For the past decades, X-ray crystallography has been the superior method for determining molecular structures and has brought us knowledge of tremendous importance throughout the years. So it is not surprising that new methods to remedy some of the shortcomings of X-ray crystallography, such as the need for crystalline samples, have started to emerge. One promising alternative is single particle diffraction, which utilizes ultrashort X-ray free-electron laser (XFEL) pulses to outrun radiation damage of the macromolecule of interest while retaining the structural information. Unfortunately, as the heavily ionized sample immediately explodes following exposure, it is troublesome to link the recovered diffraction pattern to the spatial orientation of the particle. In this work we use molecular dynamics (MD) simulations to replicate a vast number of such experiments of varying conditions to investigate if the explosion pattern can provide insight into the initial orientation of the sample.
We consider mainly four different proteins: the synthesized 20-residue polypeptide Trp-Cage, the C-terminal domain of L7/L12 from E. coli, the human regulatory protein ubiquitin, and lysozyme from hen egg white. The dynamics of these proteins encapsulated in water has been subject to earlier research by Marklund et al. in vacuum simulations. Using the output files from their study, we allow for small deviations in tertiary structures and expose these systems to a femtosecond XFEL-pulse. The trajectories of the ions leaving the sample are then tracked so that explosion patterns can be analyzed, and compared, to evaluate their level of reproducibility. This directly implies the degree of usefulness in orientational determination.