Learning How the SARS Virus Spikes Its Quarry

Armen Hareyan's picture


Researchers have determined the first detailed molecular images of a piece of the spike-shaped protein that the deadly SARS virus uses to grab host cells and initiate the first stages of infection. These structural images, which show how the spike protein grasps its receptor, may help scientists learn new details about how the virus infects cells and could also help in identifying potential weak points that novel drugs or vaccines could exploit.

A worldwide SARS (severe acute respiratory syndrome) outbreak in 2002-2003 affected more than 8,000 people and killed 774 before being brought under control. Public health experts worry about another outbreak of the virus, which originates in animals such as civet cats.

The research team, led by Howard Hughes Medical Institute investigator Stephen C. Harrison at Children's Hospital and Harvard Medical School, and colleague Michael Farzan, also at Harvard Medical School, reported its findings in the September 16, 2005, issue of the journal Science.

Prior to these studies, researchers already knew that a key step in SARS infection is the attachment of the virus's spike protein to a receptor on the surface of target cells, Harrison says. This attachment permits the virus to fuse with a host cell and inject its RNA inside to infect the cell.

A detailed understanding of how the spike protein complexes with its receptor, ACE2 (angiotensin-converting enzyme 2), could have important clinical implications.

"This virus jumps from animals to humans, laterally among humans, and in some cases from animals to humans but without subsequent human-to-human transmission," says Harrison. "We know that those modes of transmission depend on specific mutations in the spike protein that affect its interaction with the receptor. One of the critical issues in a SARS epidemic would be to predict whether a given variant of the virus will jump species or move laterally from one human to the other. Understanding the structure of this complex will help us understand what these mutations in the spike protein mean in terms of infectivity."

Farzan and colleague Hyeryun Choe in the Children's Hospital Boston pulmonary department laid the scientific groundwork for determining the structure of the spike-ACE2 complex. In 2003, they discovered that the ACE2 protein is the receptor for the SARS virus and identified a specific fragment of the spike protein that is involved in viral attachment.


With these data in hand, researchers in Harrison's and Farzan's laboratories then focused on creating crystals of the relevant fragments of the spike protein in complex with the ACE2 receptor. These crystals were then subjected to structural analysis using x-ray crystallography. In this widely used technique, x-rays are directed through crystals of a protein. The resulting diffraction pattern is analyzed to deduce the atomic structure of the protein or protein complex under study.

The x-ray structure of the spike protein fragment revealed a slightly concave surface that fits a complementary surface on the receptor, says Harrison. But more interesting, the studies revealed important new information about two amino acids on the spike protein. These were the amino acids that Farzan and his colleagues had previously determined to be the most critical for determining how the SARS virus adapted from infecting only civets to infecting humans.

"Both of these critical amino acids turned out to be right in the middle of the interface between the spike protein and the receptor," says Harrison.

Thus, the atomic structure reveals details about how even small mutations in the spike protein gene can affect the virus's ability to infect humans. Such mutations alter the identity of amino acids at those sites, changing the shape of the spike protein and affecting how well it binds to the ACE2 receptor, explains Harrison. In particular, he said, the atomic structure shows how mutation at one of the two sites can enable the animal SARS virus to infect humans, but by itself this mutation does not appear to allow subsequent human-to-human transmission.

"A dramatic epidemiological difference can result from what looks like an almost trivial mutation," said Harrison. "These findings give us the beginnings of information needed - if a new virus were isolated - to make predictive guesses about infectivity, so that we can better give advance warning."

He also noted that laboratory studies indicate that the fragment of the spike protein they used could provide the basis of a vaccine against SARS, since it appears to be recognized by the immune system.

In future studies, Harrison and his colleagues plan to explore what happens after the spike protein attaches to the receptor. They know that the spike protein undergoes a conformational change that enables the virus to fuse with the host cell.

"When there's a conformational change, it gives you an opportunity to explore the possibility of antiviral therapeutics," said Harrison. "When you have two conformational structures, you can think about how to prevent infection by inhibiting the transition from one state to another."