The interaction of cyclosporin A and cyclosporin derivatives with cyclophilins A, B, and C has been investigated by means of fluorescence measurement techniques. Since Trp-121 of cyclophilin A is in close contact with bound cyclosporins and changes its fluorescence emission upon binding, direct estimation of Kd values for cyclosporins is straightforward in this case. Cyclophilins B and C, however, display no evident binding-dependent fluorescence changes suitable for the estimation of their binding affinities. This problem can be circumvented by measuring the variations of fluorescence emission intensities of a mixture of cyclophilin A and the fluorescence measurements unsuitable for cyclosporin binder as a function of ligand concentration. Application of a mixed-mode kinetic analysis then allows the calculation of the cyclosporin binding affinity of the second binder in the system. The dissociation constant for cyclosporin A/cyclophilin A was found to be 36.8 nM. Mixed-mode kinetic calculations yielded Kd values of 9.8 and 90.8 nM for cyclophilins B and C, respectively. The analysis was extended to noncyclophilin (weak) cyclosporin binders such as calmodulin and actin, resulting in approximate Kd values of 1.2 and 5.7 microM, respectively. Using the same approach, the Kd values of a series of different cyclosporin derivatives were determined.