title: Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures.
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's stability. The unfolding of BBA1 goes through two major steps: (1) disruption of the hydrophobic core and (2) unfolding of the helix. The beta-hairpin remains stable in the unfolding because of the high stability of the type II' turn connecting the two beta-strands.
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA.
authors.forename: L
authors.initials: L
authors.lastname: Wang
authors.forename: Y
authors.initials: Y
authors.lastname: Duan
authors.forename: R
authors.initials: R
authors.lastname: Shortle
authors.forename: B
authors.initials: B
authors.lastname: Imperiali
authors.forename: P A
authors.initials: PA
authors.lastname: Kollman
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D005813:Genes, Synthetic; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D013696:Temperature
chemical_list: C097707:BBA1 protein, Synthetic; D010455:Peptides; D011506:Proteins; D012997:Solvents