Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN

Article Biochemistry & Molecular Biology

Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates

Jessica N. Rabuck-Gibbons et al.

Summary: Single-particle cryo-EM allows characterization of macromolecular structural heterogeneity. We developed a workflow to quantitatively mine cryo-EM data for structures with maximal diversity.

STRUCTURE (2022)

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Article Multidisciplinary Sciences

Structural basis of human telomerase recruitment by TPP1-POT1

Zala Sekne et al.

Summary: This study presents the structures of DNA-bound telomerase in complex with TPP1 and TPP1-POT1, revealing crucial interactions for telomerase recruitment to telomeres and providing a framework for future mechanistic work on telomerase regulation.

SCIENCE (2022)

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Article Biochemistry & Molecular Biology

Structures of radial spokes and associated complexes important for ciliary motility

Miao Gui et al.

Summary: Cryo-EM structures of radial spokes and nexin-dynein regulatory complex (N-DRC) attached to doublet microtubules isolated from Chlamydomonas reinhardtii provide a model for mechanoregulation of motile cilia.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Flexible open conformation of the AP-3 complex explains its role in cargo recruitment at the Golgi

Jannis Schoppe et al.

Summary: The study reveals the structural details of the 300 kDa yeast AP-3 complex, showing its open conformation and flexibility compared to AP-1 or AP-2. The recruitment of AP-3 to the membrane primarily depends on cargo binding, which leads to clustering and immobilization of cargo molecules. This flexible open state of AP-3 enables it to bind and collect cargo at the Golgi, facilitating coordinated vesicle formation at the trans-Golgi upon Arf1 activation.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

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Article Biochemical Research Methods

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks

Ellen D. Zhong et al.

Summary: cryoDRGN is an algorithm that uses the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. It can uncover residual heterogeneity in high-resolution datasets and visualize large-scale continuous motions of protein complexes, while also offering interactive tools for dataset visualization and analysis.

NATURE METHODS (2021)

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Article Biochemistry & Molecular Biology

3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM

Ali Punjani et al.

Summary: 3DVA is an algorithm that fits a linear subspace model of conformational change to high-resolution cryo-EM data, enabling the resolution and visualization of detailed molecular motions of proteins. It has been shown to successfully resolve multiple flexible motions in various protein complexes, providing new biological insights from single particle cryo-EM data.

JOURNAL OF STRUCTURAL BIOLOGY (2021)

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Article Biochemical Research Methods

Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM

Muyuan Chen et al.

Summary: e2gmm is a machine learning algorithm that utilizes a deep neural network and Gaussian mixture model to resolve structural heterogeneity within protein complexes, mapping changes in conformation and composition. It offers a more intuitive and flexible representation compared to other current manifold methods.

NATURE METHODS (2021)

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Proceedings Paper Computer Science, Artificial Intelligence

CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images

Ellen D. Zhong et al.

Summary: The cryoDRGN2 algorithm described in this study can jointly estimate image poses and learn a neural model of a distribution of 3D structures on real heterogeneous cryo-EM data. This method trains faster than earlier neural methods and demonstrates robustness to high noise levels of real cryo-EM images, achieving state-of-the-art performance on real datasets.

2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION (ICCV 2021) (2021)

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Review Biophysics