Long-range electrostatic interactions in proteins/peptides associating to nucleic acids are reflected in the salt-dependence of the binding process. According to the
oligocationic binding model, which is based on counterion condensation theory, only
the cationic residues of peptides/proteins near the binding interface are assumed to
affect the salt dependence in the association of peptides and proteins to nucleic acids.
This model has been used to interpret and predict the binding of oligocationic chains–such as oligoarginines/lysines–to nucleic acids, and does an excellent job in these
kinds of systems. This simple relationship, which is used to compare or count the number of ionic interactions in protein-nucleic acid complexes, does not hold when acidic
residues, i.e. glutamate and aspartate, are incorporated in the protein matrix. Here,
we report a combined molecular mechanics (by means of energy-minimization of the
structure under the influence of an empirical energy function) and Poisson-Boltzmann
(PB) study on the salt-dependence in binding to tRNA of two important enzymes that
are involved in the seminal step of peptide formation in the ribosome: Glutamine
synthetase (GluRS) and Glutaminyl synthetase (GlnRS) bound to their cognate tRNA.
These two proteins are anionic and contain a significant number of acidic residues
distributed over the entire protein. Some of these residues are located in the binding
interface to tRNA. We computed the salt-dependence in association, SKpred, of these
enzyme-tRNA complexes using both the linear and nonlinear solution to the Poisson-Boltzmann Equation (PBE). Our findings demonstrate that the SKpred obtained with
the nonlinear PBE is in good agreement with the experimental SKobs, while use of the
linear PBE resulted in the SKpred being anomalous. We conclude that electrostatic interactions between the binding partners in these systems are less favorable by means of
charge-charge repulsion between negatively charged protein residues and phosphate oxygens in the tRNA backbone but also play a significant role in the association process of proteins to tRNA. Some unfavorable electrostatic interactions are probably compensated by hydrogen-bonds between the carboxylate group of the side chain in the
interfacial acidic protein residues and the tRNA backbone. We propose that the low experimentally observed SKobs values for both GlnRS- and GluRS-tRNA depend on the
distribution and number of anionic residues that exist in these tRNA synthetases. Our
computed electrostatic binding free energies were large and unfavorable due to the
Coulombic and de-solvation contribution for the GlnRS-tRNA and GluRS-tRNA complexes, respectively. Thus, low SKobs values may not reflect small contributions from
the electrostatic contribution in complex-formation, as is often suggested in the literature. When charges are "turned off" in a computer-experiment, our results indicated
that "turning off" acidic residues far from a phosphate group significantly influences
SKpred. If cationic residues are "turned off", less impact on SKpred is observed with
respect to the distance to the nearest phosphate-group.