Enzymes are biomolecules of particular interest, as they have high substrate specificity and exhibit high catalytic efficiency. Engineering of enzymes for improved catalytic efficiency has been widely sought for industrial applications. Recently, conformational flexibility has been proposed to be a contributing factor to the catalytic efficiency of enzymes. It has been hypothesized that enzyme catalysis involves the use of conformational fluctuations in the polypeptide structure of the protein to control the structural environment in the active site to facilitate the targeted chemistry.

...it should be possible to improve the catalytic efficiency of enzyme reactions by controlled manipulation of enzyme conformational fluctuations that are associated with the targeted chemical reaction. The objective of this study was to design and test, using a model enzyme, whether the controlled modulation of enzyme conformation leads to an increase in the catalytic rate of the enzyme.

—Agarwal et al.

The team’s strategy was to introduce chemical elements on the surface of the enzyme such that the enzyme conformations could be altered by external input—i.e., light.

They introduce a light-activated molecular switch across two surface loop regions of CALB, identified by computational modeling as part of the dynamically important enzyme network. A molecular switch, containing an azobenzene derivative, was covalently attached onto the lipase via cross-linking reagents.

Using this approach, our preliminary work with CALB suggests that such a technique of introducing a compound that undergoes a light-inducible conformational change onto the surface of the protein can be used to manipulate enzyme conformation. This in turn resulted in an enhancement of the catalytic rate of the enzyme.

—Agarwal et al.

While the researchers obtained final laboratory results at industry partner AthenaES, computational modeling allowed Agarwal to test thousands of combinations of enzyme sites, modification chemistry, different wavelengths of light, different temperatures and photo-activated switches. Simulations performed on the DOE’s Jaguar supercomputer also allowed researchers to better understand how the enzyme’s internal motions control the catalytic activity.

Overall, this study has demonstrated that it is possible to combine computational and experimental engineering approaches to manipulate biomolecular activity. Here we have shown that it is possible to improve the catalytic efficiency of enzymes through conformational modulation. Further, the molecular switch designed to modulate enzyme conformations distal to active site provides an enhancement of enzyme activity. This approach has interesting applications for developing hyper-catalytic enzymes as well as new biomolecular applications for nanotechnology.

—Agarwal et al.

Funding for this work was provided by Technology Maturation Funds from Battelle Memorial Institute.

Resources

• Pratul K. Agarwal, Christopher Schultz, Aristotle Kalivretenos, Brahma Ghosh, and Sheldon E. Broedel, Jr. (2012) Engineering a Hyper-catalytic Enzyme by Photoactivated Conformation Modulation. The Journal of Physical Chemistry Letters 3, pp 1142–1146 doi: 10.1021/jz201675m