Elution Profile Analysis of SDS-induced Subcomplexes by Quantitative Mass Spectrometry

Abstract

Analyzing the molecular architecture of native multiprotein complexes via biochemical methods has so far been difficult and error prone. Protein complex isolation by affinity purification can define the protein repertoire of a given complex, yet, it remains difficult to gain knowledge of its substructure or modular composition. Here, we introduce SDS concentration gradient induced decomposition of protein complexes coupled to quantitative mass spectrometry and in silico elution profile distance analysis. By applying this new method to a cellular transport module, the IFT/lebercilin complex, we demonstrate its ability to determine modular composition as well as sensitively detect known and novel complex components. We show that the IFT/lebercilin complex can be separated into at least five submodules, the IFT complex A, the IFT complex B, the 14 -3-3 protein complex and the CTLH complex, as well as the dynein light chain complex. Understanding the orchestration and dynamics of cellular function on the molecular level is one of the challenges in biology. It is now clear that cell regulatory decisions are made by molecular switching events in large but highly dynamic, often coalescing, protein complexes (1, 2). Protein complex isolation by affinity purification is a common technique, used for the identification of the protein composition of these molecular machines (3), contributing to the elucidation of spatial and temporal patterns of large protein networks and functional modules within these networks (4). Interaction data derived from different protein complex analyses are the basis for predictions of biological pathways or disease mechanisms concerning those proteins (5). Still, in most cases it is difficult or even impossible to determine how, or even if the copurified proteins assemble as a single module in a cell, limiting the fine-grained description of the complex structure (6, 7). The possibility to integrate module and submodule information in higher order protein networks is extremely valuable for their understanding and opens the route to define pathways of information flow within and between discrete molecular machines. Zooming in on a protein mutated in early childhood blindness, lebercilin, we have previously identified proteins of the intraflagellar transport (IFT) machinery to interact with lebercilin (5). IFT appears as a physical entity driving vesicular trafficking through the connecting cilium that bridges the inner and the outer segment of vertebrate photoreceptors (8). IFT, like many other multiprotein complexes, is an example for a functionally fairly well described molecular machine with yet unknown molecular topology and mechanical properties.To determine composition, as well as protein complex topology of lebercilin and its interaction with IFT components, we developed a novel workflow, which we termed "elution profile analysis of SDS-induced subcomplexes by quantitative From the ‡Division

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