Evidence of turn and salt bridge contributions to β-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G Original Research Article

We ran and analyzed a total of eighteen, 10 ns molecular dynamics simulations of two C-terminal β-hairpins from the B1 domain of Protein G: twelve runs for the last 16 residues and six runs for the last 15 residues, G41–E56 and E42–E56, respectively. Based on their CαRMS deviation from the starting structure and the pattern of stabilizing interactions (hydrogen bonds, hydrophobic contacts, and salt bridges), we were able to classify the twelve runs on G41–E56 into one of three general states of the β-hairpin ensemble: ‘Stable’, ‘Unstable’, and ‘Unfolded’. Comparing the specific interactions between these states, we find that on average the stable β-hairpin buries 287 Å2 of hydrophobic surface area, makes 13 hydrogen bonds, and forms 3 salt-bridges. We find that the hydrophobic core prefers to make some specific contacts; however, this core does not require optimal packing. Side-chain hydrogen bonds stabilize the β-hairpin turn with strong stabilizing interactions primarily due to the carboxyl of D46 with contributions from T49 hydroxyl. Buoyed by the strength of the hydrophobic core, other hydrogen bonds, primarily main-chain, guide the β-hairpin into registration by forming a loose network of interactions, making an approximately constant number of hydrogen bonds from a pool of possible candidates. In simulations on E42–E56, where the salt bridge closing the termini is not favored, we observe that all the simulations show no ‘Stable’ behavior, but are ‘Unstable’ or ‘Unfolded’. We can estimate that the salt-bridge between the termini provides approximately 1.3 kcal/mol. Altogether, the results suggest that the β-hairpin folds beginning at the turn, followed by hydrophobic collapse, and then hydrogen bond formation. Salt bridges help to stabilize the folded conformations by inhibiting unfolded states.