Mixture of neural fields for heterogeneous reconstruction in cryo-EM Article Swipe

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Axel Levy , Rishwanth Raghu , David Shustin , Anjie Peng , Huan Li , Oliver B. Clarke , Gordon Wetzstein , Ellen D. Zhong ·

YOU? · · 2024 · Open Access · · DOI: https://doi.org/10.48550/arxiv.2412.09420

Cryo-electron microscopy (cryo-EM) is an experimental technique for protein structure determination that images an ensemble of macromolecules in near-physiological contexts. While recent advances enable the reconstruction of dynamic conformations of a single biomolecular complex, current methods do not adequately model samples with mixed conformational and compositional heterogeneity. In particular, datasets containing mixtures of multiple proteins require the joint inference of structure, pose, compositional class, and conformational states for 3D reconstruction. Here, we present Hydra, an approach that models both conformational and compositional heterogeneity fully ab initio by parameterizing structures as arising from one of K neural fields. We employ a new likelihood-based loss function and demonstrate the effectiveness of our approach on synthetic datasets composed of mixtures of proteins with large degrees of conformational variability. We additionally demonstrate Hydra on an experimental dataset of a cellular lysate containing a mixture of different protein complexes. Hydra expands the expressivity of heterogeneous reconstruction methods and thus broadens the scope of cryo-EM to increasingly complex samples.

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Type: preprint
Language: en
Landing Page: http://arxiv.org/abs/2412.09420
PDF: https://arxiv.org/pdf/2412.09420
OA Status: green
Cited By: 1
Related Works: 10
OpenAlex ID: https://openalex.org/W4405355287

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DOI: https://doi.org/10.48550/arxiv.2412.09420

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Title: Mixture of neural fields for heterogeneous reconstruction in cryo-EM

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Type: preprint

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Language: en

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Publication year: 2024

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Publication date: 2024-12-12

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Authors: Axel Levy, Rishwanth Raghu, David Shustin, Anjie Peng, Huan Li, Oliver B. Clarke, Gordon Wetzstein, Ellen D. Zhong

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Landing page: https://arxiv.org/abs/2412.09420

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PDF URL: https://arxiv.org/pdf/2412.09420

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Concepts: Artificial neural network, Computer science, Artificial intelligence, Pattern recognition (psychology)

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Cited by: 1

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