Exploring protein fitness landscapes by directed evolution

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Abstract
Directed evolution optimizes protein function by the successive generations of random mutation, artificial selection or screening. This simple design algorithm circumvents our ignorance of how sequence encodes function and provides a reliable approach to engineering proteins with new and useful properties. Directed evolution can be envisioned as an uphill walk on a protein fitness landscape, in which regions of higher elevation represent more optimized proteins. The ruggedness of this fitness landscape affects the ability to find uphill paths to fitter sequences and therefore affects the ease of evolutionary searches. Simple adaptive walks effectively optimize many protein functions, despite landscape ruggedness that arises from epistatic interactions between mutations. The many simple uphill routes to higher fitness can circumvent more convoluted paths that involve neutral or deleterious mutations. More-stable proteins can accept a wider ranger of mutations and are more evolvable. Recombination of homologous protein sequences provides access to functional sequences with many mutations. These recombined (chimeric) proteins can exhibit properties outside the range of the parental sequences, such as higher stability or even novel activities. Directed evolution studies have generated a wealth of information on the structure of protein fitness landscapes, mechanisms of adaption, pathways that are accessible under different selection pressures and the nature of trade-offs between properties during evolution.