Mechanism of Unfolding of Goat Lung Cystatin During Urea and Guanidine Hydrochloride Induced Denaturation

Cystatins essentially regulate lysosomal cysteine protease besides affecting several physiological processes. In the present study, denaturation of a high molecular weight cystatin (Mr 66.4 kDa) purified from goat lung (GLC-I) has been studied by monitoring its inhibitory activity, intrinsic fluorescence, circular dichroism (CD), and binding of ANS. It was found that increasing concentration of GdnHCl significantly enhances the inactivation and unfolding of the purified inhibitor (GLC-I) with complete loss of inhibitory activity at 4 M GdnHCl. Denaturation of GLC-I in the presence of GdnHCl is accompanied by red shift (15 nm) of the emission maximum as shown by intrinsic fluorescence. The inhibitory activity of GLC-I was increased by 1.5 fold at 2 M urea; however, it decreased with further increased of the urea concentration. Intrinsic fluorescence studies of GLC-I in the presence of 0–3 M urea shows blue shift of 5 nm, suggesting stabilization of the inhibitor followed by 5 nm red shift at higher concentration. ANS binding studies in the presence of urea indicate significant changes in the tertiary structure of the inhibitor. Thus, our result shows denaturation profile of GLC-I following simple two state transitions in the presence of GdnHCl while it proceeds through an intermediate state in the presence of urea.     

Purification,characterization and kinetics of thiol protease inhibitor from goat (<Emphasis Type="Italic">Capra hircus</Emphasis>) lung

In the present study, two molecular forms of goat lung cystatin (GLC), I and II, were purified to homogeneity by a two-step procedure including ammonium sulfate precipitation (40–60%) and ion exchange chromatography. The inhibitor forms migrated as single bands under native and SDS-PAGE with and without reducing agent giving molecular mass of 66.4 and 76.4 kDa, respectively. GLC-I possesses 0.07% and GLC-II 2.3% carbohydrate content and no -SH groups. GLC-I showed greater affinity for papain than for ficin and bromelain. Immunological studies showed that the inhibitor was pure and there was cross reactivity between anti-GLC-I serum and goat brain cystatin. Both inhibitor forms were stable in the pH range of 3–10 and up to 75°C. GLC-I was found to possess 49% α-helical structure by CD spectroscopy. The inhibitor-papain complexes showed conformational changes as invoked by UV and fluorescence spectroscopic studies. Published in Russian in Biokhimiya, 2009, Vol. 74, No. 7, pp. 963–971.     

Probing the structural interactions between methotrexate and dexamethasone with muscle cystatin: a biophysical study

Abstract

Drug protein interactions have gained considerable attention over the past many years. In the current communication the association of muscle cystatin (MC) with anti-rheumatic drugs methotrexate and dexamethasone was studied by thiol proteinase inhibitor assay, ultra violet (UV) absorption, fluorescence spectroscopy, and fluorescence transform infra-red spectroscopy (FTIR). A static pattern of quenching was noticed between muscle cystatin and methotrexate (MTX). Binding constant (K_a) of methotrexate to muscle cystatin was found to be 1?×?10^?7 M^?1 and the stoichiometry of binding was calculated to be one. Fluorescence measurement of the emission quenching reveals that the quenching process of cystatin by dexamethasone (DXN) was also static. The stoichiometry of binding and binding constant was also obtained. Additional evidence regarding MTX–MC and DXN–MC was obtained from UV spectroscopy and FTIR spectroscopic results. Such spectroscopic studies would help in modelling new candidate drugs for rheumatoid arthritis based on their cystatin binding profile.

Communicated by Ramaswamy H. Sarma     

Spectroscopic studies on the interaction of bilirubin with liver cystatin

Studies on the role of endogenous metabolites such as bilirubin and their interactions with biomolecules have attracted considerable attention over the past several years. In this work, the interaction of bilirubin (BR) with purified goat liver cystatin (LC) was studied using fluorescence and ultraviolet (UV) spectroscopy. The fluorescence data proved that the fluorescence quenching of liver cystatin by BR was the result of BR–cystatin complex formation. Stern–Volmer analysis of fluorescence quenching data showed the binding constant to be 9.27 × 10⁴ M⁻¹ and the number of binding sites to be close to unity. The conformation of the BR–cystatin complex was found to change upon varying the pH of the complex. The BR–cystatin complex was found to have reduced papain inhibitory activity. Photo-illumination of BR–cystatin complex causes perturbation in the micro-environment of goat liver cystatin as indicated by red-shift. This report summarizes our research efforts to reveal the mechanism of interaction of bilirubin with liver cystatin.     

Micronomicin/tobramycin binding with DNA: fluorescence studies using of ethidium bromide as a probe and molecular docking analysis

Two aminoglycosides, micronomicin (MN), and tobramycin (TB), binding with DNA were studied using various spectroscopic techniques including fluorescence, UV–Vis, FT-IR, and CD spectroscopy coupled with relative viscosity and molecular docking. Studies of fluorescence quenching and time-resolved fluorescence spectroscopy all revealed that MN/TB quenching the fluorescence of DNA–EB belonged to static quenching. The binding constants and binding sites were obtained. The values of ΔH, ΔS, and ΔG suggested that van der Waals force or hydrogen bond might be the main binding force. FT-IR and CD spectroscopy revealed that the binding of MN/TB with DNA had an effect on the secondary structure of DNA. Binding mode of MN/TB with DNA was groove binding which was ascertained by viscosity measurements, CD spectroscopy, ionic strength, melting temperature (T_m), contrast experiments with single stranded (ssDNA), and double stranded DNA (dsDNA). Molecular docking analysis further confirmed that the groove binding was more acceptable result.     

Calf thymus DNA binding studies of the new neodymium-naproxen complex

Fluorescence spectroscopy in combination with UV absorption spectroscopy was carried out to investigate the interaction between the neodymium-naproxen complex (Nd-NAP) and calf thymus DNA (ctDNA). The experimental results showed that Nd-NAP intercalated with the ctDNA base pairs. Analysis of fluorescence quenching data of Nd-NAP by ctDNA at different temperatures using a Stern-Volmer equation revealed that dynamic and static quenching occurred simultaneously. The binding constants and the number of binding sites at 293 and 310 K were obtained as 2.904 × 10(4) L mol(-1), 1.172 and 2.432 × 10(4) L mol(-1), 1.143, respectively. The thermodynamic parameters ΔG, ΔH, and ΔS calculated at different temperatures indicated that hydrogen bonding and van der Waals force were the main binding forces.     

Interaction of 3'-azido-3'-deamino daunorubicin with human serum albumin: investigation by fluorescence spectroscopy and molecular modeling methods

In this Letter, the binding of 3'-azido-3'-deamino daunorubicin (ADNR) to human serum albumin (HSA) was investigated at different temperatures by fluorescence spectroscopy at pH 7.4. The binding constant was determined according to Stern-Volmer equation based on the fluorescence quenching of HSA in the presence of ADNR. The thermodynamic parameters, ΔH and ΔS, were calculated according to the dependence of enthalpy change on the temperature to be -21.01 kJ mol(-1) and 24.71 J K(-l) mol(-l), respectively. The results revealed that ADNR had a strong ability to quench the intrinsic fluorescence of HSA through a static quenching procedure. The hydrophobic force played a major role in the interaction of ADNR with HSA, which was in good agreement with the results of molecular modeling study. The effect of various metal ions on the binding constants of ADNR with HSA was also investigated. All the experimental results and theoretical data indicated that ADNR could bind to HSA and be effectively transported and eliminated in body, which might be a useful guideline for further drug design.     

Cloning, in silico characterization and interaction of cysteine protease and cystatin for establishing their role in early blight disease in tomato

Cysteine protease (CP) and Cysteine protease inhibitor (CPI) or cystatin constitute a critical point in programmed cell death (PCD), a basic biological phenomenon which takes place in the plants, when they are exposed to varying biotic and abiotic stresses. In the present study we isolated and cloned cDNAs encoding cysteine protease and cystatin from early blight infected tomato plants. Using computational biology tools the sequence-structure-function relationships for the tomato cystatin and cysteine protease were elucidated. Interaction between the cystatin and cysteine protease of host and pathogen is higher as compared to interaction shown by cystatin and cysteine protease within the host. The interaction energy of (a)tomato cystatin—tomato cysteine protease, (b)tomato cystatin—fungal cysteine protease and (c)tomato cysteine protease—fungal cystatin are ?319.33 Kcal/mol, ?504.71 Kcal/mol and ?373.731 Kcal/mol respectively. Comparative protein sequence analysis with different plant cystatins and cysteine protease were also done with the sequences of cystatin and cysteine protease isolated from tomato. Structures for all the cystatin and cysteine protease were modeled along with their interactions with fungal cystatin and cysteine protease in order to explore the structural variability and its manifestation at the functional level. This helped to relate the already known functions of these proteins with their sequences as well as the predicted structures. This also served to better understand the CP-CPI interaction operational in developing this protein family and its implication in plant defense during fungal pathogenesis in tomato plants.     

Study on the interaction between isoniazid and bovine serum albumin by fluorescence spectroscopy: the effect of dimethylsulfoxide

The investigation of the binding between isoniazid (or isonicotinic acid hydrazide, INH) and serum albumin is of crucial importance to reveal the reason of resistant Mycobacterium tuberculosis strains towards INH and to increase the anti-tuberculous activity of INH. The interaction between INH and bovine serum albumin (BSA) was studied by fluorescence, UV and FT-IR spectroscopy methods. The analysis of the emission quenching at different temperatures revealed that the quenching mechanism corresponds to a static process and, as consequence; a complex INH-BSA is formed. The modified Stern-Volmer quenching constant K (a) and the corresponding thermodynamic parameters ΔH, ΔG and ΔS were calculated. The distance, r, between donor (BSA) and acceptor (INH) was calculated to be 2.14 nm based on F?rster's non-radiative energy transfer theory (FRET). The results obtained on the basis of fluorescence study of BSA solutions at the presence of dimethylsulfoxide (DMSO) were discussed in terms of the hydration properties and competitive intermolecular interactions between BSA and solvent components. The dependence of binding constant on the concentration of added DMSO as a solvent component showed non monotonous behavior. The conformational changes of BSA and its secondary structure alterations at the presence of INH were revealed.     

Molecular spectroscopy evidence of berberine binding to DNA: comparative binding and thermodynamic profile of intercalation

Berberine (BH) is an important traditional medicinal herb endowed with diverse pharmacological and biological activities. In this work, the binding characteristics and molecular mechanism of the interaction between the BH and herring sperm DNA were explored by UV-vis absorbance and fluorescence spectroscopy. In the mechanism discussion, fluorescence quenching, absorption spectra, competition experiment, and iodide quenching experiment studies hinted at an intercalative mode of binding for BH to DNA. Fluorescence studies revealed the binding constant (K) of BH-DNA was ～10(4) L·mol(-1). The effects of temperature, chemical denaturants, thermal denaturation, and pH were studied to show the factors of the interaction and provided further support for the intercalative binding mode. The results of thermodynamic parameters ΔG, ΔH, and ΔS at different temperatures indicated that the hydrogen bonds and van der Waals interactions played major roles in the reaction, and the effect of ionic strength indicated that electrostatic attraction between the BH and DNA was also a component of the interaction.     

Insights into the binding of paclitaxel to human serum albumin: multispectroscopic studies

The interaction of paclitaxel with human serum albumin (HSA) was studied using fluorescence, resonance light scattering, ultraviolet‐visible, circular dichroism and Fourier transform infrared spectroscopy at pH 7.4. Fluorescence data revealed that the fluorescence quenching of HSA by paclitaxel was a static quenching procedure. Time‐resolved fluorescence data also confirmed the quenching mode, which present a constant decay time of about 5 ns. The binding sites were approximately 1 and the binding constant suggested a weak association (324/M at 298 K), which is helpful for the release of the drug to targeted organs. The thermodynamic parameters, ΔG^○, ΔH° and ΔS° were calculated as – 1.06 × 10⁴ J/mol, 361 J/mol per K and 9.7 × 10⁴ J/mol respectively at 298 K, suggesting that binding was spontaneous and was driven mainly by hydrophobic interactions. The binding distance between HSA and paclitaxel was determined to be 2.23 nm based on the Förster theory. Analysis of circular dichroism, ultraviolet‐visible, three‐dimensional fluorescence, Fourier transform infrared and resonance light scattering spectra demonstrated that HSA conformation was slightly altered in the presence of paclitaxel and dimension of the individual HSA molecules were larger after interacting with paclitaxel. These results were confirmed by a molecular docking study. Copyright © 2013 John Wiley & Sons, Ltd.     

A multitechnique approach to probe the interaction of a therapeutic tyrosine kinase inhibitor nintedanib and bovine serum albumin

Drug and protein interaction provides a structural guideline in the rational drug designing and in the synthesis of new and improved drugs with greater efficacy. We have examined here the interaction tendency and mechanism of nintedanib (NTB), an anticancer drug (tyrosine kinase inhibitor) with bovine serum albumin (BSA), by spectroscopic techniques. The decline in Stern–Volmer quenching constants and binding constant with the temperature rise suggests that BSA forms a complex with NTB. Binding constant obtained by modified Stern–Volmer equation at 3 temperatures was realized to be of the order of ~10⁴?M^?1. Negative ΔG (~?5.93?kcal?mol^?1), ΔH (?3.74?kcal?mol^?1), and ΔS (?1.50?kcal?mol^?1) values exhibited a spontaneous and exothermic reaction between BSA and NTB. NTB molecule interacts with BSA by forming hydrogen bonds, as elucidated by fluorescence results. Moreover, a minor increment in the helical conformation of BSA upon its binding to NTB was observed by circular dichroism spectroscopy. The modification in protein’s symmetry and a decline in hydrodynamic radii were observed in the presence of NTB (from ~3.6 to ~3?nm) as obtained by the dynamic light scattering measurement results.     

Differential effects of anti-cancer and anti-hepatitis drugs on liver cystatin

The drug–protein interaction has been the subject of increasing interest over the decades. In the present communication, the interaction of liver cystatin with anti-cancer (adriamycin) and anti-hepatitis (adevofir dipivoxil) drugs was studied by thiol-protease inhibitory assay, UV absorption, fluorescence spectroscopy and circular dichroism (CD). A static type of quenching was observed between the protein and the drug molecules. Binding constant (Ka) of adriamycin to liver cystatin (LC) was found to be 1.08 × 10⁶ M⁻¹. Moreover, binding site number was found to be 2. Importantly, cystatin loses its activity in the presence of adriamycin. However, intrinsic fluorescence studies in the presence of adevofir dipivoxil showed enhancement in the fluorescence intensity suggesting that binding of adevofir to LC caused unfolding of the protein. The unfolding of the test protein was also accompanied by significant loss of inhibitory activity. CD spectroscopy result showed, both adriamycin and adevofir dipivoxil caused perturbation in the secondary structure of liver cystatin. The possible implications of these results will help in combating drug induced off target effects.Abbreviations: LC, liver cystatin; ADR, adriamycin; CD, circular dichroism; Ka, binding constant; HBV, human hepatitis B virus     

Deciphering binding mechanism between bovine serum albumin and new pyrazoline compound K4

The binding mechanism of a new and possible drug candidate pyrazoline derivative compound K4 and bovine serum albumin (BSA) was investigated in buffer solution (pH 7.4) using ultraviolet–visible light absorption and steady‐state and synchronous fluorescence techniques. The fluorescence intensity of BSA was quenched in the presence of K4 . The quenching process between BSA and K4 was examined at four different temperatures. Decrease of the quenching constants calculated using the Stern–Volmer equation and at increasing temperature suggested that the interaction BSA– K4 was realized through a static quenching mechanism. Synchronous fluorescence measurements suggested that K4 bounded to BSA at the tryptophan region. Fourier transform infrared spectroscopy results showed that there was no significant change in polarity around the tryptophan residue The forces responsible for the BSA– K4 interaction were examined using thermodynamic parameters. In this study, the calculated negative value of ΔG, the negative value of ΔH and the positive value of ΔS pointed to the interaction being through spontaneous and electrostatic interactions that were dominant for our cases. This study provides a very useful in vitro model to researchers by mimicking in vivo conditions to estimate interactions between a possible drug candidate or a drug and body proteins.     

Molecular modeling and multi‐spectroscopic approaches to study the interaction between antibacterial drug and human immunoglobulin G

Mechanistic and conformational studies on the interaction of sulfamethoxazole (SMX) with human immunoglobulin G (HIgG) were performed by molecular modeling and multi‐spectroscopic methods. The interaction mechanism was firstly predicted through molecular modeling that confirmed the interaction between SMX and HIgG. The binding parameters and thermodynamic parameters at different temperatures had been calculated according to the Stern?Volmer, Scatchard, Sips and Van ’t Hoff equations, respectively. Experimental results showed that the fluorescence intensity of HIgG was quenched by the gradual addition of SMX. The binding constants of SMX with HIgG decreased with the increase of temperature, which meant that the quenching mechanism was a static quenching. Meanwhile, the results also confirmed that there was one independent class of binding site on HIgG for SMX during their interaction. The thermodynamic parameters of the reaction, namely standard enthalpy ΔH⁰ and entropy ΔS⁰, had been calculated to be ?14.69 kJ·mol^?1 and 22.99 J·mol^?1·K^?1, respectively, which suggested that the electrostatic and hydrophobic interactions were the predominant intermolecular forces in stabilizing the SMX?HIgG complex. Furthermore, experimental results obtained from three‐dimensional fluorescence spectroscopy, UV?vis absorption spectroscopy and circular dichroism (CD) spectroscopy confirmed that the conformational structure of HIgG was altered in the presence of SMX. Copyright © 2015 John Wiley & Sons, Ltd.     

Interaction and photo-induced cleavage studies of a copper based chemotherapeutic drug with human serum albumin: spectroscopic and molecular docking study

The interaction of new dinuclear copper(ii) complex 1; [Cu(2)(glygly)(2)(ppz)(H(2)O)(4)]·2H(2)O, derived from dipeptide (glycyl glycine) and piperazine as a metallopeptide drug with human serum albumin (HSA) was examined by means of fluorescence spectroscopy which revealed that complex 1 has a strong ability to quench the intrinsic fluorescence of HSA through a static quenching procedure. The alterations of HSA secondary structure in the presence of complex 1 were confirmed by UV-visible, FT-IR, CD and 3D fluorescence spectroscopy. The binding constants (K), and binding site number (n), corresponding thermodynamic parameters ΔG, ΔH and ΔS at different temperatures were calculated. The molecular docking technique was utilized to ascertain the mechanism and mode of action towards the molecular target HSA indicating that complex 1 was located at the entrance of site I by electrostatic and hydrophobic forces, consistent with the corresponding experimental results. Complex 1 shows efficient photo-induced HSA cleavage activity, indicating the involvement of hydroxyl radicals as the reactive species. Furthermore, the cytotoxicity of 1 was examined on a panel of human tumor cell lines of different histological origins showing significant GI(50) values specifically towards MIAPACA2, A498 and A549 tumor cell lines. These results complement previous biological studies of new specific target metallopeptides, providing additional information about possibilities of their transport and disposition in blood plasma.     

Hydrogen bonding-assisted interaction between amitriptyline hydrochloride and hemoglobin: spectroscopic and molecular dynamics studies

Herein, we have explored the interaction between amitriptyline hydrochloride (AMT) and hemoglobin (Hb), using steady-state and time-resolved fluorescence spectroscopy, UV–visible spectroscopy, and circular dichroism spectroscopy, in combination with molecular docking and molecular dynamic (MD) simulation methods. The steady-state fluorescence reveals the static quenching mechanism in the interaction system, which was further confirmed by UV–visible and time-resolved fluorescence spectroscopy. The binding constant, number of binding sites, and thermodynamic parameters viz. ΔG, ΔH, ΔS are also considered; result confirms that the binding of the AMT with Hb is a spontaneous process, involving hydrogen bonding and van der Waals interactions with a single binding site, as also confirmed by molecular docking study. Synchronous fluorescence, CD data, and MD simulation results contribute toward understanding the effect of AMT on Hb to interpret the conformational change in Hb upon binding in aqueous solution.     

Effect of Chinese medicine alpinetin on the structure of human serum albumin

Alpinetin (7-hydroxy-5-methoxyflavanone), one of the main constituents from the seeds of Alpinia katsumadai Hayata, belongs to flavonoids with its usefulness as antibacterial, anti-inflammatory and other important therapeutic activities of significant potency and low systemic toxicity. In this paper, the interaction of alpinetin to human serum albumin (HSA) has been studied for the first time by spectroscopic method including Fourier transform infrared (FT-IR) spectroscopy, circular dichroism (CD), and UV-absorption spectroscopy in combination with fluorescence quenching study under physiological conditions with drug concentrations of 3.3 x 10(-6)-2.0 x 10(-5)mol/L. The results of spectroscopic measurements and the thermodynamic parameters obtained (the enthalpy change DeltaH(0) and the entropy change DeltaS(0) were calculated to be -10.20 kJ/mol and 53.97 J/molK(-1) according to the Van't Hoff equation) suggest that hydrophobic interaction is the predominant intermolecular forces stabilizing the complex, which is also good agreement with the results of molecule modeling study. The alterations of protein secondary structure in the presence of alpinetin in aqueous solution were quantitatively estimated by the evidences from FT-IR and CD spectroscopy with reductions of alpha-helices about 24%, decreases of beta-sheet structure about 2%, and increases of beta-turn structure about 21%. The quenching mechanism and the number of binding site (n approximately 1) were obtained by fluorescence titration data. Fluorescent displacement measurements confirmed that alpinetin bind HSA on site III. In addition, the effects of common ions on the constants of alpinetin-HSA complex were also discussed.     

Mechanistic and conformational studies on the interaction of sulfamethazine with human immunoglobulin G by molecular modeling and multi‐spectroscopic approach in vitro

Binding interaction of sulfamethazine (SMZ) with human immunoglobulin G (HIgG) has been explored under physiological conditions. The interaction mechanism was firstly predicted through molecular modeling which showed that several hydrogen bonds participated in stabilizing the SMZ ? HIgG complex. Fluorescence spectroscopy, ultraviolet–visible (UV–vis) light absorption and circular dichroism (CD) spectroscopy were used to analyze the binding site, binding constants and effects of SMZ on HIgG stability and secondary structure. The binding parameters and thermodynamic parameters at different temperatures for the reaction have been calculated according to the Scatchard, Sips and Van 't Hoff equations, respectively. Experimental results showed that the quenching mechanism was a static quenching and there was one independent class of binding site on HIgG for SMZ during their interaction. The thermodynamic parameters of the reaction, namely standard enthalpy ΔH⁰ and entropy ΔS⁰, had been calculated to be ?19.12 kJ · mol^?1 and 20.22 J · mol^?1 · K^?1, respectively, which meant that the electrostatic interaction was the predominant intermolecular force in stabilizing the SMZ ? HIgG complex. Moreover, the conformational changes of HIgG in the presence of SMZ were confirmed by three‐dimensional fluorescence spectroscopy, UV–vis absorption spectroscopy and CD spectroscopy. Copyright © 2014 John Wiley & Sons, Ltd.     

Probing the interaction of anticancer drug temsirolimus with human serum albumin: molecular docking and spectroscopic insight

The binding interaction between temsirolimus, an important antirenal cancer drug, and HSA, an important carrier protein was scrutinized making use of UV and fluorescence spectroscopy. Hyper chromaticity observed in UV spectroscopy in the presence of temsirolimus as compared to free HSA suggests the formation of complex between HSA and temsirolimus. Fluorescence quenching experiments clearly showed quenching in the fluorescence of HSA in the presence of temsirolimus confirming the complex formation and also confirmed that static mode of interaction is operative for this binding process. Binding constant values obtained through UV and fluorescence spectroscopy reveal strong interaction; temsirolimus binds to HSA at 298 K with a binding constant of 2.9 × 10⁴ M^?1implying the strength of interaction. The negative Gibbs free energy obtained through Isothermal titration calorimetry as well as quenching experiments suggests that binding process is spontaneous. Molecular docking further provides an insight of various residues that are involved in this binding process; showing the binding energy to be -12.9 kcal/mol. CD spectroscopy was retorted to analyze changes in secondary structure of HSA; increased intensity in presence of temsirolimus showing changes in secondary structure of HSA induced by temsirolimus. This study is of importance as it provides an insight into the binding mechanism of an important antirenal cancer drug with an important carrier protein. Once temsirolimus binds to HSA, it changes conformation of HSA which in turn can alter the functionality of this important carrier protein and this altered functionality of HSA can be highlighted in variety of diseases.