Inability to design precise enzyme movement may explain poor performance of de novo designed enzymes

Currently, there are two main approaches for improving the performance of enzymes. One approach uses purposeful designed experiments to evolve an enzyme towards particular performance targets such as ability to catalyze an atypical reaction. This is what is known as directed evolution protein engineering approach which frequently requires the use of high throughput experimentation. The other approach is rational protein design where a protein scaffold such as that for the active site is tweaked computationally using our current understanding of protein folding and enzyme catalysis to yield a structure that can be tested experimentally. Usually, the initial protein scaffold used for computational experiments is inspired by biology (i.e., a structure from a protein with a similar function), but, it could also be purely based on our theoretical understanding of structural biology and enzyme catalysis. While the approach is appealing to many researchers, de novo protein design remains an art form as we try to decipher the hidden rules that govern structure-function relationship in enzyme catalysis. The challenge is not in active site design for which we have gained considerable understanding. Rather, the difficulty lies in designing the complicated sequence of enzyme conformational changes (or allosteric changes) that accompany the process of enzyme catalysis. These shape changes can be profound both from a structural and biochemical perspective, and we currently lack the theoretical know-how to design these choreographed movement computationally. From available experimental data, de novo designed enzymes still perform poorly compared to natural enzymes, partially we lack the ability to design precision enzyme movement that governs the process of enzyme catalysis from substrate binding to formation of transition state, and final product formation and release. Future research in the field will likely have to take on the challenging task of how to design a multiple subunit enzyme that cooperatively interact with each other to enable seamless reactivity in space and time to yield the desired product in high yield and productivity.