Detailed insight into the hydrogen bonding interactions in acetone–methanol mixtures. A molecular dynamics simulation and Voronoi polyhedra analysis study

2012 ◽  
Vol 14 (17) ◽  
pp. 5979 ◽  
Author(s):  
Abdenacer Idrissi ◽  
Kamil Polok ◽  
W. Gadomski ◽  
Ivan Vyalov ◽  
Alexander Agapov ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Analysis Study ◽  
Hydrogen Bonding Interactions ◽  
Voronoi Polyhedra ◽  
Insight Into

scholarly journals The Human TSHβ Subunit Proteins and Their Binding Sites on the TSH Receptor Using Molecular Dynamics Simulation

Endocrinology ◽  
2020 ◽  
Vol 161 (9) ◽  
Author(s):  
Mihaly Mezei ◽  
Ramkumarie Baliram ◽  
M Rejwan Ali ◽  
Mone Zaidi ◽  
Terry F Davies ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulation ◽  
Binding Sites ◽  
Dynamics Simulation ◽  
Tsh Receptor ◽  
Rich Region ◽  
Monomeric Proteins ◽  
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Abstract To gain further insight into the binding of the normal and variant human TSHβ subunits (TSHβ and TSHβv), we modeled the 2 monomeric proteins and studied their interaction with the TSH receptor ectodomain (TSHR-ECD) using molecular dynamics simulation Furthermore, analyzed their bioactivity in vitro using recombinant proteins to confirm that such binding was physiologically relevant. Examining the interaction of TSHβ and TSHβv with the TSHR-ECD model using molecular dynamic simulation revealed strong binding of these proteins to the receptor ECD. The specificity of TSHβ and TSHβv binding to the TSHR-ECD was examined by analyzing the hydrogen-bonding residues of these subunits to the FSH receptor ECD, indicating the inability of these molecules to bind to the FSH receptors. Furthermore, the modelling suggests that TSHβ and TSHβv proteins clasped the concave surface of the leucine rich region of the TSHR ECD in a similar way to the native TSH using dynamic hydrogen bonding. These mutually exclusive stable interactions between the subunits and ECD residues included some high-affinity contact sites corresponding to binding models of native TSH. Furthermore, we cloned TSHβ and TSHβv proteins using the entire coding ORF and purified the flag-tagged proteins. The expressed TSHβ subunit proteins retained bioactivity both in a coculture system as well as with immune-purified proteins. In summary, we showed that such interactions can result in a functional outcome and may exert physiological or pathophysiological effects in immune cells.

Synergistic host–guest hydrophobic and hydrogen bonding interactions in the complexation between endo-functionalized molecular tube and strongly hydrophilic guest molecules in aqueous solution

2018 ◽  
Vol 20 (24) ◽  
pp. 16540-16550 ◽  
Author(s):  
Rabindranath Paul ◽  
Sandip Paul
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Guest Molecules ◽  
Hydrogen Bonding Interactions ◽  
Molecular Tube

Molecular dynamics simulation study of the recognition of hydrophilic molecules by an endo-functionalized molecular tube in aqueous solution.

The effect of amino substituents on the interactions of quinazolone derivatives with c-KIT G-quadruplex: insight from molecular dynamics simulation study for rational design of ligands

RSC Advances ◽  
2015 ◽  
Vol 5 (93) ◽  
pp. 76642-76650 ◽  
Author(s):  
Kiana Gholamjani Moghaddam ◽  
Seyed Majid Hashemianzadeh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Rational Design ◽  
Ligand Design ◽  
Dynamics Simulation ◽  
Rational Ligand Design ◽  
G Quadruplex ◽  
Ligand Interactions ◽  
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Our study provides insight into the effect of different substituents on the G-quadruplex–ligand interactions which helps us rational ligand design.

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