Base Pairing at the Stem-loop Junction in the SL1 Kissing Complex of HIV-1 RNA: A Thermodynamic Study Probed by Molecular Dynamics Simulation

Abstract

The thermodynamics of the opening/closure process of a GC base pair located at the stem-loop junction of the SL1 sequence from HIV-1_Lai genomic RNA was investigated in the context of a loop-loop homodimer (or kissing complex) using molecular dynamics simulation. The free energy, enthalpy and entropy changes for the closing reaction are 0 kcal·mol^?1, ?11 kcal·mol^?1and ?0.037 kcal·mol^?1-K^?1 at 300° K respectively. Furthermore it is found that the free energy change is the same for the formation of a 11 nucleotide loop closed with UG and for the formation of a 9 nucleotide loop closed with GC. Our study evidences the high flexibility of the nucleotides at the stem-loop junction explaining the weak stability of this structure.     

Kinetics and thermodynamics of catalysis and thermal inactivation of a novel α-amylase (Tp-AmyS) from Thermotoga petrophila

Abstract

This research is focussed on kinetic, thermodynamic and thermal inactivation of a novel thermostable recombinant α-amylase (Tp-AmyS) from Thermotoga petrophila. The amylase gene was cloned in pHIS-parallel1 expression vector and overexpressed in Escherichia coli. The steady-state kinetic parameters (V_max, K_m, k_cat and k_cat/K_m) for the hydrolysis of amylose (1.39?mg/min, 0.57?mg, 148.6?s^?1, 260.7), amylopectin (2.3?mg/min, 1.09?mg, 247.1?s^?1, 226.7), soluble starch (2.67?mg/min, 2.98?mg, 284.2?s^?1, 95.4) and raw starch (2.1?mg/min, 3.6?mg, 224.7?s^?1, 61.9) were determined. The activation energy (E_a), free energy (ΔG), enthalpy (ΔH) and entropy of activation (ΔS) at 98?°C were 42.9?kJ mol^?1, 74?kJ mol^?1, 39.9?kJ mol^?1 and ?92.3 J mol^?1 K^?1, respectively, for soluble starch hydrolysis. While ΔG of substrate binding (ΔG_E-S) and ΔG of transition state binding (ΔG_E-T) were 3.38 and ?14.1?kJ mol^?1, respectively. Whereas, EaD, Gibbs free energy (ΔG*), increase in the enthalpy (ΔH*) and activation entropy (ΔS*) for activation of the unfolding of transition state were 108, 107, 105?kJ mol^?1 and ?4.1 J mol^?1 K^?1. The thermodynamics of irreversible thermal inactivation of Tp-AmyS revealed that at high temperature the process involves the aggregation of the protein.     

Evaluation of the effect of Tb(IV)-NR complex on herring sperm DNA genetic information by mean of spectroscopic

Abstract

The interaction between Tb(IV)-NR complex and herring sperm DNA in buffer solution of Tris-HCl was investigated with the use of acridine orange(AO) as a spectral probe. The binding modes and other information were provided by the UV–spectrophotometry and fluorescence spectroscopy. The thermodynamic functions expressed that the binding constants of Tb(IV)-NR complex with DNA was K^θ_298.15K = 4.03?×?10⁵?L·mol^?1, K^θ_310.15K =1.30?×?10⁷?L·mol^?1, and the Δ_rGθ m _298.15?K＝?3.20?×?10⁴ J·mol^?1. The scatchard equation suggested that the interaction mode between Tb(IV)-NR complex and herring sperm DNA is electrostatic and weak intercalation bindings. FTIR spectroscopy results also indicate that there is a specific interaction between the Tb(IV)-NR complex and the A and G bases of DNA.     

Binding of Paeonol to Human Serum Albumin: A Hybrid Spectroscopic Approach and Conformational Study

The purpose of this study was to elucidate the binding of paeonol to human serum albumin (HSA) through spectroscopic methods. The fluorescence quenching of HSA by paeonol was a result of the formation of the HSA–paeonol complex with low binding affinity (K = 4.45 × 10³ M^?1 at 298 K). Thermodynamic parameters (ΔG^○ = –2.08 × 10⁴ J·mol^?1, ΔS^○ = 77.9 J·mol^?1·K^?1, ΔH^○ = 2.41 × 10³ J·mol^?1, k_q = 9.67 × 10¹² M^?1·s^?1) revealed that paeonol mainly binds HSA through hydrophobic force following a static quenching mode. The binding distance was estimated to be 1.91 nm by fluorescence resonant energy transfer. The conformation of HSA was changed and aggregates were formed in the presence of paeonol, revealed by synchronous fluorescence, circular dichroism, Fourier transform infrared spectroscopy, three‐dimensional fluorescence spectroscopy, and resonance light scattering results.     

Structural and functional studies on a variant of cystatin purified from brain of Capra hircus

Cystatins, known for their ubiquitous presence in mammalian system are thiol protease inhibitors serving important physiological functions. Here, we present a variant of cystatin isolated from brain of Capra hircus (goat) which is glycosylated but lacks disulphide bonds. Caprine brain cystatin (CBC) was isolated using alkaline treatment, ammonium sulphate fractionation (40–60%) and gel filtration chromatography on Sephacryl S-100HR column with an overall yield of 26.29% and 322-fold purification. The inhibitor gave a molecular mass of ~44 kDa as determined by SDS-PAGE and gel filtration behaviour. The Stokes radius and diffusion coefficient of CBC were 27.14 Å and 8.18 × 10^?7 cm² s^?1, respectively. Kinetic data revealed that CBC inhibited thiol proteases reversibly and competitively, with the highest inhibition towards papain (K_i = 4.10 nM) followed by ficin and bromelain. CBC possessed 34.7% α-helical content as observed by CD spectroscopy. UV, fluorescence, CD and FTIR spectroscopy revealed significant conformational change upon CBC-papain complex formation. Isothermal titration calorimetry (ITC) was used to measure the thermodynamic parameters – ΔH, ΔS, ΔG along with N (binding stoichiometry) for CBC-papain complex formation. Binding stoichiometry (N = .97 ± .07 sites) for the CBC-papain complex indicates that cystatin is surrounded by nearly one papain molecule. Negative ΔH (?5.78 kcal mol^?1) and positive ΔS (11.01 cal mol^?1 deg^?1) values suggest that the interaction between CBC and papain is enthalpically as well as entropically favoured process. The overall negative ΔG (?9.19 kcal mol^?1) value implies a spontaneous CBC-papain interaction.     

Kinetic studies on the binding of Streptomyces subtilisin inhibitor with subtilisin BPN′

The binding mechanism of Streptomyces subtilisin inhibitor and subtilisin BPN′ was studied kinetically with the stopped-flow method by monitoring the protein fluorescence increase due to complex formation. In the lower concentration range of proteins, the reaction followed the second-order kinetics. The pH dependence of the apparent second-order rate constant, k_on, suggested the involvement of the two ionizable groups of pK_a of 7.8 and 10 in the binding. The activation parameters were calculated from the temperature dependence of the apparent second-order rate constants. The value of the apparent activation energy (E_A = 39.7 kJ · mol^?1, 9.50 kcal · mol^?1) and insensitivity of k_on to the viscosity of the medium suggest that the binding is not a simple diffusion-controlled bimolecular association. Further studies with a much broader range of protein concentrations have revealed that the reaction tends to approach first-order kinetics as the inhibitor concentration increases. The binding reaction is, therefore, reconcilable with a two-step mechanism, in which a fast bimolecular association is followed by a slow unimolecular isomerization step; the dissociation constant of the first step, K_L, is estimated to be 1.2 × 10^?4m and the rate constant of the second step, k₊₂, to be 770 s^?1. It was also found that the increase of tryptophan fluorescence due to the complex formation occurs solely in the rate-determining unimolecular process.     

Kinetic and thermodynamics study of the pyrolytic process of the freshwater macroalga,Chara vulgaris

This is the first study where the pyrolysis of the freshwater macroalga Chara vulgaris was explored to reveal its bioenergy potential. The suitability of C. vulgaris to bioenergy conversion via pyrolysis was accessed in terms of kinetic triplet and thermodynamic parameters. For this purpose, pyrolysis experiments under a thermogravimetric scale were conducted at multiple heating rates (5, 10, and 20 °C min^?1) in an inert atmosphere. The mass-loss profiles of C. vulgaris pyrolysis showed that there are two dominant decomposition stages that are related to distinct chemical components inside its structure and that directly affect the calculated kinetic triplet and thermodynamics parameters. The average activation energy obtained using isoconversional methods of Flynn-Wall-Ozawa, Kissinger-Akahira-Sunose, Starink, and Friedman was in the range of 52.87–72.91 kJ mol^?1 for the first decomposition stage and 156.14–174.65 kJ mol^?1 for the second decomposition stage. The pyrolytic conversion of C. vulgaris initially follows a second-order reaction model (first decomposition stage), while in second decomposition stage is controlled by a second-order Avrami-Erofeev reaction model. The kinetic results derived from the non-isothermal decomposition of C. vulgaris proved its suitable characteristics for pyrolysis. Additionally, multi-stage kinetic interpretation was successfully attained based on two kinetic triplets, where reconstructed pyrolysis behavior correlated well with experimental pyrolysis behavior. The changes in enthalpy, Gibbs free energy, and entropy for first decomposition stage were 67.58±0.25 kJ mol^?1, 180.77±5.30 kJ mol^?1, and ?176.65±0.41 J mol^?1 K^?1, and for the second decomposition stage the values were 166.70±0.09 kJ mol^?1, 285.51±1.29 kJ mol^?1, and ?124.29±0.09 J mol^?1 K^?1, respectively. Based on thermodynamic aspects, C. vulgaris is particularly interesting for use as a raw material to produce biofuels and bioenergy.

     

Probing the intermolecular interactions into serum albumin and anthraquinone systems: a spectroscopic and docking approach

Intermolecular interaction study of human serum albumin (HSA) with two anthraquinones i.e. danthron and quinizarin has been performed through fluorescence, UV-vis and CD spectroscopy along with docking analysis. The titration of drugs into HSA solution brought about the quenching of fluorescence emission by way of complex formation. The binding constants were found to be 1.51 × 10⁴ L mol^?1 and 1.70 × 10⁴ L mol^?1 at λ_exc = 280 nm while at λ_exc = 295 nm, the values of binding constants were 1.81 × 10⁴ L mol^?1 and 1.90 × 10⁴ L mol^?1 which hinted toward binding of both the drugs in the vicinity of subdomain IIA. Different temperature study revealed the presence of static quenching mechanism. Moreover, more effective quenching of the fluorescence emission was observed at λ_exc = 295 nm which also suggested that both the drug molecule bind nearer to Trp-214. Thermodynamic parameters showed that hydrophobic interaction was the major force behind the binding of drugs. The UV-vis spectroscopy testified the formation of complex in both the systems and primary quenching mechanism as static one. The changes in secondary structure and α-helicity in both the systems were observed by circular dichroism spectroscopy. Furthermore, molecular docking analysis predicted the probable binding site of drugs in subdomain IIA of HSA molecule. The types of amino acid residues surrounding the drug molecule advocated that van der Waals forces, hydrophobic forces and electrostatic forces played a vital role in the stabilization of drug-protein complex formed.     

Microbial cell disruption for improving lipid recovery using pressurized CO2: Role of CO2 solubility in cell suspension,sugar broth,and spent media

The study of in situ gas explosion to lyse the triglyceride‐rich cells involves the solubilization of gas (e.g., carbon dioxide, CO₂) in lipid‐rich cells under pressure followed by a rapid decompression, which allows the gas inside the cell to rapidly expand and rupture the cell from inside out. The aim of this study was to perform the cell disruption using pressurized CO₂ as well as to determine the solubility of CO₂ in Rhodotorula glutinis cell suspension, sugar broth media, and spent media. Cell disruption of R. glutinis was performed at two pressures of 2,000 and 3,500 kPa, respectively, at 295.2 K, and it was found from both scanning electron microscopy (SEM) and plate count that a substantial amount of R. glutinis was disrupted due to the pressurized CO₂. We also found a considerable portion of lipid present in the aqueous phase after the disruption at P = 3,500 kPa compared to control (no pressure) and P = 2,000 kPa, which implied that more intracellular lipid was released due to the pressurized CO₂. Solubility of CO₂ in R. glutinis cell suspension was found to be higher than the solubility of CO₂ in both sugar broth media and spent media. Experimental solubility was correlated using the extended Henry's law, which showed a good agreement with the experimental data. Enthalpy and entropy of dissolution of CO₂ were found to be ?14.22 kJ mol^?1 and 48.10 kJ mol^?1 K^?1, 9.64 kJ mol^?1 and 32.52 kJ mol^?1 K^?1, and 7.50 kJ mol^?1 and 25.22 kJ mol^?1 K^?1 in R. glutinis, spent media, and sugar broth media, respectively. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:737–748, 2017     

Multi-spectroscopic and voltammetric evidences for binding,conformational changes of bovine serum albumin with thiamine

The interaction between thiamine hydrochloride (TA) and bovine serum albumin (BSA) was investigated by fluorescence, FTIR, UV–vis spectroscopic and cyclic voltammetric techniques under optimised physiological condition. The fluorescence intensity of BSA is gradually decreased upon addition of TA due to the formation of a BSA–TA complex. The binding parameters were evaluated and their behaviour at different temperatures was analysed. The quenching constants (K_sv) obtained were 2.6 × 10⁴, 2.2 × 10⁴ and 2.0 × 10⁴ L mol^?1 at 288, 298 and 308 K, respectively. The binding mechanism was static-type quenching. The values of ΔH° and ΔS° were found to be 26.87 kJ mol^?1 and 21.3 J K^?1 mol^?1, and indicated that electrostatic interaction was the principal intermolecular force. The changes in the secondary structure of BSA upon interaction with TA were confirmed by synchronous and 3-D spectral results. Site probe studies reveal that TA is located in site I of BSA. The effects of some common metal ions on binding of BSA–TA complex were also investigated.     

Complex formation with alkali and alkaline earth metal ions of cyclic octapeptides,cyclo(Phe-Pro)4, cyclo(Leu-Pro)4, and cyclo[Lys(Z)-Pro]4

Complex formation with alkali and alkaline earth metal ions of cyclic octapeptides, cyclo(Phe-Pro)₄, cyclo(Leu-Pro)₄, and cyclo[Lys(Z)-Pro]₄ was investigated in relation to conformation. In an alcohol solution, cyclo(Phe-Pro)₄ did not form complexes. However, cyclo(Leu-Pro)₄ and cyclo[Lys(Z)-Pro]₄ formed complexes selectively with Ba²⁺ and Ca²⁺ ions. Changing the solvent from alcohol to acetonitrile, the complexation behavior was very different. In acetonitrile, cyclo(Phe-Pro)₄ was found to form a complex with Ba²⁺, and CD spectra of cyclo(Leu-Pro)₄ and cyclo[Lys(Z)-Pro]₄ changed sharply on complexation with K⁺. Rate constants of the complex formation between the cyclic octapeptides and metal salts were in the range of 0.7–12 L mol^?1 min^?1 in an alcohol solution. One of the two types of complex formation in acetonitrile was much faster than that in an alcohol solution.     

Interaction between tryptophan‐Sm(III) complex and DNA with the use of a acridine orange dye fluorophor probe

The interaction of the Trp–Sm(III) complex with herring sperm DNA (hs‐DNA) was investigated with the use of acridine orange (AO) dye as a spectral probe for UV‐vis spectrophotometry and fluorescence spectroscopy. The results showed that the both the Trp–Sm(III) complex and the AO molecule could intercalate into the double helix of the DNA. The Sm(III)–(Trp)₃ complex was stabilized by intercalation into the DNA with binding constants: K^?_25°C = 7.14 × 10⁵ L·mol^?1 and K^?_37°C = 5.28 × 10⁴ L·mol^?1, and it could displace the AO dye from the AO–DNA complex in a competitive reaction. Computation of the thermodynamic functions demonstrates that Δ_rH_m^? is the primary driving power of the interaction between the Sm(III)(Trp)₃ complex and the DNA. The results from Scatchard and viscometry methods suggested that the interaction mode between the Sm(III)(Trp)₃ complex and the hs‐DNA is groove binding and weak intercalation binding. Copyright © 2015 John Wiley & Sons, Ltd.     

Dynamics of molecular organization in agarose sulphate

Nongelling solutions of structurally regular chain segments of agarose sulphate show disorder–order and order–disorder transitions (as monitored by the temperature dependence of optical rotation) that are closely similar to the conformational changes that accompany the sol–gel and gel–sol transitions of the unsegmented polymer. The transition midpoint temperature (T_m) for formation of the ordered structure on cooling is ～25 K lower than T_m for melting. Salt-induced conformational ordering, monitored by polarimetric stopped-flow, occurs on a millisecond time scale, and follows the dynamics expected for the process 2 coil ? helix. The equilibrium constant for helix growth (s) was calculated as a function of temperature from the calorimetric enthalpy change for helix formation (ΔH_cal = ?3.0 ± 0.3 kJ per mole of disaccharide pairs in the ordered state), measured by differential scanning calorimetry. The temperature dependence of the nucleation rate constant (k_nuc), calculated from the observed second-order rate constant (k_obs) by the relationship k_obs = k_nuc(1 ? 1/s) gave the following activation parameters for nucleation of the ordered structure of agarose sulphate (1 mg mL^?1; 0.5M Me₄NCl or KCl): ΔH* = 112 ± 5 kJ mol^?1; ΔS* = 262 ± 20 J mol^?1 K^?1; ΔG*₂₉₈ = 34 ± 6 kJ mol^?1; (k_nuc)₂₉₈ = (7.5 ± 0.5) × 10⁶ dm³ mol^?1 s^?1. The endpoint of the fast relaxation process corresponds to the metastable optical rotation values observed on cooling from the fully disordered form. Subsequent slow relaxation to the true equilibrium values (i.e., coincident with those observed on heating from the fully ordered state) was monitored by conventional optical rotation measurements over several weeks and follows second-order kinetics, with rate constants of (2.25 ± 0.07) × 10^?4 and (3.10 ± 0.10) × 10^?4 dm³ mol^?1 s^?1 at 293.7 and 296.2 K, respectively. This relaxation is attributed to the sequential aggregation processes helix + helix → dimer, helix + dimer → trimer, etc., with depletion of isolated helix driving the much faster coil–helix equilibrium to completion. Light-scattering measurements above and below the temperature range of the conformational transitions indicate an average aggregate size of 2–3 helices.     

Studies on the Redox Characteristics of Ferrioxamine E

Thermodynamic parameters for the reduction of ferrioxamine E as calculated from redox potentials determined at four different temperatures were found to be ΔH ^≠ =7.1±3.4 kJ mol^?1 and ΔS^≠=?146 J mol^?1 K^?1. The negative entropy value is large, because the decrease in the charge at the metal center and an increase in its ionic radius force the structure of the complex to become less rigid and resemble the desferrisiderophore. The hydrophilic groups of the system are now (relatively more) available for solvent interaction. Thus, a large negative entropy change accompanies the reduction of the complex. Kinetics of reduction of ferrioxamine by V^II, Cr^II, Eu^II, and dithionite were measured at different temperatures and by dithionite at different pH values. The Cr^II and Eu^II reactions proceed by an inner‐sphere mechanism and have second‐order rate constants at 25° of 1.37×10⁴ and 1.23×10⁵ M ^?1 s^?1, respectively. For the V^II reduction, the corresponding rate constant was 1.89×10³ M ^?1 s^?1. The activation parameters for the V^II reduction were ΔH^≠ = 8.3 kJ mol^?1; ΔS^≠ = ?154 J mol^?1 K^?1. These values are indicative of an outer‐sphere mechanism for V^II reduction. The reduction by dithionite is half order in dithionite concentration indicating that SO ^. is the sole reducing species. log of reduction rate constants of different trihydroxamates by this reductant were correlated with their respective redox potentials, and the variation was found to be in approximate correspondence with the expectations of Marcus relationship.     

The uptake of nitrate and ammonium nitrogen in Chara hispida L.: the contribution of the rhizoid

Abstract The uptake of ammonium and nitrate nitrogen by cultured plants of the green freshwater alga Chara hispida L. has been compared quantitatively with the contribution of its rhizoidal tissue. In the short-term, the rhizoid takes up 7–20% of the ammonium nitrogen, and about 15% of the nitrate that is taken up by whole plants under similar conditions. The uptake was studied over a range of both temperatures and external concentrations. The apparent activation energy for the uptake of NH₄⁺ and NO₃^? by the whole plant was found to be 50 kJ mol^?1 and 30 kJ mol^?1, respectively. For the rhizoid, the values were similar for both nitrogenous ions, 106 kJ mol^?1 and 70–100 kJ mol^?1. The rhizoidal uptake mechanism for ammonium nitrogen operates more efficiently compared to that in the whole plant. Nitrate is taken up by the rhizoid by a mechanism with a substrate affinity higher than in the plant taken as a whole. The possible ecological significance of the results is discussed.     

Quantification of oxygen production and respiration rates in mixotrophic cultivation of microalgae in nonstirred photobioreactors

Online monitoring and controlling of different cellular parameters are key issues in aerobic bioprocesses. Since mixotrophic cultivation, in which we observe a mixture of cellular respiration and oxygen production has gained more popularity, there is a need for an on‐process quantification of these parameters. The presented and adapted double gassing‐out method applied to a mixotrophic cultivation of Galdieria sulphuraria , will be a tool for monitoring and further optimization of algal fermentation in nonstirred photobioreactors (PBR). We measured the highest net specific oxygen production rate (opr _net) as 5.73 · 10^?3 mol_O2 g^?1 h^?1 at the lowest oxygen uptake rate (OUR) of 1.00 · 10^?4 mol_O2 L^?1 h^?1. Due to higher cell densities, we also demonstrated the increasing shading effect by a decrease of opr _net, reaching the lowest value of 1.25 10^?5 mol_O2 g^?1 h^?1. Nevertheless, with this on process measurement, we can predict the relation between the zone in which oxygen is net produced to the area where cell respiration dominates in a PBR, which has a major impact to optimize cell growth along with the formation of different products of interest such as pigments.     

Structurally symmetrical,easily polarizable hydrogen bonds between side chains in proteins and proton-conducting mechanisms. III

(L -Cys)_n, (L -Lys)_n, and (L -Glu)_n were studied by ir spectroscopy in terms of their degree of deprotonation or protonation. It is shown that structurally symmetrical, easily polarizable SH ?S^? ? ^?S ?HS, N⁺H ?N ? N ?H⁺N, and OH ?O^? ? ^?O ?HO hydrogen bonds are formed between the side chains. The different wave number distributions of the ir continua caused by these hydrogen bonds show that the barrier in the double-minimum proton potential decreases in the series of these hydrogen bonds. The stability of these hydrogen bonds against hydration increases in this series. The OH ?O^? ? ^?O ?HO bonds are not broken by small amounts of water. With (L -Cys)_n the formation of easily polarizable hydrogen bonds and a β-structure–coil transition are strongly interdependent. As a result of this coupling effect, the β-structure–coil transition becomes cooperative. With (L -Glu)_n, the formation of the polarizable hydrogen bonds and the observed conformational change are independent processes. The (L -Glu)_n conformation changes from α-helix to coil only if more than 80% of the residues are deprotonated. Finally, on the basis of the various types of easily polarizable hydrogen bonds, charge shifts in active centers of enzymes and the proton-conducting mechanism through hydrophobic regions of biological membranes are discussed.     

The Interaction of Chromium(VI) with Urease in Solution

The interaction between K₂Cr₂O₇ and urease was investigated using fluorescence, UV-vis absorption, and circular dichroism (CD) spectroscopy. The experimental results showed that the fluorescence quenching of urease by K₂Cr₂O₇ was a result of the formation of K₂Cr₂O₇–urease complex. The apparent binding constant K _A between K₂Cr₂O₇ and urease at 295, 302, and 309 K were obtained to be 2.14?×?10⁴, 1.96?×?10⁴, and 1.92?×?10⁴ L mol^?1, respectively. The thermodynamic parameters, ΔH° and ΔS° were estimated to be ?5.90 kJ mol^?1, 43.67 J mol^?1 K^?1 according to the Van’t Hoff equation. The electrostatic interaction played a major role in stabilizing the complex. The distance r between donor (urease) and acceptor (K₂Cr₂O₇) was 5.08 nm. The effect of K₂Cr₂O₇ on the conformation of urease was analyzed using UV-vis absorption, CD, synchronous fluorescence spectroscopy, and three-dimensional fluorescence spectra, the environment around Trp and Tyr residues were altered.     

Thermodynamics of the slow–fast transition in bacteriophage T2L

We have measured the thermodynamic parameters of the slow-fast tail-fiber reorientation transition on T2L bateriophage. Proportions of the virus in each form were determined from peak-height measurements in sedimention-velocity runs and from average diffusion coefficients obtained by quasielastic laser light scattering. Computer simulation of sedimentation confirmed that there were no undetected intermediates in the transition, which was analyzed as a two-state process. Van't Hoff-type plots of the apparent equilibrium constant and of the pH midpoint of the transition as function of reciprocal temperature led to the following estimates of the thermodynamic parameters for the transition at pH 6.0 and 20°C: ΔH° = ?139 ± 18Kcal mol^?1, ΔS° = ?247 ± 46 cal K^?1 mol^?1, and ΔG° = ?66 ± 22 kcal mol^?1. Per mole of protons taken up in the transition, the analogous quantities were ?15.9 ± 1.7 kcal mol^?1, ?26.3 ± 2.2 cal K^?1 mol^?1, and ?8.22 ± 1.8 kcal mol^?1. The net number of protons taken up was about 8.5 ± 1.5. The large values of the thermodynamic functions are consistent with a highly cooperative reaction and with multiple interactions between the fibres and the remainder of the phage. The negative entropy of the transition is probably due to immobilization of the fibres.     

Interaction of a tyrosine kinase inhibitor,vandetanib with human serum albumin as studied by fluorescence quenching and molecular docking

Interaction of a tyrosine kinase inhibitor, vandetanib (VDB), with the major transport protein in the human blood circulation, human serum albumin (HSA), was investigated using fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and molecular docking analysis. The binding constant of the VDB–HSA system, as determined by fluorescence quenching titration method was found in the range, 8.92–6.89?×?10^3?M^?1 at three different temperatures, suggesting moderate binding affinity. Furthermore, decrease in the binding constant with increasing temperature revealed involvement of static quenching mechanism, thus affirming the formation of the VDB–HSA complex. Thermodynamic analysis of the binding reaction between VDB and HSA yielded positive ΔS (52.76 J?mol^?1 K^?1) and negative ΔH (?6.57?kJ?mol^?1) values, which suggested involvement of hydrophobic interactions and hydrogen bonding in stabilizing the VDB–HSA complex. Far-UV and near-UV CD spectral results suggested alterations in both secondary and tertiary structures of HSA upon VDB-binding. Three-dimensional fluorescence spectral results also showed significant microenvironmental changes around the Trp residue of HSA consequent to the complex formation. Use of site-specific marker ligands, such as phenylbutazone (site I marker) and diazepam (site II marker) in competitive ligand displacement experiments indicated location of the VDB binding site on HSA as Sudlow’s site I (subdomain IIA), which was further established by molecular docking results. Presence of some common metal ions, such as Ca²⁺, Zn²⁺, Cu²⁺, Ba²⁺, Mg²⁺, and Mn²⁺ in the reaction mixture produced smaller but significant alterations in the binding affinity of VDB to HSA.