Design of Ni(II)-metallopeptides and their interactions with DNA
Abstract
A unique tripeptide based on the sequence ($\delta$)-Orn-Gly-His was created to circumvent the limitation of placing Cu(II)/Ni(II)$\cdot$Gly-Gly-His only at the amino terminus of a protein or oligopeptide. ($\delta$)-Orn-Gly-His has been successfully incorporated at the carboxy terminus and within an oligopeptide chain. This novel, versatile metallopeptide was demonstrated to (1) form a complete, high affinity metal binding site within three contiguous amino acids, (2) possess catalytic properties analogous to Gly-Gly-His, and (3) retain the overall secondary structure of an $\alpha$-helical protein once incorporated within the helices. In addition to incorporating a versatile, metal binding domain similar to Gly-Gly-His into larger oligopeptides, low molecular weight peptides that bind metal ions and interact directly with the DNA helix as stand-alone species were also examined. Upon examination of a series of peptides of the general form Ni(II)$\cdot$Xaa-Xaa-His, Ni(II)$\cdot$Gly- scD-Asn-His was found to display a unique DNA selectivity for $5\sp\prime$-CCT-$3\sp\prime$ sites when activated with the oxidizing agent oxone. Molecular modeling showed that both the amide side chain of the Asn and the carboxy terminal amide are directed toward the same face of the square-planar complex. Based on DNA cleavage results from Ni(II)$\cdot$Gly- scD-Xaa-His derivatives and DNA binding data of proteins and drugs that also bind to CCT sites, it is proposed that the source of the DNA site selectivity produced by Ni(II)$\cdot$Gly- scD-Asn-His is due to (1) an initial shape selection due to the conformational flexibility of the CCT sequence, followed by (2) specific hydrogen bond contacts provided by the exocyclic amines of the guanines to both the scD-Asn amide side chain and the carboxy terminal amide. These observations suggest the possibility of exploiting the chemical diversity and chirality of peptides in the further design of DNA binding and modifying agents. Low molecular weight metallopeptides could provide ideal templates through which to study mechanisms of DNA molecular recognition by complex proteins and drugs.
Degree
Ph.D.
Advisors
Long, Purdue University.
Subject Area
Biochemistry|Chemistry
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