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Updated: Feb 26, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

Kien Xuan Ngo^1,2, Takashi Sumikama^1,3,4, Rémi Vuillemot⁵

¹Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.

|February 25, 2026

Summary

This summary is machine-generated.

This study introduces SimHS-AFMfit-MD, a novel method combining high-speed atomic force microscopy (HS-AFM) and molecular dynamics (MD) simulations to visualize dynamic protein structures at atomic resolution.

Keywords:

AFMfit-MD AFMfit-NMA Alpha-actinin HS-AFM MD Simulations NMA PCA SimHS-AFMfit-MD

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Last Updated: Feb 26, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Area of Science:

Biophysics
Structural Biology
Computational Biology

Background:

Flexible molecular systems like proteins present challenges for traditional structural biology techniques.
Conformational heterogeneity hinders detailed atomic-level analysis.

Purpose of the Study:

To develop an integrative framework for inferring dynamic protein conformations at atomic resolution.
To visualize real-time protein dynamics bridging simulation and imaging.

Main Methods:

Introduced SimHS-AFMfit-MD, integrating high-speed atomic force microscopy (HS-AFM) with molecular dynamics (MD) simulations.
Employed AFMfit-based structural modeling, enhanced by nonlinear normal-mode analysis (AFMfit-NMA) and MD trajectory guidance (AFMfit-MD).
Applied the method to alpha-actinin, an actin cross-linking protein.

Main Results:

AFMfit-NMA improved structural fitting accuracy.
AFMfit-MD significantly enhanced fitting performance, aligning with all-atom MD simulations.
Generated atomic-scale conformational ensembles from thousands of HS-AFM images.
Revealed Ca2+-dependent conformational transitions in alpha-actinin.

Conclusions:

SimHS-AFMfit-MD enables atomic-scale visualization of protein dynamics.
The hybrid approach effectively bridges computational and experimental methods.
This framework advances the study of flexible molecular systems.