Heavy-element damage seeding in proteins under X-ray free electron laser illumination conditions

The emerging technique of serial femtosecond X-ray crystallography (SFX) can be used to study the structure and dynamics of biological macromolecules to high spatial and temporal resolutions. An ongoing challenge for SFX is the damage caused by the ultrabright X-ray free electron laser pulse. Though it is often assumed that sufficiently femtosecond pulses `outrun' radiation damage, in reality electronic damage processes commence during exposure. We model the electronic damage to protein nanocrystals using a plasma model that tracks the continuous changes to the energy distribution of the unbound electrons. Tracking the continuous energy distribution is of particular importance for distinguishing the influence of differing elements on secondary damage processes. Heavy atoms have a ubiquitous but small presence in protein targets - typically as integral components of the macromolecule and as salts in the solvent. We find that these atoms considerably influence the simulated ionization and scattering behavior of realistic targets due to their rapid seeding of secondary ionization processes. In lysozyme, even the presence of native sulfur atoms significantly contributes to theoretical measures of damage-induced noise for >= 6 keV, 15 fs pulses. Contributing to the effect is that heavy atoms seed `intermediate' energy electron cascades that are particularly effective at ionizing the target on the femtosecond timescale. In addition, the disproportionate effect of heavy atoms means the damage to a protein crystal can be sensitive to their presence in the solvent. Outside of reducing the concentration of heavy atoms in the target, these results suggest the dose limits of SFX targets will be higher where the ionization of deep >  6 keV absorption edges is minimized, or, to a lesser extent, when such edges are only ionized with X-rays >> 2 keV above their binding energy.