Cryo-EM reconstruction algorithms seek to determine a molecule's 3D density map from a series of noisy, unlabeled 2D projection images captured with an electron microscope. Although reconstruction algorithms typically model the 3D volume as a generic function parameterized as a voxel array or neural network, the underlying atomic structure of the protein of interest places well-defined physical constraints on the reconstructed structure. In this work, we exploit prior information provided by an atomic model to reconstruct distributions of 3D structures from a cryo-EM dataset. We propose Cryofold, a generative model for a continuous distribution of 3D volumes based on a coarse-grained model of the protein's atomic structure, with radial basis functions used to model atom locations and their physics-based constraints. Although the reconstruction objective is highly non-convex when formulated in terms of atomic coordinates (similar to the protein folding problem), we show that gradient descent-based methods can reconstruct a continuous distribution of atomic structures when initialized from a structure within the underlying distribution. This approach is a promising direction for integrating biophysical simulation, learned neural models, and experimental data for 3D protein structure determination.
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the Protein Data Bank. However, if for some complexes atomic resolution is reached, this is not true for all. This is also the case in cryo-electron tomography where the achievable resolution is still limited. Furthermore the resolution in a cryo-EM map is not a constant, with often outer regions being of lower resolution, possibly linked to conformational variabi…
Fold'EM: Direct atomic structure inference from Cryo-EM particles
Institute of Science and Technology Austria（奥地利科学技术研究所）；University of Zurich（苏黎世大学）；Frankfurt Institute for Advanced Studies（法兰克福高等研究院）；Princeton University（普林斯顿大学）；Broad Institute of MIT and Harvard（麻省理工学院和哈佛大学博德研究所）
SLAC National Accelerator Laboratory（SLAC国家加速器实验室）；Stanford University（斯坦福大学）；University of California Santa Barbara（加州大学圣巴巴拉分校）
Cryogenic electron microscopy (cryo-EM) provides a unique opportunity to study the structural heterogeneity of biomolecules. Being able to explain this heterogeneity with atomic models would help our understanding of their functional mechanisms but the size and ruggedness of the structural space (the space of atomic 3D cartesian coordinates) presents an immense challenge. Here, we describe a heterogeneous reconstruction method based on an atomistic representation whose deformation is reduced to a handful of collective motions through normal mode analysis. Our implementation uses an autoencoder…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with machine learning algorithms, provides a way to reveal the dynamics within the protein system from noisy micrographs. Here, we introduce an improved computational method that uses Gaussian mixture models for protein structure representation and deep neural networks for conformation space embedding. By integrating information from molecular models into the heterogen…
King Abdullah University of Science and Technology（阿卜杜拉国王科技大学）；Xi’an Jiaotong University（西安交通大学）；Peking University（北京大学）；Carnegie Mellon University（卡内基梅隆大学）
Cryo-electron tomography (Cryo-ET) is a 3D imaging technique that enables the systemic study of shape, abundance, and distribution of macromolecular structures in single cells in near-atomic resolution. However, the systematic and efficient $\textit{de novo}$ recognition and recovery of macromolecular structures captured by Cryo-ET are very challenging due to the structural complexity and imaging limits. Even macromolecules with identical structures have various appearances due to different orientations and imaging limits, such as noise and the missing wedge effect. Explicitly disentangling th…
Electron cryo-microscopy (cryo-EM) produces three-dimensional (3D) maps of the electrostatic potential of biological macromolecules, including proteins. Along with knowledge about the imaged molecules, cryo-EM maps allow de novo atomic modelling, which is typically done through a laborious manual process. Taking inspiration from recent advances in machine learning applications to protein structure prediction, we propose a graph neural network (GNN) approach for automated model building of proteins in cryo-EM maps. The GNN acts on a graph with nodes assigned to individual amino acids and edges …
Stanford University（斯坦福大学）；SLAC National Accelerator Laboratory（SLAC国家加速器实验室）；Atomwise, Inc.（Atomwise公司）
Single particle, cryogenic electron microscopy (cryo-EM) experiments now routinely produce high-resolution data for large proteins and their complexes. Building an atomic model into a cryo-EM density map is challenging, particularly when no structure for the target protein is known a priori. Existing protocols for this type of task often rely on significant human intervention and can take hours to many days to produce an output. Here, we present a fully automated, template-free model building approach that is based entirely on neural networks. We use a graph convolutional network (GCN) to gene…
CryoNet.Refine: A One-step Diffusion Model for Rapid Refinement of Structural Models with Cryo-EM Density Map Restraints
State Key Laboratory of Membrane Biology, Beijing Frontier Research Center of Biological Structures, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China（膜生物学国家重点实验室，北京生物结构前沿研究中心，清华大学-北京大学联合生命科学中心，生命科学学院，清华大学，北京，中国）；State Key Laboratory of Membrane Biology–Membrane Structure and Artificial Intelligence Biology Branch, Hangzhou, China（膜生物学国家重点实验室——生物结构与人工智能生物学分支，杭州，中国）；State Key Laboratory of Membrane Biology, Beijing Tsinghua Institute for Frontier Interdisciplinary Innovation, Beijing, China（膜生物学国家重点实验室，北京清华大学前沿交叉创新研究院，北京，中国）
Cryo-electron microscopy is a revolutionary technique that can provide 3D density maps at near-atomic resolution. However, map validation is still an open issue in the field. Despite several efforts from the community, it is possible to overfit the reconstructions to noisy data. Here, inspired by modern statistics, we develop a novel methodology that uses a small independent particle set to validate the 3D maps. The main idea is to monitor how the map probability evolves over the control set during the refinement. The method is complementary to the gold-standard procedure, which generates two …
