Exploring the ‘Dark Matter’ of the Cell

Tom Maresca
Tom Maresca

There is a little-understood realm inside cells that cell biologist Tom Maresca likes to think of as the cell’s dark matter, something like the largely unknown stuff that is so abundant in space.

Maresca recently received a four-year, $1.3 million grant renewal from the National Institute of General Medical Sciences to use specialized tools to learn more about this less-studied inner universe of the cell.

“It’s a pretty good metaphor,” he says. “We know there’s a lot of it out there, but it’s difficult to study and defining its functions inside cells is complicated.”

He explains that a foundational aspect of how scientists think about biology is called the structure-function paradigm, referring to how many proteins adopt specific and highly reproducible folded shapes that allow them to carry out their functions. For these, shape and function are inextricably linked. “These would be analogous to regular matter and they can be studied with conventional biochemical methods and techniques like X-ray crystallography and cryo-electron microscopy,” Maresca says.

“But there are also many proteins that are predicted to have no specific structure, and they’re not as easy to study as well-folded proteins. They’re called intrinsically disordered proteins, which means they are unstructured,” he adds.

Sometimes referred to as the Dark Proteome, these shapeless proteins “appear to be very abundant, we just don’t know much about them. There’s been tremendous progress in understanding structure-function; now we hope to make progress in this other important area of how unstructured proteins function.”

For the new grant, Maresca and colleagues will collaborate with biophysicist Nathan Derr at Smith College to focus on unstructured proteins in an essential structure called the kinetochore. It ensures that chromosomes are evenly split between cells when they divide. Failure to achieve this, Maresca explains, leads to cells acquiring an incorrect number of chromosomes, which is known as aneuploidy ­– a condition that causes miscarriage, genetic disorders, tumorigenesis and possibly cancer metastasis. The long-term goal is to identify basic cell processes that can be targeted by therapies to control aneuploidy.

“We are going to be using some exciting methods to look at these things,” Maresca says of their planned multi-pronged approach. Force sensors inserted into kinetochores in Maresca’s lab measure the amount of force being applied to them during cell division. Derr uses techniques on single molecules, pulling on them “to see how much they extend and whether pulling on them changes their ability to bind to other proteins,” Maresca explains.

The kinetochore is a particularly interesting place to study these proteins, he adds, because there are many, very large, disordered proteins in it. An added layer of complexity is that disordered proteins are very likely subjected to forces that alter their properties in interesting ways, he notes.

“Through evolution, what’s been conserved are these really large proteins, and we don’t know why. But we suspect their unstructured nature and the fact that they can adopt a range of possible conformations and lengths in response to forces is important. Somehow the very large, unstructured nature of these proteins is essential for their function, but we don’t understand how yet.”