Molecular Dynamics Studies of β-Hairpin Folding with the Presence of the Sodium Ion

摘要

Metal ions are ubiquitous in protein systems and play a significant role during their folding processes.Nineteen independent structures were obtained for the Na+/β-hairpin interacting systems,and their folding pathways are different:(i) For Nas47,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 NaB41,NaB52,NaB54,Nas55 and NaB56,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 initialpositions 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.