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author:("Li, pinghui")
1.  Structural and Functional Studies of the Potent Anti-HIV Chemokine Variant P2-RANTES 
Proteins  2010;78(2):295-308.
The N-terminal region of the chemokine RANTES is critical for its function. A synthesized N-terminally modified analog of RANTES, P2-RANTES, was discovered using a phage display selection against living CCR5-expressing cells, and has been reported to inhibit HIV-1 env-mediated cell-cell fusion at subnanomolar levels [Hartley et al J. Virol 77, 6637–44 (2003)]. In the present study we produced this protein using E. coli overexpression and extensively studied its structure and function. The X-ray crystal structure of P2-RANTES was solved and refined at 1.7 Å resolution. This protein was found to be predominantly a monomer in solution by analytical ultracentrifugation, but a tetramer in the crystal. In studies of glycosaminoglycan binding, P2-RANTES was found to be significantly less able to bind heparin than wild type RANTES. We also tested this protein for receptor internalization where it was shown to be functional, in cell-cell fusion assays where recombinant P2-RANTES was a potent fusion inhibitor (IC50= 2.4 ± 0.8 nM), and in single round infection assays where P2-RANTES inhibited at sub-nanomolar levels. Further, in a modified fusion assay designed to test specificity of inhibition, P2-RANTES was also highly effective, with a 65-fold improvement over the fusion inhibitor C37, which is closely related to the clinically approved inhibitor T-20. These studies provide detailed structural and functional information for this novel N-terminally modified chemokine mutant. This information will be very useful in the development of more potent anti-HIV agents.
doi:10.1002/prot.22542
PMCID: PMC4306592  PMID: 19722264
HIV fusion inhibitor; chemokine; GAG binding; quaternary state; competition fusion assay
2.  Cyclic GMP-AMP Synthase is Activated by Double-stranded DNA-Induced Oligomerization 
Immunity  2013;39(6):10.1016/j.immuni.2013.10.019.
Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor mediating innate antimicrobial immunity. It catalyzes the synthesis of a noncanonical cyclic dinucleotide 2′,5′ cGAMP that binds to STING and mediates the activation of TBK1 and IRF-3. Activated IRF-3 translocates to the nucleus and initiates the transcription of the IFN-β gene. The structure of mouse cGAS bound to an 18 bp dsDNA revealed that cGAS interacts with dsDNA through two binding sites, forming a 2:2 complex. Enzyme assays and IFN-β reporter assays of cGAS mutants demonstrated that interactions at both DNA binding sites are essential for cGAS activation. Mutagenesis and DNA binding studies showed that the two sites bind dsDNA cooperatively and site B plays a critical role in DNA binding. The structure of mouse cGAS bound to dsDNA and 2′,5′ cGAMP provided insight into the catalytic mechanism of cGAS. These results demonstrated that cGAS is activated by dsDNA-induced oligomerization.
doi:10.1016/j.immuni.2013.10.019
PMCID: PMC3886715  PMID: 24332030
3.  Structural Basis of Substrate Selectivity of E. coli Prolidase 
PLoS ONE  2014;9(10):e111531.
Prolidases, metalloproteases that catalyze the cleavage of Xaa-Pro dipeptides, are conserved enzymes found in prokaryotes and eukaryotes. In humans, prolidase is crucial for the recycling of collagen. To further characterize the essential elements of this enzyme, we utilized the Escherichia coli prolidase, PepQ, which shares striking similarity with eukaryotic prolidases. Through structural and bioinformatic insights, we have extended previous characterizations of the prolidase active site, uncovering a key component for substrate specificity. Here we report the structure of E. coli PepQ, solved at 2.0 Å resolution. The structure shows an antiparallel, dimeric protein, with each subunit containing N-terminal and C-terminal domains. The C-terminal domain is formed by the pita-bread fold typical for this family of metalloproteases, with two Mg(II) ions coordinated by five amino-acid ligands. Comparison of the E. coli PepQ structure and sequence with homologous structures and sequences from a diversity of organisms reveals distinctions between prolidases from Gram-positive eubacteria and archaea, and those from Gram-negative eubacteria, including the presence of loop regions in the E. coli protein that are conserved in eukaryotes. One such loop contains a completely conserved arginine near the catalytic site. This conserved arginine is predicted by docking simulations to interact with the C-terminus of the substrate dipeptide. Kinetic analysis using both a charge-neutralized substrate and a charge-reversed variant of PepQ support this conclusion, and allow for the designation of a new role for this key region of the enzyme active site.
doi:10.1371/journal.pone.0111531
PMCID: PMC4213023  PMID: 25354344
4.  Structural Insights into the Functions of TBK1 in Innate Antimicrobial Immunity 
Structure (London, England : 1993)  2013;21(7):1137-1148.
SUMMARY
Tank-binding kinase 1 (TBK1) is a serine/threonine protein kinase mediating innate antimicrobial immunity. TBK1 is involved in the signaling of TLRs, RLRs, and STING-mediated sensing of cytosolic DNA. Stimulation of these receptors results in the activation of TBK1, which phosphorylates interferon regulatory factor IRF-3. Phosphorylated IRF-3 translocates into the nucleus to initiate the transcription of the IFN-β gene. Here we show that TBK1 is activated by autophosphorylation at residue Ser172. Structures of TBK1 bound to two inhibitors showed that TBK1 has the IκB kinase fold with three distinct domains: the kinase domain, the ubiquitin like domain, and the scaffold and dimerization domain. However, the overall structures of TBK1 monomer and its dimer are different from IKKβ in the arrangements of the three domains and in dimer formation. Phosphorylation of IRF-3 by TBK1 in vitro results in its oligomerization, and phosphorylation of residue Ser386 plays a key role in IRF-3 activation.
doi:10.1016/j.str.2013.04.025
PMCID: PMC3702631  PMID: 23746807
5.  The Structural Basis of Iron Sensing by the Human F-box Protein FBXL5 
doi:10.1002/cbic.201200043
PMCID: PMC4046841  PMID: 22492618
Crystal Structure; F-box; FBXL5; Iron Homeostasis; Iron Sensing
6.  Single Nucleotide Polymorphisms of Human STING Can Affect Innate Immune Response to Cyclic Dinucleotides 
PLoS ONE  2013;8(10):e77846.
The STING (stimulator of interferon genes) protein can bind cyclic dinucleotides to activate the production of type I interferons and inflammatory cytokines. The cyclic dinucleotides can be bacterial second messengers c-di-GMP and c-di-AMP, 3’5’-3’5’ cyclic GMP-AMP (3’3’ cGAMP) produced by Vibrio cholerae and metazoan second messenger 2’5’-3’5’ Cyclic GMP-AMP (2’3’ cGAMP). Analysis of single nucleotide polymorphism (SNP) data from the 1000 Genome Project revealed that R71H-G230A-R293Q (HAQ) occurs in 20.4%, R232H in 13.7%, G230A-R293Q (AQ) in 5.2%, and R293Q in 1.5% of human population. In the absence of exogenous ligands, the R232H, R293Q and AQ SNPs had only modest effect on the stimulation of IFN-β and NF-κB promoter activities in HEK293T cells, while HAQ had significantly lower intrinsic activity. The decrease was primarily due to the R71H substitution. The SNPs also affected the response to the cyclic dinucleotides. In the presence of c-di-GMP, the R232H variant partially decreased the ability to activate IFN-βsignaling, while it was defective for the response to c-di-AMP and 3’3’ cGAMP. The R293Q dramatically decreased the stimulatory response to all bacterial ligands. Surprisingly, the AQ and HAQ variants maintained partial abilities to activate the IFN-β signaling in the presence of ligands due primarily to the G230A substitution. Biochemical analysis revealed that the recombinant G230A protein could affect the conformation of the C-terminal domain of STING and the binding to c-di-GMP. Comparison of G230A structure with that of WT revealed that the conformation of the lid region that clamps onto the c-di-GMP was significantly altered. These results suggest that hSTING variation can affect innate immune signaling and that the common HAQ haplotype expresses a STING protein with reduced intrinsic signaling activity but retained the ability to response to bacterial cyclic dinucleotides.
doi:10.1371/journal.pone.0077846
PMCID: PMC3804601  PMID: 24204993
7.  Crystallographic characterization of mouse AIM2 HIN-200 domain bound to a 15 bp and an 18 bp double-stranded DNA 
AIM2 is an innate immune sensor of microbial double-stranded DNA. The HIN-200 domain of mouse AIM2 bound to a 15 bp and an 18 bp dsDNA were crystallized and diffract to about 4.0 Å.
AIM2 (absent in melanoma 2) is an innate immune receptor for cytosolic double-stranded DNA (dsDNA). The engagement of dsDNA by AIM2 activates the AIM2 inflammasome, resulting in the cleavage of pro-interleukin-1β by caspase-1. The DNA-binding HIN-200 domain of mouse AIM2 bound to a 15 bp dsDNA and to an 18 bp dsDNA was purified and crystallized. The AIM2 HIN-200 domain in complex with the 15 bp DNA crystallized in the cubic space group I23 or I213, with unit-cell parameter a = 235.60 Å. The complex of the AIM2 HIN-200 domain and the 18 bp DNA crystallized in a similar unit cell. Diffraction data for the two complexes were collected to about 4.0 Å resolution. Mutagenesis and DNA-binding studies suggest that mouse AIM2 uses a similar surface to human AIM2 to recognize DNA.
doi:10.1107/S174430911203103X
PMCID: PMC3433203  PMID: 22949200
mouse AIM2; HIN-200 domain; DNA binding
8.  Structure of STING bound to c-di-GMP Reveals the Mechanism of Cyclic Dinucleotide Recognition by the Immune System 
STING, stimulator of interferon genes, is an innate immune sensor of cyclic dinucleotides that regulates the induction of type I interferons. STING C-terminal domain forms a V-shaped dimer and binds a c-di-GMP molecule at the dimer interface through direct and solvent-mediated hydrogen bonds. The guanine bases of c-di-GMP stack against the phenolic rings of a conserved tyrosine residue. Mutations at the c-di-GMP binding surface reduce nucleotide binding and affect signaling.
doi:10.1038/nsmb.2331
PMCID: PMC3392545  PMID: 22728658
9.  Peli1 negatively regulates T-cell activation and prevents autoimmunity 
Nature immunology  2011;12(10):1002-1009.
T-cell activation is subject to tight regulation to avoid inappropriate responses against self-antigens. Here we show that genetic deficiency in an ubiquitin ligase, Peli1, causes hyper activation of T cells and renders T cells refractory to suppression by T regulatory cells and transforming growth factor (TGF)-β. As a result, Peli1 knockout mice spontaneously develop autoimmunity, characterized by multiorgan inflammation and autoantibody production. Peli1 deficiency results in accumulation of nuclear c-Rel, a member of the NF-κB family of transcription factors with pivotal roles in T-cell activation. Peli1 negatively regulates c-Rel by mediating its K48 ubiquitination. These results identify Peli1 as a critical factor in the maintenance of peripheral T-cell tolerance and reveal a novel mechanism of c-Rel regulation.
doi:10.1038/ni.2090
PMCID: PMC3178748  PMID: 21874024
10.  New monoclonal anti-mouse DC-SIGN antibodies reactive with acetone-fixed cells 
Journal of immunological methods  2010;360(1-2):66-75.
Mouse DC-SIGN CD209a is a type II transmembrane protein, one of a family of C-type lectin genes syntenic and homologous to human DC-SIGN. Current anti-mouse DC-SIGN monoclonal antibodies (MAbs) are unable to react with DC-SIGN in acetone fixed cells, limiting the chance to visualize DC-SIGN in tissue sections. We first produced rabbit polyclonal PAb-DSCYT14 against a 14-aa peptide in the cytosolic domain of mouse DC-SIGN, and it specifically detected DC-SIGN and not the related lectins, SIGN-R1 and SIGN-R3 expressed in transfected CHO cells. MAbs were generated by immunizing rats and DC-SIGN knockout mice with the extracellular region of mouse DC-SIGN.. Five rat IgG2a or IgM MAbs, named BMD10, 11, 24, 25, and 30, were selected and each MAb specifically detected DC-SIGN by FACS and Western blots, although BMD25 was cross-reactive to SIGN-R1. Two mouse IgG2c MAbs MMD2 and MMD3 interestingly bound mouse DC-SIGN but at 10 fold higher levels than the rat MAbs. When the binding epitopes of the new BMD and two other commercial rat anti-DC-SIGN MAbs, 5H10 and LWC06, were examined by competition assays, the epitopes of BMD11, 24, and LWC06 were identical or closely overlapping while BMD10, 30, and 5H10 were shown to bind different epitopes. MMD2 and MMD3 epitopes were on a 3rd noncompeting region of mouse DC-SIGN. DC-SIGN expressed on the cell surface was sensitive to collagenase treatment, as monitored by polyclonal and MAb. These new reagents should be helpful to probe the biology of DC-SIGN in vivo.
doi:10.1016/j.jim.2010.06.006
PMCID: PMC2924951  PMID: 20558171
Monoclonal Antibody; Polyclonal Antibody; DC-SIGN; CD209a; Dendritic Cells
11.  The Structural Basis of 5′ Triphosphate Double-stranded RNA Recognition by RIG-I C-terminal Domain 
Structure (London, England : 1993)  2010;18(8):1032-1043.
SUMMARY
RIG-I is a cytosolic sensor of viral RNA that plays crucial roles in the induction of type I interferons. The C-terminal domain (CTD) of RIG-I is responsible for the recognition of viral RNA with 5′ triphosphate (5′ ppp). However, the mechanism of viral RNA recognition by RIG-I is still not fully understood. Here we show that RIG-I CTD binds 5′ ppp dsRNA or ssRNA, as well as blunt-ended dsRNA, and exhibits the highest affinity for 5′ ppp dsRNA. Crystal structures of RIG-I CTD bound to 5′ ppp dsRNA with GC- and AU- rich sequences revealed that RIG-I recognizes the termini of the dsRNA and interacts with the 5′ triphosphate through extensive electrostatic interactions. Mutagenesis and RNA binding studies demonstrated that similar binding surfaces are involved in the recognition of different forms of RNA. Mutations of key residues at the RNA binding surface affected RIG-I signaling in cells.
doi:10.1016/j.str.2010.05.007
PMCID: PMC2919622  PMID: 20637642
12.  Crystal structure of RIG-I C-terminal domain bound to blunt-ended double-strand RNA without 5′ triphosphate 
Nucleic Acids Research  2010;39(4):1565-1575.
RIG-I recognizes molecular patterns in viral RNA to regulate the induction of type I interferons. The C-terminal domain (CTD) of RIG-I exhibits high affinity for 5′ triphosphate (ppp) dsRNA as well as blunt-ended dsRNA. Structures of RIG-I CTD bound to 5′-ppp dsRNA showed that RIG-I recognizes the termini of dsRNA and interacts with the ppp through electrostatic interactions. However, the structural basis for the recognition of non-phosphorylated dsRNA by RIG-I is not fully understood. Here, we show that RIG-I CTD binds blunt-ended dsRNA in a different orientation compared to 5′ ppp dsRNA and interacts with both strands of the dsRNA. Overlapping sets of residues are involved in the recognition of blunt-ended dsRNA and 5′ ppp dsRNA. Mutations at the RNA-binding surface affect RNA binding and signaling by RIG-I. These results provide the mechanistic basis for how RIG-I recognizes different RNA ligands.
doi:10.1093/nar/gkq974
PMCID: PMC3045611  PMID: 20961956

Results 1-12 (12)