Introduction Life rests on a web of molecular recognition;1,2 the folding of proteins, the hybridization of nucleic acids, the recognition of signaling molecules by receptors, and the interaction of enzymes with substrates and cofactors all require molecular recognition. Molecular recognition is based on shape-sensitive, noncovalent interactions between molecules or fragments of molecules.3-6 The energetics of molecular recognition can reflect van der Waals, hydrophobic, hydrogen bonding, and electrostatic interactions; all include both enthalpic and entropic contributions. The role of van der Waals interactions in molecular recognition in aqueous ionic solutions is well understood; they contribute to molecular recognition primarily through unfavorable steric interactions that exclude ligands with noncomplementary shapes from the recognition site of the protein. Hydrophobic interactions, although still a challenge to describe theoretically, can be estimated empirically from the observed partitioning of model compounds between aqueous and hydrocarbon solvents.7 Hydrogen bonds are best thought of as a specific type of localized electrostatic interaction;8 they are also well understood qualitatively. Although much theoretical and experimental work has gone into understanding the electrostatic properties and interactions that are central to biomolecular recognition events9-11(for a review, see ref 12), it has been difficult to measure and evaluate these interactions quantitatively. One of the central electrostatic properties of proteins is their charge, which is determined, in principle, by the sequence and structure of the protein and the properties of the solvent. Although one can measure the isoelectric point of proteins (the value of pH at which the charge of the protein is zero), there has been no general way of measuring the charge of a protein at other values of pH or as a function of the properties of the solution. Previous attempts to estimate the effects of electrostatic interactions on the affinities of proteins for ligands have focused on the use of site-directed mutagenesis.10,13-15 This technique, although powerful, is labor intensive, and the number of mutated sites that can be explored practically is limited. In this Account we describe the use of protein charge ladders in combination with capillary electrophoresis (CE) as a new biophysical tool with which to measure the electrostatic properties and interactions that are central to biomolecular recognition events involving proteins. The partial acetylation of amino groups on a protein changes the charge of the protein and generates a protein charge ladder, that is, a series of derivatives of a protein differing in values of charge but having similar coefficients of friction. The distribution of protein derivatives group, in terms of their values of electrophoretic mobility, into the “rungs” of a charge ladder, which appear in CE as a set of peaks; each successive peak in the charge ladder differs incrementally in the number of acetylated amino groups (Scheme 1). Charge ladders in combination with CE have been used to estimate the charge of the unmodified protein16 and the values of pKa of individual ionizable groups.17,18 Charge ladders in combination with affinity capillary electrophoresis (ACE) make it possible to quantify the contributions of electrostatics to the free energies of binding of charged ligands to proteins.19 Although we have developed this approach primarily using charge ladders of bovine carbonic anhydrase II (BCA II, EC 4.2.1.1.) as a model system (Figure 1),16,19 we have demonstrated the formation of charge ladders with a range of other proteins and biological molecules.17,18,20-23