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Five ways recent mass spec developments enhance structural biology

SBKB [doi:10.1038/sbkb.2010.56]
Technical Highlight - December 2010
Short description: Recent technical developments have helped mass spectrometry take its place as an essential structural biology tool.

Dr Min Zhou at the ion mobilty mass spectrometer used for determining collision cross sections. This information is used to constrain the subunit architecture of a macromolecular complex.

Proteomic studies are producing vast arrays of information about interacting proteins and their regulation. Structural biology and, in particular, structural genomics is producing many structures and boosting our ability to produce accurate homology models. But the challenge is to integrate these different forms of information. Zhou and Robinson propose that mass spectrometry (MS) is the key. Here are five ways in which it can help.

1. Recent improvements in hardware and methodology have extended the use of the high mass-to-charge (m/z) region, so higher-order structural information can now be gathered from noncovalent protein complexes.

2. Not only can subunit stoichiometry of intact complexes be determined, but details of the heterogeneity of the complex and the changes in interactions in response to certain conditions can now be detected. Analysis of complex dynamics during the cell cycle, for example, is not far off.

3. Ion mobility (IM)-MS has advanced to the stage where it can be used to examine large intact complexes. Intact large assemblies can be further broken down into subcomplexes, and the subunit contacts can be used as constraints for building three-dimensional models of the subunit architecture.

4. For technical reasons, many post-translational modifications are removed from proteins in order to solve the structure. MS is now the essential tool for identifying and quantifying post-translational modifications. Phosphorylation sites in particular have been well analyzed by MS.

5. Membrane proteins, which are difficult to analyze by X-ray crystallography or NMR spectroscopy, are beginning to be tractable to MS. The first report of the determination of a membrane protein complex's subunit and lipid-binding stoichiometry, after release from a detergent micelle and detection by MS, came out last year 2 . This is likely to be an area of rapid development.

Maria Hodges

References

  1. M. Zhou & C.V. Robinson When proteomics meets structural biology.
    Trends Biochem. Sci. 35, 522-529 (2010). doi:10.106/j.tibs.2010.04.007

  2. N.P. Berrera et al. Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions.
    Nat. Methods 8, 585-587 (2009). doi:10.1038/nmeth.1347

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