Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis

Observing a single biomolecule performing its function is fundamental in biophysics as it provides important information for elucidating the mechanism. High-speed atomic force microscopy (HS-AFM) is a unique and powerful technique that allows the observation of biomolecular motion in a near-native environment. However, the spatial resolution of HS-AFM is limited by the physical size of the cantilever tip, which restricts the ability to obtain atomic details of molecules. In this study, we propose a novel computational algorithm designed to derive atomistic models of conformational dynamics from AFM images. Our method uses normal-mode analysis to describe the expected motions of the molecule, allowing these motions to be represented with a limited number of coordinates. This approach mitigates the problem of overinterpretation inherent in the analysis of AFM images with limited resolution. We demonstrate the effectiveness of our algorithm, NMFF-AFM, using synthetic data sets for three proteins that undergo significant conformational changes. NMFF-AFM is a fast and user-friendly program that requires minimal setup and has the potential to be a valuable tool for biophysical studies using HS-AFM.