contributed talk at the 7th Users' conference of IT4Innovations in Ostrava, Czechia.
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Atomistic simulations of ancient ribosomes and their parts
Michal H. Kolář
Bing via DALL-E 3: ribosome predecessor synthesizing a protein in the premordial soup of molecules, black-white line art with blue details, dark background.
Mechanism of amino acid polymerization as occured more than 3.5 billion years ago
23-05557S, 23-05764S
Hlouchová group
Protein Synthesis: Pre-Attack
Protein Synthesis: Bonds Re-Arrangement
Protein Synthesis: Product State
Ribosome evolution
Petrov et al. 2015, PMID: 26621738
big protoribosome: 610 nucleotides
tunnel view
tRNA view
small protoribosome: 134 nucleotides
tunnel view
tRNA view
Summary of simulated systems
big protoribosome (ca 365,000 atoms)
rRNA
rRNA + peptides
small protoribosome (ca 136,000 atoms)
rRNA
rRNA + pL2
rRNA + pL3
rRNA + pL4
rRNA + pL2 + pL3 + pL4
Technical setup
- classical all-atom MD simulations in GROMACS
- Amber family of force fields + SPC/E water + JC ions
- three independent unbiased trajectories 1.1 μs each
GROMACS
- open source code
- mixed openMP/MPI parallelization
- optional GPU accelleration
take this home:
Peptides stabilize ancestral ribosomal RNA (and promote protoribosome aggregation).
