How simple is too simple? Computational perspective on importance of second-shell environment for metal-ion selectivity

Physical Chemistry Chemical Physics : PCCP
Ondrej Gutten, Lubomír Rulíšek

Abstract

The metal-ion selectivity in biomolecules represents one of the most important phenomena in bioinorganic chemistry. The open question to what extent is the selectivity in the complex bioinorganic structures such as metallopeptides determined by the first-shell ligands of the metal ion is answered herein using six model peptides complexed with the set of divalent metal ions (Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), and Hg(2+)) and their various first-shell representations. By calculating the differences among the free energies of complexation of metal ions in these peptides and their model (truncated) systems it is quantitatively shown that the definition of the first shell is paramount to this discussion and revolves around the chemical nature of the binding site. Despite the vast conceivable diversity of peptidic structures, that suggest certain fluidity of this definition, major contributing factors are identified and assessed based on their importance for capturing metal-ion selectivity. These factors include soft/hard character of ligands and various non-covalent interactions in the vicinity of the binding site. The relative importance of these factors is considered and specific suggestions for effective cons...Continue Reading

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Citations

Dec 23, 2015·Biochemistry·Dhruva K ChakravortyKenneth M Merz
Oct 6, 2016·Dalton Transactions : an International Journal of Inorganic Chemistry·Lindsay E Roy, Leigh R Martin
Mar 30, 2017·Dalton Transactions : an International Journal of Inorganic Chemistry·Annaleizle FerrancoHeinz-Bernhard Kraatz
Nov 13, 2019·Scientific Reports·Jesica UrbinaLynn J Rothschild

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