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by The Ohio State University
June 20, 2016
from
PHYS
Website
Credit: George
Hodan/public domain
Scientists are getting closer to directly observing how and why
water is essential to life as we know it...
A study (Dynamics
and Mechanism of Ultrafast Water-Protein Interactions) in
this week's Proceedings of the National Academy of Sciences (PNAS)
provides the strongest evidence yet that proteins - the large and
complex molecules that fold into particular shapes to enable
biological reactions - can't fold themselves.
Rather, the work
of folding is done by much smaller
water molecules, which surround proteins and push and pull at them
to make them fold a certain way in fractions of a second, like
scores of tiny origami artists folding a giant sheet of paper at
blazingly fast speeds.
Dongping Zhong, leader of the research group at
The Ohio State University that
made the discovery, called the study a "major step forward" in the
understanding of water-protein interactions and said it answers a
question that's been dogging research into protein dynamics for
decades.
"For a long time, scientists have
been trying to figure out how water interacts with proteins.
This is a fundamental problem that
relates to protein structure, stability, dynamics and - finally
- function," said Zhong, who is the Robert Smith Professor of
physics at Ohio State.
"We believe we now have strong
direct evidence that on ultrafast time scales (picoseconds, or
trillionths of a second), water modulates protein fluctuations,"
he concluded.
Zhong, who is also a professor of
chemistry and biochemistry, and his team used ultrafast laser
pulses to take snapshots of water molecules moving around a DNA
polymerase, the kind of protein that helps
DNA reproduce.
The key to getting a good view of the interaction was to precisely
locate optical probes on the protein surface, he said. The
researchers inserted molecules of the amino acid
tryptophan into the protein as a
probe, and measured how water moved around it.
Water molecules typically flow around each other at
picosecond speeds, while proteins
fold at
nanosecond speeds - 1,000 times
slower.
Previously, Zhong's group demonstrated
that water molecules slow down when they encounter a protein. Water
molecules are still moving 100 times faster than a protein when they
connect with it, however.
In the new study, the researchers were able to determine that the
water molecules directly touched the protein's "side chains," the
portions of the protein molecule that bind and unbind with each
other to enable folding and function.
The researchers were also able to note
the timing of movement in the molecules.
Computer simulations at the Ohio Supercomputer Center (OSC)
helped the researchers visualize what was going on:
where the water moved a certain way,
the protein folded nanoseconds later, as if the water molecules
were nudging the protein into shape.
Water can't arbitrarily shape a protein,
Zhong explained.
Proteins can only fold and unfold
in a few different ways depending on the amino acids they're made
of.
"Here, we've shown that the final
shape of a protein depends on two things:
We can now say that, on ultrafast
time scales, the protein surface fluctuations are controlled by
water fluctuations.
Water molecules work together like a
big network to drive the movement of proteins."
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