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Song X, Hu R, Chen Y, Xiao M, Zhang H, Wu S, Lu Q. The structure of TRAF7 coiled-coil trimer provides insight into its function in zebrafish embryonic development. J Mol Cell Biol 2024:mjad083. [PMID: 38178633 DOI: 10.1093/jmcb/mjad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
TRAF7 serves as a crucial intracellular adaptor and E3 ubiquitin ligase involved in signal transduction pathways, contributing to immune responses, tumor progression, and embryonic development. Somatic mutations within the coiled-coil (CC) domain and WD40 repeat domain of TRAF7 could cause brain tumors, while germline pathogenic mutations contribute to severe developmental abnormalities. However, the precise molecular mechanism underlying TRAF7 involvement in embryonic development remains unclear. In this study, we employed zebrafish as an in-vivo model system. TRAF7 knockdown caused defects in zebrafish embryonic development. We determined the crystal structure of TRAF7 CC domain at 3.3 Å resolution and found that the CC region trimerization was essential for TRAF7 functionality during zebrafish embryonic development. Additionally, disease-causing mutations in TRAF7 CC region could impair the trimer formation, consequently impacting early embryonic development of zebrafish. Therefore, our study sheds light on the molecular mechanism of TRAF7 CC trimer formation and its pivotal role in embryonic development.
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Affiliation(s)
- Xiaozhen Song
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Ruixing Hu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yi Chen
- Laboratory of Development and Diseases and State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Man Xiao
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Hong Zhang
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Shengnan Wu
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
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Zhu R, Xu XG, Zhang TX, Wang XP, Zhang CH, Wang CY, Wang C, Wu JX, Yu B, Yu XH. Molecular Mechanism of Adenovirus Late Protein L4-100K Chaperones the Trimerization of Hexon. J Virol 2023; 97:e0146722. [PMID: 36475768 DOI: 10.1128/jvi.01467-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Assembly of the adenovirus capsid protein hexon depends on the assistance of the molecular chaperone L4-100K. However, the chaperone mechanisms remain unclear. In this study, we found that L4-100K was involved in the hexon translation process and could prevent hexon degradation by the proteasome in cotransfected human cells. Two nonadjacent domains, 84-133 and 656-697, at the N-terminal and C-terminal regions of human adenovirus type 5 L4-100K, respectively, were found to be crucial and cooperatively responsible for hexon trimer expression and assembly. These two chaperone-related domains were conserved in the sequence of L4-100K and in the function of hexon assembly across different adenovirus serotypes. Different degrees of cross-activity of hexon trimerization with different serotypes were detected in subgroups B, C, and D, which were proven to be controlled by the interaction between the C-terminal chaperone-related domain of L4-100K and hypervariable regions (HVR) of hexon. Additionally, HVR-chimeric hexon mutants were successfully assembled with the assistance of the 1-697 mutant. Structural analysis of 656-697 by nuclear magnetic resonance and structural prediction of L4-100K using Robetta showed that the two conserved domains are mainly composed of α-helices and are located on the surface of the highly folded core region. Our research provides a more complete understanding of hexon assembly and guidance for the development of hexon-chimeric adenovirus vectors that will be safer, smarter, and more efficient. IMPORTANCE Adenovirus vectors have been widely used in clinical trials of vaccines and gene therapy, although some deficiencies remain. Chimeric modification of the hexon was expected to improve the potency of preexisting immune evasion and targeting, but in many cases, viral packaging is prevented by the inability of the chimeric hexon to assemble correctly. So far, few studies have examined the mechanisms of hexon trimer assembly. Here, we show how the chaperone protein L4-100K contributes to the assembly of the adenovirus capsid protein hexon, and these data will provide a guide for novel adenovirus vector design and development, as we desired.
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Thangaraj R, Fiser B, Qiu X, Li C, Viskolcz B, Szőri M. An Ab Initio Investigation on Relevant Oligomerization Reactions of Toluene Diisocyanate (TDI). Polymers (Basel) 2022; 14:4183. [PMID: 36236129 DOI: 10.3390/polym14194183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
2,4- and 2,6-isomers of toluene diisocyanates (2,4-TDI and 2,6-TDI) are important raw materials in the polyurethane industry. These reactive compounds associate even under ambient conditions to form oligomers, changing the physicochemical properties of the raw material. Kinetically and thermodynamically relevant dimerization reactions were selected based on G3MP2B3 calculations from all possible dimers of phenyl isocyanate using these isocyanates as proxies. As it turned out, only the formation of the diazetidine-2,4-dione ring (11-dimer, uretdione) resulted in a species having an exothermic enthalpy of formation (−30.4 kJ/mol at 298.15 K). The oxazetidin-2-one ring product (1-2-dimer) had a slightly endothermic standard enthalpy of formation (37.2 kJ/mol at 298.15 K). The mechanism of the relevant cyclodimerization reactions was investigated further for 2,4-TDI and 2,6-TDI species using G3MP2B3 and SMD solvent model for diazetidine as well as oxazetidin-2-one ring formation. The formation of the uretdione ring structures, from the 2,4-TDI dimer with both NCO groups in the meta position for each phenyl ring and one methyl group in the para and one in the meta position, had the lowest-lying transition state (Δ#E0 = 94.4 kJ/mol) in the gas phase. The one- and two-step mechanisms of the TDI cyclotrimerization were also studied based on the quasi-G3MP2B3 (qG3MP2B3) computational protocol. The one-step mechanism had an activation barrier as high as 149.0 kJ/mol, while the relative energies in the two-step mechanism were significantly lower for both transition states in the gas phase (94.7 and 60.5 kJ/mol) and in ODCB (87.0 and 54.0 kJ/mol).
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Zhou J, Zhang C, Huo H, Zhang J, Meng Z, Yu T, Liu Y, Fu X, Qiu L, Wang B. Comparative Studies on Thermal Decompositions of Dinitropyrazole-Based Energetic Materials. Molecules 2021; 26:7004. [PMID: 34834092 PMCID: PMC8625743 DOI: 10.3390/molecules26227004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/24/2022] Open
Abstract
Dinitropyrazole is an important structure for the design and synthesis of energetic materials. In this work, we reported the first comparative thermal studies of two representative dinitropyrazole-based energetic materials, 4-amino-3,5-dinitropyrazole (LLM-116) and its novel trimer derivative (LLM-226). Both the experimental and theoretical results proved the active aromatic N-H moiety would cause incredible variations in the physicochemical characteristics of the obtained energetic materials. Thermal behaviors and kinetic studies of the two related dinitropyrazole-based energetic structures showed that impressive thermal stabilization could be achieved after the trimerization, but also would result in a less concentrated heat-release process. Detailed analysis of condensed-phase systems and the gaseous products during the thermal decomposition processes, and simulation studies based on ReaxFF force field, indicated that the ring opening of LLM-116 was triggered by hydrogen transfer of the active aromatic N-H moiety. In contrast, the initial decomposition of LLM-226 was caused by the rupture of carbon-nitrogen bonds at the diazo moiety.
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Affiliation(s)
- Jing Zhou
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (J.Z.); (Z.M.)
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China; (C.Z.); (H.H.); (J.Z.); (T.Y.); (Y.L.)
| | - Chongmin Zhang
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China; (C.Z.); (H.H.); (J.Z.); (T.Y.); (Y.L.)
| | - Huan Huo
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China; (C.Z.); (H.H.); (J.Z.); (T.Y.); (Y.L.)
| | - Junlin Zhang
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China; (C.Z.); (H.H.); (J.Z.); (T.Y.); (Y.L.)
| | - Zihui Meng
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (J.Z.); (Z.M.)
| | - Tao Yu
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China; (C.Z.); (H.H.); (J.Z.); (T.Y.); (Y.L.)
| | - Yingzhe Liu
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China; (C.Z.); (H.H.); (J.Z.); (T.Y.); (Y.L.)
| | - Xiaolong Fu
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China; (C.Z.); (H.H.); (J.Z.); (T.Y.); (Y.L.)
| | - Lili Qiu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (J.Z.); (Z.M.)
| | - Bozhou Wang
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China; (C.Z.); (H.H.); (J.Z.); (T.Y.); (Y.L.)
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Mittal N, Sengupta N, Malladi SK, Reddy P, Bhat M, Rajmani RS, Sedeyn K, Saelens X, Dutta S, Varadarajan R. Protective Efficacy of Recombinant Influenza Hemagglutinin Ectodomain Fusions. Viruses 2021; 13:v13091710. [PMID: 34578291 PMCID: PMC8473191 DOI: 10.3390/v13091710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
In current seasonal influenza vaccines, neutralizing antibody titers directed against the hemagglutinin surface protein are the primary correlate of protection. These vaccines are, therefore, quantitated in terms of their hemagglutinin content. Adding other influenza surface proteins, such as neuraminidase and M2e, to current quadrivalent influenza vaccines would likely enhance vaccine efficacy. However, this would come with increased manufacturing complexity and cost. To address this issue, as a proof of principle, we have designed genetic fusions of hemagglutinin ectodomains from H3 and H1 influenza A subtypes. These recombinant H1-H3 hemagglutinin ectodomain fusions could be transiently expressed at high yield in mammalian cell culture using Expi293F suspension cells. Fusions were trimeric, and as stable in solution as their individual trimeric counterparts. Furthermore, the H1-H3 fusion constructs were antigenically intact based on their reactivity with a set of conformation-specific monoclonal antibodies. H1-H3 hemagglutinin ectodomain fusion immunogens, when formulated with the MF59 equivalent adjuvant squalene-in-water emulsion (SWE), induced H1 and H3-specific humoral immune responses equivalent to those induced with an equimolar mixture of individually expressed H1 and H3 ectodomains. Mice immunized with these ectodomain fusions were protected against challenge with heterologous H1N1 (Bel/09) and H3N2 (X-31) mouse-adapted viruses with higher neutralizing antibody titers against the H1N1 virus. Use of such ectodomain-fused immunogens would reduce the number of components in a vaccine formulation and allow for the inclusion of other protective antigens to increase influenza vaccine efficacy.
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MESH Headings
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Cross Protection/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/administration & dosage
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Mice
- Mice, Inbred BALB C
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/prevention & control
- Vaccine Efficacy
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
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Affiliation(s)
- Nidhi Mittal
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
| | - Nayanika Sengupta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
| | - Sameer Kumar Malladi
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
| | - Poorvi Reddy
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India; (P.R.); (M.B.)
| | - Madhuraj Bhat
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India; (P.R.); (M.B.)
| | - Raju S. Rajmani
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium; (K.S.); (X.S.)
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium; (K.S.); (X.S.)
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
| | - Somnath Dutta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
| | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
- Correspondence: ; Tel.: +91-80-22932612; Fax: +91-80-23600535
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Li J, Jiang S, Ding L, Wang L. Reaction kinetics and properties of MDI base poly (urethane-isocyanurate) network polymers. Des Monomers Polym 2021; 24:265-273. [PMID: 34471398 PMCID: PMC8405120 DOI: 10.1080/15685551.2021.1971858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/19/2021] [Indexed: 11/25/2022] Open
Abstract
Since the trimerization of isocyanate occurs easily and controllably to form a clear trifunctional isocyanate ring, this reaction is an ideal candidate for the synthesis of a clear poly(urethane-isocyanurate) network polymer. Poly(urethane-isocyanurate) network polymer (PUI) was prepared from diphenylmethane diisocyanate (MDI) and propylene glycol (PPG) by cyclotrimerization of isocyanate group (NCO). It was proved that the expected product was successfully prepared by NCO determination, fourier transform infrared (FTIR) and gel permeation chromatography (GPC) characterization. The mechanical and thermal properties were characterized. Through the effects of catalyst dosage, polyurethane prepolymer molecular weight, reaction time, reaction temperature and MDI addition on the reaction process, it is determined that under certain other conditions, the step heating method is better for cyclotrimerization reaction. Generally, the better heating conditions are 60 °C/1 h + 80 °C/4 h + 100 °C/2 h + 120 °C/2 h + 140 °C/2 h + 160 °C/2 h. The results of thermogravimetric analysis (TGA) and mechanical properties showed that with the increase of cross-linking points in the polymer structure, the thermal stability, tensile strength, tensile modulus and hardness of PUI increased, while the elongation at break decreased significantly. The glass transition temperature (Tg) of PUI is around 45 °C, and it can be seen that the elastic modulus of the material can range from 58 to 1980 MPa. X-ray diffraction results show that the rubber phase represented by the flexible segment and the plastic phase represented by the rigid structure are amorphous.
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Affiliation(s)
- Juan Li
- Department of Polymer and Composite Material, School of Materials Science and Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Shengling Jiang
- Key Laboratory of Carbon Fiber and Functional Polymers of Ministry of Education, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Liang Ding
- Department of Polymer and Composite Material, School of Materials Science and Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Lingfang Wang
- Department of Polymer and Composite Material, School of Materials Science and Engineering, Yancheng Institute of Technology, Yancheng, China
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Javaid N, Patra MC, Seo H, Yasmeen F, Choi S. A Rational Insight into the Effect of Dimethyl Sulfoxide on TNF-α Activity. Int J Mol Sci 2020; 21:E9450. [PMID: 33322533 DOI: 10.3390/ijms21249450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
Direct inhibition of tumor necrosis factor-alpha (TNF-α) action is considered a promising way to prevent or treat TNF-α-associated diseases. The trimeric form of TNF-α binds to its receptor (TNFR) and activates the downstream signaling pathway. The interaction of TNF-α with molecular-grade dimethyl sulfoxide (DMSO) in an equal volumetric ratio renders TNF-α inert, in this state, TNF-α fails to activate TNFR. Here, we aimed to examine the inhibition of TNF-α function by various concentrations of DMSO. Its higher concentration led to stronger attenuation of TNF-α-induced cytokine secretion by fibroblasts, and of their death. We found that this inhibition was mediated by a perturbation in the formation of the functional TNF-α trimer. Molecular dynamics simulations revealed a transient interaction between DMSO molecules and the central hydrophobic cavity of the TNF-α homodimer, indicating that a brief interaction of DMSO with the TNF-α homodimer may disrupt the formation of the functional homotrimer. We also found that the sensitizing effect of actinomycin D on TNF-α-induced cell death depends upon the timing of these treatments and on the cell type. This study will help to select an appropriate concentration of DMSO as a working solvent for the screening of water-insoluble TNF-α inhibitors.
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Azad T, Singaravelu R, Crupi MJ, Jamieson T, Dave J, Brown EE, Rezaei R, Taha Z, Boulton S, Martin NT, Surendran A, Poutou J, Ghahremani M, Nouri K, Whelan JT, Duong J, Tucker S, Diallo JS, Bell JC, Ilkow CS. Implications for SARS-CoV-2 Vaccine Design: Fusion of Spike Glycoprotein Transmembrane Domain to Receptor-Binding Domain Induces Trimerization. Membranes (Basel) 2020; 10:membranes10090215. [PMID: 32872641 PMCID: PMC7557813 DOI: 10.3390/membranes10090215] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic presents an urgent need for an effective vaccine. Molecular characterization of SARS-CoV-2 is critical to the development of effective vaccine and therapeutic strategies. In the present study, we show that the fusion of the SARS-CoV-2 spike protein receptor-binding domain to its transmembrane domain is sufficient to mediate trimerization. Our findings may have implications for vaccine development and therapeutic drug design strategies targeting spike trimerization. As global efforts for developing SARS-CoV-2 vaccines are rapidly underway, we believe this observation is an important consideration for identifying crucial epitopes of SARS-CoV-2.
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Affiliation(s)
- Taha Azad
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Ragunath Singaravelu
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mathieu J.F. Crupi
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Taylor Jamieson
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jaahnavi Dave
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Emily E.F. Brown
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Reza Rezaei
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Zaid Taha
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Stephen Boulton
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Nikolas T. Martin
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Abera Surendran
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Joanna Poutou
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mina Ghahremani
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
| | - Kazem Nouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
| | - Jack T. Whelan
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jessie Duong
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Sarah Tucker
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jean-Simon Diallo
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - John C. Bell
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Carolina S. Ilkow
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; (T.A.); (R.S.); (M.J.F.C.); (T.J.); (J.D.); (E.E.F.B.); (R.R.); (Z.T.); (S.B.); (N.T.M.); (A.S.); (J.P.); (J.T.W.); (J.D.); (S.T.); (J.-S.D.); (J.C.B.)
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Correspondence: ; Tel.: +1-613-737-8899 (ext. 75208)
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9
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Xu F, Yang S, Jiang G, Ye Q, Wei B, Wang H. Fluorinated, Sulfur-Rich, Covalent Triazine Frameworks for Enhanced Confinement of Polysulfides in Lithium-Sulfur Batteries. ACS Appl Mater Interfaces 2017; 9:37731-37738. [PMID: 28990391 DOI: 10.1021/acsami.7b10991] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Lithium-sulfur battery represents a promising class of energy storage technology owing to its high theoretical energy density and low cost. However, the insulating nature, shuttling of soluble polysulfides and volumetric expansion of sulfur electrodes seriously give rise to the rapid capacity fading and low utilization. In this work, these issues are significantly alleviated by both physically and chemically restricting sulfur species in fluorinated porous triazine-based frameworks (FCTF-S). One-step trimerization of perfluorinated aromatic nitrile monomers with elemental sulfur allows the simultaneous formation of fluorinated triazine-based frameworks, covalent attachment of sulfur and its homogeneous distribution within the pores. The incorporation of electronegative fluorine in frameworks provides a strong anchoring effect to suppress the dissolution and accelerate the conversion of polysulfides. Together with covalent chemical binding and physical nanopore-confinement effects, the FCTF-S demonstrates superior electrochemical performances, as compared to those of the sulfur-rich covalent triazine-based framework without fluorine (CTF-S) and porous carbon delivering only physical confinement. Our approach demonstrates the potential of regulating lithium-sulfur battery performances at a molecular scale promoted by the porous organic polymers with a flexible design.
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Affiliation(s)
- Fei Xu
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Northwestern Polytechnical University and Shaanxi Joint Laboratory of Graphene (NPU) , Xi'an 710072, P. R. China
| | - Shuhao Yang
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Northwestern Polytechnical University and Shaanxi Joint Laboratory of Graphene (NPU) , Xi'an 710072, P. R. China
| | - Guangshen Jiang
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Northwestern Polytechnical University and Shaanxi Joint Laboratory of Graphene (NPU) , Xi'an 710072, P. R. China
| | - Qian Ye
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Northwestern Polytechnical University and Shaanxi Joint Laboratory of Graphene (NPU) , Xi'an 710072, P. R. China
| | - Bingqing Wei
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Northwestern Polytechnical University and Shaanxi Joint Laboratory of Graphene (NPU) , Xi'an 710072, P. R. China
- Department of Mechanical Engineering, University of Delaware , Newark, Delaware 19716, United States
| | - Hongqiang Wang
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Northwestern Polytechnical University and Shaanxi Joint Laboratory of Graphene (NPU) , Xi'an 710072, P. R. China
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10
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Tedbury PR, Novikova M, Ablan SD, Freed EO. Biochemical evidence of a role for matrix trimerization in HIV-1 envelope glycoprotein incorporation. Proc Natl Acad Sci U S A 2016; 113:E182-90. [PMID: 26711999 DOI: 10.1073/pnas.1516618113] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The matrix (MA) domain of HIV Gag has important functions in directing the trafficking of Gag to sites of assembly and mediating the incorporation of the envelope glycoprotein (Env) into assembling particles. HIV-1 MA has been shown to form trimers in vitro; however, neither the presence nor the role of MA trimers has been documented in HIV-1 virions. We developed a cross-linking strategy to reveal MA trimers in virions of replication-competent HIV-1. By mutagenesis of trimer interface residues, we demonstrated a correlation between loss of MA trimerization and loss of Env incorporation. Additionally, we found that truncating the long cytoplasmic tail of Env restores incorporation of Env into MA trimer-defective particles, thus rescuing infectivity. We therefore propose a model whereby MA trimerization is required to form a lattice capable of accommodating the long cytoplasmic tail of HIV-1 Env; in the absence of MA trimerization, Env is sterically excluded from the assembling particle. These findings establish MA trimerization as an obligatory step in the assembly of infectious HIV-1 virions. As such, the MA trimer interface may represent a novel drug target for the development of antiretrovirals.
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11
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Abstract
Biogenesis of the Gram-negative outer membrane involves the chaperone seventeen kilodalton protein (Skp). A Skp trimer is currently thought to bind its unfolded outer membrane protein (uOMP) substrates. Using sedimentation equilibrium, we discovered that Skp is not an obligate trimer under physiological conditions and that Na(+), Cl(-), Mg(2+), and PO4(3-) ions are not linked to Skp trimerization. These findings suggest that electrostatics play a negligible role in Skp assembly. Our results demonstrate that Skp monomers are populated at biologically relevant concentrations, which raises the idea that kinetic formation of Skp-uOMP complexes likely involves Skp monomer assembly around its substrate. In addition, van't Hoff analysis of Skp self-association does not support a previously proposed coupled folding and trimerization of Skp.
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Affiliation(s)
- Clifford W. Sandlin
- T.C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore MD 21218
| | - Nathan R. Zaccai
- T.C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore MD 21218
| | - Karen G. Fleming
- T.C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore MD 21218
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12
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Abstract
UNLABELLED The p75 neurotrophin receptor (p75(NTR)) is a multifunctional receptor that participates in many critical processes in the nervous system, ranging from apoptosis to synaptic plasticity and morphological events. It is a member of the tumor necrosis factor receptor (TNFR) superfamily, whose members undergo trimeric oligomerization. Interestingly, p75(NTR) interacts with dimeric ligands (i.e., proneurotrophins or mature neurotrophins), but several of the intracellular adaptors that mediate p75(NTR) signaling are trimeric (i.e., TNFR-associated factor 6 or TRAF6). Consequently, the active receptor signaling unit remains uncertain. To identify the functional receptor complex, we evaluated its oligomerization in vitro and in mice brain tissues using a combination of biochemical techniques. We found that the most abundant homotypic arrangement for p75(NTR) is a trimer and that monomers and trimers coexist at the cell surface. Interestingly, trimers are not required for ligand-independent or ligand-dependent p75(NTR) activation in a growth cone retraction functional assay. However, monomers are capable of inducing acute morphological effects in neurons. We propose that p75(NTR) activation is regulated by its oligomerization status and its levels of expression. These results indicate that the oligomeric state of p75(NTR) confers differential responses and offers an explanation for the diverse and contradictory actions of this receptor in the nervous system. SIGNIFICANCE STATEMENT The p75 neurotrophin receptor (p75(NTR)) regulates a wide range of cellular functions, including apoptosis, neuronal processes remodeling, and synaptic plasticity. The goal of our work was to inquire whether oligomers of the receptor are required for function. Here we report that p75(NTR) predominantly assembles as a trimer, similar to other tumor necrosis factor receptors. Interestingly, monomers and trimers coexist at the cell surface, but trimers are not required for p75(NTR) activation in a functional assay. However, monomers are capable of inducing acute morphological effects in neurons. Identification of the oligomerization state of p75(NTR) begins to provide insights to the mechanisms of signal initiation of this noncatalytic receptor, as well as to develop therapeutic interventions to diminish its activity.
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13
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Hwang ES, Brodsky B. Folding delay and structural perturbations caused by type IV collagen natural interruptions and nearby Gly missense mutations. J Biol Chem 2012; 287:4368-75. [PMID: 22179614 PMCID: PMC3281714 DOI: 10.1074/jbc.m111.269084] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 11/29/2011] [Indexed: 11/06/2022] Open
Abstract
The standard collagen triple helix requires Gly as every third residue in the amino acid sequence, yet all nonfibrillar collagens contain sites where this repeating pattern is interrupted. To explore the effects of such natural interruptions on the triple helix, a 4- or 15-residue sequence from human basement membrane type IV collagen was introduced between (Gly-Xaa-Yaa)(n) domains within a recombinant bacterial collagen. The interruptions had little effect on melting temperature, consistent with the high thermal stability reported for nonfibrillar collagens. Although the 4-residue interruption cannot be accommodated within a standard triple helix, trypsin and thermolysin resistance indicated a tightly packed structure. Central residues of the 15-residue interruption were protease-susceptible, whereas residues near the (Gly-Xaa-Yaa)(n) boundary were resistant, supporting a transition from an alternate conformation to a well packed triple helix. Both interruptions led to a delay in triple-helix folding, with the 15-residue interruption causing slower folding than the 4-residue interruption. These results suggest that propagation through interruptions represents a slow folding step. To clarify the relation between natural interruptions and pathological mutations, a Gly to Ser missense mutation was placed three triplets away from the 4-residue interruption. As a result of this mutation, the 4-residue interruption and nearby triple helix became susceptible to protease digestion, and an additional folding delay was observed. Because Gly missense mutations that cause disease are often located near natural interruptions, structural and folding perturbations arising from such proximity could be a factor in collagen genetic diseases.
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Affiliation(s)
- Eileen S. Hwang
- From the Department of Biochemistry, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854 and
| | - Barbara Brodsky
- From the Department of Biochemistry, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854 and
- the Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155
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14
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Amblar M, Barbas A, Gomez-Puertas P, Arraiano CM. The role of the S1 domain in exoribonucleolytic activity: substrate specificity and multimerization. RNA 2007; 13:317-27. [PMID: 17242308 PMCID: PMC1800512 DOI: 10.1261/rna.220407] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
RNase II is a 3'-5' exoribonuclease that processively hydrolyzes single-stranded RNA generating 5' mononucleotides. This enzyme contains a catalytic core that is surrounded by three RNA-binding domains. At its C terminus, there is a typical S1 domain that has been shown to be critical for RNA binding. The S1 domain is also present in the other major 3'-5' exoribonucleases from Escherichia coli: RNase R and polynucleotide phosphorylase (PNPase). In this report, we examined the involvement of the S1 domain in the different abilities of these three enzymes to overcome RNA secondary structures during degradation. Hybrid proteins were constructed by replacing the S1 domain of RNase II for the S1 from RNase R and PNPase, and their exonucleolytic activity and RNA-binding ability were examined. The results revealed that both the S1 domains of RNase R and PNPase are able to partially reverse the drop of RNA-binding ability and exonucleolytic activity resulting from removal of the S1 domain of RNase II. Moreover, the S1 domains investigated are not equivalent. Furthermore, we demonstrate that S1 is neither responsible for the ability to overcome secondary structures during RNA degradation, nor is it related to the size of the final product generated by each enzyme. In addition, we show that the S1 domain from PNPase is able to induce the trimerization of the RNaseII-PNP hybrid protein, indicating that this domain can have a role in the biogenesis of multimers.
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Affiliation(s)
- Mónica Amblar
- Instituto de Tecnologia Química e Biológica/Universidade Nova de Lisboa, Oeiras, Portugal
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15
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Abstract
The structure of a trimeric domain-swapped form of barnase (EC 3.1. 27.3) was determined by x-ray crystallography at a resolution of 2.2 A from crystals of space group R32. Residues 1-36 of one molecule associate with residues 41-110 from another molecule related through threefold symmetry. The resulting cyclic trimer contains three protein folds that are very similar to those in monomeric barnase. Both swapped domains contain a nucleation site for folding. The formation of a domain-swapped trimer is consistent with the description of the folding process of monomeric barnase as the formation and subsequent association of two foldons.
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Affiliation(s)
- I Zegers
- Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Vlaams Interuniversitair Instituut voor Biotechnologie, Paardenstraat 65, B-1640 St. Genesius Rode, Belgium.
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