Pei Zhou

Overview:

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 conformation variability of protein complexes in crucial biomedical processes using state-of-the-art NMR techniques.

Positions:

Professor of Biochemistry

Biochemistry
School of Medicine

Professor of Chemistry

Chemistry
Trinity College of Arts & Sciences

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

Ph.D. 1998

Harvard University

Post-Doct Fellow, Biological Chemistry

Harvard University

Grants:

Structural Biology and Biophysics Training Program

Administered By
Basic Science Departments
Awarded By
National Institutes of Health
Role
Mentor
Start Date
End Date

Biochemical and functional investigation of the novel enzymatic activities of MESH1

Administered By
Molecular Genetics and Microbiology
Awarded By
National Institutes of Health
Role
Co-Principal Investigator
Start Date
End Date

Regulation of Germline Stem Cell Division in Drosophila

Administered By
Cell Biology
Awarded By
National Institutes of Health
Role
Consultant
Start Date
End Date

High sensitivity multi-purpose electron paramagnetic resonance spectroscopy for biotechnological and biomedical research

Administered By
Biochemistry
Role
Collaborating Investigator
Start Date
End Date

Discovery and validation of broadly effective LpxH inhibitors as novel therapeutics against multi-drug resistant Gram-negative pathogens

Administered By
Biochemistry
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Publications:

MESH1 is a cytosolic NADPH phosphatase that regulates ferroptosis

© 2020, The Author(s), under exclusive licence to Springer Nature Limited. Critical to the bacterial stringent response is the rapid relocation of resources from proliferation toward stress survival through the respective accumulation and degradation of (p)ppGpp by RelA and SpoT homologues. While mammalian genomes encode MESH1, a homologue of the bacterial (p)ppGpp hydrolase SpoT, neither (p)ppGpp nor its synthetase has been identified in mammalian cells. Here, we show that human MESH1 is an efficient cytosolic NADPH phosphatase that facilitates ferroptosis. Visualization of the MESH1–NADPH crystal structure revealed a bona fide affinity for the NADPH substrate. Ferroptosis-inducing erastin or cystine deprivation elevates MESH1, whose overexpression depletes NADPH and sensitizes cells to ferroptosis, whereas MESH1 depletion promotes ferroptosis survival by sustaining the levels of NADPH and GSH and by reducing lipid peroxidation. The ferroptotic protection by MESH1 depletion is ablated by suppression of the cytosolic NAD(H) kinase, NADK, but not its mitochondrial counterpart NADK2. Collectively, these data shed light on the importance of cytosolic NADPH levels and their regulation under ferroptosis-inducing conditions in mammalian cells.
Authors
Ding, CKC; Rose, J; Sun, T; Wu, J; Chen, PH; Lin, CC; Yang, WH; Chen, KY; Lee, H; Xu, E; Tian, S; Akinwuntan, J; Zhao, J; Guan, Z; Zhou, P; Chi, JT
MLA Citation
Ding, C. K. C., et al. “MESH1 is a cytosolic NADPH phosphatase that regulates ferroptosis.” Nature Metabolism, vol. 2, no. 3, Mar. 2020, pp. 270–77. Scopus, doi:10.1038/s42255-020-0181-1.
URI
https://scholars.duke.edu/individual/pub1435738
Source
scopus
Published In
Nature Metabolism
Volume
2
Published Date
Start Page
270
End Page
277
DOI
10.1038/s42255-020-0181-1

Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics.

The UDP-2,3-diacylglucosamine pyrophosphate hydrolase LpxH is an essential lipid A biosynthetic enzyme that is conserved in the majority of gram-negative bacteria. It has emerged as an attractive novel antibiotic target due to the recent discovery of an LpxH-targeting sulfonyl piperazine compound (referred to as AZ1) by AstraZeneca. However, the molecular details of AZ1 inhibition have remained unresolved, stymieing further development of this class of antibiotics. Here we report the crystal structure of Klebsiella pneumoniae LpxH in complex with AZ1. We show that AZ1 fits snugly into the L-shaped acyl chain-binding chamber of LpxH with its indoline ring situating adjacent to the active site, its sulfonyl group adopting a sharp kink, and its N-CF3-phenyl substituted piperazine group reaching out to the far side of the LpxH acyl chain-binding chamber. Intriguingly, despite the observation of a single AZ1 conformation in the crystal structure, our solution NMR investigation has revealed the presence of a second ligand conformation invisible in the crystalline state. Together, these distinct ligand conformations delineate a cryptic inhibitor envelope that expands the observed footprint of AZ1 in the LpxH-bound crystal structure and enables the design of AZ1 analogs with enhanced potency in enzymatic assays. These designed compounds display striking improvement in antibiotic activity over AZ1 against wild-type K. pneumoniae, and coadministration with outer membrane permeability enhancers profoundly sensitizes Escherichia coli to designed LpxH inhibitors. Remarkably, none of the sulfonyl piperazine compounds occupies the active site of LpxH, foretelling a straightforward path for rapid optimization of this class of antibiotics.
Authors
Cho, J; Lee, M; Cochrane, CS; Webster, CG; Fenton, BA; Zhao, J; Hong, J; Zhou, P
MLA Citation
Cho, Jae, et al. “Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics.Proc Natl Acad Sci U S A, vol. 117, no. 8, Feb. 2020, pp. 4109–16. Pubmed, doi:10.1073/pnas.1912876117.
URI
https://scholars.duke.edu/individual/pub1431154
PMID
32041866
Source
pubmed
Published In
Proc Natl Acad Sci U S A
Volume
117
Published Date
Start Page
4109
End Page
4116
DOI
10.1073/pnas.1912876117

Metabolic engineering of Escherichia coli to produce a monophosphoryl lipid A adjuvant.

Monophosphoryl lipid A (MPLA) species, including MPL (a trade name of GlaxoSmithKline) and GLA (a trade name of Immune Design, a subsidiary of Merck), are widely used as an adjuvant in vaccines, allergy drugs, and immunotherapy to boost the immune response. Even though MPLA is a derivative of lipopolysaccharide (LPS), a component of the outer membrane of Gram-negative bacteria, bacterial strains producing MPLA have not been found in nature nor engineered. In fact, MPLA generation involves expensive and laborious procedures based on synthetic routes or chemical transformation of precursors isolated from Gram-negative bacteria. Here, we report the engineering of an Escherichia coli strain for in situ production and accumulation of MPLA. Furthermore, we establish a succinct method for purifying MPLA from the engineered E. coli strain. We show that the purified MPLA (named EcML) stimulates the mouse immune system to generate antigen-specific IgG antibodies similarly to commercially available MPLA, but with a dramatically reduced manufacturing time and cost. Our system, employing the first engineered E. coli strain that directly produces the adjuvant EcML, could transform the current standard of industrial MPLA production.
Authors
Ji, Y; An, J; Hwang, D; Ha, DH; Lim, SM; Lee, C; Zhao, J; Song, HK; Yang, EG; Zhou, P; Chung, HS
MLA Citation
Ji, Yuhyun, et al. “Metabolic engineering of Escherichia coli to produce a monophosphoryl lipid A adjuvant.Metab Eng, vol. 57, Jan. 2020, pp. 193–202. Pubmed, doi:10.1016/j.ymben.2019.11.009.
URI
https://scholars.duke.edu/individual/pub1423417
PMID
31786244
Source
pubmed
Published In
Metab Eng
Volume
57
Published Date
Start Page
193
End Page
202
DOI
10.1016/j.ymben.2019.11.009

The Lipid A 1-Phosphatase, LpxE, Functionally Connects Multiple Layers of Bacterial Envelope Biogenesis.

Although distinct lipid phosphatases are thought to be required for processing lipid A (component of the outer leaflet of the outer membrane), glycerophospholipid (component of the inner membrane and the inner leaflet of the outer membrane), and undecaprenyl pyrophosphate (C55-PP; precursors of peptidoglycan and O antigens of lipopolysaccharide) in Gram-negative bacteria, we report that the lipid A 1-phosphatases, LpxEs, functionally connect multiple layers of cell envelope biogenesis in Gram-negative bacteria. We found that Aquifex aeolicus LpxE structurally resembles YodM in Bacillus subtilis, a phosphatase for phosphatidylglycerol phosphate (PGP) with a weak in vitro activity on C55-PP, and rescues Escherichia coli deficient in PGP and C55-PP phosphatase activities; deletion of lpxE in Francisella novicida reduces the MIC value of bacitracin, indicating a significant contribution of LpxE to the native bacterial C55-PP phosphatase activity. Suppression of plasmid-borne lpxE in F. novicida deficient in chromosomally encoded C55-PP phosphatase activities results in cell enlargement, loss of O-antigen repeats of lipopolysaccharide, and ultimately cell death. These discoveries implicate LpxE as the first example of a multifunctional regulatory enzyme that orchestrates lipid A modification, O-antigen production, and peptidoglycan biogenesis to remodel multiple layers of the Gram-negative bacterial envelope.IMPORTANCE Dephosphorylation of the lipid A 1-phosphate by LpxE in Gram-negative bacteria plays important roles in antibiotic resistance, bacterial virulence, and modulation of the host immune system. Our results demonstrate that in addition to removing the 1-phosphate from lipid A, LpxEs also dephosphorylate undecaprenyl pyrophosphate, an important metabolite for the synthesis of the essential envelope components, peptidoglycan and O-antigen. Therefore, LpxEs participate in multiple layers of biogenesis of the Gram-negative bacterial envelope and increase antibiotic resistance. This discovery marks an important step toward understanding the regulation and biogenesis of the Gram-negative bacterial envelope.
Authors
Zhao, J; An, J; Hwang, D; Wu, Q; Wang, S; Gillespie, RA; Yang, EG; Guan, Z; Zhou, P; Chung, HS
MLA Citation
Zhao, Jinshi, et al. “The Lipid A 1-Phosphatase, LpxE, Functionally Connects Multiple Layers of Bacterial Envelope Biogenesis.Mbio, vol. 10, no. 3, June 2019. Pubmed, doi:10.1128/mBio.00886-19.
URI
https://scholars.duke.edu/individual/pub1393235
PMID
31213552
Source
pubmed
Published In
Mbio
Volume
10
Published Date
DOI
10.1128/mBio.00886-19

Unbiased measurements of reconstruction fidelity of sparsely sampled magnetic resonance spectra.

The application of sparse-sampling techniques to NMR data acquisition would benefit from reliable quality measurements for reconstructed spectra. We introduce a pair of noise-normalized measurements, and , for differentiating inadequate modelling from overfitting. While and can be used jointly for methods that do not enforce exact agreement between the back-calculated time domain and the original sparse data, the cross-validation measure is applicable to all reconstruction algorithms. We show that the fidelity of reconstruction is sensitive to changes in and that model overfitting results in elevated and reduced spectral quality.
Authors
Wu, Q; Coggins, BE; Zhou, P
MLA Citation
Wu, Qinglin, et al. “Unbiased measurements of reconstruction fidelity of sparsely sampled magnetic resonance spectra.Nat Commun, vol. 7, July 2016, p. 12281. Pubmed, doi:10.1038/ncomms12281.
URI
https://scholars.duke.edu/individual/pub1138923
PMID
27459896
Source
pubmed
Published In
Nature Communications
Volume
7
Published Date
Start Page
12281
DOI
10.1038/ncomms12281