Supporting Information for “On the Affinity Regulation of the Metal Ion Dependent Adhesion Sites in Integrins.” January 25, 2006 Eider San Sebastian 1,4 , Jose Maria Mercero 1,4 , Roland Stote 2 , Annick Dejaegere 3 , Fernando P. Coss´ ıo 1,* , Xabier Lopez 1,4,* 1. Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 1072, 20080 Donostia, Spain 2. Lab. de Chimie Biophysique, ULP - ISIS, 8, all´ ee Gaspard Monge, Strasbourg France 3. UMR 7104 Biocomputing Group, Structural Biology & Genomics Dept., Ecole Sup´ erieure de Biotechnologie de Strasbourg-IGBMC; BP 10413 - F- 67412 Illkirch, France 4. Donostia International Physics Center (DIPC), E20018 Donostia, Spain * Corresponding Authors: fp.cossio@ehu.es (F.P.C.); xabier.lopez@ehu.es 1 Supplementary Material 1.1 Calibration of the method In previous studies on Mg 2+ , Ca 2+ and Zn 2+ complexes by Peschke et. al. 1 and Dudev et. al, 2–4 it is suggested that calculations at the more expensive B3LYP/6-311++G(d,p) or B3LYP/6-31++G(2d,2p) level, respectively, are needed to converge to results in good agreement with experimental values. To assess whether the use of pseudopotentials, B3LYP/6-311++G(2df,2p)//B3LYP/SKBJ*, leads to reasonable re- sults for the cases of complexes with Zn 2+ and Ca 2+ dications, the affinity free energy of the 1S op MIDAS model was evaluated at the three different levels mentioned before, using Mg 2+ , Ca 2+ or Zn 2+ as central cations and with acetate as the incoming ligand (scheme 1). Table S1: ΔG g aff values (kcal/mol) in the gas phase for Mg 2+ -, Ca 2+ - and Zn 2+ - bound open MIDAS in the ligand binding reaction. In parenthesis, the relative affinity free energies with respect to the Mg 2+ -bound MIDAS, namely, ΔΔG g aff = ΔG g aff (M - MIDAS ) - ΔG g aff (Mg - MIDAS ) with M=Ca 2+ ,Zn 2+ . Metal 6-311++G(d,p) 1 6-31+G(2d,2p) 4 This work * Mg 2+ -193.3 -196.2 -196.6 (0.0) (0.0) (0.0) Ca 2+ -184.6 -187.2 -187.0 (+8.7) (+9.0) (+9.6) Zn 2+ -195.6 -198.3 -198.8 (-2.3) (-2.1) (-2.2) * B3LYP/6-311++G(2df,2p)//B3LYP/SBKJ+*