The interaction between initiation factor 3 and 30 S ribosomal subunits studied by high-resolution 1H NMR spectroscopy.
The interaction between Escherichia coli translational initiation factor 3 (IF-3) (Mr = 20668) and 30 S ribosomal subunits or fragmented 16 S rRNA was followed by 1H NMR spectroscopy. Upon addition of increasing yet largely substoichiometric amounts of deuterated 30 S ribosomal subunits, selective line broadenings and some chemical shift changes were observed. These effects can be fully reversed by increasing the temperature and/or the ionic strength. The selective line broadenings, which are explained by a medium-fast to fast exchange dynamics between free and bound IF-3 with loss of internal mobility of the protons, shed light on the amino acid residues of IF-3 involved in or affected by the binding to the 30 S subunits. Some effects (i.e. implication of 1 tyrosine, 1 phenylalanine, and some arginine and lysine residues) are seen with both 30 S subunits and rRNA while others (i.e. implication of a second tyrosine or phenylalanine residue of a group of hydrophobic residues and, possibly, of the single histidine residue), seen only or preferentially with 30 S subunits, may reflect additional interactions exclusively occurring at the ribosomal level.
D000596:Amino Acids / Q000032:analysis; D004926:Escherichia coli; D046911:Macromolecular Substances; D009682:Magnetic Resonance Spectroscopy; D009994:Osmolar Concentration; D010448:Peptide Initiation Factors / Q000032:analysis / Q000378:metabolism*; D039665:Prokaryotic Initiation Factor-3; D012335:RNA, Ribosomal / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*; D013329:Structure-Activity Relationship; D013696:Temperature
D000596:Amino Acids; D046911:Macromolecular Substances; D010448:Peptide Initiation Factors; D039665:Prokaryotic Initiation Factor-3; D012335:RNA, Ribosomal