title: Mixed-salt effects on the conformation of a short salt-bridge-forming α helix: a simulation study.
abstract: The structure of a single alanine-based ACE-AEAAAKEAAAKA-NH2 peptide in explicit aqueous solutions with mixed inorganic salts (NaCl and KCl) is investigated by using molecular simulations. The concentration of Na(+), c(Na(+)), varies from 0.0M to 1.0M, whereas the concentration of K(+) is 1-c(Na(+)). The simulated peptide is very sensitive to the change of concentration ratio between Na(+) and K(+). When the concentration ratio between Na^{+} and K^{+} is changed from 0.5/0.5, the structure of the peptide becomes loose or disordered. This specific phenomenon is confirmed via checking the changes of helix parameters and mapping the free energy along different coordinates. The higher normalized probability of forming direct and indirect salt bridges between residues Glu7(+) and Lys11(+) and the smallest probability of forming ringlike structures should be responsible for the stabilized helix structure in the 0.5 Na(+)/0.5 K(+) solution. Furthermore, a noticeable conformational transition from an extended helix to an α helix is found in the 0.5 Na(+)/0.5 K(+) solution, where a local ion cloud shows that some Na(+) ions in the inner shells are still directly binding with the peptide, while K(+) in the outer shells are moving into the inner shells, keeping the peptide in the collapsed state.
authors.affiliation: The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China and Beijing Radiation Center, Beijing 100875, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Shen
authors.affiliation: The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China and Beijing Radiation Center, Beijing 100875, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Cheng
authors.affiliation: The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China and Beijing Radiation Center, Beijing 100875, China and Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou 730000, China.
authors.forename: Feng-Shou
authors.initials: FS
authors.lastname: Zhang
mesh_terms: D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D012492:Salts / Q000737:chemistry*
chemical_list: D011506:Proteins; D012492:Salts