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Protein Structure Yields to Determined Predoctoral Fellow

Summary

Hyock Joo Kwon has helped to determine the structure of the active site of bacteriophage lambda integrase, a well-studied protein that had proven difficult to visualize.

Elucidating the structure of a protein molecule is an achievement usually reserved for experienced scientists. Hyock Joo Kwon, an HHMI predoctoral fellow working in the laboratory of Tom Ellenberger at Harvard Medical School, just got an early and extremely satisfying taste of success.

In a paper published in Science on April 4, Kwon, Ellenberger and their colleagues described the structure of the active site of bacteriophage lambda integrase, a well-studied protein that had proven difficult to visualize. The paper was published in the middle of Kwon's third year of graduate school.

All the elements that make structural biology difficult were present when Kwon took over the lambda integrase project. It was hard to obtain pure crystals of the protein, which orchestrates the integration of the bacteriophage DNA into the DNA of the host bacterium. Eventually, Kwon was able to obtain crystals of pure protein. He then quickly moved through the complex lab experiments and calculations required to determine the structure of the active site from the diffraction patterns his crystals produced.

The structure revealed that the active site of lambda integrase contains a long, flexible chain of protein that is tethered to the rest of the protein like a watch fob. When the integrase protein approaches the DNA of the bacterial host, the loop swings in, and one link in the chain forms a bond with the host DNA. This is the first step in integrating phage DNA into that of the host. Loops are a familiar motif in DNA-binding proteins; however, the three-dimensional structure of the integrase protein contains features that were "apparently unprecedented," said Kwon.

The results resolved a thorny debate in phage biology. As many as 58 members of the integrase family had been isolated and sequenced, with sequences so similar that they seemingly had to act by the same mechanism: a single molecule of integrase opening the host DNA. Paradoxically, however, a large volume of data emerged pointing to a mechanism with two protein molecules.

Kwon's new data put the paradox to rest. The protein chain is long and flexible enough that the integrase can open up the host DNA either way--as a single protein or a pair of proteins. "That alleviated a lot of concern about the other experiments," said Kwon. "It showed us that both sets of results were still possible."

Kwon's HHMI fellowship, which provides up to five years of support for full-time study toward the Ph.D. or Sc.D. degree in specified biological disciplines, allowed him to join Ellenberger's lab and pursue the interest in structural biology that he acquired as an undergraduate at the University of California, Berkeley.