Cellular Coordinate System Reveals Secrets of Active Matter

All humans who have ever lived were once each an individual cell, which then divided countless times to produce a body made up of around 10 trillion cells. These cells have busy lives, executing all kinds of dynamic movement: contracting every time we flex a muscle, migrating toward the site of an injury, and rhythmically beating for decades on end.

Cells are an example of active matter. As inanimate matter must burn fuel to move, like airplanes and cars, active matter is similarly animated by its consumption of energy. The basic molecule of cellular energy is adenosine triphosphate (ATP), which catalyzes chemical reactions that enable cellular machinery to work.

Caltech researchers have now developed a bioengineered coordinate system to observe the movement of cellular machinery. The research enables a better understanding of how cells create order out of chaos, such as during embryonic development or in the organized movements of chromosomes that are a prerequisite to faithful cell division.

The work was conducted in the laboratories of Rob Phillips, the Fred and Nancy Morris Professor of Biophysics, Biology, and Physics, and Matt Thomson, Professor of Computational Biology and Heritage Medical Research Institute Investigator. A paper describing the study appears in the journal Proceedings of the National Academy of Sciences.

The basic units of cellular machinery are motors and filaments made of proteins, which act like the muscles and skeleton of the cell. These structures self-assemble, like little protein robots, to enable cells to move. In 2018, former graduate student Tyler Ross (PhD '21) engineered a system of these components that can be controlled by light in a lab setting, enabling researchers to observe and experiment upon their movements. Each experimental system is only the width of a human hair, containing thousands of individual motors and filaments.

In the new work, led by former graduate student Soichi Hirokawa (PhD '23), the team developed additional light patterns that create a grid, or coordinate system, upon the mixture of motors and filaments. To understand this, imagine a sheet of rubber with a grid patterned on it—as the rubber stretches and deforms, the grid does as well. Once a set of regularly spaced squares, the grid's deformation gives a measure of which regions are being stretched or squeezed and by how much. In this way, the team can track the movements of a collection of filaments and motors—they are too small to be seen themselves, but the light-patterned grid, each square about 12-by-12 micrometers, is visible with a microscope.

"The system allows us to observe how these biomolecules reorganize as they collectively form a structure," says Hirokawa. "With it, we can distinguish the processes that contribute to the deformations that we observe on these squares."

This new system enabled the team to measure the competing dynamics of active shrinking and a process that influences cellular self-assembly, called diffusion. Taking a mixture of motors and filaments, the researchers triggered the components to contract inward, like a shrinking circle. But each component naturally still experiences some random movement, or diffusion, jiggling every which way as the whole contracts. The deforming coordinate system enabled the team to watch this competition between active contraction and random diffusion, and characterize it. Interestingly, they found that the more ATP is in the system, the more the molecules randomly diffuse.

"The formation of patterns and structure in biology has to fight against this randomness," says Phillips. "The system is able to organize despite the forces of chaos."

The dynamic coordinate system introduced here could be used in other contexts as well.

"Order is particularly important in processes like embryonic development," says staff scientist and co-author Heun Jin Lee. "An early embryo gastrulates, folding into a tube that ultimately becomes the digestive tract. You could imagine decorating the surface of an embryo with a coordinate system that stretches as the embryo folds."

The paper is titled "Motor-driven microtubule diffusion in a photobleached dynamical coordinate system." In addition to Hirokawa, Lee, Thomson, and Phillips, Caltech co-authors are former graduate student Rachel Banks (PhD '22), graduate student Ana Duarte, and postdoctoral scholar Bibi Najma. Funding was provided by the Maximizing Investigators Research Awards and the Foundational Questions Institute. Matt Thomson is an affiliated faculty member with the Tianqiao and Chrissy Chen Institute for Neuroscience at Caltech.