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Incorporation of second coordination sphere d-amino acids alters Cd(II) geometries in designed thiolate-rich proteins

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Abstract

We use a de Novo protein design strategy to demonstrate that the second coordination sphere of a metal site plays a key role in controlling coordination geometries of Cd(II)-tris-thiolate complexes. Specifically, we show that alteration of chirality within the core hydrophobic packing region of a three-stranded coiled coil (3SCC) can control the coordination number of Cd(II) by limiting steric encumbrance to the metal center. Within a specific class of 3SCCs [Ac-G-(LKALEEK) n -G-NH2], where n = 4 is TRI and n = 5 is GRAND, one l-Leu may be substituted by l-Cys to generate a planar tris-thiolate array capable of metal binding. In the native peptide containing only the l-configuration of leucine, the three-Cys ligand site leads to a mixture of 3- and 4-coordinate Cd(II). When the l-Leu above (toward the N-terminus) the tris-Cys site is substituted with d-Leu, solely a 3-coordinate structure [Cd(II)S3] was obtained. When d-Leu is located below (toward the C-terminus), a mixture of two coordination geometries, presumably Cd(II)S3O and Cd(II)S3O2, is observed, while substitution with d-Leu both above and below the tris-Cys plane yields a higher percentage of 4-coordinate Cd(II)S3O species. Thus, the use of d-amino acids around a metal’s coordination sphere provides a powerful tool for controlling the properties of future designed metalloproteins.

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Acknowledgements

This manuscript is dedicated to Prof. Dr. Helmut Sigel on the occasion of his 80th birthday. Prof. Sigel’s contributions over 5 decades have been immense. His description of metal interactions with nucleotides has been groundbreaking and authoritative, while his inexhaustible energy to the community with his book series and service roles to the Society of Biological Inorganic Chemistry and the International Conference on Biological Inorganic Chemistry has helped place the discipline of bioinorganic chemistry as a major field of scientific endeavor. The authors acknowledge funding from the National Institutes of Health (L.R. and V.L.P., ES012236; A.D. and J.E.P.-H., GM 38047) for support of this research. Synchrotron measurements were made at the Stanford Synchrotron Radiation Laboratory, which is supported by the NIH Research Resource Program and the US Department of Energy.

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Authors and Affiliations

  1. Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA

    Leela Ruckthong, Aniruddha Deb, James E. Penner-Hahn & Vincent L. Pecoraro

  2. Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA

    Leela Ruckthong & Vincent L. Pecoraro

  3. Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark

    Lars Hemmingsen

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  1. Leela Ruckthong
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Correspondence to Vincent L. Pecoraro.

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Ruckthong, L., Deb, A., Hemmingsen, L. et al. Incorporation of second coordination sphere d-amino acids alters Cd(II) geometries in designed thiolate-rich proteins. J Biol Inorg Chem 23, 123–135 (2018). https://doi.org/10.1007/s00775-017-1515-7

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