Factor H (FH) is a 155-kDa plasma protein that regulates the alternative pathway of the complement system. Its 20 CCP modules, of 51-62 amino acid residues each, are linked by short stretches (“linkers’) of three to eight residues. We set out to test the hypothesis that long linkers towards the middle of FH play a role in ensuring that its architecture allows binding sites near its N- and C-termini to engage cooperatively with the main target, C3b, which is the key complement pathway-triggering product of C3 cleavage. In initial work, site-directed mutagenesis was used to test whether two mutations, R53H and R78G, located within CCP 1 and linked to the kidney disease atypical hemolytic uremic syndrome, are functionally deficient. Mutant versions and a native-sequence version of CCPs 1-4 of FH (i.e. FH 1-4) were tested for their ability to act as a cofactor for the FI-mediated cleavage of C3b, and accelerate the decay of the C3 convertase. It was shown that FH 1-4 R53H binds normally to C3b but has no regulatory activity while FH 1-4 R78G binds very poorly and is also deficient in cofactor and decay-accelerating activities. In subsequent work, mutagenesis was used to make the eight-residue CCPs 12-13 linker shorter (SL), or more flexible through introduction of glycine residues (3xGLY), within recombinant (r) module pair FH 12-13, and in rFH 10-15 and rFH 8-15 as well as full-length rFH. NMR showed CCPs 12 and 13 remain intact following mutation of the linker but (in FH 12-13) are more flexibly mutually disposed, as expected. SAXS indicated that both FH 10-15 SL and FH 10-15 3xGLY nonetheless have similar compact structures to native sequence (WT) FH 10-15. On the other hand, FH linker mutants interact with C3b (according to surface plasmon resonance) somewhat less well than WT FH and in the case of FH SL, affinity is similar to that of FH 19-20, i.e. there is no evidence that both C3b-binding sites in this mutant bind to the target simultaneously. Nonetheless, the bacterial protein PspCN boosts binding of linker mutants to C3b by a similar factor (three-to-fivefold) to that observed for FH WT. Thus, while interactions between non-sequential CCPs are important for FH architecture, a bend at the 12-13 linker is needed for full-length FH to adopt a fully biological activity confirmation. The use of EPR for structural studies of rFH and its mutants was explored. Free cysteines were engineered in so they could have spin labels site-specifically attached. Alternatively, a recognition site for transglutaminase was introduced so a spin label could be incorporated. These strategies were applied to rFH 12-13 and rFH 10-15 as a prelude to studies of full-length FH. Several suitably engineered proteins were prepared but only one paramagnetically labeled sample (of FH 12-13) made it for EPR; this yielded results commensurate with the NMR-derived structure. Taken together, these promising data lay the groundwork for a future, potentially very insightful, combined mutagenesis and EPR study of FH architecture and its role in complement activation.