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BP: Fachverband Biologische Physik
BP 2: Protein Structure \& Dynamics
BP 2.8: Talk
Monday, March 14, 2011, 12:30–12:45, ZEU 260
Simulation of protein charge inversion by trivalent metal ion binding — •Sara Leibfarth1, Felix Roosen-Runge1, Fajun Zhang1, Nina Fischer2, Oliver Kohlbacher2, Sophie Weggler3, Michael Ziller1, Andreas Hildebrandt3, Elena Jordan1, and Frank Schreiber1 — 1Institut für Angewandte Physik, Universität Tübingen — 2Zentrum für Bioinformatik, Universität Tübingen — 3Zentrum für Bioinformatik, Universität des Saarlandes
Experiments indicate that the effective charge of proteins in solution can be inverted by binding trivalent metal ions [1]. In addition, X-ray diffraction data show that metal ions bind to negatively charged carboxylic groups on the protein surface. In order to elucidate the binding of trivalent metal ions, two simulation approaches were carried out in the dilute protein limit for the case of Y3+. Firstly, a classical protonation titration approach was adopted to trivalent ion binding [1,2]. This approach yields binding probabilities for the binding sites of the protein. The effective charge of the protein as a function of yttrium concentration was calculated at different concentrations of monovalent salt. The results are in accordance with the experimentally observed phase transition in protein solution from the dissolved to the condensed phase. Secondly, a classical molecular dynamics simulation was performed, yielding the dynamic binding behavior of yttrium to the protein. With this approach, also the binding of several carboxylic groups to one yttrium ion is observed, which is consistent with the crystallographic findings. [1] Zhang et al., Proteins, 78:3450, 2010; [2] Zhang et al., Phys Rev Lett, 101:148101, 2008