Ligand effects on the protein ensemble: unifying the descriptions of ligand binding, local conformational...

Detailed description of the structural and physical basis of allostery, cooperativity, and other manifestations of long-range communication between binding sites in proteins remains elusive. Here we describe an ensemble-based structural-thermodynamic model capable of treating explicitly the coupling between ligand binding reactions, local fluctuations in structure, and global conformational transitions. The H(+) binding reactions of staphylococcal nuclease and the effects of pH on its stability were used to illustrate the properties of proteins that can be described quantitatively with this model. Each microstate in the native ensemble was modeled to have dual structural character; some regions were treated as folded and retained the same atomic geometry as in the crystallographic structure while other regions were treated thermodynamically as if they were unfolded. Two sets of pK(a) values were used to describe the affinity of each H(+) binding site. One set, calculated with a standard continuum electrostatics method, describes H(+) binding to sites in folded parts of the protein. A second set of pK(a) values, obtained from model compounds in water, was used to describe H(+) binding to sites in unfolded regions. An empirical free energy function, parameterized to reproduce folding thermodynamics measured by differential scanning calorimetry, was used to calculate the probability of each microstate. The effects of pH on the distribution of microstates were determined by the H(+) binding properties of each microstate. The validity of the calculations was established by comparison with a number of different experimental observables.