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Updated: Dec 25, 2025
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Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules
Published on: April 25, 2025
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Nonaffine Displacements Encode Collective Conformational Fluctuations in Proteins.
Dube Dheeraj Prakashchand1, Navjeet Ahalawat1,2, Satyabrata Bandyopadhyay1
1Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India.
Journal of Chemical Theory and Computation
|March 26, 2020
Summary
This study introduces a novel method using nonaffine displacements to efficiently analyze biomacromolecular dynamics and free energy landscapes. This approach reveals essential motions and maps conformational transitions for complex macromolecules.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Understanding biomacromolecular dynamics is key to their function.
- Resolving the free energy landscape requires identifying subtle conformational changes.
Purpose of the Study:
- To develop a more efficient method for filtering essential macromolecular motions.
- To quantitatively resolve the free energy landscape of complex macromolecules.
Main Methods:
- Utilized a collective variable approach originally for crystalline solids.
- Applied time-structured independent component analysis to nonaffine displacements.
- Projected out homogeneous fluctuations to isolate nonaffine modes.
Main Results:
- The collective variable efficiently filters essential macromolecular motions.
- Nonaffine displacements encode functionally relevant conformations.
- Successfully resolved the free energy landscape for various macromolecules.
- Mapped kinetics of conformational transitions using a Markov state model.
Conclusions:
- Nonaffine modes are crucial for local structural changes during conformational transitions.
- This method provides a quantitative framework for understanding macromolecular dynamics and free energy landscapes.
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