In biology, enzymes have evolved for millions of years to boost chemical reactions. The scientists of the Max Planck Institute for dynamics and self-organization (MPI-DS) now derived the universal rules to allow the of novo Optimal enzyme design. As an example, they considered the enzymatic reaction of breaking a dimer in two monomer molecules. Taking into account the geometry of such enzyme-collection of substrate, they identified three gold rules that should be considered to build a functional enzyme.
First, the enzyme and molecule interface must be located at its smallest end. In this way, a strong coupling between the two can be achieved. For the same reason, the conformational change in the enzyme should not be less than in the reaction. Finally, the conformational change of the enzyme must take place quick enough to maximize the chemical force of the reaction.
“We build our research in two main pillars,” Ramin Golestanian, director of MPI-DS, describes the approach. “Conservation of the impulse and the coupling between the reaction coordinates,” he continues. Therefore, the researchers expanded the vision of a classic two -dimensional reaction coordinate. Typically, the models for enzymatic reactions define an energy barrier that must be overcome so that the reaction takes place.
“As in our model we also consider enzymatic dynamics and coupling, we go beyond this existing concept, considering two reaction coordinates,” says Michalis Chatzittofi, first author of the study. “Instead of overcoming an energy barrier, you can now imagine alternative ways to ignore taking alternative routes,” he concludes.
These results provide a new basis for the design of molecular machines, avoiding the tedious and technically challenging approach to simulate the dynamics of each atom individually.