Insights from molecular dynamics and metadynamics simulations into nucleotide-regulated and species-specific...

Era, an essential GTPase in Escherichia coli, is involved in ribosome biogenesis by associating with the 30S ribosomal subunit in its GTP bound state. However, the molecular mechanism underlying its nucleotide-dependent association and dissociation with the 30S subunit remains unknown. Superposition of Era structures from different species bound to distinct nucleotides revealed differences in N- and C-domain orientations. These observations raise the question of whether domain orientations are driven by nucleotide binding to facilitate Era-30S association/dissociation or whether they result from species-specific sequence variations. To investigate this, molecular dynamics simulations of E. coli Era were performed in different nucleotide bound states. Furthermore, well-tempered metadynamics was performed using the E. coli sequence modeled on the S. aureus template structure. This template-exchange simulation approach was used to investigate whether the E. coli sequence, when modeled on the S. aureus structure, can maintain the S. aureus domain orientation or reverts to its native E. coli orientation. The results showed that both nucleotide-binding and species-specific sequences influenced the conformation of Era. While the nucleotide state modulates the C-tail and N1 region conformation, influencing their interactions with the 30S subunit, species-dependent sequence variations govern the N- and C-domain orientation.