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A helicase (blue) moves rapidly on a highly
flexible DNA track. Such movement may prevent the accumulation of
toxic proteins on the DNA.
Graphic courtesy Taekjip Ha
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Taekjip Ha, a professor of physics at the
University of Illinois at Urbana-Champaign and a Howard Hughes Medical
Institute investigator, likens the biological scenario to Boston Red
Sox baseball; the team rolls along only to hit a late-season obstacle
called the New York Yankees. Then, like the always-anticipated annual
cry from Chicago Cubs fan, it's back to square one next year.
However, instead of causing more misery, as is the
case for a baseball fan, this motor protein's starting over may serve
a beneficial purpose, clearing other, undesired proteins from the DNA,
Ha said. The research was done in vitro, using purified proteins and
studied with a technique that visualizes individual molecules on DNA.
Whether the scenario plays out in real cells in not known and under
exploration.
The discovery appears in the Oct. 27 issue of the
journal Nature, along with a separate "News & Views" article by
Eckhard Jankowsky, a biochemist at the Center for RNA Molecular
Biology in Case Western University's School of Medicine, who wrote
about the potential importance of the findings.
Ha's postdoctoral fellow Sua Myong led the study,
looking at the Rep helicase from an E-coli bacterium. Rep is known to
be involved in restarting DNA replication stalled by DNA damage. As a
single protein, a monomer, Rep can travel one way along a single
strand of DNA but by itself cannot unzip it. Rep's progress was
visualized using the single molecule fluorescence resonance energy
transfer (FRET) technique that Ha had developed.
By tagging the protein and DNA with green and red
dyes, Myong measured FRET changes as Rep traveled along single DNA
strands, which are short segments extending out from double strands.
Each time the protein reached either the junction of the full
double-stranded DNA or hit an artificially created protein obstacle,
Rep instantly returned to near the beginning of the single strand on
which it had initially bound.
Upon closer examination using FRET, researchers
discovered that Rep's configuration gradually closed as it reached the
obstacle in its path. Then, conformational changes of Rep allow it to
grab and transfer to the end of the single-stranded DNA, leading to
the next cycle.
"Although the very flexible single strand of DNA
likely bombards the protein constantly, the protein doesn't seem to
pay attention to this overture until it hits a physical blockade," Ha
said.
Researchers had theorized that obstacles would
force motor proteins to disengage from DNA. "The finding was totally
unexpected and may indicate a new function for the protein," Ha said.
Jankowsky wrote that scientists "should not immediately search for the
helix that the enzyme unzips, but instead remember how Rep snaps
back."
In cells, single strands of DNA often occur when
something is wrong, Ha said. The recycling action, he said, may
represent a desirable function of the protein by keeping it engaged on
a single strand, allowing time for repairs that allow normal DNA
replication.
The human body has more than 200 types of helicases
involved in replication, transcription, repair and other genetic
processes, Ha said. Defective helicases have been linked to increased
cancer risks and premature aging.
Co-authors with Myong and Ha were Ivan Rasnik, a
former postdoctoral fellow who now is a professor of physics at Emory
University in Atlanta; Chirlmin Joo, a doctoral student in Ha's lab;
and Timothy M. Lohman, a professor of biochemistry and molecular
biophysics at the Washington University School of Medicine in St.
Louis. |
