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At Nashville Proteomics Conference, Systems Biology Meets the Proteome Blues

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Many roads lead to the networks of systems biology, and last week’s meeting “Proteomics: The Next Grand Biological Challenge” at Vanderbilt University in Nashville provided a glimpse into how such a roadmap might be established. In three days of talks and workshops led by academics, and attended by about 240 participants, it became clear that proteomics is more than just mass spectrometry and parts lists, and that studying the function of proteins will rely on a variety of approaches.

In fact, these approaches often complement each other, as illustrated by examples from computational biology and x-ray crystallography to mass spectrometry and high-throughput biochemistry. Systems biology, as outlined by Leroy Hood in his keynote address, is the ultimate goal, but to understand how the parts of biology work together will require scientists from different backgrounds “working together at a level that they have maybe never done before,” said Richard Caprioli from Vanderbilt in his concluding remarks.

In his talk earlier in the meeting, Caprioli presented a use of MALDI mass spectrometry with potential clinical and drug discovery applications: as an imaging technique to visualize the distribution of proteins or drugs in tissue sections. Like the pixels in a digital photograph, a MALDI laser scans different spots on the tissue and records a spectrum of the masses of proteins or the drugs present, typically around 500 proteins. Put together, these spots can yield a complete picture for each of these molecules. However, the method is geared towards proteins below 50 kDa, and Caprioli and his colleagues are still working on improving the current resolution of 30-50 microns, by building a more focused laser and decreasing the matrix droplet size. They are also trying to record more proteins from each sample, including membrane proteins, and are developing software for acquiring and processing the data in collaboration with Applied Biosystems. The technology could eventually complement traditional histology, as well as gene expression studies and LC-MS from tissue homogenates, Caprioli said.

Several speakers pointed out that most of the recently published large protein interaction datasets are incomplete. Judging by the number of presentations, determining the composition of individual protein complexes by mass spectrometry remains an important way to understand the function of unknown proteins and discover new functions for those already known.

Don Hunt from the University of Virginia said he had identified 28 components of a protein complex that assembles ribosomes in yeast, results that are about to be published in Nature.

Andrew Link from Vanderbilt University impressed attendees with his complete study of the TFIID transcription complex in yeast, pulling down each of the 15 subunits with a polyclonal antibody and studying the associated proteins. This work will be published in the journal Molecular and Cellular Biology later this summer, he said.

Melissa Jurica from Brandeis University presented her recent characterization of the human spliceosome, which involved tandem mass spectrometry.

Many participants eagerly awaited two talks on protein chips, as this appears to be the up-and-coming proteomics technology. Gavin MacBeath from Harvard University has developed an array format combining glass slides and 384-well plates that allows the study of protein-protein interactions and their disruption by small molecules. Grace Bio-Labs, he said, is in the process of licensing the technology. He also presented data from an antibody array using two differentially labeled secondary antibodies to measure both the relative expression levels and the phosphorylation status of proteins.

Mike Snyder from Yale University talked about his “version 1.0” yeast proteome chip published in Science last fall, but said he was working on a more complete 2.0 version, which will include C-terminally tagged yeast proteins he is developing in collaboration with Erik Phizicky at the University of Rochester. In the meantime, he has increased the number of screens for interactions with proteins, lipids, small molecules, and for posttranslational modifications, and has used the proteome chips to perform kinase assays. Last year, Snyder co-founded a company, Protometrix, to commercialize the technology.

Looking even farther ahead, two speakers explored how to engineer protein function with the help of computational biology. Steve Mayo from the California Institute of Technology, for example, talked about in vitro protein recombination, where fragments of related proteins are reshuffled to yield a chimera with an altered function. Based on interactions between amino acid residues, he calculated in advance the disruption caused by swapping different parts or schemas between two specific proteins and found a correlation between the disruption score and the function of the chimera. His results will be published soon in Nature Structural Biology, he said, and the approach could be used to recombine proteins from libraries of randomized building blocks.

Functions of novel enzymes are frequently misannotated in the database because structural homology does not always correlate with function. Patricia Babbitt from the University of California in San Francisco spoke about a possible solution: correlating structural superfamilies of enzymes with a common step in the chemical reactions they catalyze. Apart from correcting misannotations, this approach could be used to correctly infer the function of novel proteins, as well as in protein engineering, she said. In a collaboration with Maxygen, she has taken advantage of the conserved chemistry across a superfamily to convert one enzyme activity into another by making a small number of mutations. She is also working on a database that will integrate enzymatic functional information with structural data.

Lastly, a meeting in country music capital Nashville would not be complete without a singers’ night. Featuring the unexpected musical talents of David Friedman, Phil Hieter, Eric Phizicky and Mike Snyder, the “Proteome Blues” showed that scientists can interact not only when writing papers, but also when composing lyrics. Lamenting the lack of funding, Nature rejections, and dreaming about a trip to Stockholm, the four speakers’ ended their rendition on a blue note, yet high in spirits.

— JK

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