Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 23, Issue 16, Pages -Publisher
MDPI
DOI: 10.3390/ijms23168872
Keywords
AlphaCryo4D; cryogenic electron microscopy; biomolecular complex; structural dynamics; conformational space; energy landscape; deep learning; manifold learning; particle voting
Funding
- Beijing Natural Science Foundation [Z180016]
- National Natural Science Foundation of China [11774012, 12125401]
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This study introduces a deep manifold learning framework, called AlphaCryo4D, which enables the reconstruction of the conformational space of biomolecular complexes using cryo-electron microscopy. The method achieves high classification accuracy on simulated datasets and can reconstruct conformational changes of biomolecular complexes in experimental data. It has the potential to explore previously invisible conformational space or transient states. When combined with time-resolved cryo-EM, it allows visualization of conformational changes at the atomic level in non-equilibrium states, potentially enabling therapeutic discovery for dynamic biomolecular targets.
The cellular functions are executed by biological macromolecular complexes in nonequilibrium dynamic processes, which exhibit a vast diversity of conformational states. Solving the conformational continuum of important biomolecular complexes at the atomic level is essential to understanding their functional mechanisms and guiding structure-based drug discovery. Here, we introduce a deep manifold learning framework, named AlphaCryo4D, which enables atomic-level cryogenic electron microscopy (cryo-EM) reconstructions that approximately visualize the conformational space of biomolecular complexes of interest. AlphaCryo4D integrates 3D deep residual learning with manifold embedding of pseudo-energy landscapes, which simultaneously improves 3D classification accuracy and reconstruction resolution via an energy-based particle-voting algorithm. In blind assessments using simulated heterogeneous datasets, AlphaCryo4D achieved 3D classification accuracy three times those of alternative methods and reconstructed continuous conformational changes of a 130-kDa protein at sub-3 angstrom resolution. By applying this approach to analyze several experimental datasets of the proteasome, ribosome and spliceosome, we demonstrate its potential generality in exploring hidden conformational space or transient states of macromolecular complexes that remain hitherto invisible. Integration of this approach with time-resolved cryo-EM further allows visualization of conformational continuum in a nonequilibrium regime at the atomic level, thus potentially enabling therapeutic discovery against highly dynamic biomolecular targets.
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