We emulate evolution in the laboratory in order to create new proteins with desirable properties. This approach circumvents our profound ignorance of how amino acid sequence encodes protein function and exploits the remarkable ability of biological systems to evolve and adapt. Here I will describe the laboratory evolution of P450PMO, a cytochrome P450 whose activity and coupling efficiency on the non-native substrate propane rival those of non-P450 monooxygenases in alkane-degrading organisms. This example shows how a specialized bacterial P450 fatty acid hydroxylase passed through a series of functional, relatively promiscuous intermediates to become re-specialized for a reaction catalyzed in nature by structurally and mechanistically unrelated enzymes. This work demonstrates the versatility of cytochrome P450 and illustrates how readily new and improved catalytic functions can be acquired through point mutation and/or recombination combined with screening for the desired properties. While yielding useful biocatalysts for chemical synthesis, these studies also provide insights into the mechanisms underlying evolution of natural enzymes.

Scientists' dreams of constructing new forms of life—either to enhance human well-being or just to prove that we can do it—are somewhat grander than the reality, because we are profoundly ignorant of the mapping from DNA sequence to biological function. Details of molecular interactions rule function, and we just don't understand the details. For forward engineering of biological systems, I argue that we should look to the design algorithm that has produced the entire biological world: evolution. This simple algorithm works at all scales of complexity, from single proteins to ecosystems, and can be ‘directed' by controlling the molecular diversity (mutations) and applying artificial selection.

By emulating evolution in the laboratory we create new, finely-tuned biological molecules that exhibit desired properties. And, by uncoupling evolution from biological function, we can explore what is physically possible versus what is merely biologically relevant at the time. These experiments provide insight into the remarkable ability of biological systems to evolve and adapt, and may help us understand how today's proteins came about.

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