Isothermal Titration Calorimetric Studies Research Articles

Interfacial and aggregation behavior of ionic liquid-bile salt conjugates

Bile salt derived nontoxic surface-active ionic liquids (SAILs), 1-butyl-3-methylimidazolium cholate ([bmim]C) and deoxycholate ([bmim]DC) were synthesized by reacting [bmim] tetrafluoroborate separately with sodium cholate (NaC) and sodium deoxycholate (NaDC) which were subsequently characterized by FTIR, 1H-NMR, 13C-NMR, HRMS, PXRD, and TGA-DTA studies. Interfacial and aggregation behavior of the SAILs were assessed by surface tension, conductance, pyrene fluorescence, dynamic light scattering, and isothermal titration calorimetric studies. Critical micelle concentration values were substantially lower than their precursor sodium salts. SAILs were less surface active than their corresponding sodium salts due to enhanced aqueous solubility induced by the ionic liquid cation. Both the aggregation number and size of the SAIL micelles were higher/larger where the SAIL micelles were more compact than NaC/NaDC. Exothermic changes in the enthalpy of micellization were higher for SAILs, where the micellization processes were found to be entropy driven. Such comprehensive studies can shed further light on the microstructure, besides the fundamental understanding on SAIL aggregation. The combined advantages of surfactant and ionic liquid in the SAILs can result in superior amphiphilic characteristics. Such nontoxic aggregates are capable to enhance the limited solubility of organic compounds in water besides their possible uses in catalysis, drug delivery, and energy storage, etc.

Contrasting effects of molecular crowding on the membrane-perturbing and chaperone-like activities of major bovine seminal plasma protein, PDC-109

Crowded environments inside cells and biological fluids greatly affect protein stability and activity. PDC-109, a polydisperse oligomeric protein of the bovine seminal plasma selectively binds choline phospholipids on the sperm cell surface and causes membrane destabilization and lipid efflux, leading to acrosome reaction. PDC-109 also exhibits chaperone-like activity (CLA) and protects client proteins against various kinds of stress, such as high temperature and low pH. In the present work, we have investigated the effect of molecular crowding on these two different activities of PDC-109 employing Dextran 70 (D70) – a widely used polymeric dextran – as the crowding agent. The results obtained show that presence of D70 markedly increases membrane destabilization by PDC-109. Isothermal titration calorimetric studies revealed that under crowded condition the binding affinity of PDC-109 for choline phospholipids increases approximately 3-fold, which could in turn facilitate membrane destabilization. In contrast, under identical conditions, its CLA was reduced significantly. The decreased CLA could be correlated to reduced surface hydrophobicity, which was due to stabilization of the protein oligomers. These results establish that molecular crowding exhibits contrasting effects on two different functional activities of PDC-109 and highlight the importance of microenvironment of proteins in modulating their functional activities.

Synthesis of covalent organic pillars as molecular nanotubes with precise length, diameter and chirality

The construction of nanotubes with well-defined structures, although synthetically challenging, offers the prospect of studying novel chemical reactions and transportation within confined spaces, as well as fabricating molecular devices and nanoporous materials. Here we report a discrete molecular nanotube, namely the covalent organic pillar COP-1, synthesized through a [2 + 5] imine condensation reaction involving two penta-aldehyde macrocycles and five phenylenediamine linkers. A pair of enantiomeric nanotubes, obtained in a quantitative and diastereoselective manner, were characterized and resolved readily. NMR spectroscopy, isothermal titration calorimetric and X-ray crystallographic studies revealed that the 2-nm-long and 4.7-Å-wide one-dimensional channel inside COP-1 can accommodate α,ω-disubstituted n-alkyl chains with complementary lengths and electron density distributions. Furthermore, in a length-mismatched host–guest pair, we found that the nonamethylene dibromide thread not only displays a diminished binding constant in solution, but adapts an energetically unfavoured gauche conformation inside COP-1 in the solid state.

Compromised conformation and kinetics of catalase in the presence of propylthiouracil: A biophysical study and alleviation by curcumin

In the present study, the inhibitory effect of propylthiouracil (PTU) on bovine liver catalase (BLC) activity was studied in the presence of curcumin (CUR). The results suggest that the PTU-induced decrease in BLC activity was caused by a change in conformation of BLC with reduced α-helical content and decrease in zeta potential. Nevertheless, temperature-dependent activation of CUR protects the activity of BLC by restoring the secondary conformation and zeta potential of BLC. CUR inhibited the time-induced reduction in BLC activity and the protection was increased with increasing concentrations of CUR and found to be significant even from 1:0.1 molar ratios. The enzyme kinetics confirmed the high catalytic efficiency of BLC in presence of CUR than PTU. The protective role of CUR was due to the formation of a more stabilized complex as demonstrated by molecular docking, and fourier-transform infrared study. Isothermal titration calorimetric study supports for a favourable reaction between BLC and PTU or CUR due to the negative ΔH, and positive TΔS. Although the number of binding sites for PTU and CUR was found to be 10 and 7, respectively, the binding affinity between CUR and BLC is approximately 3.72 fold stronger than BLC-PTU complex. The increased melting temperature of BLC was noticed in presence of CUR suggesting the protective potential of CUR towards biomolecules. Indeed, this is the first biophysical study to describe the molecular mechanism of PTU-induced reduction in BLC activity and alleviation by CUR with detail kinetics. Thus, CUR can be further extended to other antioxidant enzymes or compromised biomolecules for therapeutic interventions.

Rim-differentiation vs. mixture of constitutional isomers: A binding study between pillar[5]arene-based glycoclusters and lectins from pathogenic bacteria

Macrocycle-based glycoclusters, on account of their promising anti-adhesive properties against bacteria, are potential therapeutic alternatives to classic antibiotics through the much less explored anti-adhesive strategy. In this study, a series of constitutionally-pure pentavalent glycoclusters was prepared by conjugating assorted azido-carbohydrates onto a penta-propargyl rim-differentiated pillar[5]arene (RD-P[5]) scaffold through Cu(I)-catalyzed azide–alkyne cycloaddition “click” reactions. Their binding towards therapeutically relevant bacterial lectins, such as LecA and LecB from Pseudomonas aeruginosa and concanavalin A (ConA), were evaluated subsequently by isothermal titration calorimetric studies. Most of these isomer-free RD-P[5] pentavalent glycoclusters, except the fucosylated ones, display good affinities to lectins. Nonetheless, the dissociation constants observed are similar to those displayed by an analogous pentavalent glycocluster consisting of four P[5] constitutional isomers, in which the RD-P[5] component merely accounts for 7% in the mixture. Our results revealed that high constitutional purity is not essential for achieving effective multivalent interactions between P[5]-based glycoclusters and lectins, presumably as a result of the conformationally labile nature of the P[5] scaffold. This information provides valuable design principles for low-cost and facile syntheses of glycosylated P[5]s for biomedical applications.

Isothermal titration calorimetric study of the formation and decay of the P- form of cytochrome c oxidase

Isothermal titration calorimetric study of the formation and decay of the P- form of cytochrome c oxidase

Biophysical interaction between lanthanum chloride and (CG)n or (GC)n repeats: A reversible B-to-Z DNA transition

The transition from right-handed to left-handed DNA is not only acts as the controlling factor for switching gene expression but also has equal importance in designing nanomechanical devices. The (CG)n and (GC)n repeat sequences are well known model molecules to study B-Z transition in the presence of higher concentration of monovalent cations. In this communication, we report a cyclic transition in (CG)6 DNA using millimolar concentration of trivalent lanthanide salt LaCl3. The controlled and reversible transition was seen in (CG)12, and (GC)12 DNA employing CD spectroscopy. While LaCl3 failed to induce B-Z transition in shorter oligonucleotides such as (CG)3 and (GC)3, a smooth B-Z transition was recorded for (CG)6, (CG)12 and (GC)12 sequences. Interestingly, the phenomenon was reversible (Z-B transition) with addition of EDTA. Particularly, two rounds of cyclic transition (B-Z-B-Z-B) have been noticed in (CG)6 DNA in presence of LaCl3 and EDTA which strongly suggest that B-Z transition is reversible in short repeat sequences. Thermal melting and annealing behaviour of B-DNA are reversible while the thermal melting of LaCl3-induced Z-DNA is irreversible which suggest a stronger binding of LaCl3 to the phosphate backbone of Z-DNA. This was further supported by isothermal titration calorimetric study. Molecular dynamics (MD) simulation indicates that the mode of binding of La3+ (of LaCl3) with d(CG)8.d(CG)8 is through the minor groove, wherein, 3 out of 11 La3+ bridge the anionic oxygens of the complementary strands. Such a tight coordination of La3+ with the anionic oxygens at the minor groove surface may be the reason for the experimentally observed irreversibility of LaCl3-induced Z-DNA seen in longer DNA fragments. Thus, these results indicate LaCl3 can easily be adopted as an inducer of left-handed DNA in other short oligonucleotides sequences to facilitate the understanding of the molecular mechanism of B-Z transition.

Exploring binding mechanism of naringenin to human transferrin using combined spectroscopic and computational methods: Towards therapeutic targeting of neurodegenerative diseases

Excessive iron deposition is linked to the pathology of neurodegenerative, signifying the importance of iron homeostasis. Together with ferritin, human transferrin (hTf) play significant roles in iron homeostasis. Naringenin (Nag) is a flavanone known to have neuroprotective action. Inhibition of hTf, which reduces the free iron, is an attractive strategy to treat neurodegenerative diseases. This study explores the binding of Nag to hTf employing in-silico and in vitro approaches. Molecular docking studies deciphered binding of Nag to hTf with a high affinity through metal coordination bonding. Further, 200 ns all-atom molecular dynamic simulation studies were performed to understand the hTf-Nag complex dynamics. No significant structural alterations occur in hTf upon binding of Nag, suggesting the stability of the hTf-Nag complex. Computational studies were supported by experimental methods. Fluorescence binding studies suggested that Nag binds to hTf with an excellent affinity. Isothermal titration calorimetric studies further validated the spontaneous nature of binding of Nag to hTf and provided various thermodynamic parameters of the hTf-Nag complex. The present work provides a platform to use Nag in therapeutic strategies to manage neurodegenerative disorders.

Binding studies of dopamine HCl drug with the mixed {sodium bis(2-ethylhexyl) sulfosuccinate + sodium dodecylsulfate} micelles: Physicochemical, spectroscopic, calorimetric and computational approach

Taking into consideration the importance of dopamine HCl as neurotransmitter in controlling central nervous system activities, the studies of binding interactions of dopamine HCl drug with micellar system (imitator of biomembranes) have been conducted by utilizing experimental as well as computational techniques. The systematic knowledge of physicochemical, spectroscopic and calorimetric properties is helpful to understand the physiological actions of biologically active additives in the living organisms. Therefore, mixed aggregation behavior of sodium bis(2-ethylhexyl) sulfosuccinate, AOT and sodium dodecylsulfate, SDS has been explored at diverse mole fractions of AOT, αAOT = 0.25, 0.39 and 0.50 in (1, 2 and 3) × 10−3 mol kg−1 dopamine HCl(aq) solutions by employing different techniques. From conductivity studies, the thermodynamic parameters (∆G°m, ∆H°m and ∆S°m), the molecular interaction parameter (βint) and the excess Gibbs free energy of micellization (∆Gmex) were ascertained at T = (298.15, 308.15, and 318.15) K. Isentropic compressibility (κs), partial specific volume (φv) and partial specific isentropic compressibility (φκ) parameters were computed from the density and sound velocity studies. Binding constant (Kb) and standard Gibbs free energy of binding (∆Gbο) have been evaluated from UV–visible absorption studies for dopamine HCl(aq) solutions at all the studied mole fractions of surfactant mixtures. Through dynamic light scattering (DLS) measurements, the hydrodynamic diameters (Dh) of mixed micellar aggregates have been acquired. Isothermal titration calorimetric (ITC) studies were executed to obtain the values of partitioning constant / binding constant (K), standard molar enthalpy of binding (ΔrHᴼ), standard molar entropy of binding (ΔrSᴼ), and stoichiometry of partitioning / binding (n) of drug with micellar system. Through density functional theory (DFT) calculations, the band gap between HOMO and LUMO for the dopamine-HCl bound mixed micelle system, and interactive features have been obtained. Aforementioned studies favor the supremacy of hydrophilic-hydrophilic / ionic and electrostatic interactions causing the binding among the hydrophilic / ionic groups of dopamine HCl (−OH, H+, Cl−), AOT (–SO3−, –OCO, Na+), and SDS (–OSO3−, Na+).

Spectroscopic and theoretical evidences for the surface binding of voglibose drug with DNA

Binding of voglibose (VOG), an alpha glucosidase inhibitor, with CT-DNA has been investigated using various spectroscopic techniques including UV–Vis, fluorescence and circular dichroism (CD) coupled with relative viscosity. Isothermal titration calorimetric studies have been used to calculate the thermodynamic parameters such as ΔH (0.0188 cal/mol), ΔS (63.3 cal/mol/K) and ΔG (-18.8 kcal/mol), which reveal that the binding is a spontaneous process and hydrophobic and H-bonding interactions play major roles in the binding process. Effect of ionic strength confirms the existence of hydrophobic interaction between VOG and CT-DNA. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 suggest that VOG possibly binds on the surface of CT-DNA. Viscosity measurements also disclose that the binding could be mainly surface binding. Corroborating the experimental observations, metadynamics molecular simulation studies confirm that VOG binding on the surface of the DNA molecule through hydrophobic interactions and direct and water molecule mediated H-bonding.

Unusual human serum albumin fibrillation inhibition by ketoprofen and fenoprofen: Mechanistic insights

Development of efficient therapeutic strategies to combat protein misfolding and fibrillation is of great clinical significance. In the current study, efforts have been made to obtain qualitative and quantitative insights into interactions of anti-inflammatory drugs; ketoprofen and fenoprofen with the transport protein HSA and their inhibitory action on fibrillation by employing a combination of calorimetric, spectroscopic, microscopic, and molecular docking methods. Interestingly, both ketoprofen and fenoprofen are able to completely inhibit fibrillation of HSA when added at a concentration of 0.5 mM for fenoprofen or 1 mM ketoprofen. Further, no amorphous aggregates are formed. Isothermal titration calorimetric studies highlight the predominant role of polar interactions of these drugs with protein in prevention of fibrillation. The role of conformational flexibility of benzoyl and phenoxy groups of drugs has been correlated with inhibition efficiency. Such studies highlight the role of functionality required for an inhibitor in addressing neurodegenerative diseases.

Characterization of different intermediate states in myoglobin induced by polyethylene glycol: A process of spontaneous molecular self-organization foresees the energy landscape theory via in vitro and in silico approaches

Practically proteins perform their functions exposed to various molecules (macro/micro) of different shapes, sizes, and high concentrations. In such conditions, proteins fold through various intermediate states to execute their type of functions. There are various in vitro studies that showed that proteins yield intermediate states (either pre-molten globule, PMG or molten globules, MG) in changing environments (pH, temperature, and co-solute). Here, we investigate that myoglobin (Mb) yields two intermediate states in the presence of polyethylene glycol, PEG (4 kDa molecular weight) at two different concentrations. These intermediates were characterized by various spectroscopic techniques, further; we demonstrated that these changes in the structure of the protein were due to soft interactions which were confirmed by isothermal titration calorimetric and computational studies. Besides, in silico (molecular dynamic simulations) studies were exploited to know the atomic-level details of the protein which are useful to comprehend the functional characteristics of the bio-molecule with structural change and to study atomic motions and inter-atomic interactions in the bio-molecular systems. This is the first time that two intermediates (MG and PMG state) in the protein (Mb) at two different concentrations in the presence of solo size of PEG are yielded. This study shows folding of a protein does not follow a singular and specific pathway but occurs through routes down a folding funnel more like rain flowing down a funnel, hence foresees the energy landscape theory. Moreover, the study provides the significance of crowding concentrations in the cellular organism.

Physicochemical studies on the interfacial and aggregation behavior of immidazolium- and pyrrolinidium-dodecyl sulfate in aqueous medium

Salt free surface active ionic liquids (SAILs), 1-butyl-3-methylimidazolium dodecyl sulfate ([bmim]DS) and N-butyl-N-methylpyrrolidinium dodecyl sulfate ([bmp]DS) were synthesised by stoichiometric mixing of ionic liquid (IL) and sodium dodecyl sulfate (SDS). SAILs were characterised by FTIR, 1H NMR, 13C NMR and thermogravimetric analysis and differential thermal analysis (TGA-DTA). Interfacial and aggregation behavior of the SAILs were investigated by surface tension, conductance, UV–visible absorption, emission spectroscopy, dynamic light scattering and isothermal titration calorimetric studies. Results were compared with the precursor surfactant SDS. Critical micelle concentration (CMC) of the surfactants followed the sequence: SDS > [bmp]DS > [bmim]DS. Lower surface excess values of SAILs were due to electrostatic interaction between IL cation and DS-, besides the higher aqueous solubility of DS-, induced by the IL cations. Negative Gibbs free energy of micellization and higher fraction of counter ion binding values further support the proposition. Aggregation number (n) and size (dh) of the micelles were determined by fluorescence quenching and dynamic light scattering studies respectively; both ‘n’ and ‘dh’ values were higher for SAILs than SDS ([bmim]DS > [bmp]DS > SDS). SAIL aggregates, although larger in size with higher aggregation number, were more compact than SDS micelles. Enthalpies of micellization, being exothermic in nature, were higher for SAILs although the micellization processes were entropically controlled. SAILs are considered to have dual advantages of surfactant and IL with substantial decrease in toxicity level.

Interaction of a hydrophilic molecule with bovine serum albumin: A combined multi-spectroscopic, microscopic and isothermal calorimetric study in the presence of graphene oxide

One of the most widely studied plasma protein is bovine serum albumin (BSA), and it plays a crucial role in the binding and transportation of many exogenous and endogenous drugs. Coumarin derivatives play a crucial role as an analgesic, anticancer, and anticoagulant agent. Here in this report, we have studied the binding interaction between a 7-amino coumarin derivative, namely 7-(N, N′-diethylamino)coumarin-3-carboxylic acid (7-DCCA) with BSA and also have found out the effect of graphene oxide (GO) on the binding interaction. The binding interaction was probed by employing various spectroscopic, microscopic, isothermal titration calorimetric (ITC), and by using molecular docking studies. The change in absorption and emission maxima position of BSA and 7-DCCA in the absence and presence of GO along with the change in absorbance and emission intensity when we titrated by 7-DCCA or BSA respectively indicates the strong complexation between 7-DCCA and BSA. From the fluorescence resonance energy transfer study, the average distance between tryptophan 213 of the BSA (donor), and the 7-DCCA (acceptor) is found ~50 Ǻ. From excited-state lifetime and fluorescence lifetime imaging (FLIM) studies, we observed that the average lifetime of 7-DCCA is much higher in the presence of BSA compared to buffer medium and in the presence of BSA a heterogeneous environment was created around 7-DCCA. Again in the presence of GO, the formation of a complex of 7-DCCA with a low concentration of BSA shows greater binding interaction as compared to that in the absence of GO. Time-resolved fluorescence anisotropy measurement shows that the addition of GO provides a restricted environment surrounding the 7-DCCA molecule in the presence of both low and high concentrations of BSA. CD study demonstrates the same extent of reduction of α-helical content of BSA protein on binding with 7-DCCA in the absence and presence of GO. ITC study revealed that the interaction between 7-DCCA and BSA is favoured by negative enthalpy change and positive entropy change. Also, from the ITC study, we find out that GO doesn't inflict significant change in the overall global binding interaction pattern, rather it inflicts changes in the mechanistic pathways of binding between 7-DCCA and BSA. Step-scan FTIR studies show the modification of amide I and amide II bonds with time when complexation occurs between BSA and 7-DCCA in the absence and presence of GO. The docking result reveals that the deprotonated form of 7-DCCA has positioned at a distance of ~3.7 nm from Trp 213. Thus these interactions play a central role in the development of coumarin derivative based small molecules to be used for both academic and industrial purposes.

Phycocyanin of marine Oscillatoria sp. inhibits lipoxygenase by protein-protein interaction-induced change of active site entry apace: A model for non-specific biofunctions of phycocyanins

An overview of the biological properties of phycocyanin (PC) amply illustrates that it may not have any specific functional feature towards any system at which it may elicit a specific function, but for the molecular interactions. Nevertheless, based on existing evidences, it is hypothesized that PC has more than one functional target with the interacting systems; therefore, it has diversity of effects. The mechanism of PC action remains elusive of a comprehensive idea. The present investigation focuses on the pro inflammatory enzyme, lipoxygenase (LOX) inhibiting property of PC purified from Oscillatoria sp. Enzyme kinetics studies show that the molecular composite of PC is required for its inhibition shown on LOX. Isothermal titration calorimetric study proves that one molecule of PC interacts with two molecules of LOX. Molecular dynamics simulation study pertaining to PC-LOX interactions shows it to be appropriate as a model to give molecular mechanistic insight into the varied biological properties of PC, demonstrated elsewhere in experimental studies including animal model studies. It explains that the PC-LOX interaction is of a function-freezing, protein-protein interaction in nature. The wide spectrum of properties of PC might be due to its function as a powerful protein hub showing non-specific protein-protein interactions.

Activation of SIRT1/PGC 1α/SIRT3 pathway by melatonin provides protection against mitochondrial dysfunction in isoproterenol induced myocardial injury

AimsPreventing mitochondrial dysfunction and enhancing mitochondrial health and biogenesis is a crucial therapeutic approach to ameliorate injury following acute myocardial infarction. Although the antioxidant role of melatonin against ischemia/reperfusion injury has been reported, the exact mechanism of protection, in vivo, remains poorly understood. This study aims to identify and elaborate upon mechanism of melatonin protection of rat cardiac mitochondria against acute myocardial infarction. Main methodsRats were pre-treated with melatonin (10 mg/kg body weight (b.w.); intraperitoneally, i.p.) before isoproterenol bitartrate (ISO) administration (25 mg/kg body weight (b.w.) subcutaneously,s.c.) and their effect on rat heart mitochondrial structure and function was studied. Biochemical changes in activity of biomarkers of oxidative stress, antioxidant enzymes as well as Krebs' cycle enzymes were analyzed. Gene expression studies and Isothermal titration calorimetric studies with pure catalase and ISO were also carried out. Key findingsMelatonin was shown to reduce ISO induced oxidative stress, by stimulating superoxide dismutase activity and removing the inhibition of Krebs' cycle enzymes. Herein we report for the first time in rat model that melatonin activates the SIRT1-PGC-1α-SIRT3 signaling pathways after ISO administration, which ultimately induces mitochondrial biogenesis. Melatonin exhibited significant protection of mitochondrial architecture and topology along with increased calcium ion permeability and reactive oxygen species (ROS) generation induced by ISO. Isothermal calorimetric studies revealed that melatonin binds to ISO molecules and sequesters them from the reaction thereby limiting their interaction with catalase along with occupying the binding sites of catalase themselves. SignificanceActivation of SIRT1-PGC-1α-SIRT3 pathway by melatonin along with its biophysical properties prevents ISO induced mitochondrial injury in rat heart.

Potent Inhibition of Mandelate Racemase by Boronic Acids: Boron as a Mimic of a Carbon Acid Center.

Boronic acids have been successfully employed as inhibitors of hydrolytic enzymes. Typically, an enzymatic nucleophile catalyzing hydrolysis adds to the electrophilic boron atom forming a tetrahedral species that mimics the intermediate(s)/transition state(s) for the hydrolysis reaction. We show that para-substituted phenylboronic acids (PBAs) are potent competitive inhibitors of mandelate racemase (MR), an enzyme that catalyzes a 1,1-proton transfer rather than a hydrolysis reaction. The Ki value for PBA was 1.8 ± 0.1 μM, and p-Cl-PBA exhibited the most potent inhibition (Ki = 81 ± 4 nM), exceeding the binding affinity of the substrate by ∼4 orders of magnitude. Isothermal titration calorimetric studies with the wild-type, K166M, and H297N MR variants indicated that, of the two Brønsted acid-base catalysts Lys 166 and His 297, the former made the greater contribution to inhibitor binding. The X-ray crystal structure of the MR·PBA complex revealed the presence of multiple H-bonds between the boronic acid hydroxyl groups and the side chains of active site residues, as well as formation of a His 297 Nε2-B dative bond. The dramatic upfield change in chemical shift of 27.2 ppm in the solution-phase 11B nuclear magnetic resonance spectrum accompanying binding of PBA by MR was consistent with an sp3-hybridized boron, which was also supported by density-functional theory calculations. These unprecedented findings suggest that, beyond substituting boron at carbon centers participating in hydrolysis reactions, substitution of boron at the acidic carbon center of a substrate furnishes a new approach for generating inhibitors of enzymes catalyzing the deprotonation of carbon acid substrates.

Differential interaction of cerium chloride with bovine liver catalase: A computational and biophysical study

In this study, Cerium chloride-induced conformational changes of Bovine Liver Catalase (BLC) has been investigated by molecular docking and further supported by various biophysical techniques. The temporal change of catalytic activity of BLC has also been studied in presence of Ce(III) with different buffer solution in vitro at 25 °C. The differential binding of Ce(III) to BLC observed by simulation study was well supported by the differential regulation of BLC activity in different buffers. After 1 h of incubation with CeCl3, the reduction in activity of BLC was maximum in MOPS, HEPES and Tris buffer, whereas no change in activity was noticed in phosphate buffer. Isothermal Titration Calorimetric (ITC) study also supports the differential binding of Ce(III) to BLC in different buffers. Ce(III)-induced conformational transition in BLC was followed as a function of concentration. Nevertheless, with 24 h incubation of CeCl3 the activity of BLC was highest with higher molar concentration of CeCl3 suggesting the conformational stability of BLC in presence of Ce(III). The compromised activity of BLC in response to Ce(III) is due to the induced conformational change and the degree of change in secondary conformation of BLC was maximum in MOPS, HEPES and Tris and least in phosphate buffer. Therefore, the reduced activity of BLC is controlled by the direct interaction of Ce(III) in the active site of BLC in Tris buffer or indirect interaction of Ce(III) in the non-active site of BLC in MOPS and HEPES buffer.

Alkali induced unique partially folded state of bovine serum albumin: qualitative and quantitative insights

Qualitative and quantitative understanding of partially folded states of protein is essential in gaining deeper insights into folding pathways. We have observed a partially folded state of bovine serum albumin (BSA) in the presence of 2,2,2-trifluoroethanol at pH11.2 which does not resembles the properties of the molten globule state. ThT, a frequently used marker for protein fibrils have two order of greater affinity towards the intermediate state at pH11.2 compared to native BSA at pH7.4. Surprisingly, the binding of ANS with this partially folded state is weaker than that of native state of BSA. Combined fluorescence, circular dichroism spectroscopy and isothermal titration calorimetric studies indicate that for such partially folded state, ThT is a better marker compared to ANS. The results have highlighted the importance of dyes like ThT in characterizing partilally folded states of protein which might appear as intermediates in the funnel moldel describing the protein folding pathway.

Chitooligosaccharide binding to CIA17 (Coccinia indica agglutinin). Thermodynamic characterization and formation of higher order complexes

CIA17 is a PP2-like, homodimeric lectin made up of 17 kDa subunits present in the phloem exudate of ivy gourd (Coccinia indica). Isothermal titration calorimetric (ITC) studies on the interaction of chitooligosaccharides [(GlcNAc)2–6] showed that the dimeric protein has two sugar binding sites which recognize chitotriose with ~70-fold higher affinity than chitobiose, indicating that the binding site is extended in nature. ITC, atomic force microscopic and non-denaturing gel electrophoresis studies revealed that the high-affinity interaction of CIA17 with chitohexaose (Ka = 1.8 × 107 M−1) promotes the formation of protein oligomers. Computational studies involving homology modeling, molecular docking and molecular dynamics simulations on the binding of chitooligosaccharides to CIA17 showed that the protein binding pocket accommodates up to three GlcNAc residues. Interestingly, docking studies with chitohexaose indicated that its two triose units could interact with binding sites on two protein molecules to yield dimeric complexes of the type CIA17-(GlcNAc)6-CIA17, which can extend in length by the binding of additional chitohexaose and CIA17 molecules. These results suggest that PP2 proteins play a role in plant defense against insect/pathogen attack by directly binding with the higher chain length chitooligosaccharides and forming extended, filamentous structures, which facilitate wound sealing.