Recent advances in high-throughput DNA sequencing have led to an explosion of the available genomic data from model organisms. Genomes of entire organisms can now be fully sequenced in a matter of weeks. There are well over one million gene entries in the NCBI database, encoding comparable numbers of proteins and their homologs and variants. These data provide us with a blueprint – describing a cell’s potential. What cells do however, is conferred, not by a static picture or blueprint, but by the dynamic interactions of the players defined by that blueprint. Fundamentally, this is the essence of biology that gives rise to the emergent properties of life. Current technologies are not suitable to reveal dynamic interactions between macromolecules at sufficient scale, with sufficient reliability or with sufficient sensitivity to keep pace with the genomic revolution brought about by sequencing technologies. At current pace, it will take us thousands of years to annotate the human proteome with respect to function and dynamic interactions. Thus, there is a desperate need for technologies that can reveal the cellular interactome, not simply to annotate function, or reveal possible (high affinity) interactions, but to illuminate the actual dynamic interplay of the macromolecular characters in cells that define life. We therefore propose innovative and dramatically new approaches to the isolation, detection and analysis of macromolecular complexes that will enable scientists to realize the full potential of the revolution brought about by genomics, interdisciplinary research, and proteomics technologies.

What form must this revolution take?

Arguably, a revolution in proteomics has already begun. Several high-throughput proteomics studies on model organisms have been published by consortia and specialized centers. Drugs companies are using high-throughput proteomic screening approaches to screen for new drugs; the anticancer drug Gleevec, an inhibitor of the oncogenic Bcr-Abl tyrosine kinase, was developed by Novartis Pharmaceuticals using such approaches. However, it is evident that the true revolution in genomics occurred when both the high-throughput output (sequence databases) and high-throughput methodologies (cloning, PCR, rapid DNA sequencing, microarrays) were made available to the whole scientific community. Thus, consortia projects are not enough – routine high-throughput proteomics and interactomics methodologies must be developed and made widely available. Like genomics, proteomics and interactomics methodologies must be put within the reach of all researchers.

What kinds of methodologies are needed?

Let us take the phenomenal improvements seen in the last decade or so of cellular imaging as a comparison. By the end of the 1970s, many considered microscopy – meaning electron microscopy and light microscopy – to have reached their performance limitations. However, by the 1980s, it was becoming clear this was not the case, and from the 1990s up to the present day, microscopic imaging has been in the process of a revolution. The microscopy revolution has included the addition of occasional new platforms (atomic force microscopy), but has in fact occurred mainly by building on existing platforms (the light and electron microscope). Established principles of physics and materials technology were applied together in new ways to these existing platforms (e.g. the field emission gun, cryogenic preservation of electron microscope samples, low-dose imaging, and tomographic reconstruction for electron microscopy; fluorescence imaging, confocal microscopy, and deconvolution microscopy for light microscopy). These advances overcame traditional bottlenecks and limitations (throughput, speed, signal-to-noise, out-of-focus sample interference, resolution). Each addition of new technology individually gave either incremental or large steps; but together, light microscopy and electron microscopy have been taken to whole new levels, the former now imaging the dynamic movement of individual molecules in the living cell, the latter now beginning to bridge the structural resolution gap between X-ray crystallographic studies on individual macromolecules, and the assemblies that these macromolecules form.

Similarly, we envision that revolutions in proteomics and interactomics will build on existing platforms (such as affinity isolation of macromolecular complexes, mass spectrometry, microarrays). However, by adding new technologies to address bottlenecks and limitations to the current techniques (throughput, speed, signal-to-noise, data integration), these technologies will bring proteomic and interactomic studies to a whole new level: the ability to form dynamic pictures of how macromolecular assemblies form and function in the living cell.

NCDIR Team

The National Center for Dynamic Interactome Research couples together an established mass spectrometry resource, a cell biology / protein chemistry laboratory, a high-throughput systems biology resource, and a computational biology center. The team which oversees the various technology cores in this center is made of acknowledged experts in their respective fields. Thus, the Cell Biology and Biochemistry Core is supervised by Michael Rout, who is a pioneer in subcellular fractionation and the elucidation of macromolecular structures through the affinity purification of proteins. In particular, he is most noted for his studies on the nuclear pore complex and yeast spindle organizer. The Macromolecular Analysis Core is divided into two subsections: a Mass Spectrometry Core Subsection overseen by Brian Chait, and a Microarray Core Subsection overseen by John Aitchison. Brian Chait is a leader in biological mass spectrometry, having designed and constructed many new mass spectrometers (18 U.S. patents) and developed numerous groundbreaking mass spectrometry – based techniques for the identification, characterization and quantitation of macromolecules. John Aitchison is a founding member of the Institute for Systems Biology where he exploits the tools of systems biology for the study the cell biology, organelle biogenesis and nuclear transport. He is co-inventor of genomic tagging and isolation procedures, which lie at the heart of this proposal and is a leader in the fields of yeast genetics, molecular biology, and microarray technologies. Andrej Sali, who will direct the Bioinformatics Core, is one of the pre-eminent figures in computational structural biology. His work is focused on using computation, grounded in the laws of physics and evolution, to study the structure and function of proteins, leading to structure-based functional annotation of proteins and macromolecular complexes. His structure modeling programs are widely used by the scientific community.

For more detailed information on the specific research please visit our research section.

Contact Information

PRINCIPAL INVESTIGATOR:
Michael Rout,
Associate Professor