An explanation of biphasic characters of mRNA translocation in the ribosome

Translocation is an essential step in the elongation cycle of protein synthesis in which mRNA that is coupled with tRNAs by codon-anticodon interaction is moved through the ribosome. It has been well documented that the kinetics of mRNA translocation generally shows biphasic character. However, the physical basis of the phenomenon is unclear. Here, to explain the phenomenon we consider two models. In one model (Model I), besides the classical non-rotated and rotated conformations of the ribosome there also exists an intermediate conformation between the two classical conformations. The mRNA translocation occurs via proceeding from the rotated (hybrid) pretranslocation to intermediate to non-rotated posttranslocation state. In another model (Model II), only the classical non-rotated and rotated conformations are considered. Before EF-G binding, the ribosomal complex is in either the classical non-rotated or rotated (hybrid) pretranslocation state, with the equilibrium with each other. EF-G can bind to both states and then the mRNA translocation occurs via proceeding either directly from the hybrid to non-rotated posttranslocation state or from the non-rotated pretranslocation to hybrid to non-rotated posttranslocation state. Analytical studies showed that Model I is unable to explain the biphasic character of mRNA translocation. By contrast, Model II can not only provide a good explanation of the biphasic character of mRNA translocation but also explain the kinetics of the reverse ribosomal rotation from the rotated to non-rotated conformation, which can be fit to a single exponential. Thus, Model II could be the appropriate one for the kinetic pathway of mRNA translocation.