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
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