Tag Archives: catalysis

Hybrid bacterial genes and virus shell combined to create ‘nano reactor’ for hydrogen biofuel

Turning water into fuel may seem like an almost biblical project (e.g., Jesus turning water to wine in the New Testament) but scientists at Indiana University are hopeful they are halfway to their goal. From a Jan. 4, 2016 news item on ScienceDaily,

Scientists at Indiana University have created a highly efficient biomaterial that catalyzes the formation of hydrogen — one half of the “holy grail” of splitting H2O to make hydrogen and oxygen for fueling cheap and efficient cars that run on water.

A Jan. 4, 2016 Indiana University (IU) news release (also on EurekAlert*), which originated the news item, explains further (Note: Links have been removed),

A modified enzyme that gains strength from being protected within the protein shell — or “capsid” — of a bacterial virus, this new material is 150 times more efficient than the unaltered form of the enzyme.

“Essentially, we’ve taken a virus’s ability to self-assemble myriad genetic building blocks and incorporated a very fragile and sensitive enzyme with the remarkable property of taking in protons and spitting out hydrogen gas,” said Trevor Douglas, the Earl Blough Professor of Chemistry in the IU Bloomington College of Arts and Sciences’ Department of Chemistry, who led the study. “The end result is a virus-like particle that behaves the same as a highly sophisticated material that catalyzes the production of hydrogen.”

The genetic material used to create the enzyme, hydrogenase, is produced by two genes from the common bacteria Escherichia coli, inserted inside the protective capsid using methods previously developed by these IU scientists. The genes, hyaA and hyaB, are two genes in E. coli that encode key subunits of the hydrogenase enzyme. The capsid comes from the bacterial virus known as bacteriophage P22.

The resulting biomaterial, called “P22-Hyd,” is not only more efficient than the unaltered enzyme but also is produced through a simple fermentation process at room temperature.

The material is potentially far less expensive and more environmentally friendly to produce than other materials currently used to create fuel cells. The costly and rare metal platinum, for example, is commonly used to catalyze hydrogen as fuel in products such as high-end concept cars.

“This material is comparable to platinum, except it’s truly renewable,” Douglas said. “You don’t need to mine it; you can create it at room temperature on a massive scale using fermentation technology; it’s biodegradable. It’s a very green process to make a very high-end sustainable material.”

In addition, P22-Hyd both breaks the chemical bonds of water to create hydrogen and also works in reverse to recombine hydrogen and oxygen to generate power. “The reaction runs both ways — it can be used either as a hydrogen production catalyst or as a fuel cell catalyst,” Douglas said.

The form of hydrogenase is one of three occurring in nature: di-iron (FeFe)-, iron-only (Fe-only)- and nitrogen-iron (NiFe)-hydrogenase. The third form was selected for the new material due to its ability to easily integrate into biomaterials and tolerate exposure to oxygen.

NiFe-hydrogenase also gains significantly greater resistance upon encapsulation to breakdown from chemicals in the environment, and it retains the ability to catalyze at room temperature. Unaltered NiFe-hydrogenase, by contrast, is highly susceptible to destruction from chemicals in the environment and breaks down at temperatures above room temperature — both of which make the unprotected enzyme a poor choice for use in manufacturing and commercial products such as cars.

These sensitivities are “some of the key reasons enzymes haven’t previously lived up to their promise in technology,” Douglas said. Another is their difficulty to produce.

“No one’s ever had a way to create a large enough amount of this hydrogenase despite its incredible potential for biofuel production. But now we’ve got a method to stabilize and produce high quantities of the material — and enormous increases in efficiency,” he said.

The development is highly significant according to Seung-Wuk Lee, professor of bioengineering at the University of California-Berkeley, who was not a part of the study.

“Douglas’ group has been leading protein- or virus-based nanomaterial development for the last two decades. This is a new pioneering work to produce green and clean fuels to tackle the real-world energy problem that we face today and make an immediate impact in our life in the near future,” said Lee, whose work has been cited in a U.S. Congressional report on the use of viruses in manufacturing.

Beyond the new study, Douglas and his colleagues continue to craft P22-Hyd into an ideal ingredient for hydrogen power by investigating ways to activate a catalytic reaction with sunlight, as opposed to introducing elections using laboratory methods.

“Incorporating this material into a solar-powered system is the next step,” Douglas said.

Here’s a link to and a citation for the paper,

Self-assembling biomolecular catalysts for hydrogen production by Paul C. Jordan, Dustin P. Patterson, Kendall N. Saboda, Ethan J. Edwards, Heini M. Miettinen, Gautam Basu, Megan C. Thielges, & Trevor Douglas. Nature Chemistry (2015) doi:10.1038/nchem.2416 Published online 21 December 2015

This paper is behind a paywall.

*(also on EurekAlert) added on Jan. 5, 2016 at 1550 PST.

An enzyme’s atoms are in a subtle dance that can affect protein function

This research comes from Québec’s Institut national de la recherche scientifique (INRS) according to a Dec. 10, 2015 news item on ScienceDaily,

Infinitesimal fluctuations occurring on the milli- and even nano-second time scales within the three-dimensional structure of enzymes may be one of the keys to explaining protein function. Professor Nicolas Doucet’s team at INRS has demonstrated that even when certain amino acids are far from the active site of an enzyme, a change in their flexibility and atomic fluctuations can significantly impact enzyme activity. This phenomenon, which has been underestimated up to now, could explain certain protein engineering failures and help improve the way synthetic functional enzymes are designed.

A Dec. 10, 2015 INRS news release on EurekAlert, which originated the news item, provides an explanation of an enzyme’s functions and what the researchers found out,

Enzymes are nanomachines that are exceptionally efficient at catalyzing a chemical reaction. They play a role in all cellular mechanisms. Like all proteins, they are made up of amino acid chains that are folded and assembled in a very precise 3D structure. Some enzymes, like ribonuclease A, are so efficient that they catalyze the transformation of chemical molecules thousands of times per second.

In this study, Donald Gagné, a researcher in Professor Doucet’s lab holding a PhD in biology from INRS, analyzed the impact of removing a methyl group located near a loop distant from the reaction site of ribonuclease A–a very slight change that presumably would have no effect. The mutation does not perturb the 3D structure of the enzyme. However, it did result in a four-fold reduction in the affinity of ribonuclease A for nucleotides (molecules to which it must bind to carry out its function). How is this possible?

Using crystallography techniques and nuclear magnetic resonance to examine the enzyme at atomic resolution, Donald Gagné compared normal ribonuclease A with the mutated enzyme. He observed that when ribonuclease A is modified, the nucleotides do not position themselves correctly and have a harder time binding to the active site. It appears that this repositioning is due to an increase in enzyme fluctuations caused by the elimination of this distant methyl group, which we can picture as creating vibrations that spread through the enzyme structure all the way to the site of catalysis.

This demonstration of the importance of enzyme dynamics could change our understanding of protein and enzyme mechanisms. While it remains a challenge to measure fluctuations at this atomic scale, researchers have studied the three-dimensional structure of proteins to understand how they function. Despite the staggering complexity of this phenomenon, we now know that proteins are increasingly regulated by the subtle dance of their atoms.

Here’s a link to and a citation for the paper,

Perturbation of the Conformational Dynamics of an Active-Site Loop Alters Enzyme Activity by Donald Gagné, Rachel L. French, Chitra Narayanan, Miljan Simonović, Pratul K. Agarwal, Nicolas Doucet. Structure Volume 23, Issue 12, p2256–2266, 1 December 2015 DOI: http://dx.doi.org/10.1016/j.str.2015.10.011

This paper is behind a paywall.