Suparna Rudra

Binding interaction of an anionic amino acid surfactant with bovine serum albumin: physicochemical and spectroscopic investigations combined with molecular docking study

The interaction of a synthesised amino acid surfactant, sodium-N-dodecanoylphenylalaninate (AAS) with a transport protein, bovine serum albumin (BSA) has been uncovered employing various physicochemical and spectroscopic techniques like tensiometry, electro kinetic potential measurements, steady-state fluorometry, time-resolved measurements and circular dichroism (CD) at physiological pH and 298 K. The difference in tensiometric responses of AAS in the absence and presence of BSA indicates a significant interaction operative between them. The zeta (ξ) potential measurements have been taken into account in assigning the type of binding interaction between them. The steady-state fluorescence study reveals the sequential unfolding of BSA with stepwise addition of AAS. Stern–Volmer and modified Stern–Volmer plots, Scatchard plots and thermodynamic parameters have been employed to find the type of binding of AAS to BSA. Life-time measurements have been carried out to shed light on the relative amplitude of binding of AAS to the two Trp residues of BSA namely Trp-134 and Trp-213. The changes in protein secondary structure induced by AAS are unveiled by CD measurements. Quantum mechanical calculations involving density functional theory (DFT) and molecular docking analysis have been undertaken to highlight the interactive phenomenon between the two. Thus this work shows a total inspection of an amino acid surfactant–BSA interaction.

Binding affinities of Schiff base Fe(II) complex with BSA and calf-thymus DNA: Spectroscopic investigations and molecular docking analysis.

The binding interaction of a synthesized Schiff base Fe(II) complex with biological macromolecules viz., bovine serum albumin (BSA) and calf thymus(ct)-DNA have been investigated using different spectroscopic techniques coupled with viscosity measurements at physiological pH and 298K. Regular amendments in emission intensities of BSA upon the action of the complex indicate significant interaction between them, and the binding interaction have been characterized by Stern Volmer plots and thermodynamic binding parameters. On the basis of this quenching technique one binding site with binding constant (Kb=(7.6±0.21)×10(5)) between complex and protein have been obtained at 298K. Time-resolved fluorescence studies have also been encountered to understand the mechanism of quenching induced by the complex. Binding affinities of the complex to the fluorophores of BSA namely tryptophan (Trp) and tyrosine (Tyr) have been judged by synchronous fluorescence studies. Secondary structural changes of BSA rooted by the complex has been revealed by CD spectra. On the other hand, hypochromicity of absorption spectra of the complex with the addition of ct-DNA and the gradual reduction in emission intensities of ethidium bromide bound ct-DNA in presence of the complex indicate noticeable interaction between ct-DNA and the complex with the binding constant (4.2±0.11)×10(6)M(-1). Life-time measurements have been studied to determine the relative amplitude of binding of the complex to ct-DNA base pairs. Mode of binding interaction of the complex with ct-DNA has been deciphered by viscosity measurements. CD spectra have also been used to understand the changes in ct-DNA structure upon binding with the metal complex. Density functional theory (DFT) and molecular docking analysis have been employed in highlighting the interactive phenomenon and binding location of the complex with the macromolecules.

Binding interaction of sodium-N-dodecanoyl sarcosinate with hemoglobin and myoglobin: Physicochemical and spectroscopic studies with molecular docking analysis

The interaction of an amino acid surfactant, sodium-N-dodecanoyl sarcosinate (SDDS), with two heme proteins, hemoglobin (Hb) and myoglobin (Mb), has been studied employing various physicochemical and spectroscopic techniques like tensiometry, UV-Vis spectroscopy, steady-state fluorometry, time-resolved fluorometry, circular dichroism (CD) spectroscopy, calorimetry and stopped flow kinetics at physiological pH of 7.2 and 298K. Tensiometric and fluorometric analysis suggest that the interaction between SDDS and protein starts with the monomer form of the surfactant which produces small induced micelles. The micelles bind to protein backbone causing denaturation of the protein structure, and finally free micelles are formed on further addition of surfactant. Life-time measurements have been performed to shed light on the binding of surfactant around the tryptophan moieties present in the heme proteins. The changes in protein secondary structure induced by AAS collected from CD measurements reveals that the proteins are quite perturbed upon action of SDDS. The enthalpy change values of each stepwise interaction process have been found from isothermal titration calorimetry (ITC). The kinetics of the protein-surfactant interaction process has been studied using stopped flow technique. Quantum mechanical calculations involving density functional theory (DFT) and molecular docking analysis have been performed to highlight the interactive phenomenon between the surfactant and heme proteins. Thus the entire study shows a total inspection of an amino acid surfactant-heme protein interaction.

Kinetic exploration supplemented by spectroscopic and molecular docking analysis in search of the optimal conditions for effective degradation of malachite green

The degradation of malachite green (MG) by an alkaline hydrolytic process has been explored spectrophotometrically. The kinetics of the reaction have been meticulously studied under the influence of cationic alkyltrimethylammonium bromide (DTAB, TTAB and CTAB) surfactants, α-, β- and γ-cyclodextrins (CDs) and surfactant–β-CD mixed systems applying pseudo-first order conditions at 298 K. The surfactants and cyclodextrins individually catalyze the hydrolytic rate, whereas surfactant–β-CD mixed systems exhibit both an inhibiting and catalytic influence depending on the surfactant concentrations. The kinetic results have been explained precisely based on the pseudo-phase ion exchange (PIE) model of micelles and CD-catalyzed model of CD systems. The surfactants exhibit micellar surface catalysis, while CDs accelerate the rate by forming MG–CD inclusion complexes, thereby facilitating nucleophilic attack of its ionized secondary hydroxyl group on the carbocation center of MG. The encapsulation of MG within the supramolecular host cavity of the CDs has been investigated diligently using a steady-state absorption spectroscopic technique. The result shows 1 : 1 host–guest complexation with different relative orientations of the guest (MG) inside the hosts. Studies employing density functional theory (DFT) as well as molecular docking analysis provide valuable insight on the insertion mechanism. The results reveal that quantitative analysis can be utilized to predict the optimum conditions for the fastest degradation of MG in ambient environments.

Characterization of domain-specific interaction of synthesized dye with serum proteins by spectroscopic and docking approaches along with determination of in vitro cytotoxicity and antiviral activity

The interaction between a synthesized dye with proteins, bovine, and human serum albumin (BSA, HSA, respectively) under physiological conditions has been characterized in detail, by means of steady-state and time-resolved fluorescence, UV–vis absorption, and circular dichroism (CD) techniques. An extensive time-resolved fluorescence spectroscopic characterization of the quenching process has been undertaken in conjugation with temperature-dependent fluorescence quenching studies to divulge the actual quenching mechanism. From the thermodynamic observations, it is clear that the binding process is a spontaneous molecular interaction, in which van der Waals and hydrogen bonding interactions play the major roles. The UV–vis absorption and CD results confirm that the dye can induce conformational and micro-environmental changes of both the proteins. In addition, the dye binding provokes the functionality of the native proteins in terms of esterase-like activity. The average binding distance (r) between proteins and dye has been calculated using FRET. Cytotoxicity and antiviral effects of the dye have been found using Vero cell and HSV-1F virus by performing MTT assay. The AutoDock-based docking simulation reveals the probable binding location of dye within the sub-domain IIA of HSA and IB of BSA.

Characterization of the binding of strychnine with bovine β-lactoglobulin and human lysozyme using spectroscopic, kinetic and molecular docking analysis

The binding interaction of a well known alkaloid strychnine (STN) with the mammalian milk protein β-lactoglobulin and human lysozyme has been explored by using several spectroscopic techniques along with computational studies. Steady-state and time-resolved fluorescence spectral data reveal that quenching of protein fluorescence proceeds through ground state complexation, i.e., a static quenching mechanism. However, the drug–protein binding constant has been found to vary proportionately with temperature. This anomalous result is explained on the basis of Arrhenius theory. Thermodynamic parameters have been estimated from temperature dependent fluorometric analysis in conjunction with isothermal titration calorimetric (ITC) study. Moreover, modification of native protein conformation due to drug binding has been investigated by UV-Vis spectroscopy, NMR spectroscopy and circular dichroism (CD) measurements. Drug–protein association kinetics has been studied using stopped flow kinetics. Furthermore, molecular dynamics study has provided accurate insights into the binding of STN with both the proteins in accordance with the experimental results obtained. Overall, our present studies report the moderately strong binding affinity of the alkaloid with bovine β-lactoglobulin and human lysozyme, which would be helpful for the medical and environmental sciences.

Deciphering the role of the head group of cationic surfactants in their binding interactions with heme protein and their release by β-cyclodextrin

A consideration of the physiochemical properties of protein–surfactant interactions is important for understanding their behavior in biological systems. The binding interactions of the different head groups of two cationic surfactants, CTAB and CPC, with heme protein, hemoglobin (Hb), have been extensively divulged through the use of various physicochemical and spectroscopic techniques such as tensiometry, UV-Vis spectroscopy, steady-state fluorometry, time-resolved fluorometry, circular dichroism (CD) spectroscopy, calorimetry, dynamic light scattering (DLS), stopped flow kinetics and cyclic voltammetry at the physiological pH of 7.4 at 298 K. The enthalpy change values of each stepwise addition of surfactant for the binding interaction process with Hb have been obtained through an isothermal titration calorimetric (ITC) study. The surfactant–protein association kinetics have been examined using a stopped flow technique. The binding of surfactant with the protein backbone results in a substantial alteration in the protein’s conformation and causes a denaturation of the protein’s structure. β-Cyclodextrin (β-CD) effectively releases the surfactant from the denatured Hb, thus regaining the native structure of the Hb. A molecular docking study also reveals the role of the head group of the surfactants in their binding interactions with Hb and subsequent release by β-CD.