Effect of sodium halides on the structure of methanol-water mixture — MD simulation studies

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.

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Molecular dynamics study of the hydrophobic 6,6-ionene oligocation in aqueous solution with sodium halides

Pure and Applied Chemistry ◽

10.1351/pac-con-09-10-41 ◽

2010 ◽

Vol 82 (10) ◽

pp. 1943-1955 ◽

Cited By ~ 4

Author(s):

Maksym Druchok ◽

Vojko Vlachy

Keyword(s):

Molecular Dynamics ◽

Md Simulation ◽

Distribution Functions ◽

Low Molecular Weight ◽

Specific Effects ◽

Sodium Cations ◽

Counter Ions ◽

Sodium Halides ◽

Explicit Water ◽

Pair Distribution Functions

An explicit water molecular dynamics (MD) simulation is presented of a solution modeling aliphatic 6,6-ionene oligocations mixed with low-molecular-weight electrolytes. In all cases, the co-ions were sodium cations and the counterions were fluoride, chloride, bromide, or iodide anions. The simple point charge/extended (SPC/E) model was used to describe water. The results of the simulation at T = 278 K (the data for 298 K were obtained earlier) and T = 318 K are presented in the form of pair distributions between various atoms and/or between ions in the system. We were interested in how temperature variation modifies the ion-specific effects, revealed by the various pair distribution functions (PDFs). The results were compared with previous calculations for the less hydrophobic 3,3-ionene solutions. Simulations of 6,6-ionene solutions containing mixtures of fluoride and iodide counter-ions at T = 298 K were also presented.

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Carbon fullerene acts as potential lead molecule against prospective molecular targets of biofilm-producing multidrug-resistant Acinetobacter baumanni and Pseudomonas aerugenosa: computational modeling and MD simulation studies

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2020.1726821 ◽

2020 ◽

pp. 1-17

Author(s):

Sinosh Skariyachan ◽

Dharshini Gopal ◽

Sanjana Pratab Kadam ◽

Aditi G Muddebihalkar ◽

Akshay Uttarkar ◽

...

Keyword(s):

Computational Modeling ◽

Md Simulation ◽

Molecular Targets ◽

Multidrug Resistant ◽

Simulation Studies

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

Computational Biology and Chemistry ◽

10.1016/j.compbiolchem.2018.12.017 ◽

2019 ◽

Vol 78 ◽

pp. 398-413 ◽

Cited By ~ 11

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

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

New Journal of Chemistry ◽

10.1039/d0nj03085f ◽

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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