Mar
26
Man Made Enzymes for Oil and Medicine
March 26, 2008 | 7 Comments
Monday the news broke that a team from the University of Washington, Seattle and the Weizmann Institute of Science, Israel, broke through to making an original enzyme, one that hasn’t existed before in nature.
Enzymes are molecules that initiate chemical reactions, and act to catalyze reactions in biological processes. These molecules exist throughout the plant and animal kingdoms and factually speaking make higher forms of life possible. The principal effect is that reactions can take place thousands of even millions of times faster.
Enzymes are primarily strings of amino acids that fold up into proteins. The team sought to create an enzyme for a specific chemical reaction in which a proton in the form of a positively charged hydrogen atom is removed from carbon, a well-known and demanding step in many chemical processes. As no enzymes exist for this specific task, they would be very beneficial in speeding up a process.
The first step the team took on was to design a “heart” or active site in the enzyme where chemical reactions could take place. The second step was to set up a framework or skeleton to hold the sequence of amino acids that make up a protein structure. With 200 amino acids and essentially and unlimited number of ways to arrange a sequence a set, 20 were selected in this effort, into a working reactive group. What prior experience has shown is that only a limited number of possibilities would work. This is because specific sequences determine the structure and the structure in turn determines the enzyme’s work.
Professor David Baker of the University of Washington used his novel computational methodologies to scan tens of thousands of sequence possibilities narrowing the list to about 60 sequences that could do the proposed work. With the 60 to test, 8 advanced to the next step by showing that they were biologically active. From the 8, 3 showed the best by being the most active. Then Dr. Orly Dym and Dr. Shira Albeck at the Weizmann Institute solved the structure of one and confirmed the that the enzymes made by man were almost identical to the computational prediction.
However, the efficiency of the man made enzymes didn’t compare well with naturally evolved enzymes in nature. Man was looking to be trumped again until Professor Dan Tawfik and research student Olga Khersonsky of the Weizmann Institute joined and developed a method allowing the man synthesized enzymes to under go an “evolution” in their lab. Their method is based on repetitions of random mutations followed by scanning the mutants to find the ones that show the most improvement in efficiency.
More repetitions followed, after seven, the efficiency gained 200 fold over the original computer designed template prediction. The 200 fold increase results in a million fold increase in reaction rates compared to reactions that take place without the assistance of an enzyme.
The team found that the mutations occurring in the region next to the active part or “heart” only caused minor structural changes that resulted in increased chemical reaction rates. The mutations seem to have corrected the computational design’s faults and show the team what was lacking in the original design. Other mutations improved the enzymes flexibility that also increased the speed of release of substrates from the active part of the enzyme.
While this is an interesting story, the payoff ranges from beyond fuel production on to medicine production and back to poison neutralization. This area of research offers a much better understanding of enzymes and the possible ways to make them and put them to work. The understanding and the newly formed path to production of synthesized enzymes can reach far beyond the demands of nature and enter the concepts of mankind and its needs.
Currently the biofuel field is centered on yeast for ethanol production with various bacteria microorganisms coming to market soon. We’ll be looking at more of these as harder data gets released, but the enzyme field has much to offer and the biological designs are just getting started in the level of quantity and quality that will drive to the most cost efficient and CO2 reuse levels. Enzymes may solve some of the microorganism problems that occur when leaving the lab and going on to industrial sized use. The fossil oil market is getting a little pressure now and much more is coming to compete against it. Bio oil is looking more and more a sure thing by each passing week.
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This is true nanotechnology, achieved through biochemistry. This approach has always been the most realistic way to enter molecular manufacturing–designed enzymes. The lessons learned here will open up entire new worlds of nano-potential.
Now comes the comprehensive work to see what can be achieved with “enzyme systems” made up of artifical enzymes, cofactors, metals etc. Artificial amino acids with corresponding artificial nucleic acids incorporated into designed biological systems of production.
Finally, devising ways to incorporate new, high-efficiency designed bio-catalysts (enzymes) in robust pseudo-cells that can keep catalysing reactions long after normal micro-organisms would have been killed off by toxic products of the basic reaction.
didn’t help!!!!!!!!
What is the enzyme called?
Good article for me to give my students. Trying to get them to see the connection between what they are learning in the classroom and what is happening in “real world” laboratories.
please keep me informed re biofuels
What a great resource!
See, the real question I have is whether we’ll ever be able to incorporate a microflora or microfauna into a full-blown biochemical system. It’s all well and good to make bacteria in a lab that make useful enzymes, but there’s something entirely different about having bacteria in a tank in some back-country garage making products useful to mankind.
Here’s an illustration of what I mean: The internal combustion engine was a huge advancement in technology, but it didn’t change society one bit until it stopped being a rich man’s toy and started appearing in the garages of the average Joe. To make any dent in fossil fuel consumption, we’ll need to change the average Joe, and the best way to do that is to make the technology accessible.
If you give the average Joe a cheap car and cheap fuel, and show him just how easy it is to use a car, he’ll give up his horse and buggy without a second thought. Likewise, if you give the average Joe a tank of pond scum that he can put on his roof to pump out diesel, he’ll put it right there in the air and sun and get his free fuel without hesitation. He’ll probably even tinker around with it a bit to try and improve the design.
That is exactly the kind of revolution we need, the kind that changes whole lifestyles. These enzymes are great and all, but they’ll have little societal impact unless they can be used in conjunction with oil-producing bacteria or solar-power-producing bacteria, or anything else useful and tangible.