contributed talk given at MDAnalysis User Group Meeting, King's College London, UK
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Computer simulations of the ribosome
Michal H. Kolář
Vibrio alginolyticus
Vibrio Export Monitoring Polypeptide (VemP)
photo courtesy: Dr. Gary Gaugler, Visuals Unlimited, Inc.
Simulations
- GROMACS 2019
- Amber12sb + SPC/E water (CHARMM36m + TIP3P water)
- four independent trajectories in ribosome (1500 ns/traj)
- eight independent trajetories in water (4000 ns/traj)
Analysis
- MDAnalysis to interface between Gromacs and Python
- 2M atoms including solvent
- PDB (150 MB) and XTC file formats (5 GB)
- PDB with 150k non-hydrogen atoms
- segid selection keyword critical
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Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel
Classification algorithms
in MD simulations
Simulations
- GROMACS 2019
- Amber12sb + SPC/E water
- four independent simulations for PDF+ and PDF−
- 1000 ns/traj
Analysis
- Functional Mode Analysis by Hub et al. PMID 19714202
- built on top of PCA module of MDAnalysis
- later combined with scikit-learn
- major bottleneck was handling large XTC files
Prediction accuracy
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The presence or absence of PDF can be predicted from conformations of distant ribosome parts.
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Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior.
Computer simulations of the ribosome
Michal H. Kolář
Structural analysis
