Poisson-Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E

Biophys Chem. 2009 Mar;140(1-3):16-23. doi: 10.1016/j.bpc.2008.11.002. Epub 2008 Nov 17.

Abstract

The electrostatic free energy of binding of two analogues of the 5'-mRNA cap, differing in size and electric charge, to the wild type and mutated eukaryotic initiation factor eIF4E was computed using the finite difference solutions to the Poisson-Boltzmann equation. Two definitions of the solute-solvent dielectric boundary were used: van der Waals model, solvent exclusion (SE) model. The computed electrostatic energies were supplemented by estimations of the non polar and entropic contributions. A comparison with experimental data for the investigated systems was done. It appears that the SE model with additional contribution fits experimental findings better than the van der Waals model does.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Computer Simulation
  • Eukaryotic Initiation Factor-4E / chemistry*
  • Eukaryotic Initiation Factor-4E / genetics
  • Eukaryotic Initiation Factor-4E / metabolism*
  • Humans
  • Models, Chemical
  • Mutant Proteins / chemistry
  • Mutant Proteins / genetics
  • Mutant Proteins / metabolism
  • Osmolar Concentration
  • Protein Binding
  • Protein Conformation
  • Protons
  • RNA Cap Analogs / chemistry*
  • RNA Cap Analogs / metabolism*
  • Static Electricity
  • Structure-Activity Relationship
  • Thermodynamics

Substances

  • Eukaryotic Initiation Factor-4E
  • Mutant Proteins
  • Protons
  • RNA Cap Analogs