Huilin Li, Ph.D. Associate Professor Department of Biochemistry and Cell Biology Center for Structural Biology 142 Centers for Molecular Medicine Stony Brook University Stony Brook, NY 11794-5215 Office telephone: 631-632-1041 Fax: 631-632-8575 E-mail: Huilin.Li@stonybrook.edu
		Joint Appointment: Biology Department, Brookhaven National Laboratory
Research Description

Our research is aimed at understanding the function of biological macromolecules via structural analyses, primarily by cryo-electron microscopy. Cryo-EM is capable of revealing low to medium resolution structures of large protein complexes that are proven difficult for X-ray crystallography or NMR methods.

Structural basis of eukaryotic DNA replication initiation

The yeast origin recognition complex (ORC) is a six-protein assembly discovered in 1992 in the lab of Bruce Stillman at Cold Spring Harbor Laboratory. ORC is conserved in all eukaryotes from yeast to human. Yeast ORC constitutively binds to and marks the replication origin throughout the cell cycle. Licensing of the DNA replication origin starts when the cell division cycle protein Cdc6p binds to ORC. Despite recent breakthrough in structures of prokaryotic replication initiators, structural information on eukaryotic ORC has been rather limited. My lab has been investigating the structural basis of the yeast DNA replication initiation by cryo-EM method.

The M. tuberculosis proteasome pathway

Proteasome is widespread in eukaryotes and archaea, but very rare in eubacteria. Recently, the bacterium M. tuberculosis (Mtb) was found to possess a ubiquitin-like proteasome pathway. Furthermore proteasome was found to be required for Mtb resistance to killing by the host immune system. Proteasome and proteasomal ATPase appear to protect Mtb against nitric oxide from macrophage by degrading damaged proteins after exposure to nitric oxide. Thus, Mpa and the Mtb proteasome may be promising targets for the development of anti-TB chemotherapeutics. We study the structure and inhibition of the Mtb proteasome system.

Structural biology of membrane protein assemblies

We have been collaborating with David Thanassi group in Microbiology department on cryo-EM of the PapC usher, a bacterial outer membrane protein that orderly secrets and assembles the bacterial surface pili. We also image the yeast oligosaccharyl transferase, a nine-protein complex that glycosylates the nascent polypeptide chains at the endoplasmic reticulum membrane. This work is in collaboration with Bill Lennarz’s lab in this department. Another interesting project that we are working with Dennis Selkoe and Michael Wolfe groups at Harvard Medical School is the human γ-secretase. -Secretase is an intramembranous aspartyl protease that is required for the processing of many membrane proteins, including Notch and amyloid precursor protein.

Selected publications

1. Li H, Lee S, Jap BK. Molecular Design of Aquaporin-1 Water Channel as Revealed by Electron Crystallography. Nature Struct. Biol. 1997;4:263-265.
2. Li H, Sui HX, Ghanshani S, Lee S, Walian PJ, Wu CL, Chandy KG, Jap BK. Two-dimensional Crystallization and Projection Structure of KcsA Potassium Channel. J. Molec. Biol. 1998;282:211-216.
3. Löwe J, Li H, Downing KH, Nogales E. Refined Structure of αβ-tubulin at 3.5 Å Resolution. J. Molec. Biol. 2001;313:1045-1057.
4. Li H, DeRosier DJ, Nicholson WV, Nogales E, Downing KH. The Microtubule Structure at 8 Å Resolution. Structure. 2002;10:1317-1328.
5. Chen ZQ, Green TJ, Luo M, Li H. Visualizing the RNA Molecule in the Bacterially-Expressed Vesicular Stomatitis Virus Nucleoprotein-RNA Complex, Structure. 2004;12:227-235.
6. Nettles JH, Li H, Cornett B, Krahn JM, Snyder JP, Downing KH. The Binding Mode of Epothilone-A on α/β-tubulin by Electron Crystallography. Science. 2004;305:866-869.
7. Surana NK, Grass S, Hardy GG, Li H, Thanassi DG, St Geme JW III. Evidence for Conservation of Architecture and Physical Properties of Omp85-like Proteins Throughout Evolution. Proc. Natl. Acad. Sci. U.S.A. 2004;101:14497-14502.
8. Li H, Qian L, Chen ZQ, Thibault D, Liu G, Liu TB, Thanassi DG. The Outer Membrane Usher Forms a Twin-Pore Secretion Complex. J. Molec. Biol. 2004;344:1397-1407.
9. Speck C, Chen ZQ, Li H, Stillman B. ATPase-dependent, Cooperative Binding of ORC and Cdc6p to Origin DNA. Nature Struct. and Molec. Biol. 2005;12:965-971.
10. Darwin KH, Lin G, Chen ZQ, Li H, Nathan, CF. Characterization of a Mycobacterium tuberculosis proteasomal ATPase homologue. Molecular Microbiology. 2005;55:561–571.
11. Hu GQ, Lin G, Wang M, Dick L, Xu R, Nathan C, Li H. Structure of the Mycobacterium tuberculosis Proteasome and Mechanism of Inhibition by a Peptidyl Boronate. Molec. Microbiol. 2006;59:1417-1428.
12. Chavan M, Chen Z, Li G, Schindelin H, Lennarz WJ, Li H. Dimeric Organization of the Yeast Oligosaccharyl Transferase Complex. Proc. Natl. Acad. Sci. U.S.A. 2006;103:8947-52.
13. Lazarov VK, Fraering PC, Ye W, Wolfe MS, Selkoe DJ, Li H. Electron Microscopic Structure of Purified, Active Gamma-secretase Reveals an Aqueous Intramembrane Chamber and Two Pores. Proc. Natl. Acad. Sci. U.S.A. 2006;103:6889-6894.
14. Li H, Grass S, Wang T, Liu T, St Geme JW 3rd. Structure of the Haemophilus Influenzae HMW1B Translocator Protein: Evidence for a Twin-pore. J. Bacteriol. 2007;189:7497-7502.
15. Li Hua, Chavan M, Schindelin H, Lennarz W., Li H. Structure of the oligosaccharide transferase complex at 12 Å resolution. Structure. 2008;16:432-440.
16. Remaut H, Tang C, Henderson N, Pinkner J, Wang T, Hultgren SJ, Thanassi DG, Waksman G, Li H. Fiber formation across the bacterial outer membrane by the chaperone/usher pathway. Cell. 2008, 133, 640-652.
17. Chen Z, Speck C, Wendel P, Tang C, Stillman B, Li H. The architecture of the DNA replication origin recognition complex in S. cerevisiae. Proc Natl Acad Sci U S A, 105, 10326-31 (2008).
18. Osenkowski P, Li H, Ye W, Li D, Aeschbach L, Fraering PC, Wolfe MS, Selkoe DJ, Li H. Cryoelectron microscopy structure of purified gamma-secretase at 12 Å resolution. J Mol Biol. 385, 642-52, (2009)
19. Li, H, Wolfe MS, Selkoe DJ. Toward structural elucidation of the γ-secretase complex (review). Structure. 2009, 17, 326-34.
20. Hayashi M, Tang C, Giannini V, Narayanan R, Stearns MH, Xu RM, Li H, C. Sala, Hayashi Y. Structural framework of the postsynaptic density formed by a high-order complex between Homer and Shank. Cell. 2009, 137, 159-171.
21. Harada Y, Li Hua, Li H, Lennarz WJ. Oligosaccharyltransferase directly binds to ribosome: Reconstitution of a complex involved in cotranslational N-glycosylation. Proc Natl Acad Sci U S A. 2009, Early edition, doi 10.1073 pnas.0812489106.
22. Li H, Thanassi DG. Use of a combined cryo-EM and X-ray crystallography approach to reveal molecular details of bacterial pilus assembly by the chaperone/usher pathway. Current opinion in Microbiology (Review) Early online publication.

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