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Updated: Jun 23, 2026
13:26
Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry
Published on: September 13, 2014
Linear response theory in dihedral angle space for protein structural change upon ligand binding
Satoshi Omori1, Sotaro Fuchigami, Mitsunori Ikeguchi
1Department of Supramolecular Biology, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
Journal of Computational Chemistry
|April 18, 2009
Summary
Dihedral linear response theory improves protein structure prediction by accurately modeling rotational motions. This method enhances predictions of structural changes upon ligand binding, crucial for understanding protein dynamics.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Protein motion and ligand binding are linked, often explained by linear response theory.
- Existing linear response theory uses Cartesian coordinates, which can be less accurate for rotational motions.
Purpose of the Study:
- To improve the prediction accuracy of protein structural changes upon ligand binding.
- To investigate the efficacy of dihedral linear response theory compared to Cartesian-based methods.
Main Methods:
- Applied dihedral linear response theory to predict the ligand-bound form of Ferric-binding protein from its ligand-free form.
- Derived the variance-covariance matrix using linear conversion from Cartesian coordinates to dihedral angles.
Main Results:
- Dihedral linear response theory demonstrated improved prediction accuracy for protein structural changes.
- The use of dihedral angles provided a more accurate description of protein domain rotational motions.
Conclusions:
- Describing protein rotational motion using dihedral angles is essential for accurate structural change prediction.
- Dihedral linear response theory offers a more refined approach to modeling protein-ligand interactions and conformational changes.
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