Three-dimensional distribution function theory for the prediction of protein-ligand binding sites and affinities: application to the binding of noble gases to hen egg-white lysozyme in aqueous solution.
The three-dimensional distribution function theory of molecular liquids is applied to lysozyme in mixtures of water and noble gases. The results indicate that the theory has the capability of predicting the protein-ligand binding sites and affinities. First, it is shown that the theory successfully reproduces the binding sites of xenon found by X-ray crystallography. Then, the ability of the theory to predict the size selectivity of noble gases is demonstrated. The effect of water on the selectivity is clarified by a theoretical analysis. Finally, it is demonstrated that the dose-response curve, which is employed in experiments for examining the binding affinity, is realized by the theory.
Imai
Takashi
T
Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan. t-imai@is.ritsumei.ac.jp
Hiraoka
Ryusuke
R
Seto
Tomoyoshi
T
Kovalenko
Andriy
A
Hirata
Fumio
F
D000818:Animals; D001665:Binding Sites; D002645:Chickens; D018360:Crystallography, X-Ray; D004527:Egg Proteins / Q000737:chemistry*; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D012996:Solutions; D014978:Xenon / Q000737:chemistry*