Completed Cells, Biochemistry & Physiology Genetics & Molecular Biology

Three-dimensional proteomics: Mapping the geometry of large protein assemblies using cross-linking, mass spectrometry, and bioinformatics.

Funder Wellcome Charity-funded
Recipient organisation University of Edinburgh
Funding £1.6M
Period Jun 2009 — May 2014

In plain English

AI plain-English summary

Proteins often work in large, multi-part teams, but scientists struggle to map the physical arrangement of these teams, especially when they are large, fragile, or insoluble. This project aims to turn a technique called 3D proteomics into a reliable, automated tool for doing exactly that. The method works by chemically stitching neighbouring proteins together, then using mass spectrometry to identify which proteins were linked, revealing their spatial geometry. The researchers have already generated unprecedented amounts of this cross-linking data and automated its interpretation. They now plan to build a general platform for analysing protein complexes both in test tubes and inside living cells. As a final test, they will tackle the kinetochore—a massive, dynamic protein assembly that controls chromosome separation during cell division and has resisted all existing structural techniques. If successful, this work will provide a new way to map the architecture of protein complexes that are currently invisible to X-ray crystallography or electron microscopy. This is fundamental science: it will not produce a drug or a diagnostic tomorrow, but understanding how these molecular machines are built is a prerequisite for knowing how they break in disease.

View original technical description
The aim of this project is to understand how structural information on protein complexes can be obtained in a facile and reliable way. We hypothesize that cross-linking, mass spectrometry and bioinformatics (3D proteomics) does provide this information. We propose to demonstrate that 1) 3D proteomics can deliver structural information on protein complexes, 2) 3D proteomics can even deliver structural information on large and insoluble protein assemblies, possibly entire cells and 3) 3D proteomic s can capture dynamic information on protein complexes. We have succeeded in detecting cross-link data by mass spectrometry in unprecedented amounts and in automating the data interpretation. We will expand this initial success into a general platform for the analysis of protein complexes in vitro and in vivo. We will synthesise novel cross-linkers for the purification of cross-linked peptides, further develop our database search software and develop concepts and tools for the visualization of c ross-link data and the integration of cross-link data with the results of other technologies. Ultimately, we will analyze the kinetochore, a large, fragile, insoluble and dynamic protein assembly that is refractory (and likely to remain so) to structural analyses utilizing current technologies.

View the original record at the funder ↗

Researchers

Juri Rappsilber (EPMC Awardee)

Related Research

Grants with similar aims, by meaning.

Developing new mass spectrometry methodologies for the determination of structures of heterogeneous protein complexes
Computational methods to enable construcution of 3D models of protein complexes by integrating mass spectrometry and biochemical data
Mass spectrometry of protein complexes - from networks to structures
An integrative approach for modelling large protein complexes using mass spectrometry-based strategies and computational analyses.
Determination of protein-protein complexes from sparse experimental data

Original classification

Senior Research Fellowship Basic

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