Department of Biochemistry
Duke University Medical Center

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

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)

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 ------ 

P7. A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada. He C, Hus JC, Sun LJ, Zhou P, Norman DP, Dotsch V, Wei H, Gross JD, Lane WS, Wagner G, Verdine GL. Mol Cell 20, 117-129 (2005).  (PDF)

P6.  A solubility-enhancement tag (SET) for NMR studies of poorly behaving proteins. Pei Zhou, Alexey A. Lugovskoy and Gerhard Wagner. J Biomolecular NMR 20, 11-14 (2001) (PDF)

P5.  Solution structure of DFF40 and DFF45 N-terminal domain complex and mutual chaperone activity of DFF40 and DFF45. Pei Zhou, Alexey A. Lugovskoy, John S. McCarty, Peng Li and Gerhard Wagner. Proc. Natl. Acad. Sci. USA 98, 6051-6055 (2001) (PDF)

P4.  Solution structure of the CIDE-N domain of CIDE-B and a model for CIDE-N/CIDE-N interactions in the DNA fragmentation pathway of apoptosis. Alexey A. Lugovskoy , Pei Zhou, James J. Chou, John S. McCarty, Peng Li and Gerhard Wagner. Cell 99, 747-755 (1999) (PDF)

P3.  Solution structure of Apaf-1 CARD and its interaction with caspase-9 CARD: A structural basis for specific adaptor/caspase interaction. Pei Zhou, James J. Chou, Roberto Sanchez Olea, Junying Yuan and Gerhard Wagner. Proc. Natl. Acad. Sci. USA 96, 11265-11270 (1999) (PDF)

P2.  Solution Structure of the Core NFATC1/DNA complex. Pei Zhou, Li Jing Sun, Volker Dötsch, Gerhard Wagner and Gregory L. Verdine. Cell 92, 687-696 (1998) (PDF)

P1. Unusual Rel-like Architecture in the DNA-binding Domain of the Transcription Factor NFATc. Scot A. Wolfe, Pei Zhou, Volker Dötsch, Lin Chen, Angie You, Steffan N. Ho, Gerald R. Crabtree, Gerhard Wagner, and Gregory L. Verdine. Nature 385, 172-176 (1997). (PDF)

 Duke University

Medical Center  

Department of Biochemistry