scholarly journals Why the Orientational Mobility in Arginine and Lysine Spacers of Peptide Dendrimers Designed for Gene Delivery Is Different?

2020 ◽  
Vol 21 (24) ◽  
pp. 9749
Author(s):  
Valeriy V. Bezrodnyi ◽  
Oleg V. Shavykin ◽  
Sofia E. Mikhtaniuk ◽  
Igor M. Neelov ◽  
Nadezhda N. Sheveleva ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Gene Delivery ◽  
Structural Properties ◽  
Dynamics Simulation ◽  
Contour Length ◽  
Pairing Effect ◽  
Slowing Down ◽  
Peptide Dendrimers ◽  
Peptide Dendrimer

New peptide dendrimer with Lys-2Arg repeating units was recently studied experimentally by NMR (RSC Advances, 2019, 9, 18018) and tested as gene carrier successfully (Int. J. Mol. Sci., 2020, 21, 3138). The unusual slowing down of the orientational mobility of 2Arg spacers in this dendrimer was revealed. It has been suggested that this unexpected behavior is caused by the Arg-Arg pairing effect in water, which leads to entanglements between dendrimer branches. In this paper, we determine the reason for this slowing down using atomistic molecular dynamics simulation of this dendrimer. We present that the structural properties of Lys-2Arg dendrimer are close to those of the Lys-2Lys dendrimer at all temperatures (Polymers, 2020, 12, 1657). However, the orientational mobility of the H-H vector in CH2-N groups of 2Arg spacers in Lys-2Arg dendrimer is significantly slower than the mobility of the same vector in the Lys-2Lys dendrimer. This result is in agreement with the recent NMR experiments for the same systems. We revealed that this difference is not due to the arginine-arginine pairing, but is due to the semiflexibility effect associated with the different contour length from CH2-N group to the end of the side arginine or lysine segment in spacers.

scholarly journals MD Simulation of AEDG Peptide Complexes with New K2R Dendrimer and Dendrigraft

2022 ◽  
Vol 16 ◽  
pp. 73-81
Author(s):  
E.I. Fatullaev ◽  
V.V. Bezrodnyi ◽  
I.M. Neelov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Complex Formation ◽  
Md Simulation ◽  
Ion Pairs ◽  
Computational Approach ◽  
Dynamics Simulation ◽  
Peptide Dendrimers ◽  
Peptide Complexes ◽  
Peptide Dendrimer

Biocompatible peptide dendrimers and dendrigrafts have useful properties for application in biomedicine. In previous papers the computational approach for study lysine dendrimers and dendrigrafts as well as their complexes with various medical peptides was used. In this paper the comparison of complex formation between molecules of therapeutic AEDG tetrapeptide and novel K2R peptide dendrimer or DG2 dendrigraft of near the same size and charge was fulfilled. The systems consisting of 16 therapeutic AEDG tetrapeptide molecules and one dendrimer or one dendrigraft were studied by molecular dynamics simulation. Full atomic models of these molecules in water with explicit counterions were used for this goal. First of all, the process of complex formation was studied. It was obtained that peptide molecules were attracted by both branched molecules and were quickly adsorbed by them. Times of complexes formation as well as size, anisotropy and structure of each complex were calculated. It was demonstrated that both K2R dendrimer and DG2 dendrigraft are effective for complexation of these peptide molecules but new dendrimer complex is more stable than dendrigraft complex because it has almost twice more hydrogen bonds with peptide molecules and 33% more ion pairs with their charged groups.

Molecular Dynamics Simulation of Transport and Structural Properties of CO2 Using Different Molecular Models

2015 ◽  
Vol 60 (8) ◽  
pp. 2188-2196 ◽  
Author(s):  
Haimin Zhong ◽  
Shuhui Lai ◽  
Jinyang Wang ◽  
Wenda Qiu ◽  
Hans-Dietrich Lüdemann ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structural Properties ◽  
Dynamics Simulation ◽  
Molecular Models

scholarly journals Thermodynamics and structural properties of CaO: A molecular dynamics simulation study

2020 ◽  
Vol 152 (8) ◽  
pp. 084503 ◽  
Author(s):  
Cecilia M. S. Alvares ◽  
Guillaume Deffrennes ◽  
Alexander Pisch ◽  
Noël Jakse
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structural Properties ◽  
Simulation Study ◽  
Dynamics Simulation

scholarly journals Structural Properties of Nonionic Tween80 Micelle in Water Elucidated by Molecular Dynamics Simulation

2012 ◽  
Vol 3 ◽  
pp. 287-297 ◽  
Author(s):  
Roghayeh Abedi Karjiban ◽  
Mahiran Basri ◽  
Mohd Basyaruddin Abdul Rahman ◽  
Abu Bakar Salleh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structural Properties ◽  
Dynamics Simulation

A coarse grained molecular dynamics simulation study on the structural properties of carbon nanotube–dendrimer composites

Soft Matter ◽  
2018 ◽  
Vol 14 (16) ◽  
pp. 3151-3163 ◽  
Author(s):  
Sajjad Kavyani ◽  
Mitra Dadvar ◽  
Hamid Modarress ◽  
Sepideh Amjad-Iranagh
Keyword(s):  
Drug Delivery ◽  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulation ◽  
Structural Properties ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Hydrophobic Properties ◽  
Coarse Grained Molecular Dynamics

By coarse grained molecular dynamics, the effect of the size and hydrophilic/hydrophobic properties of the interior/exterior structures of the dendrimers in carbon nanotube–dendrimer composites has been studied, to find a stable composite with the capability to be used in drug delivery.

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