Comparing mutagenesis and simulations as tools for identifying functionally important sequence changes for protein thermal adaptation

Significance Comparison of 26 cytosolic malate dehydrogenase (cMDH) orthologs of marine molluscs adapted to temperatures ranging from −1.9 °C (Antarctica) to ∼55 °C (South China coast) shows how amino acid usage in different regions of the enzyme varies with adaptation temperature. In vitro site-directed mutagenesis approaches and in silico molecular dynamics simulations were compared as tools for deducing functionally important sequence changes. Whereas these key amino acid substitutions invariably lie outside of the mobile regions (MRs) essential for function, they transmit their flexibility-modulating effects to the MRs through linked interactions among surface residues. Thus, regions of the protein surface lying outside of the site of catalysis can help establish an enzyme’s thermal responses and foster evolutionary adaptation of function.