Biologists learn structure of enzyme needed to power 'molecular motor'

Researchers at Purdue University and The Catholic University of America have discovered the structure of an enzyme essential for the operation of "molecular motors" that package DNA into the head segment of some viruses during their assembly.

The enzyme, called an ATPase, provides energy to run the motor needed to insert DNA into the capsid, or head, of the T4 virus, which is called a bacteriophage because it infects bacteria. The same kind of motor, however, also is likely present in other viruses, including the human herpes virus.

"This is the first time a structure has been determined of an ATPase involved in a DNA packaging motor," said Michael Rossmann, the Hanley Distinguished Professor of Biological Sciences in Purdue's College of Science.

The article's lead author is Siyang Sun (pronounced See-Young Sun), a postdoctoral research associate working in Rossmann's lab. The researchers have proposed a mechanism for how the motor works.

Findings are detailed in a paper published Thursday (March 22) in the journal Molecular Cell. The paper was written by Sun; Kiran Kondabagil, a postdoctoral research associate at The Catholic University of America; Petra Gentz, a former visiting doctoral student at Purdue; Rossmann; and Venigalla B. Rao, a professor of biology at The Catholic University of America.

"The virus first assembles the protein shell of the head and then packages the DNA into this empty capsid," Rossmann said. "This process could be likened to building a house and then filling it with furniture."

The DNA is a complete record of a virus' properties, and the capsid protects this record from damage and ensures that the virus can reproduce by infecting a host organism.

"This research represents a significant step forward to understanding how DNA genetic material is packaged in viruses," Rao said.

Energy to run the packaging motor is produced when the ATPase enzyme breaks down a biological compound called adenosine triphosphate, or ATP, turning it into adenosine diphosphate, or ADP. Specifically, the enzyme breaks a bond between a chemical group called a phosphate and the ADP.

The researchers determined the structure of the particular ATPase used to break the high-energy bond that links the phosphate to ADP. This release of energy is used to run the molecular motor in the T4 virus.

The virus consists of a head and tail portion. The DNA-packaging motor is located in the same place where the tail eventually connects to the head. The motor falls off after the packaging step is completed, allowing the tail to attach to the capsid.

DNA is made of four different kinds of "nucleotides" identified by a specific "base." The bases are paired together to form the rungs of a ladderlike, double-stranded helical structure. Because there is a negative charge associated with each nucleotide, they repel each other when compressed together, creating a pressure inside the confining space of the capsid. A motor is needed to counteract this pressure, in effect pumping the DNA into the head.

The authors of the research paper have proposed a mechanism for how the motor works by comparing its structure to those of other, similar enzymes called helicases. The helicases are needed to separate double-stranded DNA into single strands during gene replication, a fundamental process of life required to pass on genetic information from one generation to another.

Helicases alternatively bind to and release their grip on DNA during replication, progressively moving along the helix to separate the strands in a motion similar to an inchworm's movement. The authors proposed that the motor uses a similar inchworm mechanism to package the DNA into the virus.

"While the helicases use the mechanism to unwind double-stranded DNA, this ATPase uses the mechanism to pump genetic material into the virus capsid," Sun said.

The researchers determined the enzyme structure using a technique called X-ray crystallography. This technique involves crystallizing a substance like the ATPase and then passing X-rays through the crystals, creating a "diffraction pattern" that can be interpreted with various computational procedures to produce an image.

Because herpes and other viruses contain similar DNA packaging motors, the findings could help scientists to design drugs that would interfere in the function of these motors and hence mitigate the result of some viral infections. The findings also could have other applications, such as development of tiny "nanomotors" in future machines, Rossmann said.

"But it's really premature to discuss possible practical applications of this knowledge because this work is really in the realm of basic research," Rossmann said. "When the Greeks observed the planets, they never thought such information would be helpful centuries later for designing spacecraft trajectories."

Source: Purdue University

Related stories:

A breakthrough, then a surge, in stem cell research
Less than a year after a Wisconsin team helped discover a major alternative to human embryonic stem cells, the Madison scientists say more than 800 labs have begun using the approach, suggesting that many stem-cell researchers are starting to move beyond controversial embryonic sources for their work.
Scientists discover DNA knot keeps viral genes tightly corked inside shell
A novel twist of DNA may keep viral genes tightly wound within a capsule, waiting for ejection into a host, a high-resolution analysis of its structure has revealed.
Biosensing nanodevice to revolutionize health screenings
One day soon a biosensing nanodevice developed by Arizona State University researcher Wayne Frasch may eliminate long lines at airport security checkpoints and revolutionize health screenings for diseases like anthrax, cancer and antibiotic resistant Staphylococcus aureus (MRSA).
Researchers probe a DNA repair enzyme
Researchers have taken the first steps toward understanding how an enzyme repairs DNA. Enzymes called helicases play a key role in human health, according to Maria Spies, a University of Illinois biochemistry professor.
Evolutionary comparison finds new human genes
Using supercomputers to compare portions of the human genome with those of other mammals, researchers at Cornell have discovered some 300 previously unidentified human genes, and found extensions of several hundred genes already known.
Powerful Molecular Motor Permits Speedy Assembly of Viruses
A team of physicists at the University of California, San Diego and biologists at Catholic University of America, Washington D.C. has shown that a tiny viral motor generates twice as much power, relative to its size, as an automobile engine. The finding explains why even very large viruses can self-assemble so rapidly.
New vaccine prevents CMV infection and disease in mice
Researchers at the University of California, San Diego (UCSD) Skaggs School of Pharmacy and Pharmaceutical Sciences have patented a strategy for developing a human vaccine to prevent against Human Cytomegalovirus (hCMV) infection and disease.
Researchers reprogram normal tissue cells into embryonic stem cells
Researchers at the Institute for Stem Cell Biology and Medicine at UCLA were able to take normal tissue cells and reprogram them into cells with the same unlimited properties as embryonic stem cells, the cells that are able to give rise to every cell type found in the body.

News discussion:

General Science news