New protein structure found - important for drug discovery

Understanding and replicating the diverse ways in which cellular proteins fold and interconnect is key to understanding life processes and major disorders, such as Parkinson's disease.

Now, new research from biochemists and structural biologists at Weill Cornell Medical College in New York City suggests the challenge in replicating those connections will be more difficult than scientists have imagined. But the promise of doing so using "bioengineering" may be much greater for medical science, too.

As reported recently in the Proceedings of the National Academy of Sciences, the researchers discovered that the structure of one of the most common protein-to-protein "hook-ups" -- the alpha helical "coiled coil" -- is more variable than previously believed.

Coiled coils are formed from the intertwining of spiral structures that stick because they have regularly spaced greasy patches on their surface. "Coiled coils occur when a ubiquitous protein structure, called an alpha helix, comes together with another alpha helix," explains Dr. Lu. "The coil that's formed is made up of repeats of seven amino acids."

Coiled coils can involve two or more individual strands. For example, the muscle protein myosin has two chains wrapped in a spiral. Proteins with three to five strands have also been found.

"Now, in a real first, we have discovered what biochemists call a 'seven-helix coiled coil,'" says senior researcher Dr. Min Lu, associate professor of biochemistry at Weill Cornell Medical College.

"Each new structure we identify in the coiled coil repertory adds exciting possibilities for deciphering structures in nature and designing functional analogs, for use in drug discovery," Dr. Lu explains. "Previously, people had thought coiled coils were constructed of -- at most -- five helices."

"Our discovery of a seven-helix coiled coil means rational designs based on protein engineering just got more intricate," adds the study's lead researcher, Dr. Jie Liu, assistant research professor in the Department of Biochemistry at Weill Cornell.

What exactly is protein engineering? As Dr. Lu explains, every day the body uses its genes to encode and express tens of thousands of different proteins that fold together in complex, three-dimensional ways to perform specific functions.

"Understanding, fixing and even reproducing these interrelationships is really the next scientific frontier, with unlimited potential for the health sciences and beyond. Right now, however, we know relatively little about the way proteins work," Dr. Lu says.

One of the few types of protein-protein bonds that scientists thought they understood was the "coiled coil."

Engineering protein match-ups that involve one or two of these helical bonds has not proven too difficult. But as the number of helices rises, the resulting configurations become much more difficult to predict or replicate.

"It's like rolling dice -- the more dice in your hand, the more the possible configurations," Dr. Lu says.

In their current work, the Weill Cornell team observed changes in structural biochemistry of one recombinant protein, a "leucine zipper" called GCN4-pR. In their experiment, they swapped out certain amino acids lying on the protein's helix, allowing the structure to form novel configurations and create a new GCN4 variant they dubbed "GCN4-pAA."

The results were surprising.

"We saw an unexpected level of complexity in this newly engineered coiled coil -- seven helices," Dr. Liu says. "This goes beyond the five-helix coiled coil 'limit' that scientists had heretofore imagined."

The interacting, cross-sectional geometry observed in the seven-helix coiled coil means that accurate, effective protein engineering might be tougher than researchers have anticipated.

Dr. Lu explains: "I really believe that this work shows that our understanding of coiled coil architecture is still incomplete. The coiled coil is actually one of our best-understood structures, and it is already revealing a higher level of subtlety than we ever imagined."

The new finding could help shed light on protein-protein link-ups that trigger disease, however.

"This process, called 'biological sampling,' occurs naturally in cells," Dr. Lu says. "Proteins that should stand on their own sometimes form larger protein complexes that affect the life of cells. In this work, we're using atomic-level structures to better understand how they form complexes."

So, while the existence of a seven-helix coiled coil means protein-engineered drug discovery may be more difficult than we thought, there's a plus side to this research, too.

"A deeper understanding of these protein-protein connections helps us better understand the fundamental biological mechanisms and thereby the roots of disease and -- potentially -- new ways to fight it," Dr. Lu says.

This work was funded by the U.S. National Institutes of Health, the Irma T. Hirschl Trust and the National Science Council of Taiwan.

Co-researchers include Dr. Qi Zheng, Dr. Yiqun Deng, Dr. Chao-Sheng Chen -- all of Weill Cornell Medical College in New York City, and Dr. Neville R. Kallenbach of New York University in New York City.

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