Mixed-salt effects on the conformation of a short salt-bridge-formingαhelix: 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.

Structural conservation of the short α-helix in modified higher and lower polarity water solutions

“…This short peptide model has been extensively studied because of its biological importance, as its basic constituents and saltbridged electroneutral structure can fundamentally reect the responses to modied water models without articial factors, such as added foreign ions for neutralization. 19,20,62 Furthermore, this peptide is very sensitive to the subtle changes in the solution environment 63 and provides an ideal model for exploring the structural responses. The initial conformation of this peptide was created using Molden soware, 64 corresponding to a segment of an ideal a-helix structure.…”

Solvation of halogen ions in aqueous solutions at 500 K–600 K under 100 atm

“…[13,14] Corresponding researches on the hydration of DNA, proteins have also been revealed in detail. [15][16][17][18][19] Compared to other simple organic liquids, water has more complex phase diagrams, in that a number of triple points and one, probably two, critical points can be found. [20][21][22][23] Critical water, [24][25][26] near the critical point of the phase diagram, is such a special fluid that many strange properties, such as the decrease of dielectric constant, the special density change, and the coexisting phases, are all observed.…”