Four‐dimensional imaging for cryo‐electron microscopy experiments using molecular simulations and manifold learning

Abstract

Elucidating protein conformational changes is essential because conformational changes are closely related to the functions of proteins. Cryo‐electron microscopy (cryo‐EM) experiment can be used to reconstruct protein conformational changes via a method that involves using the experimental data (two‐dimensional protein images). In this study, a reconstruction method, referred to as the “four‐dimensional imaging,” was proposed. In our four‐dimensional imaging technique, the protein conformational change was obtained using the two‐dimensional protein images (the three‐dimensional electron density maps used in previously proposed techniques were not used). The protein conformation for each two‐dimensional protein image was obtained using our original protocol with molecular dynamics simulations. Using a manifold‐learning technique and two‐dimensional protein images, the protein conformations were arranged according to the conformational change of the protein. By arranging the protein conformations according to the arrangement of the protein images, four‐dimensional imaging is constructed. A simulation for a cryo‐EM experiment demonstrated the validity of our four‐dimensional imaging technique.