Genomic sequences specify protein sequences, but they don't necessarily clarify how proteins interact. Protein-protein interactions form the basis of many important activities, not onlyn within cells, but in organisms as a whole, including antigen-antibody reactions, enzyme activation and inhibition, cellular signaling, and protein localization. Deciphering these interactions is challenging, in part due to the size and flexibility of many proteins of interest, the wide range of concentrations possible for partners in an interaction, the multiple pathways a given protein may affect, and the difficulties in predicting binding sites from structures. Approaches that are being employed include inhibiting specific protein-protein interactions by designing molecules that are “larger than the small molecules chemists love,” according to Samuel H. Gellman, Professor, Department of Chemistry, University of Wisconsin, Madison, WI, and engineering new proteins containing interactive domains from other proteins and mining databases for potential interactions that can be confirmed experimentally.
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The approach taken by Gellman and his group is to design inhibitors of therapeutically relevant protein interactions that he calls “foldamers,” polymers with a strong tendency to adopt a specific, well-defined, compact conformation. This is useful where small molecules won't work, such as when the contact surface between the interacting proteins is large. The use of foldamers “embodies molecular design the way nature builds its most powerful molecules, nucleic acids and proteins,” which are polymeric, Gellman notes. His group synthesizes building blocks of oligomers that fold into set shapes and display particular side chains and uses them to probe cellular functions By using β-amino acids, which are not recognized by natural cellular proteases, and incorporating small ring structures, they have been able to synthesize short oligomers (β-pep-tides) that form stable helical strucures in an aqueous environment. These helical β-peptides can be used as scaffolds to display functional groups mimicking protein surfaces and structures and to replace one partner in an interactive pair. Two areas of research for Gellman's group concern members of the Bcl-2 family, which are involved in apoptosis (programmed cell death), and proteins participating in the membrane fusion steps that allow cytomegalovirus, a human pathogen in the herpesvirus family, to enter and infect cells.
Enough to Go AroundAlthough, like Gellman, Tony Pawson, Senior Investigator, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada, recognizes the therapeutic potential of understanding protein-protein interactions in human cells, he deems examining how these cells are organized interesting in their own right. His lab focuses on the role of particular protein domains in protein-protein interactions. Now that the human genome is sequenced, he notes, “one of the really interesting, obvious issues is how do so few genes specify the complicated behaviors that cells display? It seems like there is very little to go around, so how do you get such huge biological complexity with limited information?” He suggests that “everything must be combinatorial.” That is, if each gene and its product only did one thing, there wouldn't be enough genes and proteins to do everything cells are capable of in all tissues and organs. Part of the answer lies in posttranslational modifications (e.g., phosphorylation, ubiquitination, acetylation, and SUMOylation), allowing a given protein to display different modifications for different cellular activities, states, or tissues. This allows a relatively simple initial repertoire of proteins or their component domains to expand into more complex, cell-specific interactions.
With a long-term goal of understanding how proteins form large networks, Pawson acknowledges that they are just starting to scratch the surface. Some of the technologic advances he sees as furthering the understanding of protein-protein interactions are chip-based approaches and using biological mass spectrometry, which he calls a “fantastic tool to identify proteins and posttranslational modifications that one couldn't imagine a few years ago.” A high-throughput tool called LUMIER, developed by a colleague, Jeff L. Wrana, Senior Scientists of Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, and a professor at the University of Toronto, is a mass spectroscopic-based approach that allows one to take a given protein and look at all of its binding partners. Pawson likens using it to being able to perform yeast two hybrid-like experiments in mammalian cells.
