Analysis of the experimental binding thermodynamics for approximately 100 protein-ligand complexes provides important insights into the factors governing ligand affinity and efficiency. The commonly accepted correlation between enthalpy and -TΔS is clearly observed for this relatively diverse data set. It is also clear that affinity (i.e., ΔG) is not generally correlated to either enthalpy or -...

curcumin (cur) is the active curcuminoid with many physiological, biochemical, and pharmacological properties. solubility and stability of cur is the limiting factors for realizing its therapeutic potential. bovine β-casein is an abundant milk protein that is highly amphiphilic and self-assembles into stable micellar nanoparticles in aqueous solution. β-casein nanoparticle can solubilize cur mo...

To understand water-protein interactions in solution, the electrostatic field is calculated by solving the Poisson-Boltzmann equation, and the free energy surface of water is mapped by translating and rotating an explicit water molecule around the protein. The calculation is applied to T4 lysozyme with data available on the conservation of solvent binding sites in 18 crystallographically indepe...

In this unit, protocols are provided for predicting RNA secondary structure with the user-friendly RNAstructure desktop computer program and the RNAstructure Web server. The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented. © 2016 by Jo...

We review recent theoretical and algorithmic advances for the modeling of protein ligand binding free energies. We first describe a statistical mechanics theory of noncovalent association, with particular focus on deriving the fundamental formulas on which computational methods are based. The second part reviews the main computational models and algorithms in current use or development, pointin...

We study the effective interaction between DNA-binding proteins that arises from elastic stresses in the DNA when tension is applied. Using the wormlike chain model, we calculate the free energy cost of introducing multiple nearby bends in the DNA. We find that the bend deformation energy promotes aggregation to straighten the linker DNA, while twist resistance of the linker leads to damped osc...

In this study at first , an azo dye, 2,7- naphthalenediol, 2-[(4-Bromophenyl)azo (BPAND) as a ligand has been synthesized by addition of p-Bromoaniline to the modified montomorillonite K10 clay. This ligand was characterized using 1H-NMR, UV-Vis and IR spectroscopies. Subsequently, its interaction with calf thymus deoxyribonucleicacid ,ct-DNA was investigated in 5 mM phosphate buffer solution, ...

In the present study, the binding isotherms for interaction of a homologous series of n-alkyltrimethyl ammonium bromides with bovine serum albumin (BSA) have been analyzed on basis of intrinsic thermodynamic quantities. In this regards, the intrinsic Gibbs free energy of binding, AGb(i,)„ has been estimated at various surfactant concentrations and its trend of variation for both binding sets ha...

in this paper, the electronic eigenstates and energy spectra of single and two-interacting electrons confined in a concentric double quantum rings with a perpendicular magnetic field in the presence of         on-center donor and acceptor impurities are calculated using the exact diagonalization method. for a single electron case, the binding energy of on-center donor and acceptor impurities ar...

the armaticity of 5 methylcytosine tautomers in the gas phase has been studied and the chemical structures of related tautomers are investigated . the electronic energy, enthalpy and free energy of each tautomer are also estimated at the b3lyp/6-31 g* // b3lyp/6-31 g* and mp2 / 6-31 g* // mp2 / 6-31 g* levels