A Census of Human Soluble Protein Complexes

Abstract

SUMMARY Cellular processes often depend on stable physical associations between proteins. Despite recent progress, knowledge of the composition of human protein complexes remains limited. To close this gap, we applied an integrative global proteomic profiling approach, based on chromatographic separation of cultured human cell extracts into more than one thousand biochemical fractions which were subsequently analyzed by quantitative tandem mass spectrometry, to systematically identify a network of 13,993 high-confidence physical interactions among 3,006 stably-associated soluble human proteins. Most of the 622 putative protein complexes we report are linked to core biological processes, and encompass both candidate disease genes and unnanotated proteins to inform on mechanism. Strikingly, whereas larger multi-protein assemblies tend to be more extensively annotated and evolutionarily conserved, human protein complexes with 5 or fewer subunits are far more likely to be functionally un-annotated or restricted to vertebrates, suggesting more recent functional innovations.

Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes

“…Apart from widely studied model organisms such as yeast [1][2][3][4][5][6][7], fruit fly [8,9] and worm [10], it is now possible to predict complexes from more sophisticated organisms including human [15]. This has provided new opportunities to study complexes under different contexts and across species, thus tracing the functional and evolutionary conservation of complexes.…”

“…Among the interesting observations is that many human complexes are ancient and slowly evolving, with roughly a quarter of the human complexes overlapping with those from lower-order organisms [15]. This has inspired several studies to look at the evolutionary conservation of complexes between human and lower-order organisms.…”

“…Beginning from classical methods by Spirin & Mirny [11] and Bader & Hogue [12] that work primarily by clustering the network of protein interactions (PPI network), computational methods have come a long way, and current methods integrate diverse information with PPI networks to predict complexes. These methods have been tested extensively on data from model organisms [13,14], and are currently being extended to identify and catalogue complexes from less extensively mapped organisms including Homo sapiens [15].…”

Separation of intact proteins by using polyhedral oligomeric silsesquioxane based hybrid monolithic capillary columns

“…In order to improve the performance of proteome analysis, it is essential to develop new liquid chromatography (LC) technologies with high separation capability and throughput. So far, a wide variety of liquid chromatography methods have been developed to reduce the complexity of the intact protein samples, such as ion exchange chromatography (IEC) [8], hydrophilic interaction chromatography (HILIC) [9], reversed-phase liquid chromatography (RPLC) [10] and so on. Among them, RPLC is the most popular one due to its high separation efficiency and compatibility to the MS detection.…”

Structural and evolutionary versatility in protein complexes with uneven stoichiometry

“…Given that protein complexes are essential to most biological processes, there is a clear need to understand the principles by which assembly occurs and quaternary structure is organized. Although proteomic analyses have provided tremendous insights into the subunit compositions of protein complexes [1][2][3] , most of the deep insight into protein complex assembly and quaternary structure has come from detailed structural investigations. We now have experimental data on the assembly, structure, dynamics and function of a wide range of protein complexes, ranging from small complexes such as haemoglobin 4,5 to large macromolecular machines such as the proteasome [6][7][8] .…”