Computer Models Explore Nano-Machines

ATP synthase
Rotary motor ATP synthase manufactures ATP for the rest of the cell. Credit: Sun Lab / JHU

“Most molecular motors operate on principles that are very similar to the way the engine in your car works,“ says Sean Sun, an assistant professor in the Department of Mechanical Engineering in the Whiting School of Engineering at Johns Hopkins University and an affiliated faculty member of the Institute for NanoBioTechnology.
“They consist of a flexible protein that performs an action when it burns a fuel molecule.“

But understanding how nano-sized machines function or how they create forces is not always this straightforward. “In any system in biology, 90 percent of it is unknown,“ Sun says.

Sun recently encountered many unknowns while conducting computational research on the biological forces generated during the reproduction of single cell organisms. Sun, doctoral student Ganhul Lan and colleague Charles Wolgemuth of the University of Connecticut, have described how a kind of molecular nanomachine called a Z-ring facilitates bacterial cell division.
The team published their findings in the Proceedings of the National Academies of Science (Oct. 9, 2007). According to report, the Z-ring produces enough force to pinch the rigid cell wall to initiate division and also helps localize the proteins needed to form a new cell wall between the daughter cells. Exactly how this force is generated is still a mystery.

“Our lab works on nanomachines of all different kinds,“ Sun says. “The Z-ring is a protein conglomerate ensemble (and) one of the interesting discoveries about the process is that very little force was required to do the job.“

Sean Sun
Sean Sun. Credit: Will Kirk / JHU

Solutions to the puzzles presented by nanomachines can be found by exploiting the synergy between computational models and experimental observations, he says. Sun also draws upon his prior training in chemistry and physics.

“Biology is making a tremendous transition from an observational science into a quantitative science,“ Sun says. “This is an area where I can really make a contribution“

Computational theories on molecule fueled nanomachines can be tested experimentally in labs like that of INBT’s associate director, Denis Wirtz, professor in the Department of Chemical and Biomoleculuar Engineering. “With Denis, we are looking at many of the biochemical details to see if they match up to the computational models,“ Sun says.

Multidisciplinary collaborations initiated by INBT will shed light on these unknowns, Sun says. “Experiments are crucial in directing where your theories and modeling ought to go…They supply you with parameters. Even if you build equations, there are still unknowns that have never been measured. It is a synergistic process.“

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