Creating more realistic models of reactions inside the cell

Microscopic interactions inside cells underlie the basic functions of complex processes occurring in an organism. For this reason, the cell is considered the functional unit of life. Almost everything that happens inside the cell boils down to reactions between molecules, controlling hundreds of specific cellular functions, such as secretion of molecules, cell movement, or differentiation into other cell types.

If we could miniaturize ourselves and travel inside a cell, we would discover that interactions between molecules occur randomly. We would also find that the interior of a cell is a crowded jungle of molecules. Interactions occur because molecules are constantly diffusing and colliding with the surrounding jungle of other molecules. However, the crowded jungle of molecules diminishes the probability of encountering specific molecules required for reactions.

University of Michigan scientists developed a computer simulation algorithm to model biochemical reactions under conditions more realistic to those found in the cell. This U-M research appears as a cover story in the March 21 issue of “Physical Chemistry Chemical Physics”.

“Our algorithm may help lay the groundwork to study reactions inside cells”, says Márcio Mourão, Ph.D., a co-author of this research.

“Modeling the reaction dynamics inside cells will be invaluable for understanding how interactions between different biological molecules make a cell function,” says the lead author, Santiago Schnell, Ph.D., associate professor of Molecular and Integrative Physiology at the U-M Medical School.

U-M scientists use a discrete model of molecules interacting in a regular grid, which is similar to concepts behind many popular video games.

Despite its simplicity, the computational algorithm simulates realistic conditions of cellular environment. The research team says “Our simulation approach will have considerable impact in understanding the role of new drug treatments for diseases”.