Although multidomain proteins predominate the proteome of all organisms and are expected to display complex folding behaviors and significantly greater structural dynamics as compared with single-domain proteins, their conformational heterogeneity and its impact on their interaction with ligands are poorly understood due to a lack of experimental techniques. The multidomain calcium-binding ␥-crystallin proteins are particularly important because their deterioration and misfolding/aggregation are associated with melanoma tumors and cataracts. Here we investigate the mechanical stability and conformational dynamics of a model calcium-binding ␥-crystallin protein, Protein S, and elaborate on its interactions with calcium. We ask whether domain interactions and calcium binding affect Protein S folding and potential structural heterogeneity. Our results from single-molecule force spectroscopy show that the N-terminal (but not the C-terminal) domain is in equilibrium with an alternative conformation in the absence of Ca 2؉ , which is mechanically stable in contrast to other proteins that were observed to sample a molten globule under similar conditions. Mutagenesis experiments and computer simulations reveal that the alternative conformation of the N-terminal domain is caused by structural instability produced by the high charge density of a calcium binding site. We find that this alternative conformation in the N-terminal domain is diminished in the presence of calcium and can also be partially eliminated with a hitherto unrecognized compensatory mechanism that uses the interaction of the C-terminal domain to neutralize the electronegative site. We find that up to 1% of all identified multidomain calcium-binding proteins contain a similarly highly charged site and therefore may exploit a similar compensatory mechanism to prevent structural instability in the absence of ligand.Multidomain proteins are highly prevalent in the proteomes of all organisms (1); however, there is still little known about their folding pathways and interaction with ligands (2), as compared with small, single-domain proteins. This is because large, multidomain proteins may exhibit significant structural dynamics and transient interactions between the domains that are rather difficult to capture and analyze. An important example of this class of proteins are the calcium-binding proteins that are effectors for stimulating cellular signals (3, 4) and buffering calcium levels (5). Currently, of particular interest are the calcium-binding ␥-crystallin proteins that are implicated in several human diseases (6 -8). The complexity of these proteins may best be understood through single-molecule methods that are able to deconvolve their conformational heterogeneity. Although there have been exciting recent single-molecule studies of the multidomain calmodulin, including the impact of domains' interactions on calcium binding (9), and studies on mechanical unfolding of ␥-crystallins that captured their interesting domain swapping behavior (10), ther...