Abstract

In this study, the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites is presented. As initially proposed by Pauling, and elaborated by many others since then, biocatalysis is efficient when the catalytic residues in the active site of an enzyme are in optimal positions for transition state stabilization. Using MD simulations, we explore the dynamical pre-organization of the active sites of designed and evolved enzymes, by analyzing the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state, and relates the populations of the catalytic conformational ensemble to enzyme activity.