Design of Motifs Interfacial Interactions by Co-evolved Analysis of D-amino Acid Dehydrogenase for Stability Enhancement

Abstract

To design D-amino acid dehydrogenase (DAADH) for enhanced stability, the interactions of the subunit interfaces of DAADH were analyzed. Interaction network analysis of DAADH indicated that there are only weak interactions between the A and B subunits. Several co-evolved residue pairs were selected for mutation to enhance interfacial interactions of subunits, and 11 designed MDHs were obtained. DA06 and DA11 were selected for experimental verification for their salt bridges are 1.4 and 1.2-fold of that of DAwild, respectively. DA11 can maintain 93% activity in 80℃, while it was only 40% for DAwild. Thermostabiliy study indicated the half-life of DA11 was 2-fold of DAwild. Molecular dynamics simulations revealed that the extraordinary stability of the DA11 was due to the formation of extra interfacial salt bridges. The paper provided a strategy of mutations outside the active site of enzyme by co-evolutionary analysis which can reduce the effect of the activity-thermostability trade-off.