The following is an edited extract from a Nature paper. It is an example of real ID research. Notice that the designers only used evolutionary techniques to very slightly tweak the enzymes scaffold structure that had been designed with “borrowed components” from existing enzymes tacked together. The novel active site was completely intelligently designed. doi:10.1038/nature06879
Kemp elimination catalysts by computational enzyme design
“We designed eight enzymes with computationally designed active sites. In vitro evolution enhanced the computational designs, demonstrating the power of combining computational protein design with directed evolution for creating new enzymes.
Natural enzymes bind their substrates in a well-defined active site with precisely aligned catalytic residues to form highly active and selective catalysts for a wide range of chemical reactions. The design of stable enzymes with new catalytic activities is of great practical interest, with potential applications in biotechnology, biomedicine and industrial processes.
We recently developed our computational enzyme design to create new enzymes for a reaction for which no naturally occurring enzyme exists.
Our in silico design process seems to be drawn towards the same structural features as naturally occurring enzyme evolution.
Following the active site design, a total of 59 designs in 17 different scaffolds were selected for experimental characterization. Eight of the designs showed initial measurable activity.
We reasoned that in vitro evolution would be an excellent complement to our computational design efforts.
Directed evolution can be valuable both in improving the designed catalysts and in stimulating improvements in the computational design methodology by shedding light on what is missing from the designs.
Seven rounds of random mutagenesis and shuffling followed by screens yielded variants that had 4–8 mutations and an improvement of 200-fold in activity.
The key aspects of the computational design, including the identities of the catalytic side chains, were not altered by the evolutionary process.
The mutations provide subtle fine-tuning of the designed enzyme.
We anticipate the successful use of the combination of computational design and molecular evolution that we have described here, for a wide range of important reactions in the years to come, including design catalysts for more complex multistep reactions.”