Protein Conformational
Dynamics Analysis
An independent computational study of protein conformational dynamics using molecular-dynamics trajectories, structural measurements, and principal component analysis.
Research question
Can the dominant motion identified by principal component analysis recover the same conformational transition captured by a physically interpretable interdomain distance?
Why this project
Molecular-dynamics simulations generate high-dimensional trajectories containing the positions of thousands of atoms over time. This project explores how dimensionality-reduction methods can be used to identify dominant protein motions and compares those results with simpler structural measurements that have a direct physical interpretation.
System
The initial analysis uses an adenylate kinase molecular-dynamics trajectory containing a large-scale closed-to-open conformational transition.
Methods
The analysis includes structural alignment, backbone RMSD, interdomain distance measurements, principal component analysis of aligned atomic coordinates, and comparison of PCA projections with geometric reaction coordinates.
- Trajectory inspection
- Structural alignment
- Backbone RMSD
- Interdomain distance
- Principal component analysis
- PCA / geometric-coordinate comparison
Figure in progress.
Figure in progress.
Figure in progress.
Figure in progress.
Figure in progress.
Results
Analysis in progress. Results and figures will be added as the project develops.
Interpretation
This section will be updated after the primary structural and PCA analyses are complete.
Limitations
Limitations will be documented as the analysis develops.
Next steps
Complete PCA analysis, interpret the dominant structural modes, and evaluate whether low-dimensional representations correspond to physically meaningful conformational states.
Tools
Python · MDAnalysis · NumPy · SciPy · pandas · Matplotlib · scikit-learn