ArticleNano letters2026
SimHS-AFMfit-MD: An Integrative Approach for Inferring Alpha-Actinin Atomic Conformational Dynamics.
Article in Nano letters, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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6 authors.
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Abstract
Many molecular systems, including intrinsically disordered proteins and flexible multidomain complexes, exhibit significant conformational heterogeneity and flexibility, making them difficult to study with conventional methods like X-ray crystallography or cryo-EM. To address this challenge, we introduce SimHS-AFMfit-MD, an integrative framework combining high-speed atomic force microscopy (HS-AFM), molecular dynamics (MD) simulations, and AFMfit-based structural modeling to infer dynamic protein conformations at atomic resolution. Using alpha-actinin, an actin cross-linking protein, as a model system, we demonstrate that nonlinear normal-mode analysis (AFMfit-NMA) enhances the accuracy of structural fitting. Additionally, guiding AFMfit with MD trajectories (AFMfit-MD) significantly improves fitting performance, aligning closely with unbiased all-atom MD simulations. This method converts thousands of 3D HS-AFM images into atomic-scale conformational ensembles, revealing key transitions between Ca
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