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Updated: Oct 14, 2025
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
15.6K
Protein conformational transitions explored by a morphing approach based on normal mode analysis in internal
Byung Ho Lee1, Soon Woo Park1, Soojin Jo2
1School of Mechanical Engineering, Sungkyunkwan University, Suwon, South Korea.
Plos One
|November 4, 2021
Summary
We developed ICONGENI, a new computational method to predict protein conformational changes. This approach accurately models protein dynamics and transition pathways, aiding in understanding protein function.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Large-scale protein conformational changes are crucial for biological function.
- Studying these rare events is challenging experimentally and computationally.
- Understanding protein dynamics is key to drug discovery and protein engineering.
Purpose of the Study:
- To introduce a novel computational method, ICONGENI, for predicting protein conformational transition pathways.
- To provide a reliable computational tool for analyzing protein dynamics.
- To explore the potential of ICONGENI in revealing complex energy landscapes.
Main Methods:
- ICONGENI uses internal coordinate normal mode analysis to guide elastic network interpolation.
- It samples intermediate protein conformations by interpolating interatomic distances.
- Degrees of freedom are constrained by low-frequency protein dynamics.
Main Results:
- ICONGENI successfully predicted reliable conformational transition pathways for proteins exhibiting open-closed transitions.
- Simulated pathways demonstrated high thermal and chemical stability compared to other methods.
- The method generated an ensemble of pathways, enabling exploration of rough energy landscapes.
Conclusions:
- ICONGENI is a robust computational tool for predicting protein conformational pathways.
- The method offers insights into protein dynamics and mechanisms, even with unknown metastable states.
- ICONGENI advances the study of protein conformational changes and their functional implications.
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