Free energy analysis of protein-DNA binding: The EcoRI endonuclease-DNA complex

A detailed theoretical analysis of the thermodynamics and functional energe tics of protein-DNA binding in the EcoRI endonuclease-DNA complex is presen ted, The standard free energy of complexation is considered in terms of a t hermodynamic cycle of seven distinct steps decomposed into a total of 24 we ll-defined components, The model we employ involves explicit all-atom accou nts of the energetics of structural adaptation of the protein and the DNA u pon complex formation; the van der Waals and electrostatic interactions bet ween the protein and the DNA; and the electrostatic polarization and screen ing effects, van der Waals components, and cavitation effects of solvation. The ion atmosphere of the DNA is described in terms of a counterion conden sation model combined with a Debye-Huckel treatment of added salt effects. Estimates of entropy loss due to decreased translational and rotational deg rees of freedom in the complex relative to the unbound species based on cla ssical statistical mechanics are included, as well as corresponding changes in the vibrational and configurational entropy. The magnitudes and signs o f the various components are estimated from the AMBER parm94 force field, g eneralized Born theory, solvent accessibility measures, and empirical estim ates of quantities related to ion release. The calculated standard free energy of formation, -11.5 kcal/mol, agrees wi th experiment to within 5 kcal/mol. This net binding free energy is discern ed to be the resultant of a balance of several competing contributions asso ciated with chemical forces as conventionally defined, with 10 out of 24 te rms favoring complexation. Contributions to binding compounded from subsets of the 24 components provide a basis for advancing a molecular perspective of binding in terms of structural adaptation, electrostatics, van der Waal s interactions, hydrophobic effects, and small ion reorganization and relea se upon complexation. The van der Waals interactions and water release favo r complexation, while electrostatic interactions, considering both intramol ecular and solvation effects, prove unfavorable. Analysis of individual con tributions to the standard free energy of complexation at the nucleotide an d amino acid residue level highlights the role of contact interactions as w ell as context effects. Some patterns in compensation effects among the var ious terms are identified and discussed. (C) 1999 Academic Press.