SimHS-AFMfit-MD: An Integrative Approach for Inferring Alpha-Actinin Atomic Conformational Dynamics

Elucidating the atomic-level structure and dynamics of biomolecules is essential for a fundamental understanding of biological phenomena. Conventional structural biology techniques, such as X-ray crystallography and cryo-electron microscopy, can reveal the atomic structure of biomolecules. However, because the structures observed are frozen at low temperatures, this is essentially a “photograph” of the biomolecules. High-speed atomic force microscopy (HS-AFM), on the other hand, can film a “movie” of biomolecules, but its spatial resolution is 1 nanometer, meaning it cannot distinguish atoms, which are approximately 0.1 nanometers in size. To address this drawback, methods have been developed by fitting atomic models to structures observed with HS-AFM, but their validity has not been fully verified.

An international collaborative research group led by Jr. Associate professor Takashi Sumikama of the Graduate School of Biostudies, Kyoto University (also a collaborating researcher at the Nano Life Science Institute, Kanazawa University), Assistant Professor Kien X Ngo of Kanazawa University, and Dr. Sergei Grudinin of the University of Grenoble Alpes in France, has developed a fitting method (AFMfit-MD) that uses structures obtained through molecular dynamics (MD) simulations as a guide for fitting. Furthermore, principal component analysis (PCA) demonstrated that the atomic-level motions observed with high-speed AFM closely resembled those obtained by MD, verifying the validity of the developed method. Furthermore, the developed method was applied to α-actinin, a key molecule that constitutes muscle, to elucidate its bending and twisting motions.

The workflow to obtain atomic-level structure and dynamics using the newly developed method (AFMfit-MD).