Featured Research

from universities, journals, and other organizations

Atomic-level snapshot catches protein motor in action

Date:
November 25, 2009
Source:
DOE/Lawrence Berkeley National Laboratory
Summary:
The atomic-level action of a remarkable class of ring-shaped protein motors has been uncovered using a state-of-the-art protein crystallography beamline at the Advanced Light Source. 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.

Side view of the Rho protein motor. To clarify the mechanism, two of the six subunits have been removed. As ATP is released from binding sites (D,E, T and T*), the subunits (green, purple, blue and gray structures) spiral around the RNA (orange) strand, pulling the strand through the hole in the hexamer ring. This rotatory action enables the Rho motor to “walk” in one direction along the RNA strand.
Credit: Image courtesy of DOE/Lawrence Berkeley National Laboratory

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, 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 the genome.

"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 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 RNA chain."

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 efforts.

"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.


Story Source:

The above story is based on materials provided by DOE/Lawrence Berkeley National Laboratory. Note: Materials may be edited for content and length.


Journal Reference:

  1. Thomsen et al. Running in Reverse: The Structural Basis for Translocation Polarity in Hexameric Helicases. Cell, 2009; 139 (3): 523 DOI: 10.1016/j.cell.2009.08.043

Cite This Page:

DOE/Lawrence Berkeley National Laboratory. "Atomic-level snapshot catches protein motor in action." ScienceDaily. ScienceDaily, 25 November 2009. <www.sciencedaily.com/releases/2009/11/091124121427.htm>.
DOE/Lawrence Berkeley National Laboratory. (2009, November 25). Atomic-level snapshot catches protein motor in action. ScienceDaily. Retrieved April 16, 2014 from www.sciencedaily.com/releases/2009/11/091124121427.htm
DOE/Lawrence Berkeley National Laboratory. "Atomic-level snapshot catches protein motor in action." ScienceDaily. www.sciencedaily.com/releases/2009/11/091124121427.htm (accessed April 16, 2014).

Share This



More Matter & Energy News

Wednesday, April 16, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Google Patents Contact Lens Cameras; Internet Is Wary

Google Patents Contact Lens Cameras; Internet Is Wary

Newsy (Apr. 15, 2014) Google has filed for a patent to develop contact lenses capable of taking photos. The company describes possible benefits to blind people. Video provided by Newsy
Powered by NewsLook.com
The Walking, Talking Oil-Drigging Rig

The Walking, Talking Oil-Drigging Rig

Reuters - Business Video Online (Apr. 15, 2014) Pennsylvania-based Schramm is incorporating modern technology in its next generation oil-drigging rigs, making them smaller, safer and smarter. Ernest Scheyder reports. Video provided by Reuters
Powered by NewsLook.com
Dutch Highway Introduces Glow-In-The-Dark Paint

Dutch Highway Introduces Glow-In-The-Dark Paint

Newsy (Apr. 14, 2014) A Dutch highway has become the first lit by glow-in-the-dark paint — a project aimed at reducing street light use. Video provided by Newsy
Powered by NewsLook.com
Google Buys Drone Maker, Hopes to Connect Rural World

Google Buys Drone Maker, Hopes to Connect Rural World

Newsy (Apr. 14, 2014) Formerly courted by Facebook, Titan Aerospace will become a part of Google's quest to blanket the world in Internet connectivity. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins