contributed talk given at RNA Club, Brno, Czechia
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Structure and dynamics of the narrowest part of the ribosome exit tunnel
Michal H. Kolář
A cross-section of the bacterial ribosome showing the exit tunnel with the tRNA in pink, uL4 in green, and uL22 in yellow.
1
Is the constriction site flexible?
Yes, is seems so. The flexibility is especially high for certain side chains of uL4 and uL22.2
Can the constriction get closed?
Temporarily yes, at least for certain lengths of the nascent peptide.3
How is the constriction affected by the nascent peptide?
Its structure and dynamics follows a non-trivial trend.PDB survey
- over 220 structural models
- E. coli ribosomes
- resolution of 4 Å or better
Atomistic simulations
- entire ribosome in explicit water
- over 2 million atoms
- bias-exchange metadynamics
Width of the constrictions site
Root mean square fluctuations
Four simulated systems
uL4
uL22
Constriction side width
Is the constriction site flexible?
Yes, is seems so. The flexibility is especially high for certain side chains of uL4 and uL22.Can the constriction get closed?
Temporarily yes, at least for certain lengths of the nascent peptide.How is the constriction affected by the nascent peptide?
Its structure and dynamics follows a non-trivial trend.
Structure and dynamics of the narrowest part of the ribosome exit tunnel
michal@mhko.science
Worthan et al. PMID: 35311583