Brownian Dynamics Simulations of Polyalanine in Salt Solutions

The distribution and dynamics of the mobile monovalent ion atmosphere around polyalanine in aqueous solution at various ionic strengths have been simulated by the Brownian dynamics method. Initial simulations of pure sodium chloride solutions were performed to examine the influence of the choice of nonbonded cutoff distance on simulation results. Simulations were then performed to study how different conformations of polyalanine affect the distribution and dynamics of the mobile monovalent ion atmosphere. We found that it was necessary to use a nonbonded cutoff >30 Å in order to get reliable results for the ion pair radial distribution functions, the ionic polarizabilities, and the auto time-correlation functions of the collective dipole moments of the sodium chloride solutions. We also found that α-helical polyalanines preferentially bound sodium ions at 0.1 M sodium chloride concentration. The preferential binding of sodium ions was still noticeable but less pronounced when the polyalanines were in the extended conformation or when the concentration of the salt was increased. The polarizability of the ions was found to be insensitive to the presence of α-helical polyalanines but became smaller in the presence of extended polyalanines. The relaxation of the collective dipole moment of the ions was also found to be affected only by polyalanines in the extended conformation but not in the α-helical conformation. The biological significance of the simulation results is discussed.