| Popis: |
Ribosomal stalling during protein synthesis in bacteria occurs in different ways and under different conditions. Stalling of specific peptide sequences can be a pre-programmed means of detecting the presence of potentially lethal antibiotics and constitute the initial step of a complex resistance pathway. An example of this is the stalling of ErmBL peptide synthesis in the presence of the antibiotic erythromycin. In other cases, stalling seems to be an effect of unusually slow, sequence dependent, rates of amino acid incorporation. This is the case for translation of proteins containing poly-proline stretches. Poly-proline sequences are known to stall ribosomes, normal translation rates are achieved only by recruiting a special elongation factor (EF-P in bacteria). Here, we investigate the stalling mechanisms in the two scenarios described above by explicit-solvent, all-atom molecular dynamics simulations of the ribosome. The simulations are started from high-resolution cryo-EM structures and performed under stalling and non-stalling conditions. We find networks of allosteric interactions between the nascent peptide chain and the ribosome that differently affect the positioning and the dynamics of the peptidyl tRNA relative to the A-site tRNA in such a way as to hinder peptide bond formation depending on the presence of the antibiotic (in the first scenario) or the absence of the elongation factor (second scenario). The simulation results not only explain the stalling mechanism, but can also predict the effect of mutations on stalling. In the case of erythromycin induced stalling, these predictions have been experimentally confirmed by a toe-printing assay. Our results illustrate the fine details of how the efficiency of peptide bond formation can be modulated by external factors in a way that depends on the specific sequence being translated. |
