Biologist Trying To Crack Communication Code Of Proteins

The Bowling Green State University biologist wants to crack the communication code of proteins, especially the ones whose "talking" aids and abets disease.

"Proteins interact; they 'talk' to each other," the associate professor says. "It's how they know what to do, and it's how most of the things that need to happen for living organisms get done."

Over the past three years he has received $300,000 in funding from the National Science Foundation for his research.

What talking proteins have to do with infectious disease is a story that unfolds in the submicroscopic world of molecular biology. It starts with bacteria, which are cloaked by an outer membrane--a defensive barrier against the harsh elements of their environment, whether toxins in nature or the protective antibodies of an infected host. Specific proteins interact to support this shield, and knowing how they communicate would provide a key to disabling it, Larsen says.

Once communication questions are answered, a goal is to develop drugs to break the barrier, rendering the bacteria more susceptible to the human body's natural defenses--antibodies--as well as certain antibiotics, he points out.

While keeping potential dangers out, the outer membrane must also be porous enough to allow nutrients in, he continues. As an analogy, he cites a house with a yard and a chain-link fence that "keeps the dogs out of the roses but lets the butterflies through."

A short distance separates the outer membrane and the rest of the organism. How the bacteria maintain their barrier when it's physically removed from the rest of the cell, and thus separated from its energy source, is where his interest lies.

"The barrier is not self-sustaining, so the bacteria must export energy to it," says Larsen, referring to protein systems that take cellular energy and use it to support the outer membrane. "It's kind of like getting oil from the Middle East."

Proteins do all the business of cells, including energy transfer, which a couple of different systems handle, according to Larsen. The TonB system, which controls certain "gates" in the outer membrane, is a good model for resolving questions of how a protein recognizes and communicates with others with whom it's exchanging energy, he says. A similar system, called the Tol system, is important in maintaining the defensive barrier, although which proteins it delivers energy to as part of that process isn't known.

Finding that answer is a long-term objective, he adds, saying it could help lead to the development of a drug that could break the barrier.

Some drugs already target the outer defenses of bacteria. Perhaps best known is penicillin, one of several existing antibiotics that successfully target specific structures required for the barrier function to work, Larsen notes. The outer membrane is stabilized by a grid of sugar polymers, and penicillin wrecks the grid, making the cells susceptible to a body's natural defenses.

Disrupting energy flow--knocking out the TonB and Tol systems--would provide another powerful weapon against disease-causing bacteria, he says, but researchers must first understand how the two systems work. They are similar enough that they have some relatively interchangeable parts, but they don't swap perfectly. He compares the situation to two people speaking different dialects of the same language--"not everything makes total sense." But the TonB-Tol "cross talk" does provide a tool for mixing and matching parts of the systems and asking what's important and what isn't.

"To begin understanding how proteins talk, we first made random mutations--we broke things and then asked what happened," Larsen says. "That strategy worked well and allowed us to identify the key 'words.' Now we want to know what the 'words' mean, and we are starting by asking what happens when we mix the 'dialects.'

"It's genetic tinker toys," and an area, he adds, in which BGSU doctoral student Kerry Brinkman is "breaking new ground."

Larsen and his graduate assistants do their work with E. coli bacteria, which he calls "the world's best Lego set" and a genetic model for 60 years, on a par with rodents in other research areas. The problem, however, is that laboratory E. coli are the "98-pound weaklings in the real world," not offering barriers as robust as other bacteria maintain outside the lab, he says.

So he has begun studying the type of bacteria that is the leading cause of shellfish poisoning in the United States. It lives, he notes, in two "incredibly different environments"--estuaries of the Gulf of Mexico and Chesapeake Bay, and the human intestinal tract. That means the types of proteins in its outer membrane must change to reflect the environment, giving researchers a "thread you can pull," he says.

Living in and adapting to different environments is "part of who they are," but also, Larsen hopes, an avenue to additional funding for his research of the bacteria, which he calls a "little brother" to the organism that causes cholera.

He has received funding from the BGSU Faculty Research Council to follow up on a finding by master's degree student Cari Smerk that a protein in the Tol system is pirated by certain viruses. "Viruses are con artists, and this one has gotten the Tol system's PIN number, so we have begun asking what the virus proteins are telling the Tol system to convince it to work for them," Larsen says. "We actually know very little about how most viruses work; this is going to tell us something interesting."