Constrained template matching using rejection sampling

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Identifying macromolecular complexes in situ using cryo-electron tomography remains challenging, with low signal-to-noise ratios, the missing wedge, and crowded backgrounds among the key limiting factors. By integrating prior knowledge on macromolecular localization, such as the preferred orientations of membrane-associated proteins, detection can be improved by constraining searches to biologically feasible orientations. Here we describe rejection sampling, an approach for integrating such constraints at voxel resolution that remains both accurate and computationally efficient. Using synthetic and experimental data, we show that these constraints improve detection, orientational assignment, and discrimination between macromolecules. The resulting picks match the performance of deep-learning methods informed by membrane structure without requiring annotated data. We further apply rejection sampling to ATP synthase on mitochondrial cristae, illustrating how it extends macromolecular detection to the large and highly curved membrane systems that pervade cells.

Authors 4

1. Lukas Grunwald Aachen Institut für Theorie der Statistischen Physik

   RWTH Aachen University · Jülich Aachen Research Alliance · Max Planck Institute for the Structure and Dynamics of Matter · Center for Free-Electron Laser Science

   Affiliation as printed

   Institut für Theorie der Statistischen Physik, RWTH Aachen University and JARA-Fundamentals of Future Information Technology, 52056 Aachen, Germany

   Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany

2. Dante Marvin Kennes Aachen Institut für Theorie der Statistischen Physik

   RWTH Aachen University · Jülich Aachen Research Alliance · Max Planck Institute for the Structure and Dynamics of Matter · Center for Free-Electron Laser Science

   Affiliation as printed

   Institut für Theorie der Statistischen Physik, RWTH Aachen University and JARA-Fundamentals of Future Information Technology, 52056 Aachen, Germany

   Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany

3. Lea Dietrich corresponding

   European Molecular Biology Laboratory · European Molecular Biology Laboratory · Max Planck Institute for Brain Research · Centre for Structural Systems Biology

   Affiliation as printed

   Max Planck Institute for Brain Research, Max-von-Laue-Straße 4, 60438, Frankfurt, Germany

   Centre for Structural Systems Biology, CSSB, Notkestraße 85, 607 Hamburg, Germany

   Molecular Systems Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 9117 Heidelberg, Germany

4. Jan Kosiński

   European Molecular Biology Laboratory · European Molecular Biology Laboratory · Centre for Structural Systems Biology

   Affiliation as printed

   Centre for Structural Systems Biology, CSSB, Notkestraße 85, 22607 Hamburg, Germany

   Molecular Systems Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany

   Structural Biology Unit, European Molecular Biology Laboratory, Notkestraße 85, 22607 Hamburg, Germany