Classification of projection images of proteins with structural polymorphism by manifold: a simulation study for x-ray free-electron laser diffraction imaging.

Abstract

Coherent x-ray diffraction imaging (CXDI) enables us to visualize noncrystalline sample particles with micrometer to submicrometer dimensions. Using x-ray free-electron laser (XFEL) sources, two-dimensional diffraction patterns are collected from fresh samples supplied to the irradiation area in the "diffraction-before-destruction" scheme. A recent significant increase in the intensity of the XFEL pulse is promising and will allow us to visualize the three-dimensional structures of proteins using XFEL-CXDI in the future. For the protocol proposed for molecular structure determination using future XFEL-CXDI [T. Oroguchi and M. Nakasako, Phys. Rev. E 87, 022712 (2013)10.1103/PhysRevE.87.022712], we require an algorithm that can classify the data in accordance with the structural polymorphism of proteins arising from their conformational dynamics. However, most of the algorithms proposed primarily require the numbers of conformational classes, and then the results are biased by the numbers. To improve this point, here we examine whether a method based on the manifold concept can classify simulated XFEL-CXDI data with respect to the structural polymorphism of a protein that predominantly adopts two states. After random sampling of the conformations of the two states and in-between states from the trajectories of molecular dynamics simulations, a diffraction pattern is calculated from each conformation. Classification was performed by using our custom-made program suite named enma, in which the diffusion map (DM) method developed based on the manifold concept was implemented. We successfully classify most of the projection electron density maps phase retrieved from diffraction patterns into each of the two states and in-between conformations without the knowledge of the number of conformational classes. We also examined the classification of the projection electron density maps of each of the three states with respect to the Euler angle. The present results suggest that the DM method is imperative for future applications of XFEL-CXDI experiments for proteins, and clarify issues to be taken care of in the future application.