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Following translation, nascent peptides are deformylated, cleaved, translocated, folded, and modified. First, peptide deformylase deformylates the N-terminal formylmethionine of each nascent peptide. Second, methionine aminopeptidase cleaves the N-terminal methionine of 35 peptides. Second, 117 integral membrane, lipoproteins, and extracellular proteins bind the SecA translocase and are translocated into and through the plasma membrane via the SecYEGDF-YidC pore. Third, diacylglyceryl is transferred to the C-terminal cysteine of the signal sequence of each lipoprotein by diacylglyceryl transferase, and the signal sequence of each lipoprotein is cleaved by signal peptidase II. Next, 85 peptides bind inorganic ions at particular sites and 64 peptides fold with the assistance of the chaperones and chaperonins DnaJ, DnaK, GroEL, GroES, and GrpE. All peptides require trigger factor to properly fold. Finally, 20 peptide species are modified at 63 sites by 3 enzymes – serine/threonine protein kinase, lipoate ligase, and alpha glutamate ligase.
Nascent peptide processing, translocation, folding, and modification are modeled motivated by mass-action kinetics similar to RNA cleavage and modification. First, the maximum maturation rate of each species is calculated. Second, maturations are successively randomly selected according to the calculated maximum rates until no further maturations can occur.
In M. genitalium, every protein requires deformylation and roughly 7% require N-terminal amino acid cleavage. In this model, if both processes are required, they must occur in the same time step, as this module is internally stateless.
Deformylation (MG_106)
N-terminal amino acid cleavage (MG_172)
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