Role of N-terminal residues on folding and stability of C-phycoerythrin: simulation and urea-induced denaturation studies

The conformational state of biliproteins can be determined by optical properties of the covalently linked chromophores. Recently determined crystal structure of truncated form of alpha-subunit of cyanobacterial phycoerythrin (alpha C-PE) from Phormidium tenue provides a new insight into the structure-function relationship of alpha C-PE. To compare their stabilities, we have measured urea-induced denaturation transitions of the full length alpha C-PE (FL-alpha C-PE) and truncated alpha C-PE (Tr-alpha C-PE) followed by observing changes in absorbance at 565nm, fluorescence at 350 and 573nm, and circular dichroism at 222nm as a function of [urea], the molar concentration of urea. The transition curve of each protein was analyzed for Delta G(D)(0), the value of Gibbs free energy change on denaturation (Delta G(D)) in the absence of urea; m, the slope (= partial differential increment G(D)/ partial differential [urea]), and C-m, the midpoint of the denaturation curve, i.e. [urea] at which Delta G(D)=0. A difference of about 10% in Delta G(D)(0) observed between FL-alpha C-PE and Tr-alpha C-PE, suggests that the two proteins are almost equally stable, and the natural deletion of 31 residues from the N-terminal side of the full length protein does not alter its stability. Furthermore, normalization of probes shows that the urea-induced denaturation of both the proteins is a two-state process. Folding of both structural variants (Tr-alpha C-PE and FL-alpha C-PE) of P. tenue were also studied using molecular dynamics simulations at 300K. The results show clearly that the stability of the proteins is evenly distributed over the whole structure indicating no significant role of N-terminal residues in the stability of both proteins.