Journal article Open Access

Structural Heterogeneity in Single Particle Imaging Using X‑ray Lasers

Thomas Mandl; Christofer Östlin; Ibrahim E. Dawod; Maxim N. Brodmerkel; Erik G. Marklund; Andrew V. Martin; Nicusor Timneanu; Carl Caleman

One of the challenges facing single particle imaging with ultrafast X-ray
pulses is the structural heterogeneity of the sample to be imaged. For the method to succeed
with weakly scattering samples, the diffracted images from a large number of individual
proteins need to be averaged. The more the individual proteins differ in structure, the lower
the achievable resolution in the final reconstructed image. We use molecular dynamics to
simulate two globular proteins in vacuum, fully desolvated as well as with two different
solvation layers, at various temperatures. We calculate the diffraction patterns based on the
simulations and evaluate the noise in the averaged patterns arising from the structural
differences and the surrounding water. Our simulations show that the presence of a minimal
water coverage with an average 3 Å thickness will stabilize the protein, reducing the noise associated with structural heterogeneity,
whereas additional water will generate more background noise.

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