IDENTIFICATION OF IONS IN PROTEINS

J. Dohnálek

Institute of Macromolecular Chemistry AS CR, Heyrovského nám. 2, 16206 Praha 6, Czech Republic

dohnalek007@gmail.com

In single crystal studies of biological macromolecules identification of ligands or generally solvent molecules very often represents an uneasy task. The studied proteins undergo a lengthy process of expression, in cell modification, and/or secretion, purification and sometimes special pre-crystallization treatment. The molecules are commonly crystallized in solutions of salts and presence of unwanted metal ions in the used chemicals is not excluded.

As a result in protein crystal structures ions or other small chemical moieties are often observed bound on the molecular surface. A majority of protein crystals do not provide diffraction data to atomic or subatomic diffraction limits (1.2 Å or better). To date some 63 thousand X-ray structures deposited in the Protein Data Bank have the high diffraction limit of data 1.2 Å or worse and about 1500 1.2 Å and better. Therefore protein crystallographers must mostly rely on other indicators of the nature of an ion than purely the height of an electron density maximum.

The sum of the utilized approaches includes anomalous scattering signal, typical coordination and bonding distances [1], statistical evaluation of typical cases, assessment of the local environment, experimental conditions such as pH, and other. Access to tunable X-ray sources with fluorescence detectors enables absorption edge checks and fluorescence analysis in some cases [2] and availability of a micrometer high energy proton beam allows element identification by microbeam Proton Induced X-ray Emission (microPIXE) [3].

Lighter ions, such as Na⁺, Mg²⁺and Cl^-, belong to a special category as their presence in protein structures either remains unnoticed or is misinterpreted. In such cases the correct assignment of an ion type and its distinction from a water molecule rely on sufficient evidence from all available information sources.

References

1. M.M. Harding, M.W. Nowicki, M.D. Walkinshaw, Crystallogr. Rev. 16, (2010), 247.

2. J. Dohnálek, T. Kovaľ, P. Lipovová, T. Podzimek, J. Matoušek, J. Sync. Rad. 18, (2011), 29.

3. E.F. Garman, G.W. Grime, Prog. Biophys. Mol. Biol. 89, (2005), 173.

Acknowledgements.

Grant support from the Czech Science Foundation is gratefully acknowledged (project no. P302/11/0855).