Exploring plant enzyme conformations and dynamics via MD simulations

Molecular dynamics (MD) simulations have been widely adopted to complement experimental techniques in exploring the structures, dynamics and functions of biological macromolecules. In this talk I will discuss my group’s work employing MD simulations to probe the structures and dynamics of several plant or fungal enzymes, including the hydroxycinnamoyltransferase (HCT), the aromatic amino acid decarboxylase (AAAD) and the isochorismoyl-glutamate pyruvoyl-glutamate lyase (IPGL). Common to these diverse systems is the critical role played by conformational dynamics, rather than static structural components alone, in mediating the unique function of each protein. I will highlight how their dynamics captured by MD have provided mechanistic insights into the substrate recognition and/or the reaction mechanism of these enzymes.