The Hsp-organizing protein (HOP) binds to the C termini of the chaperones Hsp70 and Hsp90, thus bringing them together so that substrate proteins can be passed from Hsp70 to Hsp90. Because Hsp90 is essential for the correct folding and maturation of many oncogenic proteins, it has become a significant target for anti-cancer drug design. HOP binds to Hsp70 and Hsp90 via two independent tetratricopeptide (TPR) domains, TPR1 and TPR2A, respectively. We have analyzed ligand binding using Poisson-Boltzmann continuum electrostatic calculations, free energy perturbation, molecular dynamics simulations, and site-directed mutagenesis to delineate the contribution of different interactions to the affinity and specificity of the TPR-peptide interactions. We found that continuum electrostatic calculations could be used to guide protein design by removing unfavorable interactions to increase binding affinity, with an 80-fold increase in affinity for TPR2A. Contributions at buried charged residues, however, were better predicted by free energy perturbation calculations. We suggest using a combination of the two approaches for increasing the accuracy of results, with free energy perturbation calculations used only at selected buried residues of the ligand binding pocket. Finally we present the crystal structure of TPR2A in complex with its non-cognate Hsp70 ligand, which provides insight on the origins of specificity in TPR domain-peptide recognition.The Hsp-organizing protein (HOP) 4 plays a key role in in vivo folding by bringing the chaperones Hsp70 (or its constitutively expressed isoform, Hsp70) and Hsp90 together into a complex (1) (see Fig. 1), where specific substrate proteins are passed over from Hsp70 to Hsp90. Partially folded Hsp90 client proteins are transferred from Hsp70 to Hsp90, where the final steps of folding are completed (2, 3). While bound to the Hsp90, the client protein then becomes functional, e.g. hormone receptors can bind their ligands, and then are released. Both chaperones must be brought together by their interaction with HOP to accomplish this (see Fig. 1). The whole Hsp90 functional cycle involves also other co-chaperones, such as p23, other TPR proteins, and ATP binding and hydrolysis, and is fairly complicated and incompletely understood (4). However, it is clear that HOP facilitates the interaction of Hsp70 and Hsp90 and thus is important in providing the link between the chaperones in the early part of Hps90 functional cycle. Hsp90 client proteins include nuclear hormone receptors, p53, and other transcription factors and various kinases, such as Atk and Her2. Many of these are oncogenes, making Hsp90 a significant anti-cancer drug target (5). It is therefore of considerable importance to better understand the chaperone cycle of Hsp90 and in particular its interaction with essential co-chaperones, such as HOP. The interactions of Hsp70 and Hsp90 with HOP also provide an excellent model system in which to study the contribution of electrostatics to protein-peptide interactions, as will bec...