Deep learning based mixed-dimensional GMM for characterizing variability in CryoEM

The function of most protein molecules involves structural flexibility and/or dynamic interactions with other molecules. CryoEM provides direct visualization of individual macromolecules in different conformational and compositional states. While many methods are available for classification of discrete states, characterization of continuous conformational changes or large numbers of discrete state without human supervision remains challenging. Here we present a machine learning algorithm to determine a conformational landscape for proteins or complexes using a 3-D Gaussian mixture model mapped onto 2-D particle images in known orientations. Using a deep neural network architecture, this method can automatically resolve the structural heterogeneity within the protein complex and map particles onto a small latent space describing conformational and compositional changes. This system presents a more intuitive and flexible representation than other manifold methods currently in use. We demonstrate this method on several different biomolecular systems to explore compositional and conformational changes at a range of scales.