Berlin 2012 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 7: Posters: Proteins

BP 7.12: Poster

Montag, 26. März 2012, 17:30–19:30, Poster A

Ab initio conformation trends across 20 amino acids, dipeptides, and their interaction with divalent ions — •Matti Ropo, Carsten Baldauf, Volker Blum, and Matthias Scheffler — Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany

Ion-protein interactions are of tremendous importance in cellular signalling of all organisms. For instance, the binding properties of Ca²⁺ can be mimicked by heavy metals like Pb, thus disturbing Ca-dependent functions[1]. We have constructed an exhaustive, first-principles based conformational (in vacuo) database of the 20 proteinogenic amino acids, their dipeptides, and of their interactions with the divalent cations of Ca, Sr, Ba, Cd, Pb, and Hg. The database was established using all-electron density functional theory with the van der Waals-corrected PBE functional.[2] We here use it to discuss trends of biological interest, for example: (i) a uniform binding order of ions relative to Ca²⁺—Sr²⁺ and Ba²⁺ bind weaker, Pb²⁺ binds similar, Cd²⁺ and Hg²⁺ stronger. (ii) Dipeptides bind cations stronger than amino acids alone. (iii) Interestingly, Ca²⁺ binds strongest to Arg and Tyr, not to Asp or Glu (assuming the neutral protonation state for the amino acids). (iv) We evaluate backbone conformations by means of Ramachandran plots and atomic distribution function and compare these data sets to experimental structural data from the RCSB protein data bank. Finally, we address the impact of density functionals beyond the generalized gradient approximation. [1] H.A. Godwin, Curr. Opin. Chem. Biol. 5, 223 (2001); [2] A. Tkatchenko and M. Scheffler, PRL 102, 73005 (2009).