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Protein-Protein Interactions Meeting Part II: Combining Analysis Methods Likely Pays Off

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It pays to combine different methods when analyzing protein networks, in order to reveal their true biological function, researchers said at the recent IBC Life Sciences’ “Protein-Protein Interactions” meeting in Newark, NJ, continuing the theme of variety on the third day of the conference.

Christopher Williams, a researcher at Millennium Pharmaceuticals, noted that “any one technology needs help from the others to generate relevant data.”

At Millennium, Williams uses immunoprecipitation, coupled with mass spectrometry, to analyze protein complexes, and contracts out yeast two hybrid experiments to other parties. Some of the remaining challenges of his approach, he said, include the low throughput of separation techniques such as liquid chromatography or gel electrophoresis, quantification of changes in protein abundance, and sensitive detection of posttranslational modifications. He also said Millennium is interested in antibody and protein arrays to study protein-protein interactions, developing them both in house and evaluating technologies from outside. In both cases, the company is looking for low-cost, highly stable chips with label-free detection, and sensitivity that is at least as good as an ELISA, he said. Millennium has an ongoing relationship with Biacore to develop a multi-spot label-free SPR chip. This, he said, involves two Biacore employees working full-time at Millennium. The system will be commercialized by Biacore.

At Affinium Pharmaceuticals (formerly Integrative Proteomics), researchers apply a different approach to studying protein-protein and protein-ligand interactions, coupling affinity chromatography with mass spectrometry, which requires purified proteins. But apart from finding binding partners for potential protein targets, the company emphasizes structure determination by x-ray crystallography or NMR. The researchers then use these structures, together with functional information, to prioritize the targets, according to Christian Burks, Affinium’s CSO. The company, which has 70 employees and has raised a total of $33 million in funding, is currently recruiting new employees in the areas of medicinal and computational chemistry, assay development, crystallography, and NMR.

Xerion Pharmaceuticals of Martinsried, Germany, utilizes antibody-ligand interactions to probe protein function. Stefan Henning, the company’s director of functional biology, described how scientists knock out protein function using a method called chromophore-assisted laser inactivation (CALI). Researchers attach a dye to a single-chain antibody variable region fragment (scFv) that is displayed on a phage, which then binds to a target protein on the surface or inside of a cell. Laser light then triggers a photochemical reaction in the dye which oxidates — and inactivates — the target protein. Any functional effects can then be assessed by biological assays.

Xerion was originally using CALI to help customers prioritize their drug targets. However, owing to a shift in its business model, the company, which raised € 12.3 in venture capital last month, has recently used its method primarily to find novel drug targets on the surface of cancer cells and to develop therapeutic antibodies against these. Within the last year, it has found seven new targets on cancer cell lines that might be involved in metastasis, Henning said.

— JK

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