title: The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein.
abstract: In this study, the thermal stability of a designed alpha/beta protein FSD (full sequence design) was studied by explicit solvent simulations at three moderate temperatures, 273 K, 300 K, and 330 K. The average properties of the ten trajectories at each temperature were analyzed. The thermal unfolding, as judged by backbone root-mean-square deviation and percentage of native contacts, was displayed with increased sampling outside of the native basin as the temperature was raised. The positional fluctuation of the hairpin residues was significantly higher than that of the helix residues at all three temperatures. The hairpin segment displayed certain plasticity even at 273 K. Apart from the terminal residues, the highest fluctuation was shown in the turn residues 7-9. Secondary structure analysis manifested the structural heterogeneity of the hairpin segment. It was also revealed by the simulation that the hydrophobic core was vulnerable to thermal denaturation. Consistent with the experiment, the I7Y mutation in the double mutant FSD-EY (FSD with mutations Q1E and I7Y) dramatically increased the protein stability in the simulation, suggesting that the plasticity of the hairpin can be partially compensated by a stronger hydrophobic core. As for the unfolding pathway, the breathing of the hydrophobic core and the separation of the two secondary structure elements (alpha helix and beta hairpin) was the initiation step of the unfolding. The loss of global contacts from the separation further destabilized the hairpin structure and also led to the unwinding of the helix.
authors.affiliation: Bioinformatics Program and Department of Applied Science, University of California, Davis, California 95616, USA.
authors.forename: Hongxing
authors.initials: H
authors.lastname: Lei
authors.forename: Yong
authors.initials: Y
authors.lastname: Duan
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D011506:Proteins; D012997:Solvents