SHREC: A Spectral Embedding-Based Approach for Ab-Initio Reconstruction of Helical Molecules

Abstract

Cryo-electron microscopy (cryo-EM) has emerged as a powerful technique for determining the three-dimensional structures of biological molecules at near-atomic resolution. However, reconstructing helical assemblies presents unique challenges due to their inherent symmetry and the need to determine unknown helical symmetry parameters. Traditional approaches require an accurate initial estimation of these parameters, which is often obtained through trial and error or prior knowledge. These requirements can lead to incorrect reconstructions, limiting the reliability of ab initio helical reconstruction. In this work, we present SHREC (Spectral Helical REConstruction), an algorithm that directly recovers the projection angles of helical segments from their two-dimensional cryo-EM images, without requiring prior knowledge of helical symmetry parameters. Our approach leverages the insight that projections of helical segments form a one-dimensional manifold, which can be recovered using spectral embedding techniques. Experimental validation on publicly available datasets demonstrates that SHREC achieves high resolution reconstructions while accurately recovering helical parameters, requiring only knowledge of the specimen's axial symmetry group. By eliminating the need for initial symmetry estimates, SHREC offers a more robust and automated pathway for determining helical structures in cryo-EM.