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Biological Sciences Division
Research Highlights

June 2006

Combined Methods Meet Challenge of Studying Protein Changes

Scientists at Pacific Northwest National Laboratory (PNNL) have combined mass spectrometric methods in a new way to better understand the three-dimensional structure and dynamics of proteins and other biological macromolecules in various environments, therefore meeting a central challenge of chemistry. Their work was reported in the May 15, 2006, issue of Analytical Chemistry.

Conformational changes such as protein denaturation, which causes unfolding, generally result in the loss of bioactivity. Specific protein misfolding has also been shown to cause a new activity underlying neurodegenerative diseases that in some cases apparently are caused by a small amount of misfolded protein (prion). Finding these changes requires more sensitive and specific methods for profiling protein conformations. The need to identify and quantify a misfolded protein in the presence of a dominant normal conformation, and possibly other isomers, is a particular challenge. Conventional mass spectrometric (MS) methods are generally insensitive to 3-D structure of proteins and their complexes.

The PNNL researchers characterized macromolecular conformations of bovine ubiquitin and cytochrome c, two common model proteins for structure and folding studies, using field asymmetric waveform (FAIMS) coupled to conventional ion mobility spectrometry (IMS) in conjunction with mass spectrometry. They found that for nearly all charge states, two-dimensional FAIMS/IMS separations distinguish many more conformations than either FAIMS or IMS alone, including some with very low abundance. For cytochrome c in high charge states, the researchers found several abundant "unfolded" isomer series not distinguishable by IMS.

The researchers, Alex Shvartsburg, Fumin Li, Keqi Tang, and Dick Smith, are studying larger proteins such as myoglobin and increasing the peak capacity of FAIMS/IMS through improved FAIMS resolution. Portions of this work were supported by PNNL's Biomolecular Systems Initiative, and the National Institutes of Health National Center for Research Resources. The work was done at the W.R. Wiley Environmental Molecular Sciences Laboratory.


Shvartsburg AA, F Li, K Tang, and RD Smith. 2006. "Characterizing the structures and folding of free proteins using 2-D gas-phase separations: observation of multiple unfolded conformers." Analytical Chemistry 78(10):3304-3315.

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Portrait of Dick Smith
Dick Smith
Portrait of Keqi Tang
Keqi Tang
Portrait of Alex Shvartsburg

Contact: Alex Shvartsburg