Puzzle of protein complexes in vivo: a present and future challenge for functional proteomics

Abstract

Complete description of the complex network of cellular mechanisms and use of the network to predict the full range of cellular behaviors are major goals of systems biology. A key role in contemporary biology can be played by functional proteomics, which focuses on the elucidation of protein functions and the definition of cellular mechanisms at the molecular level. The attainment of these targets is strictly dependent on the identification of individual proteins within functional complexes in vivo. Isolation of interacting proteins relies on either affinity-based or immunoprecipitation procedures in which the protein bait and its specific partners can be fished out by their specific binding to ligand molecules immobilized on insoluble supports. These approaches led to the final identification of several proteins belonging to distinct complexes endowed with different biological functions. Assignment of each protein to a specific complex constitutes a tremendous problem that can only be partially solved using protein–protein interaction databases and literature information. The development of prefractionation methodologies to separate individual protein complexes while preserving their native interactions might then represent an essential tool for the future of functional proteomics. Prepurification of single complexes can only be pursued under native conditions on the basis of their physicochemical features, such as size, dimension (gel filtration chromatography) and density (gradient ultracentrifugation). Following prefractionation, the complex associated to a specific biological function can be isolated using affinity purification techniques. Functional proteomics approaches able to describe individual proteins belonging to complexes involved in specific cellular functions will have a terrific impact on future systems biology studies.

Keywords::

• affinity purification
• functional proteomics
• gel filtration
• immunoprecipitation
• prefractionation strategies
• systems biology
• ultracentrifugation

Financial & competing interests disclosure

This work was supported in part by grants from the Italian Ministry of Education (MIUR), Prin 2007 and Progetto FIRB RBRN07BMCT, ‘Italian Human ProteomeNet’. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.