(12n) Engineering Proteins for Magnetic Resonance Imaging at Molecular and Atomic Resolutions

Imaging biological processes in intact tissue and cells with molecular specificity and high resolution presents a fundamental challenge to biomedical research. Magnetic resonance imaging (MRI), being non-invasive and not limited by tissue depth, enables whole-body imaging at sub-100μm resolution; however, the main bottleneck is the lack of compatible smart sensors that can recognize specific molecular events and accordingly output an MRI signal. On a different level of resolution, nuclear magnetic resonance (NMR) spectroscopy, a structural biology method compatible with living cells and tissues, allows the visualization of the movement of atoms inside a protein when it performs a biological task. Similarly, what prevents NMR from a wide application to the study of live cells and tissue is the lack of smart agents, which in this case, would restrict NMR signals only from those selective molecules, making atom-specific spectra a feasible goal. I propose to engineer protein-based smart agents for the two applications that non-invasively image biomolecules at the molecular and atomic resolutions.The growing genomic data from the sequencing of animals and microbes, together with the understanding and computational prediction of protein structures and functions, provides unique opportunities nowadays to repurpose and modify proteins for applications distinct from their native roles. Since these engineered proteins can be genetically encoded, they can leverage the large amount of genetic engineering methods developed over the decades to achieve functions that are difficult for synthetic agents, such as the precise localization in subcellular compartment, expression-level coupling with genes and circuits, and specificity in molecular recognition. The development of the new non-invasive molecular imaging methods could lead to various applications, such as the functional imaging of the brain in line with the BRAIN initiative, while the development of atomic-resolution imaging of biomacromolecules in live cells could lead to a new imaging paradigm and information that have not been previously accessed.

Postdoctoral Project: Genetically encoded gas nanostructures as acoustomagnetic reporters for noninvasive biological imaging.

Under supervision of Mikhail G. Shapiro, California Institute of Technology

PhD Dissertation: Development of Solid-state NMR Spectroscopy for Membrane Proteins: Application to the Mercury Transporter MerF.

Under supervision of Stanley J. Opella, University of California, San Diego (UCSD)

Research Experience:

My research has been at the interface between biology and physics. In the graduate school, I joined a laboratory that had work spanning from molecular biology, protein chemistry to quantum mechanics theory of the NMR pulse sequences and computational biology on protein structures. The overall goal of my research was to develop a general method for obtaining atomic-resolution structures of membrane proteins in their native lipid bilayer environment. I devoted a large portion of the efforts to the development of new solid-state NMR and computational methods. Besides, I also applied the new methods to solve the structure of a mercury transporter protein from microbial bioremediation pathways.

While the goal for a structural biologist is to understand a proteinâ??s native function, my current postdoctoral research in the realm of protein engineering aims to utilize such understanding to repurpose and generate new functions for the proteins. For example, we currently work on gas vesicles, a group of protein-only nanostructures whose native role is to regulate buoyancy of the microbes, and we repurpose them as a genetically encoded MRI reporter gene. During my postdoctoral training, I have also gained insights into the imaging aspects of magnetic resonance methods and the techniques for live animal imaging.

As faculty I would like to leverage my knowledge in protein engineering and magnetic resonance to develop new imaging methodology that can find utilities in various studies on live cells and animals. Just as how green fluorescent protein (GFP) changes the paradigm of optical imaging, I believe the engineering of protein-based probes can break through key bottlenecks in current non-invasive imaging methods and can potentially lead to new platforms.

Selected Publications:

Lu GJ, Tian Y, Vora N, Marassi FM, Opella SJ (2013) The structure of the mercury transporter MerF in phospholipid bilayers: a large conformational rearrangement results from N-terminalâ?¨truncation. J. Am. Chem. Soc. 135(25):9299-9302.

Lu GJ, Opella SJ (2014) Mechanism of dilute-spin-exchange in solid-state NMR. J. Chem. Phys. 140(12): 124201.

Lu GJ, Opella SJ (2014) Resonance assignments of a membrane protein in phospholipid bilayers by combining multiple strategies of oriented sample solid-state NMR. J. Biomol. NMR 58(1): 69-81.

Lu GJ, Opella SJ (2013) Motion-adapted pulse sequences for oriented sample (OS) solid-state NMR of biopolymers. J. Chem. Phys. 139(8):084203.

Lu GJ, Park SH, Opella SJ (2012) Improved 1H amide resonance line narrowing in oriented sampleâ?¨solid-state NMR of membrane proteins in phospholipid bilayers. J. Magn. Reson. 220:54-61.

Lu GJ, Son WS, Opella SJ (2011) A general assignment method for oriented sample (OS) solid- state NMR of proteins based on the correlation of resonances through heteronuclear dipolar couplings in samples aligned parallel and perpendicular to the magnetic field. J. Magn. Reson. â?¨209(2):195-206.

Lu GJ, Garen CR, Cherney MM, Cherney LT, Lee C, James MNG (2007) Expression, purification and preliminary X-ray analysis of the C-terminal domain of an arginine repressor protein from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 63(Pt 11):936-939.

Teaching Interests:

At the graduate school, I TAed in analytical chemistry laboratory course, and presented weekly seminars as the only TA for a protein biochemistry course. At CalTech, I presented a 3-hour guest lecture in the Molecular Imaging course offered from chemical engineering department. Lastly, I mentored several undergraduate students during my Ph.D. and postdoctoral studies. Although my undergraduate background was mainly on biology, the exposure to multidisciplinary research in chemistry and physics during my Ph.D. and postdoctoral studies provided me confidence and enthusiasm to teach in various disciplines.