Thermodynamic investigation of a new water-soluble porphyrin with calf thymus DNA

The equilibrium binding of a new water-soluble tetra-cationic porphyrin, 5-(1-(4-carboxybutyl)‎pyridinium-4-yl)10,15,20-tris(1-methylpyridinium-4-yl)‎porphyrin (5-CBPyP) with calf thymus DNA in comparison with meso-tetrakis(4-N-methyl‎pyridinium)porphyrin (TMPyP) has been studied in 7.5 mM phosphate buffer, pH=7.2; and at various temperatures by UV-Vis absorption, fluorescence spectroscopies and viscosity measurement. The thermodynamic parameters were calculated by van't Hoff equation at various temperatures. The values of -137.13±1.22 kJ/mol and -337.21±4.75 J/mol.K for 5-CBPyP and -159.12±1.22 kJ/mol and -406.11±4.45 J/mol.K for TMPyP, were estimated for enthalpy and entropy changes of interaction, respectively. The data indicate that the process is exothermic and enthalpy driven suggesting that electrostatic forces play a considerable role in the interaction process. The results of spectroscopic techniques and viscosity measurement represent the intercalation mode of binding for both porphyrins and higher binding affinity of TMPyP respect to 5-CBPyP

Analysis of oxygen binding by hemoglobin on the basis of mean intrinsic thermodynamic quantities

The binding data for oxygenation of human hemoglobin, Hb, at various temperatures and in the absence and presence of 2,3-diphosphoglycerate, DPG, and inositol hexakis phosphate, IHP, were analyzed for extraction of mean intrinsic Gibbs free energy, ΔGo, enthalpy, ΔHo, and entropy, ΔSo, of binding at various partial oxygen pressures. This method of analysis considers all the protein species present such as dimer and tetramer forms which were not considered by Imai et al. (Imai K et al., 1970, Biochim Biophys Acta 200: 189 - 196) , in their analysis which was based on Adair equation. In this regard, the values of Hill equation parameters were estimated with high precision at all points of the binding curve and used for calculation of ΔGo, ΔHo and ΔSo were also calculated by analysis of ΔGo values at various temperatures using van't Hoff equation. The results represent the enthalpic nature of the cooperativity in Hb oxygenation and the compensation effect of intrinsic entropy. The interpretation of results also to be, into account the decrease of the binding affinity of sites for oxygen in the presence of DPG and IHP without any considerable changes in the site - site interaction (extent of cooperativity). In other words, the interactions between bound ligands, organic phosphates and oxygen, are more due to a decreasing binding affinity and not to the reduction of the cooperative interaction between sites. The results also document the more heterotropic effect of IHP compared to DPG

Spectroscopic Studies on the Interaction of a Water-Soluble Cationic Porphyrin with Bovine Serum Albumin

The interaction of a water-soluble cationic porphyrin, Cobalt(III) 5, 10, 15, 20-tetrakis (1-methylpyridinium-4-yl) porphyrin [Co(III)TMPyP], with bovine serum albumin (BSA) has been studied in 1 mM phosphate buffer pH 7.0 containing 5 mM NaCl by UV-vis absorption, resonance light scattering (RLS) and fluorescence spectroscopies at 25°C. The results of RLS studies represent no aggregate formation of porphyrin in the surface of BSA and low tendency of this porphyrin for aggregate formation

Fluorescence spectroscopic study on interaction of retinol with β-lactoglobulin in the presence of cetylpyridinium chloride

International audienceIn our previous study thermodynamic denaturation of bovine β-lactoglobulin variant A (BLG-A), has been investigated in the presence of cetylpyridinium chloride (CPC) as a cationic surfactant. Here, the retinol binding property of BLG was determined at 298 K and pH 8.0 by spectrofluorimeter titration method, in the presence of CPC to elucidate the still unknown structure-function relationship in this protein. Comparison of the results allowed determining the binding of retinol by BLG in the presence of CPC. The two-way chemometrics method was used, to estimate the equilibrium concentration of components by analysis of fluorescence emission spectrum, in order to obtain its equilibrium concentration. The results indicate that the retinol binding properties of BLG do not show significant changes in the presence of this surfactant

Interaction of β-Lactoglobulin with Resveratrol : Molecular Docking and Molecular Dynamics Simulation Studies

International audienceIn this work, the interaction of trans-resveratrol, as a natural polyphenolic compound, and Bovine β-lactoglobulin (BLG), was studied using molecular docking and molecular dynamics simulation methods. The molecular dynamics study makes an importantcontribution to understanding the effect of the binding of resveratrol on conformational changes of BLG and the stability of a protein-drug complex system in aqueous solution. Molecular docking studies revealed that the resveratrol was bound to the surface of the protein by two hydrogen bond interactions. The binding constant and free energy change, ΔG°, for the binding of resveratrol to BLG were about 6.6 × 105 mol L–1 and –33.4 kJ mol–1, respectively. Furthermore, the results of molecular dynamics simulation represented that the rmsd of unliganded BLG and BLG-resveratrol complex reached equilibration and oscillated around the average value after 600 ps simulation time. The study of the radius of gyration (Rg) revealed that BLG and BLG-resveratrol complexeswere stabilized around 1500 ps and also exhibited no conformational change. Finally, analyzing the rms fluctuations suggested that the structure of the ligand binding site remains approximately rigid during the simulation

Thermal stability of pepsin: A predictive thermodynamic model of a multi-domain protein

Pepsin is generally used in the preparation of F(ab)2 fragments from antibodies. The antibodies that are one of the largest and fastest growing categories of bio- pharmaceutical candidates. Differential scanning calorimetric is principally suitable method to follow the energetics of a multi-domain, fragment to perform a more exhaustive description of the thermodynamics in an associating system. The thermodynamical models of analysis include the construction of a simultaneous fitting of a theoretical expression. The expression depending on the equilibrium unfolding data from multimeric proteins that have a two-state monomer. The aim of the present study is considering the DSC data in connection with pepsin going through reversible thermal denaturation. Afterwards, we calculate the homology modeling identification of pepsin in complex multi-domain families with varied domain architectures. In order to analyze the DSC data, the thermal denaturation of multimer proteins were considered, the “two independent two-state sequential transitions with domains dissociation model” was introduced by using of the effective ΔG concept. The reversible unfolding of the protein description was followed by the two-state transition quantities which is a slower irreversible process of aggregation. The protein unfolding is best described by two non-ideal transitions, suggesting the presence of unfolding intermediates. These evaluations are also applicable for high throughput investigation of protein stability

Virtual screening of Piperine analogs as Survivin inhibitors and their molecular interaction analysis by using consensus docking, MD simulation, MMPB/GBSA and alanine scanning techniques

Virtual screening of Piperine analogs as Survivin inhibitors and their molecular interaction analysis by using consensus docking, MD simulation, MMPB/GBSA and alanine scanning technique

Exploring the Interaction Mechanism of Coumarin with Bovine β-Casein: Spectrofluorometric and Molecular Modeling Studies

International audienceThis paper is designed to examine the binding behavior of Coumarin with bovine -casein (βCN) through fluorescence spectroscopy and molecular modeling techniques. The data analysis on fluorescence titration experiments at various temperatures represents the enthalpy driven nature for the formation of Coumarin-βCN complex and the prevailed role of hydrogen bonds and van der Waals interactions in the binding process. The results also represent the static quenching of tryptophan and dynamics quenching of tyrosine and phenylalanine residues due to the binding of Coumarin. It can be concluded from molecular docking studies that Coumarin binds to several polar and nonpolar residues in the hydrophobic core of βCN with the binding energy of -6.96 kcal mol-1 . Finally, analysis of molecular dynamics (MD) simulation results suggested that the interactions between βCN and Coumarin are very stable and the binding of Coumarin restricted the flexibility of important residues in the binding site of this protein