Magnesium-dependent active-site conformational selection in the Diels-Alderase Ribozyme

Molecular dynamics (MD) simulations in both crystalline and aqueous solution environments is utilized to examine the Diels-Alderase ribozyme, an in vitro-evolved ribonucleic acid enzyme which accelerates the formation of carbon-carbon bonds between an anthracene diene and a maleimide dienophile in a [4 + 2] cycloaddition. The simulation results obtained for the reaction with broad application in organic chemistry demonstrated that full catalytic activity of the reaction depends on the [Mg.sup.2+] ion concentration.