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Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes

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An Erratum to this article was published on 29 October 2004

Abstract

Divalent Mg2+ ions often serve as cofactors in enzyme or ribozyme-catalyzed phosphoryl transfer reactions. In this work, the interaction of Mg2+ ions and di-metal bridge complexes with phosphates, phosphoranes, and other biological ligands relevant to RNA catalysis are characterized with density functional methods. The effect of bulk solvent is treated with two continuum solvation methods (PCM and COSMO) for comparison. The relative binding affinity for different biological ligands to Mg2+ are quantified in different protonation states. The structure and stability of the single-metal and di-metal complexes are characterized, and the changes in phosphate and phosphorane geometry induced by metal ion binding are discussed. Di-metal bridge complexes are a ubiquitous motif and the key factors governing their electrostatic stabilization are outlined. The results presented here provide quantitative characterization of metal ion binding to ligands of importance to RNA catalysis, and lay the groundwork for design of new generation quantum models that can be applied to the full biological enzymatic systems.

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Abbreviations

DMPH:

dimethyl hydrogen phosphate

EP−:

ethylene phosphate

EPA2−:

methyl(ethylene)phosphorane

EPAH−:

methyl(ethylene)(hydrogen)phosphorane

EPH:

ethylene hydrogen phosphate

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Acknowledgements

D.Y. is grateful for financial support provided by the National Institutes of Health (grant 1R01-GM62248-01A1), and the Army High Performance Computing Research Center (AHPCRC) under the auspices of the Department of the Army, Army Research Laboratory (ARL) under Cooperative Agreement number DAAD19-01-2-0014. Computational resources were provided by the Minnesota Supercomputing Institute.

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Authors and Affiliations

  1. Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN , 55455-0431, USA

    Evelyn Mayaan, Kevin Range & Darrin M. York

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  1. Evelyn Mayaan
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  2. Kevin Range
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  3. Darrin M. York
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Correspondence to Darrin M. York.

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An erratum to this article can be found at http://dx.doi.org/10.1007/s00775-004-0608-2

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Mayaan, E., Range, K. & York, D.M. Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes. J Biol Inorg Chem 9, 807–817 (2004). https://doi.org/10.1007/s00775-004-0583-7

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