Year:    2008

Communications in Computational Physics, Vol. 3 (2008), Iss. 5 : pp. 1132–1153

Abstract

The nonlinear Poisson-Boltzmann predictions of the salt-dependent association of proteins to DNA, SK_pred, are fairly insensitive to the choice of atomic charges, radii, interior dielectric constant and treatment of the boundary between a biomolecule and the solvent. In this study we  show that the SK_pred is highly correlated with the conformational adaptability of the partners involved in the biomolecular binding process. This is demonstrated for the wild-type and mutant forms of the archaeon Pyrococcus woesi TATA-binding protein (PwTBP) in complex with DNA, on which we performed molecular mechanics energy minimizations with different protocols, and molecular dynamics simulations and then computed the SK_pred on the resulting structures. It was found that the inter-molecular non bonded force field energy between the DNA and protein correlates linearly and significantly well with the SK_pred. This correlation encompasses the wild-type and mutant variants of the PwTBP and provides us with a quick way to estimate the SK_pred from a large ensemble of structures generated with Molecular Dynamics or Monte Carlo simulations. The corresponding experimental SK_obs should also correlate with the inter-molecular non bonded force field energy between the protein and DNA, given that the underlying mechanisms in binding and salt-dependent effects are in fact the main contributors in the association of proteins/peptides to nucleic acids. We show that it is possible to fit experiments versus the inter-molecular non bonded force field energy between the protein and DNA, and use this relation to predict the SK_obs in absolute numbers. Thus, we present two novel approaches to estimate both the SKpred and the SK_obs for in silico modelled PwTBP novel mutants and even for TBPs from other organisms. This is a simple but powerful tool to suggest new experiments on the TBP-DNA type of macromolecular assemblies. We conclude by suggesting some mutants and a possible biological interpretation of how changes in solvent salinity affect the binding of proteins to DNA.