Mapping the electrostatic potential within the ribosomal exit tunnel

J Mol Biol. 2007 Aug 31;371(5):1378-91. doi: 10.1016/j.jmb.2007.06.038. Epub 2007 Jun 19.

Abstract

Electrostatic potentials influence interactions among proteins and nucleic acids, the orientation of dipoles and quadrupoles, and the distribution of mobile charges. Consequently, electrostatic potentials can modulate macromolecular folding and conformational stability, as well as rates of catalysis and substrate binding. The ribosomal exit tunnel, along with its resident nascent peptide, is no less susceptible to these consequences. Yet, the electrostatics inside the tunnel have never been measured. Here we map both the electrostatic potential and accessibilities along the length of the tunnel and determine the electrostatic consequences of introducing a charged amino acid into the nascent peptide. To do this we developed novel probes and strategies. Our findings provide new insights regarding the dielectric of the tunnel and the dynamics of its local electric fields.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / metabolism
  • Cysteine / chemistry*
  • Kinetics
  • Maleimides / chemistry
  • Microtubule-Associated Proteins / chemistry
  • Models, Molecular
  • Molecular Conformation
  • Molecular Sequence Data
  • Polyethylene Glycols / chemistry
  • Protein Biosynthesis
  • Protein Conformation
  • Protein Folding
  • Ribosomes / chemistry*
  • Static Electricity

Substances

  • Bacterial Proteins
  • Maleimides
  • Microtubule-Associated Proteins
  • maleimide
  • Polyethylene Glycols
  • Cysteine