Why are some enzymes dimers? Flexibility and catalysis in thermotoga maritima dihydrofolate reductase
Abstract
In this work, we studied the dihydrofolate reductase from Thermotoga maritima (TmDHFR), a dimeric thermophilic enzyme that catalyzes the hydride transfer from the cofactor NADPH to dihydrofolate with lower efficiency compared to other DHFR enzymes, such as the mesophilic analogue Escherichia coli DHFR (EcDHFR). Using QM/MM potentials, we analyzed the reduced catalytic efficiency of TmDHFR and demonstrated that it is likely due to differences in the amino acid sequence that stabilize the M20 loop in an open conformation. This conformation prevents the formation of specific interactions in the transition state and increases the number of water molecules in the active site. Furthermore, we provided evidence that dimerization offers two advantages to the thermophilic enzyme: it protects its structure against denaturation by reducing thermal fluctuations and results in a less negative activation entropy, mitigating the increase in activation free energy with temperature. Our molecular interpretation was confirmed by analyzing the temperature dependence of enzyme kinetic isotope effects in different DHFR enzymes.
