Determining the crystal structures of biomolecules containing metal ions, such as metalloproteins, can be problematic. The X-rays used in the techniques can damage the metals’ surroundings, altering the molecules’ structure.
Kirill Gokhberg and coworkers at Germany’s Heidelberg University have now teased apart the mechanism behind such radiation damage using computational methods. Their findings suggest that even fast X-ray methods could distort biomolecules.
The researchers show that the metal in a model [Mg(H2O)6]2+ cluster relaxes via a cascade of reactions that return the metal ion to its original charge state but damage its immediate environment (Nat. Chem. 2016, DOI: 10.1038/nchem.2429).
In the model system, X-ray absorption followed by a process that ejects electrons from the metal results in the formation of Mg4+, which can return to Mg2+ through cascades of two relaxation modes: interatomic Coulombic decay (ICD) or electron-transfer-mediated decay (ETMD). In ICD, the metal transfers excess energy to a neighboring water molecule without changing the charge on the metal, while in ETMD a neighboring water molecule transfers an electron to the metal and the metal transfers excess energy back to the donor or to another water molecule.
Both pathways result in the ionization of one or more water molecules, which then decompose into radicals that can attack other molecules. ICD takes less than one femtosecond, and ETMD takes about 20 femtoseconds.
Researchers have been turning to free-electron lasers as a way to acquire structures faster than the X-rays can damage samples. But the speed of the reactions seen in this computational model means that probably even free-electron lasers damage molecules, Gokhberg notes. “In three femtoseconds, we already start ionizing the environment,” he says.
“I for one have not previously considered possible involvement by what we all expected were innocent s-block metal ions such as Mg2+,” says Graham N. George, an X-ray spectroscopy expert at the University of Saskatchewan. “Anything that helps us really understand the process of metalloprotein photodamage in X-ray crystallography will have a substantial impact.”