Bioengineering

Meeting of the minds: Student finds ideal setting for protein research
As an undergraduate at the University of Utah, Nathan Lassig imagined the exact kind of research he wanted to do as a doctoral student. He wanted to isolate the manufacturing machinery of cells and harness it to engineer proteins. The problem was finding somewhere to do it. The lab of Stanford bioengineering and chemical engineering Professor Jim Swartz was the only place with that same vision.

“I searched for a long time all over the country to find a lab that was doing this,” says Lassig. “I didn’t even dream it would be this close to what I wanted to do.”

But Lassig came to Stanford in 2004 as a bioengineering graduate student supported by a School of Engineering fellowship. He began his research in June 2005. The stage is set for Lassig and Swartz to make important discoveries about how people can join nature in making beneficial proteins for the body. A potential application of Lassig’s research, for example, is building scaffolds of protein filaments to grow new tissues for patients who need them. Making such protein filaments could also lead to advances in nanotechnology and materials.

Custom proteins
Lassig likes to quip that proteins are protean, in that they are versatile enough to carry out a wide variety of functions in the body. Some proteins are the building blocks of muscle, or compose the fibrous framework of bone. Other proteins, principally enzymes, facilitate vital biochemical reactions. Still others bear signals. Insulin, for example, signals cells to take up sugar. Novel proteins could be engineered to do anything along these lines. There are thousands of proteins in nature and thousands more that engineers could make to meet specific needs.

Cells are naturally programmed by DNA to manufacture specific proteins and they do their jobs well, but they aren’t necessarily good contract workers. In other words, cells are difficult for researchers to use for making custom proteins because they don’t always tolerate the changes a researcher needs to impose to make a specific product.

A specialty of Swartz’s lab — the approach that Lassig was looking for — is to extract the protein-making machinery from cells into a “cell-free” environment that researchers can manipulate more freely. “I don’t want to worry about the needs of the cell that go against what we want to accomplish,” Lassig says. “If you change something then you might disrupt the cell.”

Perfected cell-free techniques would also allow researchers to make novel proteins using artificial amino acids. Working with a cell-free environment they could also specify the sequence, rate, and quantity of proteins produced in a batch. A focus of Swartz’s group is to perfect such techniques. That would make it easier for bioengineers to generate proteins to address all kinds of biological and chemical tasks, generating medical therapies, environmentally beneficial substances, and even new materials.

Weaving tissues
Lassig has long had an interest in tissue engineering, going back to his undergraduate days. Now he is in the first stages of research that, if successful, would go a long way toward fulfilling that ambition.

Using the protein-making components from cells of a harmless E.coli bacteria strain, Lassig is attempting to manufacture three proteins he’s selected to combine into filaments with desirable properties. The filaments, for example, should be rigid enough to support the tissue grown on them and Lassig should be able to control their length.

A key goal is that the proteins will assemble themselves into filaments — without Lassig having to combine them manually — based on their inherent propensity to bond. The two main constituent proteins of the filaments might form a pair, with different shapes on either end like a rail car. Each pair, or “heterodimer” would connect in series to another, forming the filament. To ensure the filament chains don’t close on themselves in a big loop, Lassig would plug up one end of the first pair.

The third protein comes into the picture to satisfy another requirement: Lassig wants the process to yield a small number of long filaments rather than a large number of short ones. A “linking” protein must be designed to exert a tension that draws proteins newly added to the mix to filaments that are already forming, thereby discouraging the formation of new filaments.

For each protein and the filaments they form, another key requirement is that their crystalline structures be well known. With that information, Lassig would be able better predict how the filaments could be modified for different uses.

Both in advancing cell-free protein manufacturing and also in making useful protein filaments, Lassig and Swartz have plenty of work to do. But Lassig, who comes across as a soft-spoken and a little reticent, nevertheless brings the eagerness and enthusiasm of a student who once wondered whether he’d even get the chance to do such a project. It was not enough for Lassig to find Swartz’s lab, for example. Lassig’s fellowship proved important in supporting him while he and Swartz sought grant funding for the nascent research.

At last the latex gloves and lab coats are on and Lassig’s project is underway. “Proteins are likely to be the most versatile approach to self-assembly of structures,” Lassig says. “Cell-free methods have a good chance to be the best approach to making different proteins.”

October 2005