W. M. Keck Foundation funds Berkeley effort to reveal inner workings of cellular machines
First-of-its-kind project will enable key research

by Camille Mojica Rey

Every living cell relies on the carefully orchestrated interactions of proteins to form molecular machines that mediate fundamental processes. The key to understanding how cells work — and, thus, the nature of disease — lies in determining the three-dimensional configuration of the proteins involved. But, because proteins are so small, revealing their structure has been slowed by the difficulty of extracting sufficient amounts of pure, intact proteins from cells and the limitations of available imaging systems.

Now, a new state-of-the-art laboratory at UC Berkeley funded by a $2 million grant from the W.M. Keck Foundation promises to expand the scope of protein-structure discovery. The Keck MacroLab will bring into focus the most elusive structures of all, those of large assemblies that make up molecular machines. The Berkeley project, which brings together seven faculty research programs, will focus on discovering the structural basis of four main processes — copying DNA strands, creating RNA copies of genes, making proteins, and dividing a single cell into two cells. To overcome key experimental limitations, the lab will combine cutting-edge biochemistry, industry-level laboratory automation and the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory (LBNL) to image essential molecular machines.

"Our goal is to solve a major bottleneck in biochemistry," said Tom Alber, principal investigator of the MacroLab and a faculty affiliate in the California Institute for Quantitative Biomedical Research (QB3). The new facility will allow a team of UC Berkeley scientists to characterize efficiently the most difficult structures: the giant assemblies of proteins and nucleic acids that make up molecular machines. These studies will show how machines assemble, communicate and cooperate to do their complex jobs.

"The lab is a great example of a partnership with a visionary foundation to create something that we couldn't accomplish in the public sector, alone," said Alber, who is also professor of biochemistry and molecular biology and a member of LBNL's Physical Biosciences Division.

The lab will allow project researchers to make complexes of proteins that are important in the life of the cell, make large quantities of these proteins, crystallize them, and image them as they interact. The lab will focus on what Alber called "big and fundamental" problems in modern biochemistry: DNA replication, gene regulation, protein synthesis and cell division. "These are things that have to happen in every form of life and we don't understand them nearly as well as we should," he said.

Keck MacroLab, which will be housed in the new Stanley Biosciences and Bioengineering Facility, promises to speed up the discovery of new drugs for treating disease, said Geoff Owen, dean of the biological sciences at Berkeley’s College of Letters & Science. "Once you know the structure of the proteins in those interactions, you can design molecules that regulate, interfere with or otherwise modulate those interactions and, ultimately, change the outcome," Owen said.

The MacroLab will likely serve as a model for other universities interested in increasing the scale of their research capabilities through on-campus collaborative ventures. "Biochemists everywhere are limited by these problems of scale. We hope that what we do here will be replicated elsewhere," Owen said. "This project is going to be extremely important," he predicted.

According to Alber, the secret to the lab's future success will be the integration of methods developed by an interdisciplinary group of Berkeley researchers. "The individuals involved have each invented pieces of the technologies that we are going to use to make a pipeline that can effect a dramatic increase in scale when it comes to isolating and analyzing molecular machines," Alber explained.

A few of the groundbreaking discoveries that will be incorporated include:

• A method worked out by Keck MacroLab director James Berger to overproduce proteins very quickly
• A new way to grow protein crystals using small samples co-invented by Berger
• Methods pioneered by Jamie Cate in determining the structure of intact ribosomes, protein-RNA machines that make proteins in all living things
• Imaging methods developed by Eva Nogales and Robert Tjian to study proteins involved in gene control
• Data analysis automation created by Alber that makes the ALS faster to use

By automating both sample production and analysis, investigators will generate much larger amounts of starting material so that they can study proteins now considered unattainable for proper study. “The scientific problems we face are increasingly large and complex, involving the most rare and complicated protein assemblies. By turning over the human work to robots, we will do more work than any one lab group could do alone,” Alber said.

The pipeline Alber envisions begins at the Keck MacroLab and ends with scientists comparing the inner workings of different molecular machines. “The lab will provide the new front-end of an experimental process that begins with making many more samples quickly and ends with using the ALS shared beamline to discover the structures of some of the cell’s most important molecular machines,” Alber said. “It will be an intellectual center, as well, where researchers working on distinct systems can compare methods and discoveries,” he added. “We will make possible discoveries that are impossible today.”

Keck MacroLab collaborators include: James Berger, professor of biochemistry and molecular biology and member of LBNL’s Physical Biosciences Division; Jamie Cate, an assistant professor of chemistry and of molecular and cell biology and a member of the Physical Biosciences Division at LBNL; Jennifer Doudna, professor of molecular and cell biology and Howard Hughes Investigator; John Kuriyan, professor of molecular and cell biology and Howard Hughes Investigator; Eva Nogales, professor of biochemistry & molecular biology and Howard Hughes Investigator; and Robert Tijan, professor of molecular and cell biology and Howard Hughes Investigator. All MacroLab collaborators listed above are also QB3 faculty affiliates.

Related Links:

Tom Alber’s Lab

ALS at LBNL

QB3