules ◽  
Low Dosage

According to analysis of the gas hydrate cage and structure of the inhibitor and simulation of molecular dynamics, the interaction between GHI1 and hydrates was discussed. The structure analysis indicated the side group of PVP can insert into the open hydrate cage, and force the hydrate growing along the polymer chain, which results in a large space resistance and inhibits gas hydrate agglomerating. The results of MD simulation show GHI1 can damage the surface cage in hydrate lattice; the hydrogen and oxygen in GHI1 can form hydrogen bonds respectively with oxygen and hydrogen in hydrates, which makes the surface molecules of the cages unstable and distorts the cages; Synergist diethylene glycol ether increases strength and range of length of hydrogen bond.

scholarly journals Investigating Liquid–Liquid Phase Separation of a Monoclonal Antibody Using Solution-State NMR Spectroscopy: Effect of Arg·Glu and Arg·HCl

2017 ◽  
Vol 14 (8) ◽  
pp. 2852-2860 ◽  
Author(s):  
Priscilla Kheddo ◽  
Jack E. Bramham ◽  
Rebecca J. Dearman ◽  
Shahid Uddin ◽  
Christopher F. van der Walle ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Phase Separation ◽  
Nmr Spectroscopy ◽  
Liquid Phase ◽  
Liquid Phase Separation ◽  
Solution State ◽  
Liquid Liquid Phase Separation

Proton-Detected NMR Spectroscopy of Nanodisc-Embedded Membrane Proteins: MAS Solid-State vs Solution-State Methods

2017 ◽  
Vol 121 (32) ◽  
pp. 7671-7680 ◽  
Author(s):  
Nils-Alexander Lakomek ◽  
Lukas Frey ◽  
Stefan Bibow ◽  
Anja Böckmann ◽  
Roland Riek ◽  
...  
Keyword(s):  
Solid State ◽  
Nmr Spectroscopy ◽  
Membrane Proteins ◽  
Solution State

Estimating the energy of intramolecular bifurcated (three-centered) hydrogen bond by X-ray, IR and 1 H NMR spectroscopy, and QTAIM calculations

2018 ◽  
Vol 1163 ◽  
pp. 185-196 ◽  
Author(s):  
Andrei V. Afonin ◽  
Irina V. Sterkhova ◽  
Alexander V. Vashchenko ◽  
Mark V. Sigalov
Keyword(s):  
Hydrogen Bond ◽  
Nmr Spectroscopy ◽  
X Ray ◽  
H Nmr

2/3D-QSAR, molecular docking and MD simulation studies of FtsZ protein targeting benzimidazoles derivatives

2019 ◽  
Vol 78 ◽  
pp. 398-413 ◽  
Author(s):  
Shahzaib Ahamad ◽  
Asimul Islam ◽  
Faizan Ahmad ◽  
Neeraj Dwivedi ◽  
Md. Imtaiyaz Hassan
Keyword(s):  
Molecular Docking ◽  
Md Simulation ◽  
Protein Targeting ◽  
3D Qsar ◽  
Simulation Studies ◽  
Ftsz Protein

Combined DFT and MD simulation studies of protein stability on imidazolium–water (ImH+Wn) clusters with aromatic amino acids

2020 ◽  
Vol 44 (41) ◽  
pp. 17912-17923
Author(s):  
Kandhan Palanisamy ◽  
Muthuramalingam Prakash ◽  
Varatharaj Rajapandian
Keyword(s):  
Amino Acids ◽  
Protein Stability ◽  
Md Simulation ◽  
Protein Denaturation ◽  
Aromatic Amino Acids ◽  
Simulation Studies ◽  
Π Stacking ◽  
Hydrated Clusters

The hydrated clusters of protonated imidazole (ImH+) can induce protein denaturation through various kinds of monovalent interactions such as cation···π (stacking), N–H⋯π (T-shaped) and water-mediated O–H⋯O H-bonds.

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