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Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in
1Physics Department, University at Buffalo, Buffalo, New York, USA. wjzheng@buffalo.edu
Biophysical Journal
|March 18, 2009
Summary
Elastic network models (ENMs) reveal protein dynamics. Nonuniform interactions reveal coupled modes crucial for protein function, as shown in myosin II.
Area of Science:
- Computational biology
- Biophysics
- Structural biology
Background:
- Elastic network models (ENMs) are effective for studying protein conformational changes.
- ENMs typically assume uniform elastic interactions between residues.
- Understanding the impact of non-uniform interactions is crucial for accurate dynamic predictions.
Purpose of the Study:
- To investigate the dynamical effects of non-uniform elastic interactions in ENMs.
- To analyze the robustness and coupling of low-frequency normal modes under perturbations.
- To explore how these analyses can reveal functionally important protein motions.
Main Methods:
- Calculated low-frequency normal modes using ENMs with non-uniform force constants.
- Applied Gaussian noise to approximate variations in elastic interactions.
- Utilized first-order perturbation theory to estimate mode robustness and coupling.
- Analyzed mode coupling and robustness in myosin II.
Main Results:
- First-order perturbation theory efficiently estimates mode robustness and coupling for perturbed ENMs.
- Mode coupling and robustness analyses identify groups of strongly coupled modes related to protein function.
- Demonstrated the application using myosin II, highlighting implications for allosteric regulation.
Conclusions:
- Non-uniform elastic interactions significantly influence protein dynamics and functional motions.
- Mode coupling and robustness analyses provide insights into allosteric regulation in proteins like myosin.
- This approach enhances the predictive power of ENMs for understanding protein function.
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