Do proteins in cells make computations?

Within the molecular machinery of living cells, information of a chemical nature flows almost as freely as the oxygen that facilitates life. Biomolecules signal each other, exchanging, updating, and using chemical data to keep the cell healthy and functioning.

"In principle, any protein that transforms an input signal into an output signal could act as a computational, or information-carrying, element," says Dennis Bray, a chemist at the University of Cambridge. For instance, "an enzyme in a biochemical pathway 'reads' the concentration of its substrate and produces a corresponding level of product."

From the viewpoint of information processing, every cell contains unique "biochemical circuits." These perform various simple computational tasks, among them amplifying, integrating, and storing information, he maintains in the July 27 Nature.

"In unicellular organisms, protein-based circuits act in place of a nervous system to control behavior," Bray states. "In the larger and more complicated cells of plants and animals, many thousands of proteins functionally connected to each other carry information from the plasma membrane to the genome."

A cell's internal and external environment affect the concentration and activities of those many macromolecules, giving rise to what Bray calls a "memory trace." As with a computer's random-access memory, which serves as temporary storage for transient information, a cell's proteins maintain a record of its ever-changing surroundings.

"Because of their high degree of interconnection, systems of interacting proteins act as neural network [computers], trained by evolution to respond appropriately to patterns of extracellular stimuli," Bray says.

Communication within such chemical networks relies on the diffusion and concentration of information-bearing molecules, a characteristic that gives them "unique features not found in conventional computer-based neural networks," he stresses.

"This area of research is very intriguing," says John Ross, a chemist at Stanford University who has measured the capacities of biomolecules to serve as logic elements. Chemical agents can serve as information processors, Ross contends, adding that by bringing analytic approaches from computer science to bear on biochemical reactions, a researcher can shed light on the flow of information within living systems.

As far back as 1943, neurophysiologists working in the field of artificial intelligence showed that a few idealized nerve cells, hooked together as feedback circuits, could perform logical processes and make simple calculations. Though scientists scoffed at the simplicity of those systems, even skeptics acknowledged that, in principle, neurons in the central nervous system could behave in similar ways.

"As with neurons, so with proteins," Bray argues. "Protein molecules are, in principle, able to perform a variety of logical or computational

operations."

Serving as logic elements, proteins provide cells with tool kits for building circuits, he adds. However, unlike silicon-based computers, cells make calculations purely for their own maintenance and survival by monitoring and responding to environmental changes.

"Many proteins in a living cell are used to build macromolecular 

structures, produce movement, degrade unwanted molecules, or synthesize specific chemical species," Bray says. "The molecular interactions that regulate chemical catalysis and direct motion merge seamlessly with those involved in the transmission of information."

As scientists look to chemical systems for computing potential, Bray concludes, nature's own methods of regulating cell functions may give insight into how molecules process information.