State-of-the-art method reveals never-before-seen atomic structures controlling the process
From: Northwestern University
March 17, 2022 -- Methanotrophic bacteria consume 30
million metric tons of methane per year and have captivated researchers for
their natural ability to convert the potent greenhouse gas into usable fuel.
Yet we know very little about how the complex reaction occurs, limiting our
ability to use the double benefit to our advantage.
By studying the enzyme
the bacteria use to catalyze the reaction, a team at Northwestern University
now has discovered key structures that may drive the process.
Their findings, to
be published Friday (March 18) in the journal Science, ultimately
could lead to the development of human-made biological catalysts that convert
methane gas into methanol.
“Methane has a very
strong bond, so it’s pretty remarkable there’s an enzyme that can do this,”
said Northwestern’s Amy Rosenzweig, senior author of the paper. “If we don’t
understand exactly how the enzyme performs this difficult chemistry, we’re not
going to be able to engineer and optimize it for biotechnological
applications.”
Rosenzweig is
the Weinberg Family Distinguished Professor of Life Sciences in
Northwestern’s Weinberg College of Arts and Sciences, where she holds
appointments in both molecular biosciences and chemistry.
The enzyme, called
particulate methane monooxygenase (pMMO), is a particularly difficult protein
to study because it’s embedded in the cell membrane of the bacteria.
Typically, when researchers
study these methanotrophic bacteria, they use a harsh process in which the
proteins are ripped out of the cell membranes using a detergent solution. While
this procedure effectively isolates the enzyme, it also kills all enzyme
activity and limits how much information researchers can gather — like
monitoring a heart without the heartbeat.
In this study, the team
used a new technique entirely. Christopher Koo, the first author and a Ph.D. candidate
in Rosenzweig’s lab, wondered if by putting the enzyme back into a membrane
that resembles its native environment, they could learn something new. Koo used
lipids from the bacteria to form a membrane within a protective particle called
a nanodisc, and then embedded the enzyme into that membrane.
“By recreating the
enzyme’s native environment within the nanodisc, we were able to restore
activity to the enzyme,” Koo said. “Then, we were able to use structural
techniques to determine at the atomic level how the lipid bilayer restored
activity. In doing so, we discovered the full arrangement of the copper site in
the enzyme where methane oxidation likely occurs.”
The researchers used
cryo-electron microscopy (cryo-EM), a technique well-suited to membrane
proteins because the lipid membrane environment is undisturbed throughout the
experiment. This allowed them to visualize the atomic structure of the active
enzyme at high resolution for the first time.
“As a consequence of
the recent ‘resolution revolution’ in cryo-EM, we were able to see the
structure in atomic detail,” Rosenzweig said. “What we saw completely changed
the way we were thinking about the active site of this enzyme.”
Rosenzweig said that the
cryo-EM structures provide a new starting point to answer the questions that
continue to pile on. How does methane travel to the enzyme active site? Or
methanol travel out of the enzyme? How does the copper in the active site do
the chemical reaction? Next, the team plans to study the enzyme directly within
the bacterial cell using a forefront imaging technique called cryo-electron
tomography (cryo-ET).
If successful, the
researchers will be able to see exactly how the enzyme is arranged in the cell
membrane, determine how it operates in its truly native environment and learn
whether other proteins around the enzyme interact with it. These discoveries would
provide a key missing link to engineers.
“If you want to
optimize the enzyme to plug it into biomanufacturing pathways or to consume
pollutants other than methane, then we need to know what it looks like in its
native environment and where the methane binds,” Rosenzweig said. “You could
use bacteria with an engineered enzyme to harvest methane from fracking sites
or to clean up oil spills.”
The study, “Recovery of
particulate methane monooxygenase structure and activity in a lipid bilayer,”
was supported by the National Institutes of Health (grant numbers R35GM118035,
T32GM008382, T32GM105538 and R01GM135651).
https://news.northwestern.edu/stories/2022/03/methane-converting-bacteria/
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