John Rubinstein

At A Glance

• Electron cryomicroscopy (cryo-EM) of macromolecular machines
• Cryo-EM method development including algorithm and software development and nano-fabrication for specimen preparation
• Study of rotary ATPases and other biomedically significant protein complexes
• Bioenergetics and pH control in intracellular compartments
• Targeted destruction of proteins
• Vacuolar ATPases in cancer, osteoporosis, cell cycle control, and the immune system

Short Bio

Dr. Rubinstein is a Senior Scientist in the Molecular Structure and Function Program at the Hospital for Sick Children, where he has worked since 2006. He is a Professor in the Departments of Medical Biophysics and Biochemistry at the University of Toronto, and a Tier 1 Canada Research Chair in Electron Cryomicroscopy. He received his PhD from Cambridge University for work done at the Medical Research Council laboratories. His accomplishments have been recognized by awards including a CIHR New Investigator Award, the GE Healthcare New Investigator Award from the Canadian Society for Molecular Biosciences, and the Burton Medal from the Microscopy Society of America

Research Synopsis

The Rubinstein laboratory studies the structure and function of macromolecular assemblies using electron cryomicroscopy (cryo-EM), image analysis, molecular biology and molecular genetics. We also develop the tools of cryo-EM so that we can answer questions that are not amenable to the techniques that currently exist. Method development usually occurs on several levels: (1) Development of new algorithms and computational approaches for image analysis (e.g. Rubinstein and Brubaker, 2015); and (2) Nanofabrication to improve specimen preparation (e.g. Marr et al., 2014). For computational method development we collaborate closely with colleagues in the Department of Computer Sciences at the University of Toronto. Recent biological projects have included the structural study of the mitochondrial ATP synthase (Zhou et al., 2015), the Vacuolar-type ATPase (Zhao et al., 2015), and the V/A-ATPase (Lau and Rubinstein, 2012). These rotary ATPases have important roles in cancer, osteoporosis, the immune system, and ischemia-reperfusion injury. We have numerous collaborative projects studying other aspects of the molecular biology of the cell from a structural perspective. Our work on the rotary ATPases and other ongoing projects has illustrated how cryo-EM can be used not only to elucidate the high-resolution structures of macromolecular assemblies, but also to understand the dynamics of biomolecular systems.

Recent Publications

•  Zhou, A., Rohou, A., Schep, D.G., Bason, J.V., Montgomery, M.G., Walker, J.E., Grigorieff, N., Rubinstein, J. L. (2015). Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM. eLife 4:e10180 [BioRxiv:11 Aug 2015]
• Rubinstein, J. L., and Brubaker, M. A. (2015). Alignment of cryo-EM movies of individual particles by optimization of image translations. J Struct Biol 192, 188-95. [ArXiv:1409.6789]
• Zhao, J., Benlekbir, S., and Rubinstein, J. L. (2015). Cryo-EM observation of rotational states in a eukaryotic V-ATPase. Nature 521, 241-5.
• Smith, M.T. J., Rubinstein, J. L. (2014). Beyond blob-ology. Science 345, 617-9.
• Marr, C. R., Benlekbir, S., and Rubinstein, J.L. (2014). Fabrication of carbon films with ~500 nm holes for cryo-EM with a direct detector device. Journal of Structural Biology 185, 42-7.
• Benlekbir, S., Bueler, S. A., and Rubinstein, J. L. (Dec 2012).  Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11 Å resolution.  Nature Struct and Mol Biol 19, 1356-62.
• Baker, L. A., Watt, I. N., Runswick, M. J., Walker, J. E., and Rubinstein, J. L. (Jul 2012).  The arrangement of subunits in intact mammalian mitochondrial ATP synthase determined by cryo-EM. Proc Natl Acad Sci (USA) 109, 11675-80.
• Lau, W. C. Y., and Rubinstein, J. L. (Jan 2012). Sub-nanometer resolution structure of the intact T. thermophilus H+-driven ATP synthase. Nature 481, 214-8.

Graduate Students

Gautier Courbon
Hui Guo
Kristine Keon
David Yanofsky