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 o f pure sodium chloride solutions were performed to examine the influen ce of the choice of nonbonded cutoff distance on simulation results. S imulations were then performed to study how different conformations of polyalanine affect the distribution and dynamics of the mobile monova lent ion atmosphere. We found that it was necessary to use a nonbonded cutoff >30 Angstrom in order to get reliable results for the ion pair radial distribution functions, the ionic polarizabilities, and the au to time-correlation functions of the collective dipole moments of the sodium chloride solutions. We also found that alpha-helical polyalanin es preferentially bound sodium ions at 0.1 M sodium chloride concentra tion. The preferential binding of sodium ions was still noticeable but less pronounced when the polyalanines were in the extended conformati on or when the concentration of the salt was increased, The polarizabi lity of the ions was found to be insensitive to the presence of alpha- helical polyalanines but became smaller in the presence of extended po lyalanines, The relaxation of the collective dipole moment of the ions was also found to be affected only by polyalanines in the extended co nformation but not in the alpha-helical conformation. The biological s ignificance of the simulation results is discussed.