Experimental and Theoretical Evaluation of Multisite Cadmium(II) Exchange in Designed Three-Stranded Coiled-Coil Peptides

Abstract

An important factor that defines the toxicity of elements such as cadmium­(II), mercury­(II), and lead­(II) with biological macromolecules is metal ion exchange dynamics. Intriguingly, little is known about the fundamental rates and mechanisms of metal ion exchange into proteins, especially helical bundles. Herein, we investigate the exchange kinetics of Cd­(II) using <i>de novo</i> designed three-stranded coiled-coil peptides that contain metal complexing cysteine thiolates as a model for the incorporation of this ion into trimeric, parallel coiled coils. Peptides were designed containing both a single Cd­(II) binding site, <b>Grand</b>L12AL16C [<b>Grand</b> = AcG-(LKALEEK)₅-GNH₂], <b>Grand</b>L26AL30C, and <b>Grand</b>L26AE28QL30C, as well as <b>Grand</b>L12AL16CL26AL30C with two Cd­(II) binding sites. The binding of Cd­(II) to any of these sites is of high affinity (<i>K</i>_A > 3 × 10⁷ M^–1). Using ¹¹³Cd NMR spectroscopy, Cd­(II) binding to these designed peptides was monitored. While the Cd­(II) binding is in extreme slow exchange regime without showing any chemical shift changes, incremental line broadening for the bound ¹¹³Cd­(II) signal is observed when excess ¹¹³Cd­(II) is titrated into the peptides. Most dramatically, for one site, L26AL30C, all ¹¹³Cd­(II) NMR signals disappear once a 1.7:1 ratio of Cd­(II)/(peptide)₃ is reached. The observed processes are not compatible with a simple “free-bound” two-site exchange kinetics at any time regime. The experimental results can, however, be simulated in detail with a multisite binding model, which features additional Cd­(II) binding site(s) which, once occupied, perturb the primary binding site. This model is expanded into differential equations for five-site NMR chemical exchange. The numerical integration of these equations exhibits progressive loss of the primary site NMR signal without a chemical shift change and with limited line broadening, in good agreement with the observed experimental data. The mathematical model is interpreted in molecular terms as representing binding of excess Cd­(II) to surface Glu residues located at the helical interfaces. In the absence of Cd­(II), the Glu residues stabilize the three-helical structure though salt bridge interactions with surface Lys residues. We hypothesize that Cd­(II) interferes with these surface ion pairs, destabilizing the helical structure, and perturbing the primary Cd­(II) binding site. This hypothesis is supported by the observation that the Cd­(II)-excess line broadening is attenuated in <b>Grand</b>L26AE28QL30C, where a surface Glu(28), close to the metal binding site, was changed to Gln. The external binding site may function as an entry pathway for Cd­(II) to find its internal binding site following a molecular rearrangement which may serve as a basis for our understanding of metal complexation, transport, and exchange in complex native systems containing α-helical bundles