A Study on Fe2+ – α-Helical-Rich Keratin Complex Formation Using Isothermal Titration Calorimetry and Molecular Dynamics Simulation

2014 ◽  
Vol 103 (4) ◽  
pp. 1224-1232 ◽  
Author(s):  
Yanyan Zhao ◽  
Jan K. Marzinek ◽  
Peter J. Bond ◽  
Longjian Chen ◽  
Qiong Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Complex Formation ◽  
Isothermal Titration Calorimetry ◽  
Dynamics Simulation ◽  
Titration Calorimetry

scholarly journals Computer simulation of complex of lysine dendrigraft with molecules of therapeutic KED peptide

2019 ◽  
Vol 24 ◽  
pp. 02008
Author(s):  
Igor Neelov ◽  
Valerii Bezrodnyi ◽  
Anna Marchenko ◽  
Emil Fatullaev ◽  
Sofia Miktaniuk
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Molecular Dynamics Simulation ◽  
Complex Formation ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Stable Complex ◽  
Target Organs ◽  
Therapeutic Peptides ◽  
Drug And Gene Delivery

Lysine dendrimers and dendrigrafts are often used in biomedicine for drug and gene delivery to different target organs or cells. In present paper the possibility of complex formation by lysine dendrigraft and 16 molecules of therapeutic KED peptide was investigated using molecular dynamics simulation method. A system containing of one dendrigraftt and 16 KED peptides in water were studied. It was shown that stable complex consisting of the dendrigraft and the peptide molecules formed and structure of this complex was studied. Similar complexes could be used in future for delivery of other therapeutic peptides to target organs.

scholarly journals Does the single-walled carbon nanotube affect the rate constant of binding of biotin to streptavidin? Molecular dynamics simulation perspective

2019 ◽  
Vol 44 (3) ◽  
pp. 234-243
Author(s):  
Orkide Soltani ◽  
Mohammad Reza Bozorgmehr ◽  
Mohammad Momen-Heravi
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulation ◽  
Complex Formation ◽  
Van Der Waals ◽  
Dynamics Simulation ◽  
Electrostatic Forces ◽  
Single Walled Carbon Nanotube ◽  
Arrhenius Dependence

The interaction of biotin and streptavidin in the presence and absence of a carbon nanotube was studied by molecular dynamics simulation. With respect to the Arrhenius dependence of the rate constants with temperature, those of streptavidin–biotin complex formation ([Formula: see text]) and streptavidin–biotin complex dissociation ([Formula: see text]) were calculated from molecular dynamics simulation trajectories. Nanotube has reduced the amount of and k1and k1. However, the biotin position in streptavidin does not change much. The results obtained from MMPBSA calculations show that the contribution of the van der Waals forces to both systems (in the absence and presence of the nanotube) was greater than that of electrostatic forces. The presence of the nanotube also led to the reduction of van der Waals and electrostatic forces in the interaction of biotin with streptavidin. However, this reduction was greater for electrostatic forces. In the absence of a nanotube, there are four hydrogen bonds between streptavidin and biotin, which are related to the residues Ser27, Tyr43, Ser45 and Ser88. In the presence of the nanotube, the hydrogen bonding of biotin with Ser45 is removed.

Multiscale simulation of surfactant–aquaporin complex formation and water permeability

RSC Advances ◽  
2014 ◽  
Vol 4 (71) ◽  
pp. 37592-37599 ◽  
Author(s):  
Xian Kong ◽  
Zhixian Li ◽  
Diannan Lu ◽  
Zheng Liu ◽  
Jianzhong Wu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Complex Formation ◽  
Water Permeability ◽  
Hydrophobic Interactions ◽  
Multiscale Simulation ◽  
Dynamics Simulation ◽  
Electrostatic And Hydrophobic Interactions

Molecular dynamics simulation reveals distinctive roles of electrostatic and hydrophobic interactions in surfactant (SDS)–protein (AqpZ) complex formation and functionality.

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