Neutrons help understand enzymes that could produce improvements in biomass processing 

An artist’s rendering of the five protein structures solved using neutrons shown on top of the MaNDi instrument detectors. Image credit - ORNL/DOE

Plants and other biomass can be converted into a variety of renewable high-value products including carbon fibers, plastics, and liquid fuels such as ethanol and biodiesel that are beneficial for reducing petroleum use and vehicle emissions. Breaking down plants in order to release energy can require many steps and harsh chemicals, so researchers are seeking efficient natural catalysts, specifically enzymes, to deconstruct plant material.

Scientists at the U.S. Department of Energy’s Oak Ridge National Laboratory are using neutron crystallography to understand enzymes and learn how to bioengineer those enzymes for large-scale improvements in the efficiency of biomass processing. Using the MaNDi instrument at ORNL’s Spallation Neutron Source (a DOE Office of Science User Facility), the LANSCE Protein Crystallography Station in Los Alamos, N.M., and the FRMII BioDiff instrument in Munich, Germany, they determined the structure of xylanase, an enzyme used to digest hemicellulose during biofuel production, at unprecedented detail.

When processing plant-based biomass, hemicellulose—an abundant polysaccharide in plant cell walls—must first be degraded to monomeric sugars that can be converted to high-value products such as biofuels. Current non-harsh methods to pretreat biomass result in very basic (high pH) conditions. Native enzymes are not very efficient in such conditions, however, preferring an acidic (low pH) environment for maximum activity. By re-engineering hemicellulose-hydrolyzing enzymes to increase their activity at high pH, researchers can improve the process, but that requires researchers to understand the intricate details of how the enzymes work.

“We need to look deeper into their structures than what X-rays usually can provide,” said ORNL’s Andrey Kovalevsky, the senior author of the study. “That is, we have to know where all of the hydrogen atoms are before, during and after a chemical reaction has occurred in an enzyme’s active site. Neutrons can give us this information.”

In fact, using neutrons, the team directly and unequivocally visualized hydrogen atoms and hydrogen bonding in xylanase at different stages of the catalytic reaction.

“No one has ever observed hydrogen atoms in a glycoside hydrolase enzyme, and until now we did not know how the catalytic glutamic acid residue is protonated,” said Kovalevsky.

Kovalevsky and his colleagues are interested in protonation because they need to know how protons move during catalysis. For example, to start the hemicellulose hydrolysis reaction, the catalytic glutamic acid must be protonated and the catalytic base must be deprotonated. Understanding the acid/base chemistry of enzymatic biomass hydrolysis is key to rationally engineering enzymes that improve biomass processing.

Kovalevsky and his colleagues determined five neutron structures of xylanase at various pH values and in complex with a ligand. The structures showed how hydrogen atoms are arranged in the active site of xylanase, where they move and how hydrogen bonding is altered due to pH changes and ligand binding. The low-pH structure, obtained from data collected on MaNDi, helped them understand how the enzyme functions.

“This enzyme, used in biofuels production, is a target for enzyme design to improve its performance in an industrial setting,” said Kovalevsky.  “Exact knowledge of its mechanism will improve protein engineering efforts.”

Nuclear density maps (green mesh) of the enzyme active site showing protonation of the catalytic glutamate residue only in the downward conformation (red mesh).
Nuclear density maps (green mesh) of the enzyme active site showing protonation of the catalytic glutamate residue only in the downward conformation (red mesh).

The team has discovered that the catalytic glutamic acid can orient itself in two different conformations that have very different affinities for a proton. When the glutamate side chain rotates down and away from a substrate, it is a weaker acid than when it adopts an upward orientation. As a result, the catalytic group obtains a proton from water only when it faces downward, but can be an efficient proton donor to the substrate to initiate the hydrolysis reaction when it is in the upward conformation.

“This is a big revelation for glycoside hydrolases, and specifically for xylanases, because we now know where to make amino acid substitutions in order to improve the enzyme,” said Kovalevsky.

The combination of neutron diffraction experiments with high-performance computing is a powerful approach for understanding how enzymes function. The researchers were curious to know how easily the glutamate side chain switches conformations. To answer that question, they turned to computer simulations.

“Using neutron structures as a starting point for molecular dynamics simulations, we showed that the glutamate can readily cycle between the two conformations,” said Jerry Parks, an ORNL researcher and co-author of the study. “With another computational approach, we also found that the acidity of the glutamate changes significantly based on how it is oriented, which agrees nicely with the neutron structures.”

This research was published in the Proceedings of the National Academy of Sciences (http://www.pnas.org/content/112/40/12384.abstract), and is the first user publication of the MaNDi instrument, which was commissioned at SNS in 2014.  The research was supported by DOE’s Office of Science.

ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science.

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