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Please send your questions, requests, or comments to:

Hongjun Zhou, Ph.D.
Director, NMR Facility
Department of Chemistry and Biochemistry
University of California
Santa Barbara, CA 93106-9510

E-mail: hzhou@chem.ucsb.edu

Phone: 805-893-2938
PSBN: 3614A

Assistant: Kaylaa Gutman

Hongjun
"The universe is everything and nothing. We are simply things in-between."

Professional Background

Driven by a keen interest in physics, I studied nuclear physics during my undergraduate education at Peking University. That interest led me to a few more years of study and research in graduate school in theoretical nuclear and particle physics. In early 1990s, the high-energy physics world faced a downturn from funding cuts, especially the killing of the Superconducting Super Collider (SSC), a once inspirational project for many young physicists. My last particle physics project was a Monte Carlo simulation of the various particles and states that may form during a high-energy heavy hadron collision, a part of the research that was inspired by the SSC project.

During that period, I explored biophysics and felt attracted to the elegant physical techniques being applied in the biochemical field that are driven by profound and precise physics, and the beautiful quantum mechanics that is put into action in NMR. It is this tunable, precise quantum wave actions of the nuclear spins that lead to the first conceptual design of a quantum computer. After I completed my doctoral degree in physics with work in protein NMR, I continued my research at the National Cancer Institute, then the University of Colorado at Boulder, before I took a position at a company in San Diego in 2000. Using both computational methods and experimental screening with NMR and X-ray, the company was among the first to explore large-scale functional data mining of the human genome following the near completion of the Human Genome Project. I joined UCSB in 2004 and continued my work in protein NMR before I took over the duty of managing the department NMR Facility.

Einstein once said: "People love chopping wood. In this activity one immediately sees results." In a different context, a big part of science is to reconstruct the tree from the pile of wood chips we manage to collect, a reverse process that is challenging and equally enjoyable. Going from the forefront of theoretical particle physics to analytical NMR, one does have a better chance not having to wait a lifetime to see verification of an idea or a model. However, the questions are no less challenging, just different. With abundant empirical data and more advanced experimental techniques, we continue to look for better ways to not only collect the wood chips properly but also reconstruct the tree quickly and accurately.

Publications
  1. Makris C., Carmichael J. R., Zhou H., and Butler A. (2022) C-Diazeniumdiolate Graminine in the Siderophore Gramibactin Is Photoreactive and Originates from Arginine. ACS Chem. Biol. 17, 11, 3140–3147. DOI: https://doi.org/10.1021/acschembio.2c00593
  2. Bartelli N.L., Passanisi V.J., Michalska K., Song K., Nhan D.Q., Zhou H., Cuthbert B.J., Stols L.M., Eschenfeldt W.H., Wilson N.G., Basra J.S, Cortes R., Noorsher Z., Gabraiel Y., Poonen-Honig I., Seacord E.C., Goulding C.W., Low D.A., Joachimiak A., Dahlquist F.W. & Hayes C.S. (2022) Proteolytic processing induces a conformational switch required for antibacterial toxin delivery. Nature Communications 13, 5078. DOI: https://doi.org/10.1038/s41467-022-32795-y
  3. Bartelli NL, Sun S, Gucinski GC, Zhou H, Song K, Hayes CS, Dahlquist FW (2019) The cytoplasm-entry domain of antibacterial cdia is a dynamic alpha-helical bundle with disulfide-dependent structural features. J. Mol. Biol. 431, 3203-3216. DOI: https://doi.org/10.1016/j.jmb.2019.05.049
  4. Carmichael J. R., Zhou H. & Butler A. (2019) A suite of asymmetric citrate siderophores isolated from a marine Shewanella species. J. Inorg. Biochem. Vol. 198, 110736.
  5. Nicklisch S, Spahn J, Zhou H, Gruian C, and Waite JH (2016) Redox capacity of an extracellular protein associated with adhesion in mytilus californianus. Biochemistry 55, 2022-2030.
  6. Wang X1, Vallurupalli P, Vu A, Lee K, Sun S, Bai WJ, Wu C, Zhou H, Shea JE, Kay LE, Dahlquist FW (2014) The linker between the dimerization and catalytic domains of the CheA histidine kinase propagates changes in structure and dynamics that are important for enzymatic activity. Biochemistry 53, 855-861.
  7. Ortega DR1, Mo G, Lee K, Zhou H, Baudry J, Dahlquist FW, Zhulin IB (2013) Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein. PLoS Comput Biol November 14, 2013.
  8. Matje DM, Zhou H, Smith DA, Neely RK, Dryden DT, Jones AC, Dahlquist FW, Reich NO. (2013) Enzyme-Promoted Base Flipping Controls DNA Methylation Fidelity. Biochemsitry 52, 1677-1685.
  9. Mo G, Zhou H, Kawamura T, Dahlquist FW. (2012) Solution structure of a complex of the histidine autokinase CheA with its substrate CheY. Biochemistry 51, 3786-3798.
  10. Levenson R, Zhou H, Dahlquist FW. (2012) Structural insights into the interaction between the bacterial flagellar motor proteins FliF and FliG. Biochemistry 51, 5052-5060.
  11. Gauglitz, J.M., Zhou, H., & Butler, A. (2012) A suite of citrate-derived siderophores from a marine Vibrio species isolated following the Deepwater Horizon oil spill. J. Inorg. Biochem. 107, 90-95.
  12. Vu, A., Wang, X., Zhou, H., & Dahlquist, F.W. (2012) The receptor-CheW binding interface in bacterial chemotaxis. J. Mol. Biol. 415, 759-767.
  13. Vu, A., Hamel, D.J., Zhou, H., & Dahlquist, F.W. (2011). The structure and dynamic properties of the complete histidine phosphotransfer domain of the chemotaxis specific histidine autokinase CheA from Thermotoga maritima. J. Biomol. NMR 51, 49-55.
  14. Kawamura, T., Vartanian, A.S., Zhou, H., & Dahlquist, F.W. (2011) The design involved in PapI and Lrp regulation of the pap operon. J. Mol. Biol. 409, 311-332.
  15. Mealman, T.D., Bagai, I., Singh, P., Goodlett, D.R., Rensing, C., Zhou, H., Wysocki, V.H., & McEvoy, M.M. (2011) Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry. Biochemistry 50, 2559-2566.
  16. Peterson, D.W., Ando, D.M., Taketa, D.A., Zhou, H., Dahlquist, F.W., & Lew, J. (2010) No difference in kinetics of tau or histone phosphorylation by CDK5/p25 versus CDK5/p35 in vitro. Proc. Natl. Acad. Sci. U S A. 207, 2884-2889.
  17. Zhou, H., Purdy, M.M., Dahlquist, F.W., & Reich, N.O. (2009) The recognition pathway for the DNA cytosine methyltransferase M.HhaI. Biochemistry 48, 7807-7816.
  18. Hao, S., Hamel, D., Zhou, H., & Dahlquist, F.W. (2009) Structural basis for the localization of the chemotaxis phosphatase CheZ by CheAS. J. Bacteriol. 18, 5842-5844
  19. Dyer, C.M., Vartanian, A.S., Zhou, H., & Dahlquist, F.W. (2009) A molecular mechanism of bacterial flagellar motor switching. J. Mol. Biol. 388, 71-84.
  20. Peterson, D.W., Zhou, H., Dahlquist, F.W., & Lew, J. (2008) A soluble oligomer of tau associated with fiber formation analyzed by NMR. Biochemistry 47, 7393-7404.
  21. Zhou. H., Shatz, W., Fera, N., Purdy, M.M., Dahlquist, F.W., & Reich, N.O. (2007) Long-range structural and dynamical changes induced by cofactor binding in DNA methyltransferase M.HhaI. Biochemistry 46, 7261-7268.
  22. Kawamura, T., Le, L.U., Zhou, H., & Dahlquist, F.W. (2007) Solution structure of Escherichia coli PapI, a key regulator of the Pap pili phase variation. J. Mol. Biol. 365, 1130-1142.
  23. Hamel, D.J., Zhou, H., Starich, M.R., Byrd, R.A., & Dahlquist, F.W. (2006) Chemical-shift-perturbation mapping of the phosphotransfer and catalytic domain interaction in the histidine autokinase CheA from Thermotoga maritima. Biochemistry 45, 9509-9517.
  24. Daughdrill, G.W., Vise, P.D., Zhou, H., Yang, X., Yu, W.F., Tasayco, M.L., & Lowry, D.F. (2004) Reduced spectral density mapping of a partially folded fragment of E. coli thioredoxin. J. Biomol. Struct. Dyn. 21, 663-670.
  25. Zhou, H., Gallina, M., Mao, H., Nietlispach, D., Betz, S.F., Fetrow, J.S., & Domaille, P.J. (2003) 1H, 13C and 15N resonance assignments and secondary structure of the human protein tyrosine phosphatase, PRL-2. J. Biomol. NMR 27, 397-398.
  26. Griswold, I.J, Zhou, H., Swanson, R.V,, McIntosh, L.P., Simon, M.I., & Dahlquist, F.W. (2002) The solution structure and interactions of chew from thermotoga maritima. Nat. Struct. Biol. 9, 121-125.
  27. Zhou, H., Vermeulen, A., Jucker, F. & Pardi, A. (2001) Incorporating residual dipolar couplings into the NMR solution structure determination of nucleic acids. Biopolymers 52, 168-80.
  28. Vermeulen, A., Zhou, H. & Pardi, A. (2000) Determining DNA global structure and DNA bending by application of NMR dipolar couplings. J. Am. Chem. Soc. 122, 9638-9647.
  29. Zhou, H., Casas-Finet, J.R., Heath Coats, R., Kaufman, J.D., Stahl, S.J., Wingfield, P.T., Rubin, J.S., Bottaro, D.P., & Byrd, R.A. (1999) Identification and dynamics of a heparin-binding site in hepatocyte growth factor. Biochemistry 38, 14793-802.
  30. Chirdadze, D.Y., Hepple, J.P., Zhou, H., Byrd, R.A., Blundell, T.L. & Gherardi, E. (1999) The crystal structure of a receptor-binding fragment of HGF/SF (NK1) suggests a novel mode for growth factor dimerization and receptor binding. Nat. Struct. Biol. 6, 72-78.
  31. Bertelson, E.B., Zhou, H., Lowry, D., Flynn, G.C., & Dahlquist, F.W. (1999) Topology and dynamics of the 10 kDa C-terminal domain of DnaK in solution. Protein Sci. 8, 343-354.
  32. Zhou, H., Mazzulla, M.J., Stahl, S.J., Wingfield, P.T., Rubin, J.S., Bottaro, D.P., & Byrd, R.A. (1998) The solution structure of the N-terminal domain of hepatocyte growth factor reveals a potential heparin-binding site. Structure 6, 109-116
  33. Altieri, A.S., Mazzulla, M.J., Zhou, H., Costantino, N., Court, D. & Byrd, R.A. (1997) Sequential assignments and secondary structure of the RNA-binding transcriptional regulator NusB. FEBS Letters 415, 221-226.
  34. Zhou, H. & Dahlquist, F.W. (1997) The phosphotransfer site of the chemotaxis-specific histidine autokinase CheA as revealed by NMR. Biochemistry 36, 699-710.
  35. Zhou, H., McEvoy, M.M., Lowry, D.F., Swanson, R.V., Simon, M. I. & Dahlquist, F.W. (1996) The phosphotransfer domain and the CheY-binding domain of the histidine kinase CheA are joined by a flexible linker. Biochemistry 35, 433-443.
  36. McEvoy, M.M., Zhou, H., Roth, A.F., Lowry, D.F., Morrison, T.B., Kay, L.E., & Dahlquist, F. W. (1995) Nuclear magnetic resonance assignments and global fold of a CheY-binding domain in CheA, the chemotaxis-specific kinase of Escherichia coli. Biochemistry 34, 13871-13880.
  37. Zhou, H., Lowry, D.F., Swanson, R.V., Simon, M.I., & Dahlquist, F.W. (1995) NMR studies of the phosphotransfer domain of the histidine kinase CheA from Escherichia coli: assignments, secondary structure, general fold, and backbone dynamics. Biochemistry 34, 13858-13870.