We demonstrate a method to quantitatively determine both Coulomb energy and the intrinsic dielectric polarizability of large, multiply protonated gas-phase protein ions. Information about the conformation and maximum charge state of these ions in the gas phase is also obtained. The apparent gas-phase basicities (GB(app)) of individual charge states are measured; these values are compared to those calculated from a relatively simple model in which charges are assigned to sites in an ion such that the overall ion free energy is minimized. For cytochrome c, we find our calculations can be fit to measured values of GB(app) of the 3+ to 15+ ions using a fully denatured ion conformation and an epsilon(r) = 2.0+/-0.2. This value is substantially higher than that of the small cyclic decapeptide gramicidin s, but below that predicted by theory for the interior of a protein. We find that the intrinsic basicity of individual basic charge sites, estimated by GB measurements of small peptides, is 13-18 kcal/mol higher than those of the corresponding individual amino acid, consistent with independent intramolecular interaction (self-solvation) of the charge site occurring in these large multiply protonated ions. For the 21+ ion in a denatured conformation, we find that the minimum Coulomb contribution to ion zero-point energy is 24 eV. This substantial Coulomb energy accounts for the increased reactivity and decreased stability of these highly charged ions. Our calculations indicate that the maximum charge state observed in electrospray mass spectra is determined by the relative apparent gas-phase basicity of the ion/solvent combination. Finally, we find that the gas-phase conformation of cytochrome c ions is consistent with a denatured form, although our calculations indicate that cytochrome c electrosprayed from an aqueous solution is initially in its native conformation subsequent to its desorption into the gas phase.