Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study
Abstract
:1. Introduction
2. Results
2.1. Generation of the ssDNA Aptamer Structure
2.2. MD Analysis
2.3. E2-Interaction Analysis
3. Discussion
3.1. Generation of the ssDNA Aptamer Structure
3.2. MD Analysis
3.3. E2-Interaction Analysis
4. Conclusions
5. Methods
5.1. Generation of the ssDNA Aptamer Structure
5.2. MD Simulation
5.3. E2-Interaction Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ACPYPE | AnteChamber PYthon Parser interfacE |
AIL | asymmetric interior loop |
AptF | aptamer-free |
E2 | 17-Estradiol |
E2AptC | E2-aptamer complex |
FEP | free energy perturbation |
GROMACS | Groningen Machine for Chemical Simulations |
H-bond | hydrogen bond |
HL | hairpin loop |
MMB | MacroMoleculeBuilder |
MD | molecular dynamics |
MM/PBSA | molecular mechanics Poisson–Boltzmann surface area |
NPT | constant number (N), pressure (P), and temperature (T) |
NVT | constant number (N), volume (V), and temperature (T) |
PLIP | Protein–Ligand Interaction Profiler |
R | Radius of gyration |
RMSD | root mean square deviation |
RMSF | root mean square fluctuation |
SELEX | systematic evolution of ligands by exponential enrichment process |
SR | stem region |
ssDNA | single stranded DNA |
SSE | secondary structure element |
SSP | secondary structure prediction |
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Sample Availability: Not available. |
Region | Base Range | RMSF [Å] of AptF | RMSF [Å] of E2AptC |
---|---|---|---|
5-end | A1 to G5 | 7.34 | 6.43 |
stem | A6 to G11 and C26 to T31 | 3.72 | 3.02 |
asymmetric interior loop | T12 and G23 to T25 | 5.61 | 3.99 |
hairpin loop | T13 to A22 | 5.14 | 4.24 |
3-end | A32 to G35 | 6.57 | 6.96 |
3*E2 binding site | T12 (asymmetric interior loop) | 3.18 | 3.10 |
T24 (asymmetric interior loop) | 5.20 | 4.31 | |
C26 (stem) | 4.20 | 3.61 | |
E2 | - | - | 2.81 |
Binding Bases | H-Bond rel. [%] | -Stacking int. rel. [%] | Water-Mediated H-Bond rel. [%] | Hydrophobic int. rel. [%] | Total rel. [%] |
---|---|---|---|---|---|
DG11 | 1.00 | 0.80 | 15.44 | 21.08 | 33.44 |
DT12 | 17.68 | 1.92 | 19.04 | 38.64 | 60.96 |
DT13 | 0.32 | 0.00 | 0.48 | 0.00 | 0.68 |
DA22 | 0.04 | 0.00 | 0.96 | 0.00 | 1.00 |
DG23 | 0.24 | 0.00 | 3.92 | 0.00 | 4.16 |
DT24 | 0.04 | 70.56 | 0.56 | 29.76 | 76.44 |
DT25 | 0.36 | 0.00 | 10.24 | 0.28 | 10.84 |
DC26 | 94.36 | 5.76 | 2.68 | 11.16 | 98.00 |
E2 Position | H-Bond abs./rel. [%] | Water-Mediated H-Bond abs./rel. [%] | Total abs./rel. [%] |
---|---|---|---|
3 | 2415/84.65 | 494/33.40 | 2909/67.15 |
17- | 438/15.35 | 985/66.60 | 1423/32.85 |
∑ | 2853/100.00 | 1479/100.00 | 4332/100.00 |
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Eisold, A.; Labudde, D. Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study. Molecules 2018, 23, 1690. https://doi.org/10.3390/molecules23071690
Eisold A, Labudde D. Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study. Molecules. 2018; 23(7):1690. https://doi.org/10.3390/molecules23071690
Chicago/Turabian StyleEisold, Alexander, and Dirk Labudde. 2018. "Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study" Molecules 23, no. 7: 1690. https://doi.org/10.3390/molecules23071690