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Gang (Gary) Ren


Ren

Staff Scientist, Imaging and Manipulation of Nanostructures

gren@lbl.gov

510.495.2375
personal website

Biography

Education

B.A., Theoretical Physics, Lanzhou University, China, 1986-1990

M.S., Theoretical Physics (General relativity and gauge theory), Lanzhou University, China, 1990-1993, Advisor: Prof. Yi-shi Duan. Thesis: "Theory and Application of 2+1 Dimensional Topological Current"

Ph.D. Material Physics (Electron microscopy), Univ. of Science and Technology Beijing, and Beijing Laboratory of Electron Microscopy, Chinese Academy of Science, Beijing, China, 1993-1997, Advisor: Profs. Lian-mao Peng (2012 chair of IUCr -Commission of Electron crystallography) and Kehsin Kuo, Thesis: "Quantitative Electron Diffraction Theory and Application"

Previous Positions

Postdoctoral Fellows (American Heart Association and University of California), Cell Biology, the Scripps Research Institute, La Jolla, CA, 1997-2003, Advisors: Profs. Alok K. Mitra and Mark Yeager

Staff Scientist (non-PI), National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, 2004-2006, Director: Prof. Wah Chiu

Keck Fellow (Principal Investigator), Dept. of Biophysics and Biochemistry, University of California, San Francisco, CA, 2006-2010

Research Interests

My research group is focused on developing a new-era electron microscopy technique, individual-particle electron tomography (IPET) for achieving 3D reconstruction of a single macromolecule structure at nanometer resolution. As an only approach for uncovering a single macromolecular structure at near nanometer resolution, IPET can uncover the interface between macromolecules; reveal the macromolecular dynamics and tracking the chemical reactions of soft and biological macromolecules. This information is critical for current biological research and drug development, as a result, IPET will bring a large amount of users to our molecular foundry.

Projects

Toward a high-resolution structure of an individual protein

The long-term goal of this lab is to develop a robust method to determine a 3D image of an individual protein at a resolution that sufficient to answer biological stories. This lab recently reported a 14Å-resolution 3D image of an individual IgG antibody from negative-staining electron tomography (NS-ET) and a 36Å-resolution 3D image of an individual HDL particle from cryo-electron tomography (cryoET) proved the concept of that an individual protein 3D map at an intermediate resolution is possible to be achieved by this lab invented method - individual particle electron tomography (IPET) (PLoS ONE, 2012, 7(1):30249).

The strategy in improvement of electron tomography is from two aspects, high-quality (includes high-resolution and high-contrast) image acquirement and high-resolution reconstruction algorithm. For high-quality imageing, this lab developed an optimized negative-staining protocol (OpNS) for high-contrast imaging (JLR, 2010, 51(5):1228-36; and JLR, 2011, 52(1):175-84), invented cryo-positive-staining (cryoPS) protocol (NBC, 2012, 8(4): 342-349) for high-resolution and high-contrast imaging, and improved cryo-electron microscopy (cryoEM) protocol for high-resolution imaging (JBC, 2010, 24;285(52):41161-71) For high-resolution reconstruction, this lab developed IPET method via a focused electron tomography reconstruction (FETR) for high-resolution reconstructing a high-resolution 3D map from high-noise images of an individual protein.

The structural dynamics of human IgG antibody

The human IgG antibody (molecular weight: ~150 kDa) is well known as naturally dynamics and fluctuation in solution. X-ray diffraction provides detail structure of IgG antibody (1iGT) that locked in their lattice positions. Thus, the structure lost the information about its dynamic and fluctuation. To uncover the dynamics and fluctuation of IgG antibody, we use IPET to track and window a targeted single-instance of an antibody particle from each tilt micrograph after CTF correction by TOMOCTF, and then FETR reconstructed the images of this particle into a 3D density map at 14 Å resolution (PLoS ONE, 2012, 7(1):30249). The 3D density map contained rich structural details, including the shape of each domain, and even the holes inside each domain. The 3D reconstruction from single-instance antibody that is free of conformational dynamics and heterogeneity can be treated as a "snapshot" of the dynamic structure of antibody. By comparing these "snapshot" IgG antibody structures from different antibody particles, this method could allow us to study antibody dynamics. For example, by aligning two docked PDB files by aligning their Fc domain, the Fab domains are different from each other in location and orientation, suggesting the equilibrium fluctuation and structural dynamic character of IgG antibody.

The structural dynamics of human high-density lipoprotein (HDL, "good-cholesterol")


Human high-density lipoprotein (HDL, so-called "good cholesterol"), a highly dynamic protein conveys excess cholesterol from peripheral tissues to the liver and steroidogenic organs for clearance during reverse cholesterol transport. HDL particles in vivo vary in size, shape, components, and biological functions. A fraction, nascent HDL is a critical intermediate between lipid-poor apoA-I and mature spherical HDL during HDL assembly. Nascent HDL contains 120-240 phospholipids and 2-3 amphipathic apolipoprotein A-I (apoA-I, MW: 28kDa) molecules (in total MW of 140-240 kDa). Although nascent HDL is small protein that is super challenging for imaging by cryoEM and cryoET and even challenging for 3D reconstruction, we have successfully imaged nascent HDL embedded in vitreous ice by cryoET (JBC, 2010, 24;285(52):41161-71) and then reconstructed at 36 Å resolution 3D map (PLoS ONE, 2012, 7(1):30249), suggesting our IPET method is a robust and powerful approach. The 3D reconstruction from a single-instance HDL particle that is free of conformational dynamics and heterogeneity can be treated as a "snapshot" of the dynamic structure of protein. By comparing these "snapshot" HDL structures, this method could allow the study of HDL structural dynamics.

3-D images from a single particle (A) a series of images of an ApoA-1 protein particle, taken from different angles as indicated. A succession of four computer enhancements (projections) clarifies the signal. In the right column is the 3-D image compiled from the clarified data. B) is a close-up of the reconstructed 3-D image. C) Analysis shows how the particle structure is formed by three ApoA-1 proteins (red, green, blue noodle-like models)

The function and mechanism of human cholesteryl ester transfer protein (CETP)

Human cholesteryl ester transfer protein (CETP) mediates the net transfer of cholesteryl ester mass from atheroprotective high-density lipoproteins to atherogenic low-density lipoproteins by an unknown mechanism. Delineating this mechanism would be an important step toward the rational design of new CETP inhibitors for treating cardiovascular diseases. Using our reported OpNS and cryoPS for imaging single-particle approach for 3D reconstruction and molecular dynamics simulation for understanding the mechanism, we discovered that: i) CETP bridges a ternary complex with its N-terminal β-barrel domain penetrating into high-density lipoproteins and its C-terminal domain interacting with low-density lipoprotein or very-low-density lipoprotein; ii) the CETP lipoprotein-interacting regions, which are highly mobile, form pores that connect to a hydrophobic central cavity, thereby forming a tunnel for transfer of neutral lipids from donor to acceptor lipoproteins. These new insights into CETP transfer provide a molecular basis for analyzing mechanisms for CETP inhibition.

Selected Publications

All Publications by Gary Ren in Foundry database »

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