A Spectroscopic and Molecular Simulation Approach toward the Binding Affinity between Lysozyme and Phenazinium Dyes: An Effect on Protein Conformation

Millan, Sabera; Satish, Lakkoji; Bera, Krishnendu; Susrisweta, Behera; Singh, Durg Vijay; Sahoo, Harekrushna

doi:10.1021/acs.jpcb.6b10991

Cited by 67 publications

(32 citation statements)

References 47 publications

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“…We have used linear interaction free energy (LIE) [18,40] to estimate the free energy (Figure S14) of binding between Lyz and BPS. We observed the statistical mean of binding energy as −18.21±1.39 kcal mol −1 , establishing the interaction of Lyz with BPS [18,40] …”

Section: Resultsmentioning

confidence: 99%

Structural Compactness in Hen Egg White Lysozyme Induced by Bisphenol S: A Spectroscopic and Molecular Dynamics Simulation Approach

et al. 2021

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The endocrine disrupting compound Bisphenol and its analogues are widely used in food packaging products and can cause serious health hazards. The protein, Lysozyme (Lyz), showing anti‐microbial properties, is used as a “natural” food and dairy preservative. Herein, we explored the interaction between Lyz and Bisphenol S (BPS) by multi‐spectroscopic and theoretical approaches. Lyz interacts with BPS through static quenching, where hydrophobic force governed the underlying interaction. Molecular docking results reveal that tryptophan plays a vital role in binding, corroborated well with near UV‐CD studies. A decrease in the radius of gyration (from 1.43 nm to 1.35 nm) of Lyz substantiates the compactness of the protein conformation owing to such an interaction. This structural alteration experienced by Lyz may alter its functional properties as a food preservative. Consequently, this can degrade the quality of the food products and thereby lead to severe health issues.

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Section: Resultsmentioning

confidence: 99%

Structural Compactness in Hen Egg White Lysozyme Induced by Bisphenol S: A Spectroscopic and Molecular Dynamics Simulation Approach

et al. 2021

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“…The stability and conformational changes of protein and ligand‐protein complexes were further evaluated using MD simulations . To measure the stability of the complexes, the root mean square deviation (RMSD) was calculated considering the backbone atoms (shown in Figure (a)).…”

Section: Resultsmentioning

confidence: 99%

Multi‐spectroscopic and molecular dynamics simulations investigation of the binding mechanism of polybrominated diphenyl ethers to hen egg white lysozyme

Zuo

Rui

et al. 2019

Luminescence

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Three PBDEs (BDE25, BDE47, and BDE154) were selected to investigate the interactions between PBDEs and hen egg white lysozyme (HEWL) by molecular modeling, fluorescence spectroscopy, and FT-IR spectra. The docking results showed that hydrogen bonds were formed between BDE25 and residue TRP63 and between BDE47 and TRP63 with bond lengths of 2.178 Å and 2.146 Å, respectively. The molecular dynamics simulations indicated that van der Waals forces played a predominant role in the binding of three PBDEs to HEWL. The observed fluorescence quenching can be attributed to the formation of complexes between HEWL and PBDEs, and the quenching mechanism is a static quenching. According to Förster's non-radiative energy transfer theory, the binding distances r were < 7 nm, indicating a high probability of energy transfer from HEWL to the three PBDEs. The synchronous fluorescence showed that the emission maximum wavelength of tryptophan (TRP) residues emerged a red-shift. FT-IR spectra indicated that BDE25, BDE47 and BDE154 induced the α-helix percentage of HEWL decreased from 32.70% ± 1.64% to 28.27% ± 1.41%, 27.50% ± 1.38% and 29.78% ± 1.49%, respectively, whereas the percentage of random coil increased from 26.67% ± 1.33% to 27.60% ± 1.38%, 29.18% ± 1.46% and 30.59% ± 1.53%, respectively. KEYWORDSbinding free energy, fluorescence spectroscopy, hen egg white lysozyme, molecular modeling, polybrominated diphenyl ethers

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“…Various binding parameters including binding constant (K) and binding site (n) per protein molecule were calculated using the following equation :

italiclog \frac{F_{0} - F}{F} = log K + n log . ([], Q)

…”

Section: Resultsmentioning

confidence: 99%

Insights into the binding interaction between copper ferrite nanoparticles and bovine serum albumin: An effect on protein conformation and activity

et al. 2018

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The binding affinity between bovine serum albumin (BSA) and copper ferrite (CuFe O ) nanoparticles in terms of conformation, stability and activity of protein was studied using various spectroscopic methods. The quenching involved in BSA-CuFe O NP interaction was static quenching as analysed by different techniques (steady-state and time-resolved fluorescence along with temperature-dependent fluorescence measurements). Among all types of possible interactions, it was revealed that the major binding forces were van der Waals interaction and hydrogen bonding, which were explored from negative values of enthalpy change (∆H = -193.85 kJ mol ) and entropy change (∆S = -588.88 J mol K ). Additionally, synchronous, circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy measurements confirmed the conformational changes in BSA upon the addition of CuFe O NP. Furthermore, thermal denaturation observations were consistent with the circular dichroism results. The interaction of CuFe O NP with BSA decreased the esterase activity in the BSA assay, revealing the affinity of copper ferrite towards the active site of BSA.

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A Spectroscopic and Molecular Simulation Approach toward the Binding Affinity between Lysozyme and Phenazinium Dyes: An Effect on Protein Conformation

Cited by 67 publications

References 47 publications

Structural Compactness in Hen Egg White Lysozyme Induced by Bisphenol S: A Spectroscopic and Molecular Dynamics Simulation Approach

Structural Compactness in Hen Egg White Lysozyme Induced by Bisphenol S: A Spectroscopic and Molecular Dynamics Simulation Approach

Multi‐spectroscopic and molecular dynamics simulations investigation of the binding mechanism of polybrominated diphenyl ethers to hen egg white lysozyme

Insights into the binding interaction between copper ferrite nanoparticles and bovine serum albumin: An effect on protein conformation and activity

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