Nav: Home

Optimized binding cavity

February 01, 2019

The impressively high conversion rates of natural enzymes partly result from increasing the catalytic activity of a selected few amino acid side chains through precise positioning within the protein binding cavity. Scientists have now demonstrated that such fine-tuning is also possible for "designer" enzymes with unnatural catalytic amino acids. In the journal Angewandte Chemie, they report that laboratory "evolution" of a designer enzyme with an aniline side chain led to variants with significantly higher activity.

The speed and selectivity with which enzymes in nature catalyze conversions are enviable. To catalytically boost unnatural reactions, researchers mimic enzymes with the help of protein frameworks realized by computer-aided protein design. Further optimization is achieved through repetition of a Darwinian cycle: 1) diversification through mutation, 2) identification of improved catalysts, and 3) amplification of the more efficient enzyme variants. This allows for the production of designer enzymes with very high activities.

Researchers led by Clemens Mayer and Gerard Roelfes at the University of Groningen (the Netherlands) have now demonstrated that this type of directed evolution is also a method for improving the efficiency of a novel class of designer enzymes: enzymes that contain an amino acid that is not utilized by nature.

Starting with a protein from Lactococcus lactis, a bacterium used in the production of dairy products such as cheese and buttermilk, the researchers synthesized a designer enzyme that contains an amino acid with an abiotic aniline side chain (aminophenylalanine). Like free aniline, this amino acid catalyzes the reaction of aldehydes with hydrazines or hydroxylamines to make hydrazones or oximes, respectively.

To increase the activity of the enzyme, the researchers produced enzyme variants with mutations at amino acids near the aniline side chain. Screening of about 400 mutants yielded two candidates with better activity, one of which was subjected to a second evolutionary round. This led to the discovery of more beneficial mutations. To identify synergetic effects, multiple favorable mutations were combined to produce further variants. In this way, it was possible to increase the conversion rate of the enzyme by a factor of 90.

The researchers emphasize that, akin to natural enzymes, "this drastic increase is based on strengthening the inherent catalytic activity of the aniline side chain. We intend to use this principle to incorporate further organic catalysts as side chains in enzymes, and to use directed evolution to convert these into highly effective designer enzymes that can rapidly and efficiently carry out synthetically important reactions that would otherwise only run very slowly."
-end-
About the Author

Dr. Gerard Roelfes is professor of biomolecular chemistry and catalysis. He is interested in catalysis research at the interface of chemisry and biology, working on topics such as the design of enzymes for abiological reactions, bio-orthogonal catalysis, and catalytic chemistry in living cells.

https://roelfesgroup.nl/

Wiley

Related Evolution Articles:

Prebiotic evolution: Hairpins help each other out
The evolution of cells and organisms is thought to have been preceded by a phase in which informational molecules like DNA could be replicated selectively.
How to be a winner in the game of evolution
A new study by University of Arizona biologists helps explain why different groups of animals differ dramatically in their number of species, and how this is related to differences in their body forms and ways of life.
The galloping evolution in seahorses
A genome project, comprising six evolutionary biologists from Professor Axel Meyer's research team from Konstanz and researchers from China and Singapore, sequenced and analyzed the genome of the tiger tail seahorse.
Fast evolution affects everyone, everywhere
Rapid evolution of other species happens all around us all the time -- and many of the most extreme examples are associated with human influences.
Landscape evolution and hazards
Landscapes are formed by a combination of uplift and erosion.
New insight into enzyme evolution
How enzymes -- the biological proteins that act as catalysts and help complex reactions occur -- are 'tuned' to work at a particular temperature is described in new research from groups in New Zealand and the UK, including the University of Bristol.
The evolution of Dark-fly
On Nov. 11, 1954, Syuiti Mori turned out the lights on a small group of fruit flies.
A look into the evolution of the eye
A team of researchers, among them a zoologist from the University of Cologne, has succeeded in reconstructing a 160 million year old compound eye of a fossil crustacean found in southeastern France visible.
Is evolution more intelligent than we thought?
Evolution may be more intelligent than we thought, according to a University of Southampton professor.
The evolution of antievolution policies
Organized opposition to the teaching of evolution in public schoolsin the United States began in the 1920s, leading to the famous Scopes Monkey trial.

Related Evolution Reading:

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Jumpstarting Creativity
Our greatest breakthroughs and triumphs have one thing in common: creativity. But how do you ignite it? And how do you rekindle it? This hour, TED speakers explore ideas on jumpstarting creativity. Guests include economist Tim Harford, producer Helen Marriage, artificial intelligence researcher Steve Engels, and behavioral scientist Marily Oppezzo.
Now Playing: Science for the People

#524 The Human Network
What does a network of humans look like and how does it work? How does information spread? How do decisions and opinions spread? What gets distorted as it moves through the network and why? This week we dig into the ins and outs of human networks with Matthew Jackson, Professor of Economics at Stanford University and author of the book "The Human Network: How Your Social Position Determines Your Power, Beliefs, and Behaviours".