Department of Biochemistry

Duke University Medical Center

Dr. Pei Zhou

Associate Professor of Biochemistry

Research Interests

Selected Publications

Contact Information

Tel. (919) 668-6409
Fax (919) 684-8885
Email peizhou@biochem.duke.edu

Lab Location
Rm 270, Sands Building

Mailing Address
Department of Biochemistry
Box 3711, DUMC
Durham, NC 27710

Education

Ph.D. (Harvard University, 1998)

News

Read more in The Chronicle.	4/10/2013. Congratulations to Yaohua (Jenny) Xue, a Duke junior working in the lab, who has won the prestigious 2013 Barry M. Goldwater Scholarship!
Read comments in Faculty of 1000.	1/30/2013. Congratulations to Jessica Wojtaszek and Chul-Jin Lee! Their article: Structural basis of Rev1-mediated assembly of a quaternary vertebrate translesion polymerase complex consisting of Rev1, heterodimeric polymerase (Pol) ζ, and Pol κ., JBC, 2012; 287(40):33836-46, has been recommended as being of special significance in its field from the F1000 Faculty: http://f1000.com/prime/717972978.
	12/20/2012. Congratulations to Jessica Wojtaszek, who has been awarded the Jo Rae Wright Fellowship for Outstanding Women in Science for academic year 2013-2014.
	Prof. Brian Coggins will present his development of the SCRUB technology for efficient collection of high resolution 4-D NOESY spectra at the 2013 Keystone Symposia. This work is described in JACS 2012; 134(45): 18619-30.
	World Health Day – 7 April 2011 Antimicrobial resistance: no action today, no cure tomorrow (Read more)
	The March, 2011 issue of The Economist published a special report on antibiotic resistance: The spread of superbugs. (Read more)
	Prof. Pei Zhou spoke at the Cambridge Healthtech Institute's (CHI) PEPTALK conference (Jan 10-14, 2011) at San Diego, CA on using Solubility-enhancement tags (SETs) for solution NMR studies of challenging proteins.
	Congratulations to Jon Werner-Allen, who has been invited for an oral presentation at the Keystone Symposium: Frontiers of NMR in Biology, Jan 8 - Jan 13, 2011, Big Sky Resort in Big Sky, Montana.
	Congratulations to Su Wang for winning the Graduate Student Poster Award at the 2010 Duke Biochemistry Departmental Retreat at the Wrightsville Beach, NC (09/17/2010-09/19/2010).

Research Interests
Protein-protein interactions play a pivotal role in the regulation of various cellular processes. The formation of higher order protein complexes is frequently accompanied by extensive structural remodeling of the individual components, varying from domain re-orientation to induced folding of unstructured elements. Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool for macromolecular structure determination in solution. It has the unique advantage of being capable of elucidating the dynamic behavior of proteins during the process of recognition. Recent advances in NMR techniques have enabled the study of significantly larger proteins and protein complexes. These innovations have also led to faster and more accurate structure determination. My research interests focus on the exploration of molecular recognition and conformational variability of protein complexes in crucial biomedical processes using state-of-the-art NMR techniques. (More)

Recent Publications

	--------- 2013 ---------
	54. Mechanistic characterization of the tetraacyldisaccharide-1-phosphate 4´-kinase LpxK involved in lipid A biosynthesis. Emptage RP, Pemble CW, York JD, Raetz CR, Zhou P. *Biochemistry*. 2013 Mar 7.
	53. Specific interaction of the transcription elongation regulator TCERG1 with RNA polymerase II requires simultaneous phosphorylation at Ser2, Ser5 and Ser7 within the carboxyl-terminal domain repeat. Liu J, Fan S, Lee CJ, Greenleaf AL, Zhou P. J Biol Chem. 2013 Feb 22. [Epub ahead of print]
	52. Mutants resistant to LpxC inhibitors by rebalancing cellular homeostasis. Zeng D, Zhao J, Chung HS, Guan Z, Raetz CR, Zhou P. *J Biol Chem.* 2013 Jan 11. [Epub ahead of print]
	--------- 2012 ---------
	51. HASH: a Program to Accurately Predict Protein Ha Shifts from Neighboring Backbone Shifts. Zeng J, Zhou P, and Donald BR. *J Biomol NMR* 2012 Dec 16. [Epub ahead of print].
	50. Rapid protein global fold determination using ultrasparse sampling, high-dynamic range artifact suppression, and time-shared NOESY. Coggins BE, Werner-Allen JW, Yan A, and Zhou P. J Am Chem Soc. 2012; 134(45): 18619-30.
Recommended by Faculty of 1000	49. Structural basis of Rev1-mediated assembly of a quaternary vertebrate translesion polymerase complex consisting of Rev1, heterodimeric Pol zeta and Pol kappa. Wojtaszek J, Lee CJ, D'Souza S, Minesinger B, Kim H, D'Andrea AD, Walker GC, and Zhou P. *J Biol Chem*. 2012 Aug 2 [Epub ahead of print]
	48. Multifaceted recognition of vertebrate Rev1 by translesion polymerases zeta and kappa. Wojtaszek J, Liu J, D'Souza S, Wang S, Xue Y, Walker GC, Zhou P. *J Biol Chem*. 2012 July 27; 287 (31): 26400-8. Epub 2012 Jun 14.
	47. Efficient acquisition of high-resolution 4-D diagonal-suppressed methyl-methyl NOESY for large proteins. Wen J, Zhou P, Wu J. *J Magn Reson*. 2012 May;218:128-32. Epub 2012 Mar 9. PMID: 22464875.
	--------- 2011 ---------
	46. Protein loop closure using orientational restraints from NMR data.Tripathy C, Zeng J, Zhou P, Donald BR. *Proteins*. 2011 Sep 26. doi: 10.1002/prot.23207. (PDF)
	45. A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs. Martin JW, Yan AK, Bailey-Kellogg C, Zhou P, Donald BR. *J Comput Biol*. 2011 Nov;18(11):1507-23. Epub 2011 Oct 28.
	44. A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data. Zeng J, Roberts KE, Zhou P, Donald BR. *J Comput Biol*. 2011 Nov;18(11):1661-79.
	43. ¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of Drosophila melanogaster Ssu72. Werner-Allen JW, Zhou P. *Biomol NMR Assign*. 2011 Jul 6. [Epub ahead of print]
	42. Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data. Zeng J, Zhou P and Donald BR. *J Biomol NMR*. 2011 Jun 25. (PDF)
	41. Lipooligosaccharide is required for the generation of infectious elementary bodies in Chlamydia trachomatis. Nguyen BD, Cunningham D, Liang X, Chen X, Toone EJ, Raetz CR, Zhou P, Valdivia RH. Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10284-9. (PDF)
	40. A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers. Martin JW, Yam AK, Bailey-Kellogg C, Zhou P and Donald BR. Protein Sci 2011; 20: 970-85. (PDF)
	39. Sparsely-sampled high-resolution 4-D experiments for efficient backbone resonance assignment of disordered proteins. Wen J, Wu J, and Zhou P. J Magn Reson 209, 94-100 (2011). (PDF)
	38. Cis proline-mediated pSer5-dephosphorylation by the RNA polymerase II CTD phosphatase Ssu72. Werner-Allen JW, Lee CJ, Liu P, Nicely NI, Wang S, Greenleaf AL, Zhou P. *Journal of Biological Chemistry* 286, 5717-5826 (2011). (PDB: 3P3Y) (PDF)
	37. Syntheses, structures and antibiotic acitivities of LpxC inhibitors based on the diacetylene scaffold. Liang X, Lee CJ, Chen X, Chung HS, Zeng D, Raetz CRH, Li Y, Zhou P, Toone EJ. *Bioorganic & Medicinal Chemistry* 19: 852-60 (2011). (PDB: 3PS1, 3PS2, 3PS3) (PDF)
	36. Species-specific and inhibitor-dependent conformations of LpxC-Implications for antibiotic design. Lee CJ, Liang X, Chen X, Zeng D, Joo SH, Chung HS, Barb AW, Swanson SM, Nicholas RA, Li Y, Toone EJ, Raetz CRH, Zhou P. *Chemistry and Biology* 18: 1-10 (2011). (PDB: 3P3C, 3P3E, 3P3G) (PDF)

(+) --------- 2009-2010 ----------

	35. HDAC6 and Ubp-M BUZ Domains Recognize Specific C-Terminal Sequences of Proteins. Hard RL, Liu J, Shen J, Zhou P, Pei D. Biochemistry 49:10737-46 (2010). (PDF)
	34. The unusual UBZ domain of Saccharomyces cerevisiae polymerase eta. Woodruff RV, Bomar MG, D'Souza S, Zhou P, Walker GC. *DNA Repair* 9: 1130-41 (2010). (PDF)
	33. Radial Sampling for Fast NMR: Concepts and Practices Over Three Decades. Coggins BE, Venters RA, and Zhou P. *Progress in Nuclear Magnetic Resonance Spectroscopy* 57: 381-419 (2010). (Review).
	32. Fast Acquisition of High Resolution 4-D Amide-Amide NOESY with Diagonal Suppression, Sparse Sampling and FFT-CLEAN. Werner-Allen JW, Coggin BE and Zhou P. J Magn Reson 204,:173-178 (2010) (PDF).
	31. Unconventional Ubiquitin Recognition by the Ubiquitin-Binding Motif within the Y Family DNA Polymerases i and Rev1. Bomar MG, D’Souza S, Bienko M, Dikic I, Walker GC, and Zhou P. Molecular Cell 37, 408-417 (2010) (PDF).
	30. Assignment of ¹H, ¹³C and ¹⁵N backbone resonances of Escherichia coli LpxC bound to L-161,240. Barb AW, Jiang L, Raetz CR and Zhou P. Biomol NMR Assign (PMID: 19941092) (PDF).
	29. Overcoming the Solubility Limit with Solubility-Enhancement Tags: Successful Applications in Biomolecular NMR Studies. Zhou P and Wagner G. J Biomolecular NMR 46: 23-31 (2010) (Review).

28. High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations. Zeng J, Boyles J, Tripathy C, Wang L, Yan A, Zhou P and Donald BR. J Biomolecular NMR 45: 265-81 (2009). (PDF).

27. Uridine-based inhibitors as new leads for antibiotics targeting E. coli LpxC. Barb AW, Leavy TM , Robins L, Guan Z , Six D, Zhou P, Bertozzi C and Raetz CRH. Biochemistry 48, 3068-77 (2009). (PDF)

(+) --------- 2006-2008 ----------

26. A Hausdorff-based NOE assignment algorithm using protein backbone determined from residual dipolar couplings and rotamer patterns. Zeng JM, Tripathy C, Zhou P and Donald BR. Comput Syst Bioinformatics Conf 2008:169-181 (2008). (PDF) (Supplementary Information)

25. Mechanism and inhibition of LpxC: an essential zinc-dependent deacetylase of bacterial lipid A synthesis. Barb AW and Zhou P. Curr Pharm Biotechnol 9, 9-15 (2008). (Review).

24. High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN. Coggins BE and Zhou P. J Biomol NMR 42, 225–239 (2008) (PDF).

23. Structure of the deacetylase LpxC bound to the antibiotic CHIR-090: time-dependent inhibition and specificity in ligand binding. Barb A, Jiang L, Raetz CRH and Zhou P. Proc Natl Acad Sci USA 104, 18433-18438 (2007). (PDF)

22. The ADAM10 prodomain is a specific inhibitor of ADAM10 proteolytic activity and inhibits cellular shedding events. Moss ML, Bomar M, Liu Q, Sage H, Dempsey P, Lenhart PM, Gillispie PA, Stoeck A, Wildeboer D, Bartsch JW, Palmisano R, Zhou P. J Biol Chem 282, 35712-35721 (2007). (PDF)

21. Drosophila PIWI associates with chromatin and interacts directly with HP1a. Brower-Toland B, Findley SD, Jiang L, Liu L, Yin H, Dus M, Zhou P, Elgin SCR and Lin H. Genes & Development 21, 2300-2311 (2007). (Cover Image)

20. The low affinity IgE receptor (CD23) is cleaved by the metalloproteinase ADAM10. Lemieux GA, Blumenkron F, Yeung N, Zhou P, Williams J, Grammer AC, Petrovich R, Lipsky PE, Moss ML, Werb Z. J Biol Chem 282, 14836-44 (2007). (PDF)

19. Solution Structure of the Ubp-M BUZ Domain, a Highly Specific Protein Module that Recognizes the C-terminal Tail of Free Ubiquitin. Pai MT, Tzeng SR, Kovacs JJ, Keaton MA, Li SS, Yao TP, Zhou P. J Mol Biol 370, 290-302 (2007). (PDF)

18. Inhibition of Lipid A Biosynthesis as the Primary Mechanism of CHIR-090 Antibiotic Activity in Escherichia coli. Barb AW, McClerren AL, Snehelatha K, Reynolds CM, Zhou P, Raetz CRH. Biochemistry 46, 3793-3802 (2007). (PDF)

17. Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase h. Bomar MG, Pai M, Tzeng S, Li S and Zhou P. EMBO reports 8, 247-251 (2007). (PDF) (Supplementary Information)

16. Sampling of the NMR time domain along concentric rings. Coggins BE and Zhou P. J Magn Reson, 184, 207-221 (2007). (PDF)

15. Fourier Transforms of Radially-Sampled NMR Data. Coggins BE and Zhou P. J Magn Reson 182, 84-95 (2006). (PDF) (Cover Image)

14. A 'just-in-time' HN(CA)CO experiment for the backbone assignment of large proteins with high sensitivity. Werner-Allen JW, Jiang L, and Zhou P. J Magn Reson 181, 177-180 (2006). (PDF) (Pulse Sequence)

13. PR-CALC: A Program for the Reconstruction of NMR Spectra from Projections. Coggins BE and Zhou P. J Biomol NMR 34, 179-95 (2006). (PDF) (Supplementary Material)

12. Evaluating the quality of NMR structures by local density of protons. Ban YA, Rudolph J, Zhou P and Edelsbrunner H. Proteins: Structure, Function, and Bioinformatics 62, 852-864 (2006). (PDF)

(+) --------- 2003-2005 ----------

11. Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1. Li M, Phatnani HP, Guan Z, Sage H, Greenleaf AL, and Zhou P. Proc Natl Acad Sci USA 102, 17636-17641 (2005). (PDF) (Supplementary Material)

10. Filtered Backprojection for the Reconstruction of a High-Resolution (4,2)D CH₃-NH NOESY Spectrum on a 29 kDa Protein. Coggins BE, Venters RA and Zhou P. J Am Chem Soc 127, 11562-11563 (2005). (PDF) (Supplementary Materials)

9. (4,2)D Projection-Reconstruction Experiments for Protein Backbone Assignment: Application to Human Carbonic Anhydrase II and Calbindin D_28K. Venters RA, Coggins BE, Kojetin D, Cavanagh J and Zhou P. J Am Chem Soc 127, 8785-8795 (2005). (PDF) (Supplementary Material)

8. Rapid assignment of protein side chain resonances using projection-reconstruction of (4,3)D HC(CCO)NH and intra-HC(C)NH experiments. Jiang L, Coggins BE and Zhou P. J Magn Reson 175, 170-176 (2005). (PDF)

7. Refined Solution Structure of the LpxC-TU-514 Complex and pKa Analysis of an Active Site Histidine: Insights into the Mechanism and Inhibitor Design. Coggins BE, McClerren AL, Jiang L, Li X, Rudolph J, Hindsgaul O, Raetz CRH, and Zhou P. Biochemistry 44, 1114-1126 (2005). (PDF)

6. Kinetic Analysis of the Zinc-Dependent Deacetylase in the Lipid A Biosynthetic Pathway. McClerren AL, Zhou P, Guan Z, Raetz CRH, and Rudolph J. Biochemistry 44, 1106-1113 (2005). (PDF)

5. Assignment of the ¹H, ¹³C and ¹⁵N Resonances of the LpxC Deacetylase from Aquifex aeolicus in Complex with the Substrate-Analog Inhibitor TU-514. Coggins BE, Li X, Hindsgaul O, Raetz CRH, Zhou P. J Biomol NMR 28, 201-202 (2004). PubMed Abstract

4. Generalized Reconstruction of n-D NMR Spectra from Multiple Projections: Application to the 5-D HACACONH Spectrum of Protein G B1 Domain. Coggins BE, Venters RA, Zhou P. J Am Chem Soc 126, 1000-1001 (2004). (PDF)

3. Structure of the LpxC deacetylase with a bound substrate-analog inhibitor. Coggins BE, Li X, McClerren AL, Hindsgaul O, Raetz CRH, Zhou P. Nat Struct Biol 10, 645-651 (2003). (PDF)

2. Characteristics of the Interaction of a Synthetic Human Tristetraprolin Tandem Zinc Finger Peptide with AU-rich Element-containing RNA Substrates. Blackshear PJ, Lai WS, Kennington EA, Brewer G, Wilson GM, Guan X and Zhou P. J Biol Chem 278,19947-19955 (2003). (PDF)

1. PACES: Protein sequential assignment by computer-assisted exhaustive search. Coggins BE and Zhou P. J Biomol NMR 26, 93-111 (2003). (PDF)

(+) Ph.D. and Postdoctoral Research

SearchPubMed for Publications

Duke University

Medical Center

Department of Biochemistry

Duke University Medical Center

News !

Research Interests

Publications

Software

Lab Members