Interaction of hen egg white lysozyme with cefpiramide sodium: multi-spectroscopic and computational simulations

Abstract

Under simulated physiological conditions (pH?=?7.40), the interaction between cefpiramide sodium and hen egg white lysozyme was studied with multi-spectroscopy and molecular docking. The results showed that cefpiramide sodium quenched the fluorescence of hen egg white lysozyme by static quenching, and the number of binding site n was about 1. The binding distance (r) between cefpiramide sodium and hen egg white lysozyme was obtained based on the Förster nonradioactive resonance energy transfer and r was less than 7?nm, which indicated that there was a non-radiative energy transition in the system. The thermodynamic parameters were obtained from the van't Hoff equation, and the Gibbs free energy ΔG?H?S?>?0, indicating hydrophobic interaction played a major role in forming the cefpiramide sodium-hen egg white lysozyme complex. Synchronous spectra, circular dichroism spectra and UV-Vis spectra showed that cefpiramide sodium changed the conformation of hen egg white lysozyme. The molecular docking results showed that the binding position of cefpiramide sodium was close to the active center composed of Asp52 and Glu35 residues, suggesting that cefpiramide sodium could change the microenvironment of amino acid residues at the catalytic active center of hen egg white lysozyme.     

Molecular mechanism investigation on the interaction of Clothianidin with human serum albumin

Abstract

With the widespread application of neonicotinoid insecticides, Clothianidin has received much attention due to the potential harm to human health and ecological environment. However, the mechanism of Clothianidin's underlying toxicity to organisms remains unclear. In this work, the interaction between Clothianidin and human serum albumin was investigated and the intrinsic fluorescence of human serum albumin got quenched via static mechanisms upon the addition of Clothianidin. The binding constants between Clothianidin and human serum albumin at three different temperature were obtained to be 3.543?×?10⁴, 2.995?×?10⁴, and 2.490?×?10⁴ M^?1, respectively. Based on the van't Hoff equation, the thermodynamic parameters, ΔH⁰ and ΔS⁰ were estimated to be ?53.885?KJ mol^?1 and ?110.535?J mol^?1K^?1, respectively. A single binding site was predicted from the binding constants at different temperatures by multiple spectroscopic techniques and the negative values of ΔH⁰ and ΔS⁰ indicated the binding of human serum albumin with Clothianidin was driven by hydrogen bonds or van der Waals forces. Furthermore, the loose and unfolded secondary structure of human serum albumin along with the addition of clothianidin had been observed through ultraviolet-visible absorption and circular dichroism spectra. In addition, it was also found that Clothianidin had polar effects of structural microenviroment not only on Trp but also Tyr residues from synchronous fluorescence analysis. This study illuminates the molecular mechanism of the interaction between human serum albumin and clothianidin for the first time and helps to construct a specific pesticide biosensor system of human health.     

Thermally Stable Schiff Base and its Metal Complexes: Molecular Docking and Protein Binding Studies

In this paper, interaction of Schiff base and its metal complexes carrying naphthalene ring in the structure with bovine serum albumin (BSA) were investigated using UV-vis absorption, fluorescence spectroscopies and molecular docking methods. The effect on the binding mechanism and properties of these compounds containing metal-free, iron and copper ions were also investigated. The fluorescence spectroscopy results showed that fluorescence intensity of BSA in the presence of different concentration of ligands was decreased through a static quenching mechanism. Binding constants (KSV, Kbin and Ka) and thermodynamic parameters (ΔG, ΔH and ΔS) for the ligand-protein interactions were also determined. ΔG values of ligand-protein interaction were calculated in the range ? 6.3 to ?5.5 kcal/mol. These negative values showed that binding process is spontaneous and, hydrogen bonding and van der Waals force were main interaction of the protein and ligands. ΔH and ΔS value were also calculated in the range of 1.10 to 1.26 kJ/mol and 0.133 to 0.135 kJ/mol. K, respectively. These positive values indicated that the binding process between ligands and BSA are endothermic and electrostatic interaction, respectively.     

Characterization of the interaction between human lactoferrin and lomefloxacin at physiological condition: Multi-spectroscopic and modeling description

The interaction between lomefloxacin (LMF) and human lactoferrin (Hlf) was studied by using fluorescence, circular dichroism (CD) spectroscopic and molecular modeling measurements. By the fluorescence quenching results, it was found that the binding constant K_A=8.69×10⁵ L mol⁻¹, and number of binding sites n=1.75 at physiological condition. Experimental results observed showed that the binding of LMF to Hlf induced conformational changes of Hlf. The participation of tyrosyl and tryptophanyl residues of protein was also estimated in the drug-Hlf complex by synchronous fluorescence. The quantitative analysis data of far-UV CD spectra from that of the α-helix 37.4% in free Hlf to 30.2% in the LMF-Hlf complex further confirmed that secondary structure of the protein was changed by LMF. Near-UV CD showed perturbations around tryptophan and tyrosine residues which involves perturbations of tertiary structure. The thermodynamic parameters like, ΔH° and ΔS°, have been calculated to be 63.411 kJ mol⁻¹ and 231.104 J mol⁻¹ K⁻¹, respectively. Thermodynamic analysis showed that hydrophobic interactions were the main force in the binding site but the hydrogen bonding and electrostatic interaction could not be excluded which in agreement with the result of molecular docking study. The distance r between donor and acceptor was obtained according to fluorescence resonance energy transfer (FRET) and found to be 1.78 nm. The interaction between LMF and Hlf has been verified as consistent with the static quenching procedure and the quenching mechanism is related to the energy transfer. Furthermore, the study of molecular modeling that LMF could bind to the α-helixes between Pro145-Asn152 and Phe167-Gln172 regions and hydrophobic interaction was the major acting force for the binding site, which was in agreement with the thermodynamic analysis.     

Interaction between flavin mononucleotide-containing azoreductase and azo dyes

ABSTRACT

Azoreductase, a flavin mononucleotide-containing oxidoreductase from Escherichia coli, can catalyze the reduction of azo dyes to form aromatic amine compounds. Few spectroscopic studies have explored the binding mode of azo dyes or the role of the arginine at site 59 in Azoreductase. In this article, protein engineering strategy has been used to construct one mutant in which the arginine residue at site 59 was mutated to glycine. Fluorescence spectroscopic data showed that the addition of Methyl Red and Methyl Orange resulted in the fluorescence quenching of the cofactor flavin mononucleotide bound to Azoreductase. The association constant was fitted using the standard binding equation instead of the Stern-Volmer equation. The results showed that the mutation from the arginine to glycine at site 59 weakened the association constant from 2.21?×?10⁵?L.mol^?1 to 4.55?×?10⁴?L.mol^?1 at 25°C. A similar phenomenon was also observed when Methyl Orange was used as a substrate. In each case, the association constant tended to decrease as the temperature increased from 25°C to 37°C. Thermodynamic parameter analysis revealed that the interaction type changed from a van der Waals interaction (between Azoreductase and the dyes) to a hydrogen bonding interaction (between the mutant and the dyes). Moleculcar docking was also performed in this work to provide some support for the binding mode and binding stability between Azoreductase/mutant and azo dyes.     

Fluorescence Interaction and Determination of Sulfathiazole with Trypsin

The mechanism of interaction of trypsin with the sulfathiazole was studied through using fluorescence quenching and UV-visible absorption spectra at pH 7.4. The Stern-Volmer quenching constants, binding constants, number of binding sites and the corresponding thermodynamic parameters ΔH^o, ΔS^o and ΔG^o were calculated at different temperatures. The effect of common metal ions on the constants was also discussed. The results suggest that sulfathiazole can interact strongly trypsin and that there is the formation of trypsin-sulfathiazole complex and the interaction can be explained on the basis of hydrogen bonds and van der Waals forces. The binding distance (r) between the donor (trypsin) and acceptor (sulfathiazole) was 3.52 nm based on the Förster’s non-radiative energy transfer theory. The detection and quantification limits of sulfathiazole were calculated as 2.52 and 8.40 μM in the presence of trypsin, respectively. The relative standard deviation (RSD) was 4.086 % for determinations (n?=?7) of a sulfathiazole solution with the concentration of 7.54 μM.     

Adsorption Kinetics and Binding Studies of Protein Quantum Dots Interaction: A Spectroscopic Approach

Protein Quantum dots interaction is crucial to investigate for better understanding of the biological interactions of QDs. Here in, the model protein Bovine serum albumin (BSA) was used to evaluate the process of protein QDs interaction and adsorption on QDs surface. The modified Stern-Volmer quenching constant (K_a), number of binding sites (n) at different temperatures (298 308 and 318 K?±?1) and corresponding thermodynamic parameters (ΔG?<?0, ΔH?<?0, and ΔS?>?0) were calculated. The quenching constant (K_s) and number of binding sites (n) is found to be inversely proportional to temperature. It signified that static quenching mechanism is dominant over dynamic quenching. The standard free energy change (ΔG?<?0) implies that the binding process is spontaneous, while the enthalpy change (ΔH?<?0) suggest that the binding of QDs to BSA is an enthalpy-driven process. The standard entropy change (ΔS?>?0) suggest that hydrophobic force played a pivotal role in the interaction process. The adsorption process were assessed and evaluated by pseudofirst-order, pseudosecond-order kinetic model, and intraparticle diffusion model.     

Ab Initio Investigation of the Microspecies and Energy in Hydrated Strontium Ion Clusters

Quantum chemistry calculations were used to study the structure and energy of strontium (Sr) ion hydrated clusters [Sr(H₂O)_1?25]²⁺. The saturated hydration number of the first hydration layer of Sr²⁺ was 8, and the hydration distance was 2.58 Å. The second hydration layer had 1–9 hydration numbers, and the hydration distance was in the range of 4.4–4.6 Å. This work also developed the relationship between the thermodynamic data (average water binding energy E_n and successive water binding energy ΔE_n,n?1, etc.) of the aforementioned low-energy structure and the hydration structures. The first hydration layer was formed by the strong electrostatic interaction between Sr²⁺ and water molecules, and the decrease in ΔE_n,n?1 was relatively large. Hydrogen bonds were formed between water molecules of the second hydration layer and water molecules of the inner layer, and the decrease in ΔE_n,n?1 was relatively small. When one water molecule was added beyond the second hydration layer, ΔE_n,n?1 was close to the hydrogen bond energy 8.88 kcal/mol (37.1 kJ/mol) of dimer water molecule, indicating that there was very weak interaction between Sr²⁺ and the water molecules beyond the second hydration layer.     

The Interaction of a New Schiff Base Ligand with Human Serum Albumin: Molecular Docking and Molecular Dynamics Simulation Studies

The interaction of a new heterocyclic Schiff base bearing pyridine and pyrimidine cycles, with human serum albumin (HSA) using molecular docking and molecular dynamics simulation methods was examined. Molecular docking studies showed that the ligand was bonded to the IB domain of the protein. It was found that there was one hydrogen bond interaction between HSA and the ligand. The standard Gibbs free energy for binding of the ligand to HSA was calculated as ?9.63 kcal.mol^?1. The results of the molecular dynamics simulation showed that the root mean square deviation (RMSD) of the non-liganded HSA and the HSA–ligand complex reached equilibration after 1000 ps. The study of the radius of gyration revealed that there was a conformational change when the HSA–ligand complex was formed. Finally, analyzing the RMS fluctuations (RMSF) suggested that the structure of the ligand binding site remained approximately rigid during the simulation.     

Luminescence quenching effect for the interaction of prulifloxacin with trypsin-Britton-Robinson buffer solution system

Prulifloxacin is a kind of new oral taking antibiotic of fluoroquinolone. Conjugation reaction of prulifloxacin with trypsin in Britton-Robinson buffer solution of pH 7.96 was analyzed by UV-vis spectrophotometry and fluorescence spectrometry. The intrinsic fluorescence of trypsin was strongly quenched by prulifloxacin. This effect was rationalized in terms of a static quenching procedure. The binding parameters have been evaluated by fluorescence quenching methods. Negative values ΔG⁰ for the formation of prulifloxacin-trypsin complex implied that both hydrogen bonds and hydrophobic interactions might play a significant role in prulifloxacin binding to trypsin. The binding distance deduced from the efficiency of energy transfer was 0.84 nm for prulifloxacin-trypsin. Furthermore, association constants and binding mechanism were successfully derived from the fluorescence spectra. UV-vis detections supported a change in the secondary structure of proteins caused by the interaction of prulifloxacin with trypsin.     

Conductometric and fluorometric studies of sodium dodecyl sulphate in aqueous solution and in the presence of amino acids

The critical micelle concentration (CMC) of sodium dodecyl sulphate (SDS) in pure water and in the presence of amino acids (0.01, 0.02 and 0.03 mol kg^?1), L-valine (Val) and L-leucine (Leu) was determined from conductometric and fluorometric methods using pyrene as luminescence probe. Depression in the CMC at low concentration of amino acids is attributed to the increased hydrophobic–hydrophobic interaction between the non-polar groups of the surfactant, while, at high concentration, amino acids bind strongly with the anion, DS^?, head groups of SDS, thereby, delaying the micelle formation, resulting in increased CMC. A pronounced decrease in the CMC, while a marked increase in λ⁰₊, with decrease in the solvated radius (rather than crystal radius) of the counterions is observed. Negative values of ΔG⁰_m and ΔH⁰_m indicate that micellisation of SDS in the presence of amino acids is thermodynamically spontaneous and exothermic. Highest negative value of ΔH⁰_m in 0.01 m Val, with lowest CMC value, shows that 0.01 m aqueous Val is the most suitable medium favouring the micellisation of SDS. Decrease in I₁/I₃ from Val to Leu confirms the relative hydrophobicity of two amino acids. The observed values of the packing parameter, P, of SDS in water and in aqueous amino acids suggest that micelles formed are spherical in nature.     

Interaction of Sulfadiazine with Model Water Soluble Proteins: A Combined Fluorescence Spectroscopic and Molecular Modeling Approach

The binding behavior of antibacterial drug sulfadiazine (SDZ) with water soluble globular proteins like bovine as well as human serum albumin (BSA and HSA, respectively) and lysozyme (LYS) was monitored by fluorescence titration and molecular docking calculations. The experimental data reveal that the quenching of the intrinsic protein fluorescence in presence of SDZ is due to the strong interaction in the drug binding site of the respective proteins. The Stern-Volmer plot shows positive deviation at higher quencher concentration for all the proteins and was explained in terms of a sphere of action model. The calculated fluorophore-quencher distances vary within 4?~?11 Å in different cases. Fluorescence experiments at different temperature indicate thermodynamically favorable binding of SDZ with the proteins with apparently strong association constant (~10⁴–10⁵ M^?1) and negative free energy of interaction within the range of ?26.0?~??36.8 kJ mol^?1. The experimental findings are in good agreement with the respective parameters obtained from best energy ranked molecular docking calculation results of SDZ with all the three proteins.     

Reaction mechanism of tylosin tartrate with lysozyme

Under simulated physiological conditions, the interaction between tylosin tartrate and lysozyme was investigated at pH?=?7.40 by fluorescence spectroscopy. The results indicated that tylosin tartrate could strongly quench the intrinsic fluorescence of lysozyme. By determining the quenching constants of the reaction between tylosin tartrate and lysozyme at different temperatures, the quenching mechanism was proven to be a static quenching process. The thermodynamic parameters (ΔH°, ΔS°) of the reaction between tylosin tartrate and lysozyme were obtained by the Van’t Hoff equation, and were 27.80?kJ mol^?1 and 166.28?J mol^?1 K^?1, respectively. The results showed that hydrophobic interaction between tylosin tartrate and lysozyme was dominant. Synchronous fluorescence spectra revealed that the conformation of lysozyme was changed. This method could be applied to measure the content of tylosin tartrate.     

Study of interaction between protein and main active components in Citrus aurantium L. by optical spectroscopy

The interaction between flavonoids and proteins was investigated by fluorescence and absorption spectroscopy. The binding parameters of drugs with proteins were obtained according to the corrected fluorescence data by an improved calculation method. The ΔH, ΔS and ΔG obtained indicate that the van der Waals or hydrogen bond, electrostatic force and hydrophobic forces all play a role in the interaction of drugs with proteins. Based on Förster's theory, the binding average distance r between the protein and drug was evaluated and found to be less than 3 nm. The interaction of drug-metal ion complexes and proteins was also investigated.     

Synthesis,CMC Determination,Antimicrobial Activity and Nucleic Acid Binding of A Surfactant Copper(II) Complex Containing Phenanthroline and Alanine Schiff-Base

A new water-soluble surfactant copper(II) complex [Cu(sal-ala)(phen)(DA)] (sal-ala = salicylalanine, phen = 1,10-phenanthroline, DA = dodecylamine), has been synthesized and characterized by physico-chemical and spectroscopic methods. The critical micelle concentration (CMC) values of this surfactant–copper(II) complex in aqueous solution were obtained from conductance measurements. Specific conductivity data (at 303, 308, 313. 318 and 323 K) served for the evaluation of the temperature-dependent CMC and the thermodynamics of micellization (ΔG⁰m, ΔH⁰m and ΔS⁰m). The interaction of this complex with nucleic acids (DNA and RNA) has been explored by using electronic absorption spectral titration, competitive binding experiment, cyclic voltammetry, circular dichroism (CD) spectra, and viscosity measurements. Electronic absorption studies have revealed that the complex can bind to nucleic acids by the intercalative binding mode which has been verified by viscosity measurements. The DNA binding constants have also been calculated (K_b?=?1.2?×?10⁵ M^?1 for DNA and K_b?=?1.6?×?10⁵ M^?1 for RNA). Competitive binding study with ethidium bromide (EB) showed that the complex exhibits the ability to displace the DNA-bound-EB indicating that the complex binds to DNA in strong competition with EB for the intercalative binding site. The presence of hydrophobic ligands, alanine Schiff-base, phenanthroline and long aliphatic chain amine in the complex were responsible for this strong intercalative binding. The surfactant–copper (II) complex was screened for its antibacterial and antifungal activities against various microorganisms. The results were compared with the standard drugs, amikacin(antibacterial) and ketokonazole(antifungal).     

Far infrared spectrum and spectroscopic constants of AsH3 in the ground state

The far ir spectrum of arsine, AsH₃, was recorded in the range 25–100 cm^?1 with a resolution of approximately 0.004 cm^?1. ΔJ = +1, ΔK = 0 rotational transitions were measured and assigned up to J″ = 12. These transitions, together with the presently available microwave and submillimeter-wave data and ground state combination differences, were analyzed on the basis of a rotational Hamiltonian which includes Δk = ±3 and Δk = ±6 interaction terms. The derived ground state molecular parameters reproduced the transition frequencies of both allowed and “perturbation allowed” transitions within the accuracy of the measurements. The equilibrium structure was determined for the AsH₃ molecule.     

Investigation of the Interaction Between Rutin and Trypsin in Solution by Multi-Spectroscopic Method

ABSTRACT

The interactions between rutin and trypsin were investigated by UV-Vis absorption, CD, fluorescence, resonance light-scattering spectra, synchronous fluorescence, and three-dimensional fluorescence spectra techniques under physiological pH 7.40. Rutin effectively quenched the intrinsic fluorescence of trypsin via static quenching. The enthalpy change and entropy change were estimated to be ?8.23 kJ·mol^?1 and 53.66 J·mol^?1·K^?1 according to the van't Hoff equation. The process of binding rutin to trypsin was a spontaneous molecular interaction procedure. This result indicates that hydrophobic and electrostatic interactions played a major role in stabilizing the complex. The conformation of trypsin was discussed by CD, synchronous, and three-dimensional fluorescence techniques.     

美洛昔康与溶菌酶作用机制的光谱分析及理论模建研究

为了探究美洛昔康与溶菌酶的作用机制,在pH=7.40的实验条件下,采用荧光光谱、同步荧光光谱和理论模建分析技术研究了类风湿性关节炎药物美洛昔康与溶菌酶分子之间的相互作用。结果表明,美洛昔康能够以静态猝灭形式有效地猝灭溶菌酶的内源荧光,形成1∶1的复合物,并使溶菌酶的构象发生改变。热力学结果表明,美洛昔康-溶菌酶体系的主要作用力类型为疏水作用力。理论模建结果表明,该体系除疏水作用外还存在氢键作用,且美洛昔康被溶菌酶的活性氨基酸残基Glu35和Asp52包围,结合作用改变了溶菌酶催化活性中心处氨基酸残基的微环境。当患者服用15 mg美洛昔康时,美洛昔康与溶菌酶的蛋白结合率W(B)为3.71%~8.79%,说明美洛昔康与溶菌酶的结合对溶菌酶自身抗炎、抗菌功能的影响不大,体系药物结合率W(Q)为1.08%~1.14%,说明溶菌酶与美洛昔康结合不会影响美洛昔康的药效。该研究从理论上证明了溶菌酶在血浆环境中与药物美洛昔康结合后,对溶菌酶本身功能和美洛昔康的药效不会产生严重影响。     

Study on the interaction of La with bovine serum albumin at molecular level

The interaction of La³⁺ to bovine serum albumin (BSA) has been investigated mainly by fluorescence spectra, UV-vis absorption spectra, and circular dichroism (CD) under simulative physiological conditions. Fluorescence data revealed that the quenching mechanism of BSA by La³⁺ was a static quenching process and the binding constant is 1.75×10⁴ L mol⁻¹ and the number of binding sites is 1 at 289 K. The thermodynamic parameters (ΔH=−20.055 kJ mol⁻¹, ΔG=−23.474 kJ mol⁻¹, and ΔS=11.831 J mol⁻¹ K⁻¹) indicate that electrostatic effect between the protein and the La³⁺ is the main binding force. In addition, UV-vis, CD, and synchronous fluorescence results showed that the addition of La³⁺ changed the conformation of BSA.     

Binding Study of Phenformin with Bovine Serum Album Using a Combined Technique of Equilibrium Dialysis with Flow-Injection Chemiluminescence Detection

ABSTRACT

The interaction between phenformin hydrochloride and bovine serum albumin (BSA) was investigated by the methods of chemiluminescence combined with equilibrium dialysis technique. A novel N-bromosuccinimide (NBS)–eosin Y (EY) chemiluminescence (CL) method was established for the determination of phenformin. The mechanism of this chemiluminescence system was proposed. Optimization studies were performed to determine the phenformin. Under the optimal conditions, the CL intensity was linear for a phenformin concentration over the range of 4.6 × 10^?8 to 5.0 × 10^?5 g/mL. The detection limit was 1.5 × 10^?8 g/mL. The data obtained by the present equilibrium dialysis–CL system were analyzed using the Klotz plot and the Scatchard analysis. The results showed that the Klotz plot and the Scatchard plot are linear with good correlation coefficient, indicating that the phenformin has only one type of binding site on BSA. The binding parameters were the number of the binding sites n (1.02) and the estimated association constant K (2.66 × 10⁴ L/mol). The chemiluminescence system combined with equilibrium dialysis developed in this work demonstrated its use for determination of interaction between drug and protein by using relatively simple instrument.