Recombination in directed evolution

While it may not be possible to cross a duck and a wolf to produce viable offspring, it is possible to combine duck and wolf proteins using directed evolution to produce exciting new proteins that wouldn’t be found naturally. Image credit: Humandescent.com

The selection and accumulation of desirable mutations – also known as natural selection – has shaped the living world. The proteins resulting from natural selection solve an impressive array of problems for the organisms that express them, from how not to be caught by a predator, to protecting against life-threatening diseases. However, all this biodiversity came about over millions of years; natural selection takes a very, very long time. Another problem with relying solely on natural selection is that it only selects for proteins that are biologically relevant. What about the other thousands of possible proteins? What if we wanted a protein that is not found naturally, but could help treat a disease – would we have to wait eons for it to evolve through natural selection? Thanks to a process called directed evolution, the answer to that question is a resounding “No way!”

Directed Evolution: a great tool for protein engineers 

Directed evolution can be a misleading term; after all, humans have been directing evolution for years using artificial selection to generate prettier tulips, faster dogs, or fatter cows. It is important to note, however, that artificial selection involves changing entire organisms. Directed evolution, on the other hand, is concerned only with modifying the properties of individual molecules, rather than the whole organism. Since we don’t know enough about the relationship between the amino acid sequence of a protein and its final structure, it’s next to impossible to design a new protein from scratch. Predicting changes in an amino acid sequence that generate a certain kind of enzymatic activity or conformational change is still extremely difficult. Starting with a functional protein, directed evolution uses repeated rounds of mutation to generate new protein variants. The fittest (or rather, the proteins that function in the way protein engineers want them to) variants are then selected for. The process of directed evolution – and natural selection, for that matter – relies on the fact that proteins are able to adapt under selection pressure and change their function or even their shape [1]. Instead of taking millennia, new proteins can be created with directed evolution in mere weeks. Indeed, several vendors at Assay Depot provide protein engineering and design services using directed evolution.

In the next posts in this series, we discuss directed evolution in more detail. We will describe strategies for carrying out the actual process of directed evolution, and in the third and final post, we shall talk about various applications.

Reference:

[1] Romero, PA and Arnold, FH. Exploring protein fitness landscapes by directed evolution. Nature Reviews Molecular Cell Biology 10 (12): 866-76. December 2009.