Scientists create protein models to explore toxic methylmercury
formation

Date:
August 25, 2020
Source:
DOE/Oak Ridge National Laboratory
Summary:
A team has created a computational model of the proteins responsible
for the transformation of mercury to toxic methylmercury, marking
a step forward in understanding how the reaction occurs and how
mercury cycles through the environment.



FULL STORY ==========================================================================
A team led by the Department of Energy's Oak Ridge National Laboratory
created a computational model of the proteins responsible for the transformation of mercury to toxic methylmercury, marking a step forward
in understanding how the reaction occurs and how mercury cycles through
the environment.


========================================================================== Methylmercury is a potent neurotoxin that is produced in natural
environments when inorganic mercury is converted by microorganisms
into the more toxic, organic form. In 2013, ORNL scientists announced
a landmark discovery: They identified a pair of genes, hgcA and hgcB,
that are responsible for mercury methylation.

Those genes encode the proteins HgcA and HgcB, whose structure and
function ORNL scientists have been working to better understand.

"Determining protein structures can be challenging," said Jerry Parks, the
head investigator and leader of the Molecular Biophysics group at ORNL.

These two proteins are difficult to characterize experimentally for
several reasons: they are produced by anaerobic microorganisms and
are therefore highly sensitive to oxygen; they are expressed at such
low levels in cells that they are barely detectable by conventional
techniques; HgcA is embedded in the membrane of a cell, making it more challenging to study than a soluble protein; and both proteins have
complex cofactors -- substances that bind to proteins and are essential
for their function.

"We don't have an experimental structure yet for these proteins, so
the next best thing is to use computational techniques to predict their structure," Parks said.



==========================================================================
The computational model was generated using a large dataset of HgcA
and HgcB protein sequences from many different microorganisms, ORNL's high-performance computing resources and bioinformatics, and structural modeling techniques as detailed in a recent article in Communications
Biology.

The result is a 3D structural model of the HgcAB protein complex and
its cofactors that scientists can use to develop new hypotheses designed
to understand the biochemical mechanism of mercury methylation and then
test them experimentally.

Scientists have been predicting protein structures from their amino
acid sequences for many years. In 2017, a team led by the University of Washington reached a milestone, modeling the structures of hundreds of previously unsolved protein families by mining large metagenomic datasets
for diverse protein sequences. This approach predicts which pairs of
amino acids in each protein are in close contact with each other, and
then uses that information to fold the proteins computationally.

Parks was eager to apply the same techniques to the mercury work, turning
to data available from DOE's Joint Genome Institute, a DOE Office of
Science user facility.

The scientists searched the JGI database for HgcA and HgcB amino acid sequences. They then performed a coevolution analysis to identify
coordinated changes that occur among pairs of amino acids. Coevolution
makes it likely that those coordinated pairs are close to each other in
the three-dimensional folded structure of the protein. This information
can be used to guide computational protein folding and predict how the
folded protein domains interact with each other.



==========================================================================
One surprising finding by the team is that the two domains of HgcA
don't interact with each other, but they both interact with the
HgcB protein. The model also suggests that conserved cysteine amino
acids in HgcB are likely involved in shuttling some forms of mercury, methylmercury, or both, to HgcA during the reaction. Some features of
these proteins are similar to other more well-studied proteins, but
others are unique and have not been observed before in any other protein.

Future research will involve experimental testing. Stephen Ragsdale's
group at the University of Michigan is working out a way to produce the
HgcA and HgcB proteins in E. coli bacteria in sufficient quantities to
enable the proteins to be studied in the laboratory using spectroscopic techniques and X-ray crystallography. "We are excited that this important experimental work is being done," said Parks. "It will be interesting
to see how well we did with our structure predictions." Mercury is a
naturally occurring element found worldwide, and scientists at ORNL have
come to realize that the microorganisms that convert inorganic mercury
to methylmercury are also widespread. "We don't know as much as we'd
like about all the different reactions and processes that mercury can
undergo," Parks added. "This work helps us understand more about one of
the most important biotransformations of mercury in nature." In addition
to gaining insight into mercury methylation, the project creates a new capability at ORNL that can be used to explore the structure and function
of other microbial proteins. In particular, Parks and colleagues are
interested in characterizing proteins from microorganisms referred to
as microbial dark matter because they are unable to be cultured in the
lab and are otherwise difficult to study.

"There is so much we still don't know about all the unusual proteins that
are produced by microorganisms," Parks said. "This technique allows us
to begin characterizing these complex, mysterious biological systems."

========================================================================== Story Source: Materials provided by
DOE/Oak_Ridge_National_Laboratory. Note: Content may be edited for style
and length.


========================================================================== Journal Reference:
1. Connor J. Cooper, Kaiyuan Zheng, Katherine W. Rush, Alexander
Johs, Brian
C. Sanders, Georgios A. Pavlopoulos, Nikos C. Kyrpides,
Mircea Podar, Sergey Ovchinnikov, Stephen W. Ragsdale, Jerry
M. Parks. Structure determination of the HgcAB complex using
metagenome sequence data: insights into microbial mercury
methylation. Communications Biology, 2020; 3 (1) DOI:
10.1038/s42003-020-1047-5 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200825121831.htm

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