Structural and Dynamic Effects of -Helix Deletion in Sso7d: Implications for Protein Thermal Stability

ABSTRACT Sso7d is a 62-residue protein from the hyperthemophilic archaeon Sulfolobus solfatari-cus with a denaturation temperature close to 100°C around neutral pH. An engineered form of Sso7d truncated at leucine 54 (L54) is significantly less stable, with a denaturation temperature of 53°C. Mo-lecular dynamics (MD) studies of Sso7d and its trun-cated form at two different temperatures have been performed. The results of theMD simulations at 300 K indicate that: (1) the flexibility of Sso7d chain at 300 K agrees with that detected from X-ray and NMR struc-tural studies; (2) L54 remains stable in the native folded conformation and possesses an overall dy-namic behavior similar to that of the parent protein. MD simulations performed at 500 K, 10 ns long, indi-cate that, while Sso7d is in-silico resistant to high temperature, the truncated variant partially unfolds, revealing the early phases of the thermal unfolding pathway of the protein. Analysis of the trajectories of L54 suggests that the unzipping of the N-terminal and C-terminal -strands should be the first event of the unfolding pathway, and points out the regions more resistant to thermal unfolding. These findings allow one to understand the role played by specific interactions connecting the two ends of the chain for the high thermal stability of Sso7d, and support re-cent hypotheses on its folding mechanism emerged from site-directedmutagenesis studies. Proteins 2004