Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures

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Abstract
BBA1 is a designed protein that has only 23 residues. It is the smallest protein without disulfide bridges that has a well‐defined tertiary structure in solution. We have performed unfolding molecular dynamics simulations on BBA1 and some of its mutants at 300, 330, 360, and 400 K to study their kinetic stability as well as the unfolding mechanism of BBA1. It was shown that the unfolding simulations can provide insights into the forces that stabilize the protein. Packing, hydrophobic interactions, and a salt bridge between Asp12 and Lys16 were found to be important to the protein' stability. The unfolding of BBA1 goes through two major steps: (1) disruption of the hydrophobic core and (2) unfolding of the helix. The β‐hairpin remains stable in the unfolding because of the high stability of the type II' turn connecting the two β‐strands.