Abstract
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.
Highlights
One of the challenges facing single particle imaging with ultrafast X-ray pulses is the structural heterogeneity of the sample to be imaged
Despite continuous development and advances, X-ray crystallography cannot be applied to all proteins, largely because they do not always form crystals of sufficient quality
Many important proteins are inherently dynamic in their interactions and form many different coexisting complexes,[1] which does not comply with the purifying nature of crystallization
Summary
The “RMSF-single” (Figure 2, top) was calculated by merging the last frame in each of the 50 sets of trajectories for a specific combination of temperature and water layer This way we compare the difference between the separate simulations, mimicking the experiment where each protein is only exposed to the X-ray pulse once. Both the previously mentioned work[13] and the current study point to the fact that a layer corresponding to 3 Å water is an optimum case Notes The authors declare no competing financial interest. ◆E-mail: christofer.ostlin@physics.uu.se
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