9 results on '"Brett Zirkle"'
Search Results
2. Antigenic variations of recent street rabies virus
- Author
-
Wenbo Wang, Jian Ma, Jianhui Nie, Jia Li, Shouchun Cao, Lan Wang, Chuanfei Yu, Weijin Huang, Yuhua Li, Yongxin Yu, Mifang Liang, Brett Zirkle, Xiaojiang S. Chen, Xuguang Li, Wei Kong, and Youchun Wang
- Subjects
Rabies virus ,glycoprotein ,vaccine ,monoclonal antibody ,neutralization ,Infectious and parasitic diseases ,RC109-216 ,Microbiology ,QR1-502 - Abstract
ABSTRACTThe genetic and/or antigenic differences between street rabies virus (RABV) and vaccine strains could potentially affect effectiveness of rabies vaccines. As such, it is important to continue monitoring the glycoprotein (G) of the street isolates. All RABVG sequences in public database were retrieved and analysed. Using a pseudovirus system, we investigated 99 naturally occurring mutants for their reactivities to well-characterized neutralizing monoclonal antibodies (mAbs) and vaccine-induced antisera. A divergence in G sequences was found between vaccine strains and recent street isolates, with mutants demonstrating resistance to neutralizing mAbs and vaccine-induced antibodies. Moreover, antigenic variants were observed in a wide range of animal hosts and geographic locations, with most of them emerging since 2010. As the number of antigenic variants has increased in recent years, close monitoring on street isolates should be strengthened.
- Published
- 2019
- Full Text
- View/download PDF
3. Understanding the structural basis of HIV-1 restriction by the full length double-domain APOBEC3G
- Author
-
Linda Chelico, Brett Zirkle, Shu-Xing Li, Robin P. Love, Fumiaki Ito, Amit Gaba, Hanjing Yang, Maocai Yan, Aaron Wolfe, Xiaojiang S. Chen, and Nazanin Mohammadzadeh
- Subjects
APOBEC ,Molecular biology ,viruses ,Science ,General Physics and Astronomy ,RNA-binding protein ,HIV Infections ,APOBEC-3G Deaminase ,Virus Replication ,Biochemistry ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Protein Domains ,Animals ,Humans ,lcsh:Science ,APOBEC3G ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,Chemistry ,Virus Assembly ,Cytosine deaminase ,RNA ,General Chemistry ,Cytidine deaminase ,Macaca mulatta ,3. Good health ,Cell biology ,Host-Pathogen Interactions ,HIV-1 ,RNA, Viral ,lcsh:Q ,Structural biology ,Linker ,Dimerization ,030217 neurology & neurosurgery ,DNA - Abstract
APOBEC3G, a member of the double-domain cytidine deaminase (CD) APOBEC, binds RNA to package into virions and restrict HIV-1 through deamination-dependent or deamination-independent inhibition. Mainly due to lack of a full-length double-domain APOBEC structure, it is unknown how CD1/CD2 domains connect and how dimerization/multimerization is linked to RNA binding and virion packaging for HIV-1 restriction. We report rhesus macaque A3G structures that show different inter-domain packing through a short linker and refolding of CD2. The A3G dimer structure has a hydrophobic dimer-interface matching with that of the previously reported CD1 structure. A3G dimerization generates a surface with intensified positive electrostatic potentials (PEP) for RNA binding and dimer stabilization. Unexpectedly, mutating the PEP surface and the hydrophobic interface of A3G does not abolish virion packaging and HIV-1 restriction. The data support a model in which only one RNA-binding mode is critical for virion packaging and restriction of HIV-1 by A3G., APOBEC3G (A3G) belongs to the DNA/RNA cytosine deaminase family that plays important roles in innate immunity against HIV and internal retroelements. Here the authors report the structures of two full-length A3G variants that provides insight into domain organization, multimerization, RNA binding, and viral restriction.
- Published
- 2020
4. Antigenic variations of recent street rabies virus
- Author
-
Shouchun Cao, Yongxin Yu, Wei Kong, Brett Zirkle, Weijin Huang, Jianhui Nie, Jia Li, Youchun Wang, Xiaojiang S. Chen, Mifang Liang, Wenbo Wang, Lan Wang, Chuanfei Yu, Xuguang Li, Jian Ma, and Yuhua Li
- Subjects
glycoprotein ,0301 basic medicine ,Rabies ,Epidemiology ,medicine.drug_class ,Guinea Pigs ,030106 microbiology ,Immunology ,Biology ,Antibodies, Viral ,medicine.disease_cause ,Monoclonal antibody ,Microbiology ,Article ,Neutralization ,03 medical and health sciences ,Vaccine strain ,Viral Envelope Proteins ,Antigen ,Neutralization Tests ,vaccine ,Virology ,Drug Discovery ,medicine ,Animals ,Humans ,chemistry.chemical_classification ,Rabies virus ,General Medicine ,neutralization ,medicine.disease ,Antibodies, Neutralizing ,Antigenic Variation ,030104 developmental biology ,Infectious Diseases ,Rabies Vaccines ,chemistry ,monoclonal antibody ,Female ,Parasitology ,Glycoprotein - Abstract
The genetic and/or antigenic differences between street rabies virus (RABV) and vaccine strains could potentially affect effectiveness of rabies vaccines. As such, it is important to continue monitoring the glycoprotein (G) of the street isolates. All RABVG sequences in public database were retrieved and analysed. Using a pseudovirus system, we investigated 99 naturally occurring mutants for their reactivities to well-characterized neutralizing monoclonal antibodies (mAbs) and vaccine-induced antisera. A divergence in G sequences was found between vaccine strains and recent street isolates, with mutants demonstrating resistance to neutralizing mAbs and vaccine-induced antibodies. Moreover, antigenic variants were observed in a wide range of animal hosts and geographic locations, with most of them emerging since 2010. As the number of antigenic variants has increased in recent years, close monitoring on street isolates should be strengthened.
- Published
- 2019
5. Understanding the Structure, Multimerization, Subcellular Localization and mC Selectivity of a Genomic Mutator and Anti-HIV Factor APOBEC3H
- Author
-
Brett Zirkle, Hanjing Yang, Fumiaki Ito, Aaron Wolfe, Vagan Arutiunian, Xiao Xiao, Shu-Xing Li, and Xiaojiang S. Chen
- Subjects
Models, Molecular ,0301 basic medicine ,RNase P ,Intracellular Space ,lcsh:Medicine ,medicine.disease_cause ,DNA-binding protein ,Article ,Substrate Specificity ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Aminohydrolases ,medicine ,Humans ,lcsh:Science ,Mutation ,Multidisciplinary ,Chemistry ,lcsh:R ,HIV ,RNA ,Genomics ,Subcellular localization ,Immunity, Innate ,Cell biology ,Protein Transport ,HEK293 Cells ,030104 developmental biology ,030220 oncology & carcinogenesis ,5-Methylcytosine ,Nucleic acid ,lcsh:Q ,Protein Multimerization ,Biogenesis ,DNA - Abstract
APOBEC3H (A3H) is a member of the APOBEC3 subfamily of DNA cytosine deaminases that are important for innate immune defense and have been implicated in cancer biogenesis. To understand the structural basis for A3H biochemical function, we determined a high-resolution structure of human A3H and performed extensive biochemical analysis. The 2.49 Å crystal structure reveals a uniquely long C-terminal helix 6 (h6), a disrupted β5 strand of the canonical five-stranded β-sheet core, and a long loop 1 around the Zn-active center. Mutation of a loop 7 residue, W115, disrupted the RNA-mediated dimerization of A3H yielding an RNA-free monomeric form that still possessed nucleic acid binding and deaminase activity. A3H expressed in HEK293T cells showed RNA dependent HMW complex formation and RNase A-dependent deaminase activity. A3H has a highly positively charged surface surrounding the Zn-active center, and multiple positively charged residues within this charged surface play an important role in the RNA-mediated HMW formation and deaminase inhibition. Furthermore, these positively charged residues affect subcellular localization of A3H between the nucleus and cytosol. Finally, we have identified multiple residues of loop 1 and 7 that contribute to the overall deaminase activity and the methylcytosine selectivity.
- Published
- 2018
6. N463 Glycosylation Site on V5 Loop of a Mutant gp120 Regulates the Sensitivity of HIV-1 to Neutralizing Monoclonal Antibodies VRC01/03
- Author
-
Xiaojiang S. Chen, Jian Ma, Jianhui Nie, Wei Kong, Wenbo Wang, Weijing Huang, Kai Gao, Youchun Wang, and Brett Zirkle
- Subjects
Protein Folding ,Glycosylation ,medicine.drug_class ,Viral protein ,Mutant ,HIV Infections ,HIV Envelope Protein gp120 ,Antibodies, Viral ,Gp41 ,Monoclonal antibody ,medicine.disease_cause ,Article ,Neutralization ,Cell Line ,chemistry.chemical_compound ,medicine ,Humans ,Pharmacology (medical) ,Infectivity ,biology ,Antibodies, Monoclonal ,Antibodies, Neutralizing ,Virology ,Molecular biology ,Infectious Diseases ,chemistry ,CD4 Antigens ,Mutation ,HIV-1 ,Mutagenesis, Site-Directed ,biology.protein ,Binding Sites, Antibody ,Antibody - Abstract
BACKGROUND HIV-1 gp120/gp41 is heavily modified by n-linked carbohydrates that play important roles either in correct folding or in shielding vulnerable viral protein surfaces from antibody recognition. METHODS In our previous work, 25 potential N-linked glycosylation sites (PNGS) of a CRF07_BC isolate of HIV-1 were individually mutated, and the resulting effects on infectivity and antibody-mediated neutralization were evaluated. To further understand the functional role of these PNGS, we generated double and multiple mutants from selected individual PNGS mutants. The effects were then evaluated by examining infectivity and sensitivity to antibody-mediated neutralization by neutralizing monoclonal antibodies (nMAbs) and serum antibodies from HIV-1 positive donors. RESULTS Infectivity results showed that, among the 12 combined PNGS mutants, only 197M.1 (N197D/N301Q) lost infectivity completely, whereas all others (except for 197M.6) showed reduced viral infectivity. In terms of neutralization sensitivity to known nMAbs, we found that adding N463Q mutation to all the gp120 mutants containing N197D significantly increased neutralization sensitivity to VRC01 and VRC03, suggesting N197 and N463 have a strong synergistic effect in regulating the neutralizing sensitivity of HIV-1 to the anti-CD4bs nMAbs VRC01/VRC03. Structural analysis based on the available structures of gp120 alone and in complex with CD4 and various nMAbs elucidates a molecular rationale for this experimental observation. CONCLUSIONS The data indicate that N463 plays an important role in regulating the CD4bs MAbs VRC01/VRC03 sensitivity in the genetic background of N197D mutation of gp120, which should provide valuable information for a better understanding of the interplay between HIV-1 and VRC01/03.
- Published
- 2015
7. Early stages of induction of anterior head ectodermal properties inXenopusembryos are mediated by transcriptional cofactorldb1
- Author
-
Carol Zygar Plautz, Malia J. Deshotel, Robert M. Grainger, and Brett Zirkle
- Subjects
Gene knockdown ,Xenopus ,Neural crest ,Ectoderm ,Biology ,biology.organism_classification ,Molecular biology ,medicine.anatomical_structure ,Lens (anatomy) ,Expression cloning ,Eye development ,medicine ,Neural plate ,Developmental Biology - Abstract
Background: Specific molecules involved in early inductive signaling from anterior neural tissue to the placodal ectoderm to establish a lens-forming bias, as well as their regulatory factors, remain largely unknown. In this study, we sought to identify and characterize these molecules. Results: Using an expression cloning strategy to isolate genes with lens-inducing activity, we identified the transcriptional cofactor ldb1. This, together with evidence for its nuclear dependence, suggests its role as a regulatory factor, not a direct signaling molecule. We propose that ldb1 mediates induction of early lens genes in our functional assay by transcriptional activation of lens-inducing signals. Gain-of-function assays demonstrate that the inductive activity of the anterior neural plate on head ectodermal structures can be augmented by ldb1. Loss-of-function assays show that knockdown of ldb1 leads to decreased expression of early lens and retinal markers and subsequently to defects in eye development. Conclusions: The functional cloning, expression pattern, overexpression, and knockdown data show that an ldb1-regulated mechanism acts as an early signal for Xenopus lens induction. Developmental Dynamics 243:1606–1618, 2014. © 2014 Wiley Periodicals, Inc.
- Published
- 2014
8. Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation
- Author
-
Yao Fang, Hanjing Yang, Xiao Xiao, Guillaume Besse, Xiaojiang S. Chen, Vagan Arutiunian, Brett Zirkle, and Cherie Morimoto
- Subjects
0301 basic medicine ,Models, Molecular ,Protein Conformation, alpha-Helical ,Amino Acid Motifs ,Gene Expression ,Plasma protein binding ,Bioinformatics ,Heterogeneous ribonucleoprotein particle ,Crystallography, X-Ray ,Heterogeneous-Nuclear Ribonucleoproteins ,Substrate Specificity ,0302 clinical medicine ,Protein structure ,Structural Biology ,Catalytic Domain ,Cloning, Molecular ,0303 health sciences ,Tryptophan ,Cytidine deaminase ,Recombinant Proteins ,3. Good health ,030220 oncology & carcinogenesis ,Erratum ,Hydrophobic and Hydrophilic Interactions ,Protein Binding ,RNase P ,Static Electricity ,Biology ,Minor Histocompatibility Antigens ,03 medical and health sciences ,Cytidine Deaminase ,Hydrolase ,Genetics ,Escherichia coli ,Humans ,Protein Interaction Domains and Motifs ,RNA, Messenger ,Binding site ,030304 developmental biology ,Binding Sites ,030102 biochemistry & molecular biology ,DNA ,Kinetics ,030104 developmental biology ,HEK293 Cells ,Mutation ,Biophysics ,Nucleic acid ,Biocatalysis ,Protein Conformation, beta-Strand - Abstract
The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species after RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.
- Published
- 2017
9. Structural Basis for HIV-1 Neutralization by 2F5-Like Antibodies m66 and m66.6
- Author
-
Krisha McKee, Gilad Ofek, John R. Mascola, Zhongyu Zhu, Yongping Yang, Nicole A. Doria-Rose, Dimiter S. Dimitrov, Baoshan Zhang, Sijy O'Dell, Ivelin S. Georgiev, Gwo-Yu Chuang, Brett Zirkle, and Peter D. Kwong
- Subjects
Models, Molecular ,Protein Conformation ,Molecular Sequence Data ,Immunology ,Context (language use) ,Antigen-Antibody Complex ,HIV Antibodies ,Gp41 ,Microbiology ,Epitope ,Neutralization ,Epitopes ,Protein structure ,Neutralization Tests ,Virology ,Vaccines and Antiviral Agents ,Humans ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Peptide sequence ,biology ,Antibodies, Neutralizing ,Complementarity Determining Regions ,Molecular biology ,HIV Envelope Protein gp41 ,Molecular Docking Simulation ,Biochemistry ,Insect Science ,Mutation ,HIV-1 ,biology.protein ,Antibody ,Peptides ,Alpha helix ,Protein Binding - Abstract
Antibodies m66.6 and 2F5 are the only effective human HIV-1-neutralizing antibodies reported thus far to recognize the N-terminal region of the membrane-proximal external region (MPER) of the gp41 subunit of the HIV-1 envelope glycoprotein. Although 2F5 has been extensively characterized, much less is known about antibody m66.6 or antibody m66, a closely related light-chain variant. Here, we report the crystal structure of m66 in complex with its gp41 epitope, along with unbound structures of m66 and m66.6. We used mutational and binding analyses to decipher antibody elements critical for their recognition of gp41 and determined the molecular basis that underlies their neutralization of HIV-1. When bound by m66, the N-terminal region of the gp41 MPER adopts a conformation comprising a helix, followed by an extended loop. Comparison of gp41-bound m66 to unbound m66.6 identified three light-chain residues of m66.6 that were confirmed through mutagenesis to underlie the greater breadth of m66.6-mediated virus neutralization. Recognition of gp41 by m66 also revealed similarities to antibody 2F5 both in the conformation of crucial epitope residues as well as in the angle of antibody approach. Aromatic residues at the tip of the m66.6 heavy-chain third complementarity-determining region, as in the case of 2F5, were determined to be critical for virus neutralization in a manner that correlated with antibody recognition of the MPER in a lipid context. Antibodies m66, m66.6, and 2F5 thus utilize similar mechanistic elements to recognize a common gp41-MPER epitope and to neutralize HIV-1.
- Published
- 2014
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.