Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation
Fig 8
Representation of mRNA translation elongation as a Markov process and assigned IFIs for a mRNA that consists of four codons.
The Markov model for translation of a short mRNA consisting of n = 4 codons includes 6n + 2 = 26 states and n + 3 = 7 assigned IFIs. Each state in the process corresponds to one biochemically resolved step: State 01 represents the initiation complex with the start codon in the ribosomal A site. States 01-41 describe initial selection, including ternary complex binding and recognition, GTPase activation, GTP hydrolysis and rearrangement of EF-Tu. This is followed by tRNA accommodation and peptide bond formation (51). Afterwards, the ribosome translocates to the second codon (02). The elongation cycle is repeated for the next three codons before the ribosome reaches the end of the truncated mRNA (E4) where the P site is occupied by the fourth codon while the A site remains empty. See refs. [39–45] for more details on the translation process. Possible transitions between the states are indicated by arrows and occur with transitions rates ωij, which is exemplified by the ternary complex binding rate ω01 and the unbinding rate ω10. The average rate of translation for one codon is denoted by ωelo. For the first codon, changes in the state-specific IFIs are assumed to occur both after peptide bond formation and translocation, and states assigned with identical IFI values have the same color. Note that due to initial synchronization of ribosomes, the two IFI changes on the first codon become visible in the ensemble fluorescence signature. For all following codons only one change in fluorescence intensity after peptide bond formation (after transition from state (4k) to state (5k)) is considered to avoid overfitting. The final intrinsic fluorescence intensity E4 corresponds to the artificial state of the ribosome at the end of the truncated mRNA. Previously published as the 6n2/n3 model in [8]. Nomenclature of IFIs for a): a generic mRNA, and b): the specific case of LepB5 mRNA.