Separation of amino acids in glucose isomerase crystal: insight from molecular dynamics simulations

The separation of amino acids (Arg, Phe and Trp) in a liquid chromatography is investigated using molecular dynamics simulations. A bioorganic nanoporous material--glucose isomerase crystal--is used as the stationary phase and water as the mobile phase. The transport velocities of amino acids decrease in the order Arg>Phe>Trp, consistent with experimental measurement. The elution order is not affected by the solute concentration or by the flowing rate of mobile phase. Arg is highly hydrophilic and charged, interacts with water the most strongly, and thus moves with flowing water the fastest. Trp has the largest van der Waals volume and encounters the largest steric hindrance, leading to the slowest velocity. From the number distributions of amino acids around protein surface, Trp and Phe are found to stay closer to protein than Arg. The solvent-accessible surface areas of amino acids and the numbers of hydrogen bonds between amino acids and water further elucidate the observed velocity difference. The simulation results provide useful microscopic insight into the retention mechanisms in chromatographic separation process and suggest that glucose isomerase crystal has the capability to separate amino acids.