Improvements in the numerical analysis of thermodynamic data from biomolecular complexes

In this work, recent improvements in the capability of the numerical solver-based binding data global analysis program, BIOEQS, are presented. These improvements represent an expansion of the types of physical models which can be considered. The first realm of improvement concerns the modeling of systems which include several species of the same stoichiometry and differing chemical potentials, or site isomers. Such an option is generally used in the analysis of binding of multiple ligands to multiple protein sites. In addition to classical ligand binding problems, such a capability is useful in considering the binding of protein to different sites on the same DNA molecule and the effects of ligation upon these equilibria. It can also be employed for consideration of the equilibrium unfolding of oligomeric proteins with folded monomeric intermediates. The effect of dilution of the protein and ligation by up to two different types of ligands at multiple binding sites upon the dissociation and unfolding properties of the oligomers is now possible. The second advance which has been incorporated into the modeling capabilities of the BIOEQS program is the option of considering perturbations to the multiple binding or folding equilibria by chemical denaturants, temperature, or high hydrostatic pressure. Additional improvements to the BIOEQS program include direct mapping of individual species or sums of species to the numerical physical experimental observable. The values of the observable corresponding to particular species or to 0 and 100% completion of a titration can be either fixed or floating parameters in the fit.(ABSTRACT TRUNCATED AT 250 WORDS)