Estimating affinities of calcium ions to proteins

Stefan Franke, Julia Herfurth, Daniel Hoffmann

Department of Bioinformatics/Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany

Abstract: Ca²⁺-ions have a range of affinities to different proteins, depending on the various functions of these proteins. This makes the determination of Ca²⁺-protein affinities an interesting subject for functional studies. We have investigated the performance of two methods – Fold-X and AutoDock vina – in the prediction of Ca²⁺-protein affinities. Both methods, although based on different energy functions, showed virtually the same correlation with experimental affinities. Guided by insight from experiment, we further derived a simple linear model based on thesolvent accessible surface of Ca²⁺ that had practically the same performance in terms of absolute errors as the more complex docking methods.

Keywords: metal ions, binding, free energy, crystal structure, solvent accessible surface