The Experts below are selected from a list of 315 Experts worldwide ranked by ideXlab platform
Adam Zlotnick - One of the best experts on this subject based on the ideXlab platform.
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Dynamics of Hepatitis B Virus Capsid Protein Dimer Regulate Assembly through an Allosteric Network.
ACS chemical biology, 2020Co-Authors: Angela Patterson, Adam Zlotnick, Zhongchao Zhao, Elizabeth Waymire, Brian BothnerAbstract:While there is an effective vaccine for Human Hepatitis B Virus (HBV), 257 million people have chronic infections for which there is no cure. The assembly process for the viral capsid is a potential therapeutic target. In order to understand the capsid assembly process, we investigated the Dimeric building blocks of the capsid. To understand what blocks assembly, we took advantage of an assembly incompetent mutant Dimer, Cp149-Y132A, located in the interDimer interface. This mutation leads to changes in Protein dynamics throughout the structure of the Dimer as measured by hydrogen-deuterium exchange mass spectrometry (HDX-MS). To further understand how the HBV capsid assembles, the homologue woodchuck HBV (WHV) capsid Protein Dimer (Cp) was used. WHV is more stable than HBV in HDX-MS and native mass spectrometry experiments. Because the WHV Cp assembles more rapidly into viral capsids than HBV, it was suspected that an increase in stability of the intraDimer interface and/or in the contact region leads to increased assembly rates. The differences in dynamics when comparing HBV and human Cp149-Y132A as well as the differences in dynamics when comparing the HBV and WHV Cps allowed us to map an allosteric network within the HBV Dimer. Through a careful comparison of structure, stability, and dynamics using four different capsid Protein Dimers, we conclude that Protein subunit dynamics regulate HBV capsid assembly.
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the integrity of the intraDimer interface of the hepatitis b virus capsid Protein Dimer regulates capsid self assembly
ACS Chemical Biology, 2020Co-Authors: Zhongchao Zhao, Joseph Cheyen Wang, Carolina Perez Segura, Jodi A Haddenperilla, Adam ZlotnickAbstract:During the hepatitis B virus lifecycle, 120 copies of homoDimeric capsid Protein assemble around a copy of reverse transcriptase and viral RNA and go on to produce an infectious virion. Assembly needs to be tightly regulated by Protein conformational change to ensure symmetry, fidelity, and reproducibility. Here, we show that structures at the intraDimer interface regulate conformational changes at the distal interDimer interface and so regulate assembly. A pair of interacting charged residues, D78 from each monomer, conspicuously located at the top of a four-helix bundle that forms the intraDimer interface, were mutated to serine to disrupt communication between the two monomers. The mutation slowed assembly and destabilized the Dimer to thermal and chemical denaturation. Mutant Dimers showed evidence of transient partial unfolding based on the appearance of new proteolytically sensitive sites. Though the mutant Dimer was less stable, the resulting capsids were as stable as the wildtype, based on assembly and thermal denaturation studies. Cryo-EM image reconstructions of capsid indicated that the subunits adopted an "open" state more usually associated with a free Dimer and that the spike tips were either disordered or highly flexible. Molecular dynamics simulations provide mechanistic explanations for these results, suggesting that D78 stabilizes helix 4a, which forms part of the intraDimer interface, by capping its N-terminus and hydrogen-bonding to nearby residues, whereas the D78S mutation disrupts these interactions, leading to partial unwinding of helix 4a. This in turn weakens the connection from helix 4 and the intraDimer interface to helix 5, which forms the interDimer interface.
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A Disulfide in HBV Core Protein Dimer Allosterically Modifies Capsid Assembly and Stability
Biophysical Journal, 2014Co-Authors: Lisa Selzer, Sarah P Katen, Adam ZlotnickAbstract:During the Hepatitis B virus (HBV) life cycle, assembly and disassembly of the capsid need to be highly regulated. The HBV capsid is formed by 120 copies of the homoDimeric core Protein. Capsid assembly is allosterically regulated, implying that Dimer transitions from assembly-inactive to assembly-active states. Indeed, the intra-Dimer interface (which is distant from the site if inter-Dimer contact) in free Dimer is substantially different than in Dimer from capsid (Packianathan et al (2010)). The intra-Dimer interface contains a pair of completely conserved cysteines at position 61 that can form a disulfide bond.Within capsid, C61-C61 oxidized 7 times faster than in free Dimer indicating Dimer within capsid adopts a conformation that strongly promotes disulfide formation. However, compared to reduced Dimer, oxidized Protein assembled slowly and into lower yields of capsid. In addition, urea disassembly studies showed that capsids formed by oxidized Dimer are less stable to urea treatment than reduced capsids.These results indicate that oxidized Protein adopts a conformation unfavorable for capsid assembly. Sucrose gradient centrifugation and electron microscopy confirmed these findings and revealed that oxidized Dimer forms a higher proportion of small, 90-Dimer particles than reduced Protein.Our results show that structural changes at the Dimer interface can dramatically alter the assembly behavior and stability of the capsid. This distal effect is consistent with allosteric regulation of assembly. Our data also suggest an unsuspected biological role for the C61-C61 disulfide bond. We propose that newly expressed, reduced Protein subunits assemble with high fidelity into capsids packaging the RNA genome. As the life cycle progresses oxidation of the capsid occurs resulting in metastable capsid particles that have a lower energy barrier to disassembly, facilitating the release of the genome.
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conformational changes in the hepatitis b virus core Protein are consistent with a role for allostery in virus assembly
Journal of Virology, 2010Co-Authors: Charles Packianathan, Sarah P Katen, Charles E Dann, Adam ZlotnickAbstract:In infected cells, virus components must be organized at the right place and time to ensure assembly of infectious virions. From a different perspective, assembly must be prevented until all components are available. Hypothetically, this can be achieved by allosterically controlling assembly. Consistent with this hypothesis, here we show that the structure of the hepatitis B virus (HBV) core Protein Dimer, which can spontaneously self-assemble, is incompatible with capsid assembly. Systematic differences between core Protein Dimer and capsid conformations demonstrate linkage between the intraDimer interface and interDimer contact surface. These structures also provide explanations for the capsid-Dimer selectivity of some antibodies and the activities of assembly effectors. Solution studies suggest that the assembly-inactive state is more accurately an ensemble of conformations. Simulations show that allostery supports controlled assembly and results in capsids that are resistant to dissociation. We propose that allostery, as demonstrated in HBV, is common to most self-assembling viruses.
Suzanne Trudel - One of the best experts on this subject based on the ideXlab platform.
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antagonism of the stat3 stat3 Protein Dimer with salicylic acid based small molecules
ChemMedChem, 2011Co-Authors: Steven Fletcher, Brent D. G. Page, Xialoei Zhang, Peibin Yue, Sumaiya Sharmeen, Jagdeep Singh, Wei Zhao, Aaron D. Schimmer, Suzanne Trudel, James TurksonAbstract:More than 50 new inhibitors of the oncogenic Stat3 Protein were identified through a structure-activity relationship (SAR) study based on the previously identified inhibitor S3I-201 (IC₅₀ =86 μM, K(i) >300 μM). A key structural feature of these inhibitors is a salicylic acid moiety, which, by acting as a phosphotyrosine mimetic, is believed to facilitate binding to the Stat3 SH2 domain. Several of the analogues exhibit higher potency than the lead compound in inhibiting Stat3 DNA binding activity, with an in vitro IC₅₀ range of 18.7-51.9 μM, and disruption of Stat3-pTyr peptide interactions with K(i) values in the 15.5-41 μM range. One agent in particular exhibited potent inhibition of Stat3 phosphorylation in both breast and multiple myeloma tumor cells, suppressed the expression of Stat3 target genes, and induced antitumor effects in tumor cells harboring activated Stat3 Protein.
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Antagonism of the Stat3–Stat3 Protein Dimer with Salicylic Acid Based Small Molecules
ChemMedChem, 2011Co-Authors: Steven Fletcher, Brent D. G. Page, Xialoei Zhang, Peibin Yue, Sumaiya Sharmeen, Jagdeep Singh, Wei Zhao, Aaron D. Schimmer, Suzanne TrudelAbstract:More than 50 new inhibitors of the oncogenic Stat3 Protein were identified through a structure-activity relationship (SAR) study based on the previously identified inhibitor S3I-201 (IC₅₀ =86 μM, K(i) >300 μM). A key structural feature of these inhibitors is a salicylic acid moiety, which, by acting as a phosphotyrosine mimetic, is believed to facilitate binding to the Stat3 SH2 domain. Several of the analogues exhibit higher potency than the lead compound in inhibiting Stat3 DNA binding activity, with an in vitro IC₅₀ range of 18.7-51.9 μM, and disruption of Stat3-pTyr peptide interactions with K(i) values in the 15.5-41 μM range. One agent in particular exhibited potent inhibition of Stat3 phosphorylation in both breast and multiple myeloma tumor cells, suppressed the expression of Stat3 target genes, and induced antitumor effects in tumor cells harboring activated Stat3 Protein.
A Haouz - One of the best experts on this subject based on the ideXlab platform.
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Structural basis of potent Zika–dengue virus antibody cross-neutralization
Nature, 2016Co-Authors: Giovanna Barba-spaeth, Wanwisa Dejnirattisai, Alexander Rouvinski, Marie Christine Vaney, Iris Medits, Arvind Sharma, Anavaj Sakuntabhai, Etienne Simon-lorière, Van-mai Cao-lormeau, A HaouzAbstract:Zika virus is a member of the Flavivirus genus that had not been associated with severe disease in humans until the recent outbreaks, when it was linked to microcephaly in newborns in Brazil and to Guillain-Barré syndrome in adults in French Polynesia. Zika virus is related to dengue virus, and here we report that a subset of antibodies targeting a conformational epitope isolated from patients with dengue virus also potently neutralize Zika virus. The crystal structure of two of these antibodies in complex with the envelope Protein of Zika virus reveals the details of a conserved epitope, which is also the site of interaction of the envelope Protein Dimer with the precursor membrane (prM) Protein during virus maturation. Comparison of the Zika and dengue virus immunocomplexes provides a lead for rational, epitope-focused design of a universal vaccine capable of eliciting potent cross-neutralizing antibodies to protect simultaneously against both Zika and dengue virus infections.
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structural basis of potent zika dengue virus antibody cross neutralization
Nature, 2016Co-Authors: Giovanna Barbaspaeth, Wanwisa Dejnirattisai, Alexander Rouvinski, Marie Christine Vaney, Iris Medits, Arvind Sharma, Etienne Simonloriere, Anavaj Sakuntabhai, Vanmai Caolormeau, A HaouzAbstract:Zika virus is a member of the Flavivirus genus that had not been associated with severe disease in humans until the recent outbreaks, when it was linked to microcephaly in newborns in Brazil and to Guillain-Barre syndrome in adults in French Polynesia. Zika virus is related to dengue virus, and here we report that a subset of antibodies targeting a conformational epitope isolated from patients with dengue virus also potently neutralize Zika virus. The crystal structure of two of these antibodies in complex with the envelope Protein of Zika virus reveals the details of a conserved epitope, which is also the site of interaction of the envelope Protein Dimer with the precursor membrane (prM) Protein during virus maturation. Comparison of the Zika and dengue virus immunocomplexes provides a lead for rational, epitope-focused design of a universal vaccine capable of eliciting potent cross-neutralizing antibodies to protect simultaneously against both Zika and dengue virus infections.
Steven Fletcher - One of the best experts on this subject based on the ideXlab platform.
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antagonism of the stat3 stat3 Protein Dimer with salicylic acid based small molecules
ChemMedChem, 2011Co-Authors: Steven Fletcher, Brent D. G. Page, Xialoei Zhang, Peibin Yue, Sumaiya Sharmeen, Jagdeep Singh, Wei Zhao, Aaron D. Schimmer, Suzanne Trudel, James TurksonAbstract:More than 50 new inhibitors of the oncogenic Stat3 Protein were identified through a structure-activity relationship (SAR) study based on the previously identified inhibitor S3I-201 (IC₅₀ =86 μM, K(i) >300 μM). A key structural feature of these inhibitors is a salicylic acid moiety, which, by acting as a phosphotyrosine mimetic, is believed to facilitate binding to the Stat3 SH2 domain. Several of the analogues exhibit higher potency than the lead compound in inhibiting Stat3 DNA binding activity, with an in vitro IC₅₀ range of 18.7-51.9 μM, and disruption of Stat3-pTyr peptide interactions with K(i) values in the 15.5-41 μM range. One agent in particular exhibited potent inhibition of Stat3 phosphorylation in both breast and multiple myeloma tumor cells, suppressed the expression of Stat3 target genes, and induced antitumor effects in tumor cells harboring activated Stat3 Protein.
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Antagonism of the Stat3–Stat3 Protein Dimer with Salicylic Acid Based Small Molecules
ChemMedChem, 2011Co-Authors: Steven Fletcher, Brent D. G. Page, Xialoei Zhang, Peibin Yue, Sumaiya Sharmeen, Jagdeep Singh, Wei Zhao, Aaron D. Schimmer, Suzanne TrudelAbstract:More than 50 new inhibitors of the oncogenic Stat3 Protein were identified through a structure-activity relationship (SAR) study based on the previously identified inhibitor S3I-201 (IC₅₀ =86 μM, K(i) >300 μM). A key structural feature of these inhibitors is a salicylic acid moiety, which, by acting as a phosphotyrosine mimetic, is believed to facilitate binding to the Stat3 SH2 domain. Several of the analogues exhibit higher potency than the lead compound in inhibiting Stat3 DNA binding activity, with an in vitro IC₅₀ range of 18.7-51.9 μM, and disruption of Stat3-pTyr peptide interactions with K(i) values in the 15.5-41 μM range. One agent in particular exhibited potent inhibition of Stat3 phosphorylation in both breast and multiple myeloma tumor cells, suppressed the expression of Stat3 target genes, and induced antitumor effects in tumor cells harboring activated Stat3 Protein.
Tetsuro Yamamoto - One of the best experts on this subject based on the ideXlab platform.
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Monocyte chemotactic S19 ribosomal Protein Dimer in atherosclerotic vascular lesion
Virchows Archiv : an international journal of pathology, 2005Co-Authors: Lei Shi, Noriko Futa, Tamami Sakamoto, Shigeyuki Tsurusaki, Tomoko Matsuda, Norikazu Nishino, Ryuji Kunitomo, Michio Kawasuji, Kazutaka Tokita, Tetsuro YamamotoAbstract:To elucidate the molecular mechanism inducing monocyte/macrophage infiltration in the atherosclerotic lesion, we measured the monocyte chemotactic capacity in the extracts of aortic lesions. Five out of seven extracts exhibited significant chemotactic activities. Immunohistochemical examination with an anti-CD68 monoclonal antibody demonstrated that the five positive lesions possessed obvious monocyte/macrophage infiltrations at the intima, whereas the two negative lesions did so at significantly lower intensities. We subjected the chemotactic extracts to immunological analyses to identify the monocyte chemoattractant in them. The monocyte chemotactic capacities of all positive extracts were removed with anti-S19 ribosomal Protein (RP S19) antibody beads and antimonocyte chemoattractant Protein-1 (MCP-1) antibody beads. In three of the five extracts, the anti-RP S19 antibody beads were more effective than the anti-MCP-1 antibody beads for removal, while in the remaining two extracts, the opposite was observed. A combined immunoabsorption with these beads depleted the monocyte chemotactic capacity of a representative sample of each group. Consistently, the chemotactic capacity of an apparently RP S19 Dimer-predominant extract was strongly inhibited by the presence of a C5a receptor antagonist. These results suggest that the RP S19 Dimer and MCP-1 play a major role in the monocyte/macrophage infiltration of the atherosclerotic vascular lesion.
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S19 ribosomal Protein Dimer augments metal-induced apoptosis in a mouse fibroblastic cell line by ligation of the C5a receptor.
Journal of cellular biochemistry, 2005Co-Authors: Hiroshi Nishiura, Jörg Zwirner, Yoko Shibuya, Sumio Tanase, Noriko Futa, Tamami Sakamoto, Adrian Higginbottom, Peter N. Monk, Tetsuro YamamotoAbstract:To analyze the role of S19 ribosomal Protein (RP S19) in apoptosis, murine NIH3T3 were transfected with either hemagglutinin peptide-tagged (HA) wild-type human RP S19 or a mutant (Gln137Asn) that is resistant to transglutaminase-catalyzed cross-linked-Dimerization. Transfection with the mutant HA-RP S19 inhibited manganese (II) (Mn II)-induced apoptosis whereas the wild-type HA-RP S19 augmented apoptosis and a mock transfection had no effect. Release of the wild-type HA-RP S19 Dimer but not the mutant HA-RP S19 was observed during the apoptosis. The reduced rate of apoptosis of the cells transfected with the mutant HA-RP S19 was overcome by addition of extracellular wild-type RP S19 Dimer. The apoptosis rates in cells transfected with either form of human HA-RP S19 and in mock transfectants were reduced to about 40% by the presence of anti-RP S19 antibody in the culture medium. Immunofluorescence staining and fluorescence-activated cell sorting (FACS) analysis showed that the cell surface expression of the receptor for cross-linked RP S19 Dimer, C5a receptor, increased during apoptosis, concomitant with phosphatidylserine exposure. The expression of the C5a receptor gene also increased twofold. Apoptosis rates in the transfected and control cell lines were also reduced by the presence of an anti-mouse C5a receptor monoclonal antibody or of a peptide C5a receptor antagonist. These results indicated the presence of an RP S19 Dimer- and C5a receptor-mediated autocrine-type augmentation mechanism during Mn II-induced apoptosis in the mouse fibroblastic cell line. In contrast to the RP S19 Dimer, C5a actually inhibited apoptosis, suggesting that signaling through the C5a receptor varies depending on the ligand bound.
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Identification of Receptor-Binding Sites of Monocyte Chemotactic S19 Ribosomal Protein Dimer
The American journal of pathology, 2001Co-Authors: Yoko Shibuya, Hiroshi Nishiura, Norikazu Nishino, Megumi Shiokawa, Takumasa Nishimura, Hiroaki Okabe, Katsumasa Takagi, Tetsuro YamamotoAbstract:The S19 ribosomal Protein (RP S19) cross-linked homo-Dimer attracts monocyte migration by binding to C5a receptor on monocytes (H Nishiura, Y Shibuya, T Yamamoto, Laboratory Investigation, 1998, 78:1615–1623). Using site-directed mutants of recombinant RP S19 and synthetic peptides mimicking RP S19 molecular regions, we currently identified the binding sites of the RP S19 Dimer to the C5a receptor. The RP S19 Dimer activated the receptor by a two-step binding mechanism as in the case of C5a. The first binding site was a basic cluster region containing a-Lys41-His42-Lys43- sequence. The second one was the-Leu131-Asp132-Arg133- moiety, localized 12 residues upstream from the COOH-terminal. The second binding triggered the chemotactic response. The first binding would have a role in achieving a high-binding affinity between the ligand and receptor. The first and second ligand-binding sites of C5a receptor seem to be shared by C5a and the RP S19 Dimer, although overall homology between the amino acid sequences of these ligands is only 4%.
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Acquired immune response as a consequence of the macrophage-dependent apoptotic cell clearance and role of the monocyte chemotactic S19 ribosomal Protein Dimer in this connection.
Laboratory investigation; a journal of technical methods and pathology, 1999Co-Authors: Arjun Shrestha, Kei Horino, Hiroshi Nishiura, Tetsuro YamamotoAbstract:A connection between the apoptotic cell clearance system and the acquired immune system was studied in vivo. When fluorescence-labeled apoptotic HL-60 cells were inoculated into footpads of guinea pigs and rabbits, monocyte/ macrophage infiltration rapidly occurred and subsequently the apoptotic cells as well as the macrophages disappeared from the lesion by 48 hours without any macroscopical signs of inflammation. Inversely, the fluorescent cell debris, which had been engulfed by the macrophages, appeared and chronologically increased in the draining lymphatics and the popliteal lymph nodes by 48 hours. Subsequently, proliferation of T and B lymphocytes in the popliteal lymph nodes was observed. Secondary inoculation of HL-60 cells in the flank skin of guinea pigs on day 3 after the initial inoculation induced an acute immunologic dermatitis with erythema, edema, vascular permeability enhancement, and polymorphonuclear leukocyte infiltration. In vitro characterizations demonstrated the presence of complement dependent cytotoxic IgM antibody against HL-60 cells in their sera. The infiltration of monocytes/macrophages at the apoptotic cell injection site and the subsequent production of the anti-HL-60 cell IgM antibodies were significantly suppressed by in situ injections of anti-S19 ribosomal Protein rabbit antibodies. These results indicated that the serial events with the rapid apoptotic cell clearance by macrophages, the macrophage migration to lymph nodes, and the antigen presentation to T lymphocytes by the macrophages acquire immunity against apoptotic cells. It was also indicated that the S19 ribosomal Protein Dimer was the major chemotactic factor in the initial monocyte/macrophage infiltration to apoptotic cells.
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a monocyte chemotactic factor s19 ribosomal Protein Dimer in phagocytic clearance of apoptotic cells
Laboratory Investigation, 1998Co-Authors: Kei Horino, Yoko Shibuya, Hiroshi Nishiura, T Ohsako, T Hiraoka, Nobuo Kitamura, Tetsuro YamamotoAbstract:HL-60 cells derived from a human promyelocytic leukemia underwent apoptosis by heat treatment. When the heat-treated HL-60 cells were injected into guinea pig skin, monocyte/macrophage infiltration was observed 24 or 36 hours later, and the apoptotic cells were phagocytically cleared by 48 hours after their injection. The infiltration and clearance patterns were quite different from those observed in injection of necrotic or boil-fixed HL-60 cells. The apoptotic cells released a monocyte chemotactic factor in vitro 24 hours after the heat treatment. The chemotactic factor generated was identified as the cross-linked homoDimer of S19 ribosomal Protein by its immunologic and physicochemical properties. A serine protease that inactivates the monocyte chemotactic factor was also released from the apoptotic cells 30 hours after the heat treatment. A super infusion of this protease into the skin where the apoptotic cells had been injected diminished the number of infiltrated monocytes. The present results indicate an important role of the S19 ribosomal Protein Dimer in the phagocytic clearance of apoptotic cells.
