Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel

Nascent polypeptide chains (NCs) are extruded from the ribosome through an exit tunnel (ET) traversing the large ribosomal subunit. The ETs irregular and chemically complex wall allows for various NC-ET interactions. Translational arrest peptides (APs) bind in the ET to induce translational arrest, a property that can be exploited to study NC-ET interactions by Force Profile Analysis (FPA). We employed FPA and molecular dynamics (MD) simulations to investigate how individual residues within a glycine-serine repeat segment of an AP-stalled NC interact with the ET to exert a pulling force on the AP and release stalling. Our results indicate that large and hydrophobic residues generate a pulling force on the AP when placed {gtrsim}10 residues away from the peptidyl transfer center (PTC). An asparagine placed 12 residues from the PTC appears to form a specific stabilizing interaction with the tip of ribosomal protein uL22 that reduces the pulling force on the AP, whereas a lysine or leucine residue in the same position increases the pulling force. Finally, the MD simulations suggest how the Mannheimia succiniciproducens SecM AP interacts with the ET to promote translational stalling. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/608737v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@d61d3forg.highwire.dtl.DTLVardef@11a3fa3org.highwire.dtl.DTLVardef@47e7ecorg.highwire.dtl.DTLVardef@cb4fb7_HPS_FORMAT_FIGEXP M_FIG C_FIG