London, March 25 : An international team of scientists has achieved a breakthrough in designing artificial enzymes that undergo evolution in a test tube.
The team of researchers from the University of Washington, Seattle, and the Weizmann Institute of Science, Israel, believe that their achievement may open the door to the development of a variety of potential applications in medicine and industry.
Enzymes are responsible for initiating chemical reactions within the body, and a valuable model for understanding the intricate works of nature.
The researchers say that their work has helped them attain a comprehensive understanding of the structure of natural enzymes, their mode of action, and advanced protein engineering techniques.
"Reproducing the breathtaking performances of natural enzymes is a daunting task, but the combination of computational design and molecular in vitro evolution opens up new horizons in the creation of synthetic enzymes," Nature magazine quoted Dan Tawfik, a professor at the Weizmann Institute's Biological Chemistry Department, as saying Tawfik.
"Thanks to this research, we have gained a better understanding of the structure of enzymes as well as their mode of action. This, in turn, will allow us to design and create enzymes that nature itself had not 'thought' of, which could be used in various processes, such as neutralizing poisons, developing medicines, as well as for many further potential applications," added Tawfik.
The researchers say that their aim was to create an enzyme for a specific chemical reaction whereby a proton (a positively charged hydrogen atom) is removed from carbon - a highly demanding reaction and rate-determining step in numerous processes for which no enzymes currently exist, but which would be beneficial in helping to speed up the reaction.
They first designed the 'heart' of the enzymatic machine, i.e. the active site where the chemical reactions take place.
Thereafter, the challenge before them was to determine the sequence of the 200 amino acids that make up the structure of the protein.
Prof. David Baker of the University of Washington, Seattle, used novel computational methodologies to scan tens of thousands of sequence possibilities, identifying about 60 computationally designed enzymes that had the potential to carry out the intended activity. Eight of such sequences advanced to the next 'round' having showed biological activity, and three of them got through to the 'final stage', which proved to be the most active.
Drs. Orly Dym and Shira Albeck of the Weizmann Institute's Structural Biology Department solved the structure of one of the final contestants, and confirmed that the enzymes created were almost identical to the predicted computational design.
The efficiency of the new enzymes, however, could not compare to that of naturally-occurring enzymes that have evolved over millions of years.
The researchers then developed a method allowing the synthetic enzymes to undergo 'evolution in a test tube' that mimics natural evolution, a technique that is based on repeated rounds of random mutations followed by scanning the mutant enzymes to find the ones who showed the most improvement in efficiency.
Results show that it takes only seven rounds of evolution in a test tube to improve the enzymes' efficiency 200-fold compared with the efficiency of the computer-designed template, resulting in a million-fold increase in reaction rates compared with those that take place in the absence of an enzyme.
The group observed that the mutations occurring in the area surrounding the enzyme's active site caused minor structural changes that, in turn, resulted in an increased chemical reaction rate. The mutations seemed to correct shortcomings in the computational design by shedding light on what might be lacking in the original designs.
Other mutations increased the flexibility of the enzymes, which helped increase the speed of substrate release from the active site.