The cold denatured state of the C-terminal domain of protein L9 is compact and contains both native and non-native structure

Cold denaturation is a general property of globular proteins, and the process provides insight into the origins of the cooperativity of protein folding and the nature of partially folded states. Unfortunately, studies of protein cold denaturation have been hindered by the fact that the cold denatured state is normally difficult to access experimentally. Special conditions such as addition of high concentrations of denaturant, encapsulation into reverse micelles, the formation of emulsified solutions, high pressure, or extremes of pH have been applied, but these can perturb the unfolded state of proteins. The cold denatured state of the C-terminal domain of the ribosomal protein L9 can be populated under native-like conditions by taking advantage of a destabilizing point mutation which leads to cold denaturation at temperatures above 0 °C. This state is in slow exchange with the native state on the NMR time scale. Virtually complete backbone ¹⁵N, ¹³C, and ¹H as well as side-chain ¹³C_β and ¹H _β chemical shift assignments were obtained for the cold denatured state at pH 5.7, 12 °C. Chemical shift analysis, backbone N-H residual dipolar couplings, amide proton NOEs, and R₂ relaxation rates all indicate that the cold denatured state of CTL9 (the C-terminal domain of the ribosomal protein L9) not only contains significant native-like secondary structure but also non-native structure. The regions corresponding to the two native α-helices show a strong tendency to populate helical - and - angles. The segment which connects α-helix 2 and β-strand 2 (residues 107-124) in the native state exhibits a significant preference to form non-native helical structure in the cold denatured state. The structure observed in the cold denatured state of the I98A mutant is similar to that observed in the pH 3.8 unfolded state of wild type CTL9 at 25 °C, suggesting that it is a robust feature of the denatured state ensemble of this protein. The implications for protein folding and for studies of cold denatured states are discussed.