Digital twin of biomacromolecular thermodynamics in cryo-EM data

The biological functions of biomacromolecules are linked to their thermodynamics. Thus, a quantitative understanding of the full scope of these dynamics, ranging from local fluctuations to large-scale conformational change on the free-energy landscape, is essential for elucidating the biomacromolecular mechanisms. Recently, cryo-electron microscopy (cryo-EM) has garnered increasing attention for determining novel static structures with large molecular sizes and complex structural assemblies. However, identifying their comprehensive thermodynamic behaviors remains challenging. In this study, we present a deep learning framework that reconstructs a provable "digital twin" of the thermodynamics recorded in cryo-EM data with a theoretically guaranteed isometric autoencoder. This framework enables a thermodynamic analysis of the heterogeneous conformational states and their transition pathways in a semi-automatic manner. We demonstrated the application of the framework to the cryo-EM data obtained from a 50S-Ribosome and two SARS-CoV-2 spike proteins, which yielded novel biological insights without supplementary assumptions. This work establishes a provable approach to achieve the quantitative analysis of biomacromolecular thermodynamics using only cryo-EM data, whereas current similar methods do not guarantee the exact construction of the free-energy landscape. Overall, our approach has the potential to advance biological foundations by uncovering the thermodynamics of complex biological systems.