scholarly journals Interaction of lysine dendrimer with 8 and 16 molecules of EDR peptide

2020 ◽  
Vol 14 ◽  
Keyword(s):  
Computer Simulation ◽  
Complex Formation ◽  
Regulatory Peptides ◽  
Stable Complex ◽  
Drug Molecules ◽  
Method Of Molecular Dynamics ◽  
Conformational Properties ◽  
Oppositely Charged ◽  
It Structure ◽  
Similar Peptide

Dendrimers are frequently used for drug molecules delivery to different cells or organs. In our previous papers we used computer simulation to study the complex formation between dendrimers and dendrigrafts with different short regulatory peptides. The goal of present paper is to study interaction and the possibility of complex formation between lysine dendrimer and molecules of therapeutic EDR peptide. The system consisting of one lysine dendrimer of the second generation and 8 or 16 therapeutic EDR peptide molecules in water with explicit counterions was studied by computer simulation. The method of molecular dynamics and full atomic model were used for this goal. It was obtained that EDR peptide molecules become adsorbed by lysine dendrimer and form stable complex with it. Structure and conformational properties of this complex were studied. It was demonstrated that formation of complex occurs mainly due to electrostatic interaction between oppositely charged dendrimer and peptide molecules. Such complexes could be used in future for delivery of these or similar peptide molecules to the targeted tissues and organs.

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 Complex formation between polyelectrolytes and oppositely charged oligoelectrolytes

2016 ◽  
Vol 144 (16) ◽  
pp. 164902 ◽  
Author(s):  
Jiajia Zhou ◽  
Matthias Barz ◽  
Friederike Schmid
Keyword(s):  
Complex Formation ◽  
Oppositely Charged

scholarly journals Interaction between Nbp35 and Cfd1 Proteins of Cytosolic Fe-S Cluster Assembly Reveals a Stable Complex Formation in Entamoeba histolytica

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e108971 ◽  
Author(s):  
Shadab Anwar ◽  
Manas Ranjan Dikhit ◽  
Krishn Pratap Singh ◽  
Rajiv Kumar Kar ◽  
Amir Zaidi ◽  
...  
Keyword(s):  
Complex Formation ◽  
Entamoeba Histolytica ◽  
Stable Complex ◽  
Cluster Assembly

scholarly journals Structural Basis of Complex Formation Between Mitochondrial Anion Channel VDAC1 and Hexokinase-II

2020 ◽  
Author(s):  
Nandan Haloi ◽  
Po-Chao Wen ◽  
Qunlii Cheng ◽  
Meiying Yang ◽  
Gayathri Natarajan ◽  
...  
Keyword(s):  
Complex Formation ◽  
Hybrid Approach ◽  
Md Simulations ◽  
Structural Basis ◽  
Stable Complex ◽  
Binary Complex ◽  
Hexokinase Ii ◽  
Insertion Depth ◽  
Form Complex ◽  
Membrane Bound

ABSTRACTComplex formation between hexokinase-II (HKII) and the mitochondrial channel VDAC1 plays a crucial role in regulating cell growth and survival; however, structural details of this complex remain elusive. We hypothesize that a conserved, hydrophobic helix (H-anchor) of HKII first inserts into the outer membrane of mitochondria (OMM) and then interacts with VDAC1 on the cytosolic leaflet of OMM to form a binary complex. To systematically investigate this process, we adopted a hybrid approach: 1) the membrane binding of HKII was first described with molecular dynamics (MD) simulations employing a membrane mimetic model with enhanced lipid diffusion, then 2) the resulting membrane-bound HKII was used to form complex with VDAC1 in millisecond-scale Brownian dynamics (BD) simulations. We show that H-anchor inserts its first 10 residues into the membrane, substantiating previous experimental findings. The insertion depth of the H-anchor was used to derive positional restraints in subsequent BD simulations to preserve the membrane-bound pose of HKII during the formation of the HKII/VDAC1 binary complex. Multiple BD-derived structural models were further refined with MD simulations, resulting in one stable complex. A major feature in the complex is the partial (not complete) blockade of VDAC1’s permeation pathway by HKII, a result supported by our comparative electrophysiological measurements of the channel in the presence and absence of HKII. Additionally, we showed how VDAC1 phosphorylation disrupts HKII binding, a feature that is verified by our electrophysiology recordings and have implications in mitochondria-mediated cell death.

Transcription factor binding is limited by the 5'-flanking regions of a Drosophila tRNAHis gene and a tRNAHis pseudogene

1984 ◽  
Vol 4 (12) ◽  
pp. 2714-2722
Author(s):  
L Cooley ◽  
J Schaack ◽  
D J Burke ◽  
B Thomas ◽  
D Söll
Keyword(s):  
Complex Formation ◽  
Hela Cell ◽  
Cell Extract ◽  
Deletion Analysis ◽  
Stable Complex ◽  
Flanking Sequence ◽  
Factor Binding ◽  
Real Gene ◽  
Hela Cell Extract ◽  
Flanking Regions

We determined the sequence of a Drosophila tRNA gene cluster containing a tRNAHis gene and a tRNAHis pseudogene in close proximity on the same DNA strand. The pseudogene contains eight consecutive base pairs different from the region of the bona fide gene which codes for the 3' portion of the anticodon stem of tRNAHis. The tRNAHis gene is transcribed efficiently in Drosophila Kc cell extract, whereas the pseudogene is not. The pseudogene is also a much poorer competitor than the real gene in a stable transcription complex formation assay, even though the sequence alteration in the pseudogene does not affect the sequence or spacing of the putative internal transcription control regions. Recombinant clones were constructed in which the 5'-flanking regions are exchanged. The transcription efficiencies and competitive abilities of the recombinant clones resemble those of the genes from which the 5' flank was derived; for example, the tRNAHis pseudogene with the 5'-flanking sequence of the tRNAHis gene is now efficiently transcribed. Deletion analysis of the pseudogene 5' flank failed to uncover an inhibitory element. Deletion analysis of the real gene showed very high dependence on the presence of the wild-type 5'-flanking sequence for factor binding to the internal control regions and stable complex formation. The 5'-flanking sequence of a Drosophila tRNAArg gene active in the Drosophila Kc cell extract does not restore transcriptional activity or stable complex formation. The tRNAHis gene and pseudogene behave atypically in HeLa cell extract. Both genes compete for HeLa transcription factors, but neither of them is efficiently transcribed. Removal of the 5'-flanking sequences of each gene and replacement with various sequences, including the tRNAArg gene 5' flank, does not allow increased transcription in HeLa cell extract.

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