title: Molecular dynamics studies of β-hairpin folding with the presence of the sodium ion.
abstract: Metal ions are ubiquitous in protein systems and play a significant role during their folding processes. Nineteen independent structures were determined for the Na(+)/β-hairpin interacting systems, and their folding pathways are different. (i) For Na(S47), the turn is rapidly shaped with the help of Na(+) and acts as the folding nucleus for the rest regions. Two intermediate states are observed and the resulted structure is the most folded. (ii) For Na(B41), Na(B52), Na(B54), Na(S55) and Na(B56), the inclusive Na(+) ions are anchored by β-strands. The local structures around the Na(+) ions and the turn regions fold simultaneously and serve as two independent folding nuclei. (iii) The other systems have no folding nuclei and correspond to low-folded structures. Long-range electrostatic interactions contribute a lot to the folding, especially from the four negatively charged residues (Glu42, Asp46, Asp47 and Glu56). The initial positions of the Na(+) ions are largely responsible for the different folding behaviors. The interactions with sidechain- rather than backbone-O atoms generally lead to more compact structures. Another factor affecting the folding is whether the O atoms are associated with native H-bonds, and those involved show decreased affinities to metal ions. The addition of water solvent does not induce obvious folding and conformational transitions to the Na(+)/β-hairpin interacting systems.
authors.affiliation: Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China.
authors.forename: Xiaomin
authors.initials: X
authors.lastname: Wu
authors.forename: Gang
authors.initials: G
authors.lastname: Yang
authors.forename: Yuangang
authors.initials: Y
authors.lastname: Zu
authors.forename: Lijun
authors.initials: L
authors.lastname: Zhou
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D002414:Cations, Monovalent; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012964:Sodium / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D000596:Amino Acids; D002414:Cations, Monovalent; D009842:Oligopeptides; D012997:Solvents; D014867:Water; D012964:Sodium