Minimal transition state charge stabilization of the oxyanion during peptide bond formation by the ribosome

Biochemistry. 2011 Dec 6;50(48):10491-8. doi: 10.1021/bi201290s. Epub 2011 Nov 9.

Abstract

Peptide bond formation during ribosomal protein synthesis involves an aminolysis reaction between the aminoacyl α-amino group and the carbonyl ester of the growing peptide via a transition state with a developing negative charge, the oxyanion. Structural and molecular dynamic studies have suggested that the ribosome may stabilize the oxyanion in the transition state of peptide bond formation via a highly ordered water molecule. To biochemically investigate this mechanistic hypothesis, we estimated the energetic contribution to catalytic charge stabilization of the oxyanion using a series of transition state mimics that contain different charge distributions and hydrogen bond potential on the functional group mimicking the oxyanion. Inhibitors containing an oxyanion mimic that carried a neutral charge and a mimic that preserved the negative charge but could not form hydrogen bonds had less than a 3-fold effect on inhibitor binding affinity. These observations argue that the ribosome provides minimal transition state charge stabilization to the oxyanion during peptide bond formation via the water molecule. This is in contrast to the substantial level of oxyanion stabilization provided by serine proteases. This suggests that the oxyanion may be neutralized via a proton shuttle, resulting in an uncharged transition state.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Catalysis
  • Catalytic Domain
  • Hydrogen Bonding
  • Peptide Biosynthesis
  • Peptides / chemistry*
  • Peptidyl Transferases / antagonists & inhibitors
  • Peptidyl Transferases / chemistry
  • Protein Stability
  • Ribosomal Proteins / biosynthesis
  • Ribosomal Proteins / chemistry*
  • Ribosomes / chemistry*
  • Ribosomes / enzymology
  • Static Electricity

Substances

  • Peptides
  • Ribosomal Proteins
  • Peptidyl Transferases