Poisson-Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E.
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.
Szklarczyk
Oliwia
O
Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warszawa, Poland.
Zuberek
Joanna
J
Antosiewicz
Jan M
JM
D000818:Animals; D001665:Binding Sites; D003198:Computer Simulation; D039561:Eukaryotic Initiation Factor-4E / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008956:Models, Chemical; D050505:Mutant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D009994:Osmolar Concentration; D011485:Protein Binding; D011487:Protein Conformation; D011522:Protons; D012314:RNA Cap Analogs / Q000737:chemistry* / Q000378:metabolism*; D055672:Static Electricity; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D039561:Eukaryotic Initiation Factor-4E; D050505:Mutant Proteins; D011522:Protons; D012314:RNA Cap Analogs