scholarly journals Lysozyme–AuNPs Interactions: Determination of Binding Free Energy

Nanomaterials ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2139
Author(s):  
Axel Gomes ◽  
Jose M. Carnerero ◽  
Aila Jimenez-Ruiz ◽  
Elia Grueso ◽  
Rosa M. Giráldez-Pérez ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Free Energy ◽  
Conformational Changes ◽  
Binding Free Energy ◽  
Aqueous Media ◽  
Plasmon Band ◽  
Low Concentrations ◽  
The Stability ◽  
20 Nm ◽  
Free Energy Of Binding

Investigation and optimization of lysozyme (Lys) adsorption onto gold nanoparticles, AuNPs, were carried out. The purpose of this study is to determine the magnitude of the AuNPs–lysozyme interaction in aqueous media by simple spectrophotometric means, and to obtain the free energy of binding of the system for the first time. In order to explore the possibilities of gold nanoparticles for sensing lysozyme in aqueous media, the stability of the samples and the influence of the gold and nanoparticle concentrations in the detection limit were studied. ζ potential measurements and the shift of the surface plasmon band showed a state of saturation with an average number of 55 Lys per gold nanoparticle. Lysozyme–AuNPs interactions induce aggregation of citrate-stabilized AuNPs at low concentrations by neutering the negative charges of citrate anions; from those aggregation data, the magnitude of the interactions has been measured by using Benesi–Hildebrand plots. However, at higher protein concentrations aggregation has been found to decrease. Although the nanocluster morphology remains unchanged in the presence of Lys, slight conformational changes of the protein occur. The influence of the size of the nanoclusters was also investigated for 5, 10, and 20 nm AuNPs, and 10 nm AuNPs was found the most appropriate.

scholarly journals Noncovalent Interactions of Tiopronin-Protected Gold Nanoparticles with DNA: Two Methods to Quantify Free Energy of Binding

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
R. Prado-Gotor ◽  
E. Grueso
Keyword(s):  
Gold Nanoparticles ◽  
Free Energy ◽  
Conformational Changes ◽  
Noncovalent Interactions ◽  
Binding Free Energy ◽  
Free Energies ◽  
Double Stranded Dna ◽  
Second Procedure ◽  
Free Energy Of Binding

The binding of gold nanoparticles capped with N-(2-mercaptopropionyl)glycine (Au@tiopronin) with double-stranded DNA has been investigated and quantified in terms of free energies by using two different approaches. The first approach follows the DNA conformational changes induced by gold nanoparticles using the CD technique. The second methodology consists in the use of pyrene-1-carboxaldehyde as a fluorescent probe. This second procedure implies the determination of the “true” free energy of binding of the probe with DNA, after corrections through solubility measurements. Working at different salt concentrations, the nonelectrostatic and electrostatic components of the binding free energy have been separated. The results obtained revealed that the binding is of nonelectrostatic character, fundamentally. The procedure used in this work could be extended to quantify the binding affinity of other AuNPs/DNA systems.

scholarly journals Hydrogen Bond Stability of Quinazoline Derivatives Compounds in Complex against EGFR using Molecular Dynamics Simulation

2019 ◽  
Vol 19 (2) ◽  
pp. 461
Author(s):  
Herlina Rasyid ◽  
Bambang Purwono ◽  
Thomas S Hofer ◽  
Harno Dwi Pranowo
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Inhibition Mechanism ◽  
Energy Calculation ◽  
Protein Receptor ◽  
The Stability

Lung cancer was a second common cancer case due to the high cigarette smoking activity both in men and women. One of protein receptor which plays an important role in the growth of the tumor is Epidermal Growth Factor Receptor (EGFR). EGFR protein is the most frequent protein mutation in cancer and promising target to inhibit the cancer growth. In this work, the stability of the hydrogen bond as the main interaction in the inhibition mechanism of cancer will be evaluated using molecular dynamics simulation. There were two compounds (A1 and A2) as new potential inhibitors that were complexed against the EGFR protein. The dynamic properties of each complexed were compared with respect to erlotinib against EGFR. The result revealed that both compounds had an interaction in the main catalytic area of protein receptor which is at methionine residue. Inhibitor A1 showed additional interactions during simulation time but the interactions tend to be weak. Inhibitor A2 displayed a more stable interaction. Following dynamics simulation, binding free energy calculation was performed by two scoring techniques MM/GB(PB)SA method and gave a good correlation with the stability of the complex. Furthermore, potential inhibitor A2 had a lower binding free energy as a direct consequence of the stability of hydrogen bond interaction.

scholarly journals Interaction of Coumarin Phytoestrogens with ERα and ERβ: A Molecular Dynamics Simulation Study

Molecules ◽  
2020 ◽  
Vol 25 (5) ◽  
pp. 1165 ◽  
Author(s):  
Ting Wang ◽  
Yunfei Wang ◽  
Xuming Zhuang ◽  
Feng Luan ◽  
Chunyan Zhao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Binding Free Energy ◽  
Human Life ◽  
Simulation Method ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Molecular Dynamics Methods ◽  
17Β Estradiol ◽  
The Stability

Coumarin phytoestrogens, as one of the important classes of phytoestrogens, have been proved to play an important role in various fields of human life. In this study, molecular simulation method including molecular docking and molecular dynamics methods were performed to explore the various effects between four classical coumarin phytoestrogens (coumestrol, 4-methoxycoumestrol, psoralen and isopsoralen), and estrogen receptors (ERα, ERβ), respectively. The calculated results not only proved that the four coumarin phytoestrogens have weaker affinity than 17β-estradiol to both ERα, and ERβ, but also pointed out that the selective affinity for ERβ is greater than ERα. In addition, the binding mode indicated that the formation of hydrogen bond and hydrophobic interaction have an important effect on the stability of the complexes. Further, the calculation and decomposition of binding free energy explored the main contribution interactions to the total free energy.

Hemoglobin bioconjugates with surface-protected gold nanoparticles in aqueous media: The stability depends on solution pH and protein properties

2017 ◽  
Vol 505 ◽  
pp. 1165-1171 ◽  
Author(s):  
Rafael del Caño ◽  
Lucia Mateus ◽  
Guadalupe Sánchez-Obrero ◽  
José Manuel Sevilla ◽  
Rafael Madueño ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Aqueous Media ◽  
Solution Ph ◽  
Protein Properties ◽  
The Stability

scholarly journals Biogenic Gold Nanoparticles Decrease Methylene Blue Photobleaching and Enhance Antimicrobial Photodynamic Therapy

Molecules ◽  
2021 ◽  
Vol 26 (3) ◽  
pp. 623
Author(s):  
Irena Maliszewska ◽  
Ewelina Wanarska ◽  
Alex C. Thompson ◽  
Ifor D. W. Samuel ◽  
Katarzyna Matczyszyn
Keyword(s):  
Methylene Blue ◽  
Gold Nanoparticles ◽  
Photodynamic Therapy ◽  
Bactericidal Effect ◽  
Antimicrobial Photodynamic Therapy ◽  
Plasmon Band ◽  
Escherichia Coli Bacteria ◽  
Average Size ◽  
20 Nm ◽  
Nanoparticle Sizes

Antibiotic resistance is a growing concern that is driving the exploration of alternative ways of killing bacteria. Here we show that gold nanoparticles synthesized by the mycelium of Mucor plumbeus are an effective medium for antimicrobial photodynamic therapy (PDT). These particles are spherical in shape, uniformly distributed without any significant agglomeration, and show a single plasmon band at 522–523 nm. The nanoparticle sizes range from 13 to 25 nm, and possess an average size of 17 ± 4 nm. In PDT, light (from a source consisting of nine LEDs with a peak wavelength of 640 nm and FWMH 20 nm arranged in a 3 × 3 array), a photosensitiser (methylene blue), and oxygen are used to kill undesired cells. We show that the biogenic nanoparticles enhance the effectiveness of the photosensitiser, methylene blue, and so can be used to kill both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria. The enhanced effectiveness means that we could kill these bacteria with a simple, small LED-based light source. We show that the biogenic gold nanoparticles prevent fast photobleaching, thereby enhancing the photoactivity of the methylene blue (MB) molecules and their bactericidal effect.

scholarly journals DEVELOPMENT OF A METHOD FOR THE SYNTHESIS OF PLASMONIC GOLD NANOPARTICLES FOR A WIDE SPECTRAL REGION 520-720 nm

2017 ◽  
Vol 12 (5) ◽  
pp. 56-64
Author(s):  
I. I. Faskhutdinova ◽  
A. S. Mikhailov ◽  
B. I. Shapiro
Keyword(s):  
Gold Nanoparticles ◽  
Colloidal Stability ◽  
Wavelength Region ◽  
Reducing Agent ◽  
Plasmon Band ◽  
Long Wavelength ◽  
Aggregation Processes ◽  
Wide Range ◽  
Minimal Quantity ◽  
The Stability

A method of the synthesis of plasmon gold nanoparticles by the reduction of HAuCl4 with organic reductants, such as formalin, sodium citrate and hydroquinone has been studied. It is shown that, depending on the concentration of the reagents, the temperature of synthesis and the type of the reducing agent, the position of the maximum of the plasmon band varies in a wide range from 520 nm to 720 nm. A one-stage method using hydroquinone as a reducing agent for the synthesis of long-wave plasmonic gold nanoparticles that form agglomerates of smaller particles with a plasmon absorption band in the red region of the spectrum is proposed. Since the resulting sol is rapidly precipitated due to the aggregation processes, it has been found necessary to use stabilizers for its subsequent application. The influence of some stabilizers (gelatin, as well as surface-active substances polydimethyldiallylammonium chloride and cetyltrimethylammonium bromid) on the stability of the gold sol synthesized by the hydroquinone method has been studied. It is shown that all the types of investigated stabilizers even in a minimal quantity provide the colloidal stability of the sol for several hours. However, only a natural polymer, gelatin, stabilizes the sol so that the maximum absorption of the plasmon band remains in the long-wavelength region of the spectrum.

scholarly journals A simple model for predicting the free energy of binding between anthracycline antibiotics and DNA.

2000 ◽  
Vol 47 (1) ◽  
pp. 1-9 ◽  
Author(s):  
W R Rudnicki ◽  
M Kurzepa ◽  
T Szczepanik ◽  
W Priebe ◽  
B Lesyng
Keyword(s):  
Free Energy ◽  
Theoretical Model ◽  
Density Functional ◽  
Binding Free Energy ◽  
Binding Energies ◽  
Free Energies ◽  
Anthracycline Antibiotics ◽  
Free Energy Of Binding ◽  
Derivatives Of ◽  
Binding Free Energies

A theoretical model for predicting the free energy of binding between anthracycline antibiotics and DNA was developed using the electron density functional (DFT) and molecular mechanics (MM) methods. Partial DFT-ESP charges were used in calculating the MM binding energies for complexes formed between anthracycline antibiotics and oligodeoxynucleotides. These energies were then compared with experimental binding free energies. The good correlation between the experimental and theoretical energies allowed us to propose a model for predicting the binding free energy for derivatives of anthracycline antibiotics and for quickly screening new anthracycline derivatives.

scholarly journals Stability of the Cross Linking Component of the Biosensor Receptor Layer after Addition of Gold Nanoparticles

2021 ◽  
Vol 25 (1) ◽  
pp. 49-52
Author(s):  
Aleksandra Kłos-Witkowska ◽  
Vasyl Martsenyuk
Keyword(s):  
Gold Nanoparticles ◽  
Conformational Changes ◽  
Cross Linking ◽  
Relative Percentage ◽  
Pure Protein ◽  
The Cross ◽  
The Stability ◽  
Changes Over Time ◽  
Over Time ◽  
Receptor Layer

In this study, the stability of the receptor layer component of a biosensor after addition of gold nanoparticles was investigated. Accelerated conformational changes under the influence of Au were demonstrated. The relative percentage changes over time between the pure protein and the Au doped protein were calculated. It was shown that these changes are greater with time and exceed 20 % in the last days of the experiment.

scholarly journals Ligand deconstruction: Why some fragment binding positions are conserved and others are not

2015 ◽  
Vol 112 (20) ◽  
pp. E2585-E2594 ◽  
Author(s):  
Dima Kozakov ◽  
David R. Hall ◽  
Stefan Jehle ◽  
Lingqi Luo ◽  
Stefan O. Ochiana ◽  
...  
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Binding Free Energy ◽  
Hot Spot ◽  
Binding Mode ◽  
Binding Potential ◽  
Binding Modes ◽  
Affinity Ligand ◽  
Ligand Binding Sites ◽  
Free Energy Of Binding

Fragment-based drug discovery (FBDD) relies on the premise that the fragment binding mode will be conserved on subsequent expansion to a larger ligand. However, no general condition has been established to explain when fragment binding modes will be conserved. We show that a remarkably simple condition can be developed in terms of how fragments coincide with binding energy hot spots—regions of the protein where interactions with a ligand contribute substantial binding free energy—the locations of which can easily be determined computationally. Because a substantial fraction of the free energy of ligand binding comes from interacting with the residues in the energetically most important hot spot, a ligand moiety that sufficiently overlaps with this region will retain its location even when other parts of the ligand are removed. This hypothesis is supported by eight case studies. The condition helps identify whether a protein is suitable for FBDD, predicts the size of fragments required for screening, and determines whether a fragment hit can be extended into a higher affinity ligand. Our results show that ligand binding sites can usefully be thought of in terms of an anchor site, which is the top-ranked hot spot and dominates the free energy of binding, surrounded by a number of weaker satellite sites that confer improved affinity and selectivity for a particular ligand and that it is the intrinsic binding potential of the protein surface that determines whether it can serve as a robust binding site for a suitably optimized ligand.

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