Barrel structure in globular proteins may transport small molecules

The ability of proteins to guide small molecules to reaction sites and across membranes is essential to many metabolic pathways, but the process is not well understood. Now, scientists at the University of Illinois at Urbana-Champaign have shown that a globular protein with a barrel structure can direct small molecules in much the same fashion as a membrane protein.

Chemistry professor Zaida Luthey-Schulten, graduate student Rommie Amaro, and Emad Tajkhorshid, assistant director of physics research at the university’s Beckman Institute for Advanced Science and Technology, used molecular dynamics simulations to study the movement of ammonia during the biosynthesis of the amino acid histidine. A paper describing the results is to be published the week of June 9 in the Online Early Edition of the Proceedings of the National Academy of Sciences. The print version will appear at a later date.

Most living organisms are composed of a set of 20 amino acids, the so-called “building blocks of life.” Each of these amino acids is produced through what can be thought of as a biological assembly line. Starting with a small part, subsequent parts are added or removed by enzymes until the final compound is formed. These final compounds become the major components of proteins and tissues.

For humans, the 20 amino acids can be divided into two groups: Eleven are made by the human body and are called “nonessential”; the other nine are not made by the body and are called “essential.” Despite their names, all 20 amino acids are crucial to human health. One of the main reasons nutritionists advise people to eat balanced diets is because the nine essential amino acids must be ingested and are found in different foods.

Histidine is one of the nine essential amino acids. Because histidine is a critical component of nearly all living systems, understanding how it is made is of great interest. Histidine’s biological assembly line consists of nine steps. Of special interest is the fifth step, where an event called substrate channeling may occur.

“Imagine that you need to move an object from one point to another, but there is a mountain standing in the way,” Amaro said. “You could drive over the mountain, you could drive around it, or you could make a tunnel and drive through it. The tunneling option, referred to as substrate channeling in proteins, is what appears to be happening in this fifth step.”

Although substrate channeling is a recurring theme in biological organisms, “this is the first time this particular enzyme — a so-called alpha-beta barrel — has been suggested to use its barrel structure as this type of channel,” Amaro said.

In bacterial cells, the fifth step of histidine synthesis begins when two proteins (hisH and hisF) come together. Once the proteins dock, a reaction occurs at the “active site” of hisH, releasing a molecule of ammonia. Studies have suggested that this ammonia molecule then diffuses across the interface and enters the hisF protein.

“This protein looks like an empty barrel; it has a narrow channel running down the center,” Luthey-Schulten said. “The ammonia enters the channel, travels through it, and is then used in another reaction that takes place at the opposite end.”

Using molecular dynamics simulations developed in the Theoretical and Computational Biophysics group at the Beckman Institute, and in conjunction with the National Center for Supercomputing Applications, the researchers were able to simulate this protein function.

“We applied a force to ammonia to pull it through the channel of the hisF protein and then watched what happened,” Luthey-Schulten said. “Our studies show that it is indeed possible — even energetically favorable — for ammonia to use the barrel as a channel to undergo protected and directed travel from one active site to another.”

Another interesting aspect of the system is that there appears to be a “gate” at the mouth of the barrel. “In all of the available crystal structures, the gate appears to be closed,” Amaro said. “When the gate is closed, it is nearly impossible for the ammonia molecule to pass through. Therefore, the reaction — and more importantly, the synthesis of histidine — can happen only when the gate opens.”

The exact mechanism of the gate opening is not known, Luthey-Schulten said. “We modeled one possible open-gate configuration and found that the energy required for the ammonia to pass into the barrel was much more reasonable.”

The simulations suggest that globular proteins, like membrane proteins, can exploit their structure to transport small molecules.

“This is an excellent example of channeling between two catalytic enzymatic sites,” Tajkhorshid said. “Generating the ammonia molecule and then delivering it directly to the reaction site means it won’t get lost in solution. This is a very efficient way of increasing the rate of a chemical reaction.”

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The National Science Foundation funded the work.