Jan 12, 2018
Prof. Joseph Loo
The Loo research team developed a mass spectrometry workflow that can be used for drug development and structural biology research.
Traditional methods of mass spectrometry reveal what proteins form a complex but usually cannot reveal how the protein complex is assembled or what parts of each protein interact. Obtaining this structural data via X-ray crystallography or NMR spectroscopy can be difficult for large protein complexes.
To address this difficulty, the team has developed a workflow using high resolution Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry (MS) to analyze intact protein complexes, which could prove useful for a variety of applications including drug development and structural biology.  Most notably, their research establishes that FTICR instruments can be used for the analysis of large macromolecular complexes.
FTICR MS can use many methods for generating protein fragments from larger protein complexes for analysis. High-energy fragmentation methods can disrupt strong protein interactions, like salt bridges. Increasing the energy of fragmentation and using different forms of dissociation methods (e.g., via photons and electrons) revealed structural data by slowly chipping off bigger and bigger protein chunks from larger protein complexes.
Other fragmentation methods can preserve noncovalent interactions, allowing for identification of where drugs or other proteins interact. Combining multiple fragmentation methods allowed the researchers to obtain snippets of 3D structural data that they used to assemble pictures of entire protein complexes.
Previous experiments have analyzed protein complexes of about 150 kDa. The Loo lab’s new method can analyze protein complexes more than 10 times larger, at 1,860 kDa. This accomplishment alleviates fears that FTICR lacked the capability to detect large protein complexes.
Moreover, traditional mass spectrometry methods lose spatial information of protein post-translational modifications (PTMs). Post-translational modifications are a common form of protein regulation, sometimes changing proteins from an open, active form to a closed, inactive form. The authors suggest their new method can be used to see how PTMs affect a protein’s conformation and interactors.
The research was published in the January 1, 2018 issue of Nature Chemistry in a paper titled “An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes”.  The first author is Loo group former postdoc Dr. Huilin Li (currently a member of the faculty at Sun Yat-Sen University in Guangzhou, China), and co-authors are postdoc alumna Dr. Hong Hanh Nguyen (Ph.D. ’15, Biochemistry, Loo group), researcher Dr. Rachel Ogorzalek Loo, Amgen senior scientist Dr. Iain Campuzano, and Prof. Joseph Loo.
On January 3, 2018, the paper was featured on GenomeWeb, an online news organization serving scientists, technology professionals, and executives who use and develop the latest advanced tools in molecular biology research and molecular diagnostics. 
In addition to being a UCLA biochemistry professor, Loo is a faculty member of the UCLA Department of Biological Chemistry, David Geffen School of Medicine, and he is a member of the UCLA-DOE Institute for Genomics and Proteomics. To learn more about the Loo group’s research, visit their website.
Many thanks to Joseph Ong for writing this article.