Low resolution structure of the human α4 protein (IgBP1) and studies on the stability of α4 and of its yeast ortholog Tap42

Abstract The yeast Tap42 and mammalian α4 proteins belong to a highly conserved family of regulators of the type 2A phosphatases, which participate in the rapamycin-sensitive signaling pathway, connecting nutrient availability to cell growth. The mechanism of regulation involves binding of Tap42 to Sit4 and PPH21/22 in yeast and binding of α4 to the catalytic subunits of type 2A-related phosphatases PP2A, PP4 and PP6 in mammals. Both recombinant proteins undergo partial proteolysis, generating stable N-terminal fragments. The full-length proteins and α4 C-terminal deletion mutants at amino acids 222 (α4Δ222), 236 (α4Δ236) and 254 (α4Δ254) were expressed in E. coli . α4Δ254 undergoes proteolysis, producing a fragment similar to the one generated by full-length α4, whereas α4Δ222 and α4Δ236 are highly stable proteins. α4 and Tap42 show α-helical circular dichroism spectra, as do their respective N-terminal proteolysis resistant products. The cloned truncated proteins α4Δ222 and α4Δ236, however, possess a higher content of α-helix, indicating that the C-terminal region is less structured, which is consistent with its higher sensitivity to proteolysis. In spite of their higher secondary structure content, α4Δ222 and α4Δ236 showed thermal unfolding kinetics similar to the full-length α4. Based on small angle X-ray scattering (SAXS), the calculated radius of gyration for α4 and Tap42 were 41.2 ± 0.8 A and 42.8 ± 0.7 A and their maximum dimension ∼142 A and ∼147 A, respectively. The radii of gyration for α4Δ222 and α4Δ236 were 21.6 ± 0.3 A and 25.7 ± 0.2 A, respectively. Kratky plots show that all studied proteins show variable degree of compactness. Calculation of model structures based on SAXS data showed that α4Δ222 and α4Δ236 proteins have globular conformation, whereas α4 and Tap42 exhibit elongated shapes.