Spectral decomposition of atomic structures in heterogeneous cryo-EM. (1st March 2023)

• Record Type: Journal Article
• Authors: Esteve-Yagüe, Carlos; Diepeveen, Willem; Öktem, Ozan; Schönlieb, Carola-Bibiane
• Is Part Of: Inverse problems. Volume 39:Number 3(2023)
• Publication Date: 2023-03-01
• Subjects: heterogeneous cryo-EM -- atomic structure decomposition -- graph Laplacian -- tomographic reconstruction; Inverse problems (Differential equations) -- Periodicals; 515.357
• DOI: 10.1088/1361-6420/acb2ba
• Languages: English
• ISSNs: 0266-5611

Abstract

Abstract: We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryogenic electron microscopy (cryo-EM) dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the macromolecule, taken from different viewing directions, and in the heterogeneous case, each cryo-EM image corresponds to a different conformation of the macromolecule. Under the assumption that the macromolecule can be modelled as a chain, or discrete curve (as it is for instance the case for a protein backbone with a single chain of amino-acids), we introduce a method to estimate the deformation of the atomic model with respect to a given conformation, which is assumed to be known a priori . Our method consists on estimating the torsion and bond angles of the atomic model in each conformation as a linear combination of the eigenfunctions of the Laplace operator in the manifold of conformations. These eigenfunctions can be approximated by means of a well-known technique in manifold learning, based on the construction of a graph Laplacian using the cryo-EM dataset. Finally, we test our approach with synthetic datasets, for which we recover the atomic model of two-dimensional and three-dimensional flexible structures from simulated cryo-EM images.