Architects often say that “form follows function” to suggest that structures should be designed to fit their intended purposes.
In three recent papers in the Proceedings of the National Academy of Science, Stanford Bioengineering Professor K.C. Huang followed a variation on that theme to make some surprising discoveries about the design principles of bacterial cells -- findings that improve our understanding of the mechanisms behind disease and health.
Cells are the basic structural units of life. They are made out of proteins, molecules that can take on different conformations, or shapes, to perform different tasks.
Scientists have long known that, when it comes to proteins and cells, form and function are intertwined. But how do millions of proteins, each focused on a specific function, work together to create the complex architecture of the cell?
“We know that cells move, change shape and interact with their environments, and that all these processes are driven by the protein machinery inside cells,” Huang said.
The three PNAS papers report on experiments in which more than a dozen Stanford and Princeton researchers sought to understand different molecular and cellular processes within E. coli, the rod-shaped bacterium that can cause food poisoning.
“Our challenge is to look at the cell as a system of interacting proteins, and to simultaneously study these interactions at the molecular and cellular scale, and even down to the level of individual atoms,” Huang explained. “It is only by bridging across these scales from cells to proteins to atoms that we can truly hope to understand the whole cell.”
In one recent PNAS paper Huang’s team examined how two key proteins interact to help cell walls grow. Working with eight co-authors, including Princeton University molecular biologist Zemer Gitai and Stanford PhD candidate Timothy Lee, he studied the proteins MreB and PBP2.
Their experiment involved some basic detective work. The researchers tagged each of these two proteins with fluorescent markers. Using advanced microscopy techniques they tracked these two proteins as they moved throughout the cell.
This approach revealed that cell wall construction involves a sort of purposeful, but highly efficient, chaos.
As Huang explained, the arrival of MreB proteins at certain locales attracts PBP2 proteins as well. But rather than remain at a single site, these proteins perform their functions quickly and then move on to another locale to do the next job, roaming around the cell wherever their services are needed.
“This leads to an incredibly robust process,” said Huang, who wonders whether nanotech engineers can draw inspiration from the way nature uses swarms of simple parts to perform an undirected but efficient self-assembly process.
In the quest to relate form and function, Huang has been seeking to more fully understand what connects the shape of proteins to the different tasks they perform.
“Instead of thinking of proteins as blocks of metal, think of them as pieces of silly putty that can change their shape in response to cues in their environment,” Huang said.
Structural biologists use the term “conformational dynamics” to describe this shape-shifting characteristic. In a second PNAS paper, Huang studied the conformational dynamics of the MreB protein, which shifts between two shapes – best visualized by holding your index finger slightly bent, then straightening it out. What mechanism made bent MreB straighten out?
They answered that question through a computational analysis of the forces that hold the atoms in MreB together.
Each of those interactions is like the push or pull you feel when bringing two magnets together, depending on whether you hold north pole to north pole, or north to south, how far apart and at what angle.
“There are so many possible interactions between the hundreds of thousands of atoms in a protein, and slight changes at any one place can exert a butterfly effect on the entire protein,” Huang explained.
Working with PhD candidate Alexandre Colavin and postdoctoral scholar Jen Hsin, Huang spent several months crunching numbers on the National Science Foundation’s XSEDE supercomputer cluster. Their analysis revealed that removing five atoms -- out of the roughly 200,000 in the protein -- can cause bent MreB to straighten out.
These five atoms are part of adenosine triphosphate, or ATP, a molecule that serves as the energy source for the cell. It also powers the conformational dynamics of proteins such as MreB. The “P” represents a phosphate group: one phosphorus atom bound to four oxygens. When a reaction inside the cell strips off these five atoms, turning ATP into adenosine diphosphate (ADP), bent MreB straightens out.
In a third PNAS paper, Huang’s team brought the cell and protein studies full circle by trying to determine how MreB helps E. coli maintain its cylindrical shape.
“How does a protein read the blueprint and direct construction inside a cell that is 1,000 times bigger than itself?” Huang asked.
His team used experimentation and computer simulation to answer this question. Eight co-authors took part, including Gitai and Joshua Shaevitz from Princeton and Tristan Ursell, a postdoctoral scholar in bioengineering at Stanford.
Experimentally, they induced E. coli cells, which are typically straight, to bend into U-shapes. Advanced imaging techniques allowed them to peer inside these cells to observe what happened in the bent regions.
They observed that MreB proteins swarmed to concave regions, filling these depressions with new wall material, thus making the U-shape more cylindrical. Biophysical computer simulations, which modeled forces and growth across the entire cell, showed that this simple mechanism was sufficient to maintain the E. coli’s rod shape.
In other words, this simple mechanism enabled a protein that is as tiny in comparison to the cell as an ant to a skyscraper to locate – and repair – defects. Or as Huang put it: “Using the local geometry as a cue for growth is sufficient to maintain the global geometry.”
Huang said that a better understand of bacterial growth and form will ultimately help researchers combat disease and promote health, and allow them to bioengineer organisms for medicinal or industrial tasks.
“Peeling back the myriad layers of cellular shape and function has required the development of new tools, both experimental and computational,” Huang said. “Nonetheless, it is comforting to find simple rules that explain something as complex as building an entire cell.”
Huang recently had another paper about cellular processes published in the Proceedings of the National Academy of Science.
Tom Abate is the Associate Director of Communications for Stanford Engineering.