Researchers use cluster analysis to study protein shape and function. Each green circle represents one potential shape of the protein mitoNEET. The longer the blue line between two circles, the greater the differences between the shapes. Most shapes are similar; they fall into three clusters that are represented by the three images of the protein. Image: Elizabeth Baxter/UCSD |
Like
a magician employing sleight of hand, the protein mitoNEET—a mysterious
but important player in diabetes, cancer and aging—draws the eye with a
flurry of movement in one location while the subtle, more crucial
action takes place somewhere else.
Using
a combination of laboratory experiments and computer modeling,
scientists from Rice University and the University of California, San
Diego (UCSD) have deciphered part of mitoNEET’s movements to get a
better understanding of how it handles its potentially toxic payload of
iron and sulfur. Their research is described this week in the
Proceedings of the National Academy of Sciences.
“We
scrutinize proteins with an unconventional approach,” said José
Onuchic, Rice’s Harry C. and Olga K. Wiess Professor of Physics and
Astronomy and co-director of the Center for Theoretical Biological
Physics. “We use biophysics to probe biology rather than the other way
around. Using computational theory, we find structures that are
possible—regardless of whether they’ve already been observed
experimentally—and we ask ourselves whether these structures might be
biologically significant.”
Study
co-leader Patricia Jennings, professor of chemistry and biochemistry at
UCSD, who has collaborated with Onuchic for 15 years, said they save a
great deal of time by using structural biophysics to guide their
experiments on a wide variety of targets. For example, Jennings’
laboratory determined less than five years ago that mitoNEET contained a
novel folded structure. Since then, her lab has been using insights
gained from static and dynamic snapshots of the protein to guide
biological and biochemical studies.
“I
think people forget that proteins are machines with moving parts,” said
study lead author Elizabeth Baxter, a UCSD graduate student who works
under the guidance of both Onuchic and Jennings. “We start with the
static snapshot and model in the functional motions.”
MitoNEET,
which binds to the diabetes drug, Actos, immediately caught the
attention of researchers when it was discovered. It has a unique ability
to bind and store iron-based molecules in an iron-sulfur cluster. Iron
is an essential element for all life, but it is also highly toxic, and
mitoNEET is the only iron-handling protein that is known to sit on the
wall of the mitochondria, one of the key structures inside a cell.
The
protein’s biological functions are still being unraveled.
Interestingly, scientists have shown that mitoNEET sits on the outer
mitochondrial wall with its potentially toxic payload of iron-sulfur
molecules facing toward the cell’s cytoplasm, the gel-like fluid that
fills the cell. Discovery of the unique binding mode of the protein’s
iron-sulfur cluster led the Jennings group to show that the cluster can
be delivered into the mitochondria. In addition, its sister protein
interacts with proteins that participate in apoptosis—the process cells
use to kill themselves when they are no longer viable.
“I
think mitoNEET is a protein that could be your best friend or your
worst enemy,” Jennings said. “There’s some evidence that it may act as a
sensor for oxidative stress and that it can lose its toxic iron-sulfur
cluster under stress conditions. Depending upon where the iron ends up,
that could lead to drastic problems inside the cell.”
Proteins
are strands of amino acids that are produced from DNA blueprints, but
their shapes can provide important clues about their function. To find
out how mitoNEET’s control and release of its iron-sulfur payload might
be related to its shape, Baxter used computer simulations to study how
the protein folds, as well as the functional motions of two similar
shapes that could be biologically important. In one of these shapes,
there is a slight intertwining of two arms that extend away from the
iron-cluster pocket. In the other, the arms also extend but are not
intertwined.
Baxter
found that both conformations were physically possible. She also found
the protein could switch between the “strand-swapped” and
“strand-unswapped” conformations without entirely unfolding. Moreover,
this change in the twining of the arms was shown to alter the shape of
the critical pocket that holds the iron-sulfur cluster; this makes the
cluster more likely to be inserted or released in situations where the
arms are untwined.
Like
the magician using misdirection, the loosening of the grip on the
cluster is subtle and happens in a different location than the flurry of
arm motions. Jennings said it’s the kind of thing that could easily be
missed if the focus of the study were the cluster itself.
Onuchic
said, “One of the advantages to our approach is that it allows us to
look for relevant biophysical properties that control distant functional
regions—like mitoNEET’s strand-swapping—that can easily be missed with a
more conventional approach.”
The research was funded by the National Science Foundation and the National Institutes of Health.
Strand swapping regulates the iron-sulfur cluster in the diabetes drug target mitoNEET
