The atomic-level action of a remarkable class of ring-shaped protein motors
has been uncovered by researchers with the Lawrence
Berkeley National Laboratory (Berkeley Lab) using a state-of-the-art protein
crystallography beamline at the Advanced Light Source (ALS). These protein motors
play pivotal roles in gene expression and replication, and are vital to the
survival of all biological cells, as well as infectious agents, such as the
human papillomavirus, which has been linked to cervical cancer.
James Berger (left) and Nathan Thomsen solved the structure of an important protein motor called the Rho transcription termination factor using the protein crystallography capabilities of Beamline 8.3.1 at Berkeley Lab’s Advanced Light Source. (Photo by Roy Kaltschmidt, Berkeley Lab Pubilc Affairs)
James Berger, a biochemist and structural biologist who holds joint appointments
with Berkeley Lab’s Physical Biosciences Division and University of California
Berkeley’s Department of Molecular and Cell Biology, and Nathan Thomsen,
a graduate student in his research group, have captured a critical action shapshot
of an enzyme known as the Rho transcription termination factor. In bacteria,
the Rho motor protein binds to a specific region of messenger RNA and translocates
along the chain to selectively terminate transcription at discrete points along
“We have shown that the Escherichia coli Rho transcription termination
factor functions like a rotary engine, much like the motors found on certain
classes of propeller airplanes,” says Berger. “As the motor spins,
fueled by the chemical energy in ATP nucleotides, it pulls RNA strands through
it’s interior, an action that enables Rho to walk along RNA chains. Interestingly,
the rotary firing order of the motor is biased so that the Rho protein can walk
in only one direction along the RNA chain.”
Berger and Thomsen are the co-authors of a paper reporting the results this
research that has been published in the journal Cell. The paper is titled: “Running
in reverse: the structural basis for translocation polarity in hexameric helicases.”
The Rho factor is a member of the hexameric helicase superfamily of enzymes
- ring-shaped proteins made up of six independent subunits or “cylinders.”
Hexameric helicases are found in all organisms and are involved in unwinding
and moving DNA and RNA strands around the cell. There are two subfamilies of
hexameric helicase enzymes: AAA+ and RecA. Rho belongs to the RecA family, which
is most common in bacteria. AAA+ motors are predominantly found in eukaryotes,
including humans, as well as some human pathogens, such as the papillomavirus.
These motors are descended from a common ancestor far back in evolution, but
have distinct properties, most notably they walk along nucleic acid tracks in
opposite directions. Scientists have wanted to know why the biased movement
of these motors differs, Berger explains.
“If you want to understand how an enzyme works, and perhaps eventually
develop therapeutic drug that will gum up the works and stop the motor from
doing its job, it helps to know what the motor looks like,” he says. “We
are the first group to determine the crystal structure of a RecA class of hexamer
helicase in a translocation state bound to both its nucleic acid track and ATP.
In doing so, we fortuitously caught the motor in the act of tracking along an
Berger and Thomsen solved the structure of this Rho protein motor using the
protein crystallography capabilities of ALS Beamline 8.3.1. The ALS is an electron
synchrotron designed to accelerate electrons to energies of nearly two billion
electron volts (GeV) and focus them into a tight beam around a storage ring.
Beams of ultraviolet and x-ray light are extracted from this electron beam through
the use of either bending, wiggler or undulator magnetic devices. These light
beams are a hundred million times brighter than those from the best x-ray tubes.
ALS Beamline 8.3.1 is powered by a superconducting bend magnet, or “superbend,”
and has experimental facilities that offer both multiple-wavelength anomalous
diffraction (MAD) and monochromatic protein crystallography capabilities.
“The high brightness of the x-ray beams and the experimental capabilities
at Beamline 8.3.1 were critical to our success,” says Berger, one of the
scientific spokespersons for the beamline.
What Berger and Thomsen found from their structural studies was that nucleic-acid
binding elements in the interior of the Rho ring spiral around six bases of
RNA. When the ATP binding sites that are coupled to this RNA segment release
their chemical energy through hydrolysis of the nucleotide, they do so in a
sequential manner that propagates around the hexameric ring. This chemical energy
is converted into mechanical motion that dictates the rotational direction of
the Rho motor based on the firing order of the ATP sites.
“Think of it like the cylinders in a radial engine,” Berger says.
“The fuel and intake come in from one side, leading to motions that cause
the cylinders to spin around a central RNA camshaft. However, because the cylinders
actually lie out of plane, they walk along the camshaft as they move.”
In their study, Berger and Thomsen found that nature has evolved a similar
rotary mechanism for the papillomavirus E1 protein, an AAA+ family hexameric
helicase. Their analysis showed that E1 motor moves in the opposite direction
along a nucleic chain because the rotational firing order of ATP sites is actually
reversed. Determining the molecular structure of protein motors and learning
how they operate is critical not only to basic understanding of the molecular
principles that control the cell, but also to aiding pharmaceutical drug discovery
“DNA and RNA are large and cumbersome macromolecular polymers which present
a challenge to the molecular machines that need to access their genetic information,”
says Berger. “There have been two other proposed models for these protein
motors in addition to the rotary, one a type of putt-putt motor, in which all
the active binding elements hydrolyze ATP simultaneously, and the other a stochastic
model, whereby ATP sites are fired at random. We’ve shown that RecA-style
motors use the rotary model.”
This research was supported by funding from the National Institutes of Health
and the G. Harold and Leila Y. Mathers Foundation.