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Aklima J, Onchaiya S, Saotome T, Velmurugan P, Motoichi T, Naima J, Kuroda Y, Ohta Y. Direct Analysis of Mitochondrial Damage Caused by Misfolded/Destabilized Proteins. Int J Mol Sci 2022; 23:ijms23179881. [PMID: 36077279 PMCID: PMC9456338 DOI: 10.3390/ijms23179881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Protein quality control is essential for cellular homeostasis. In this study, we examined the effect of improperly folded proteins that do not form amyloid fibrils on mitochondria, which play important roles in ATP production and cell death. First, we prepared domain 3 of the dengue envelope protein in wild type and four mutants with widely different biophysical properties in misfolded/aggregated or destabilized states. The effects of the different proteins were detected using fluorescence microscopy and Western blotting, which revealed that three of the five proteins disrupted both inner and outer membrane integrity, while the other two proteins, including the wild type, did not. Next, we examined the common characteristics of the proteins that displayed toxicity against mitochondria by measuring oligomer size, molten globule-like properties, and thermal stability. The common feature of all three toxic proteins was thermal instability. Therefore, our data strongly suggest that thermally unstable proteins generated in the cytosol can cause cellular damage by coming into direct contact with mitochondria. More importantly, we revealed that this damage is not amyloid-specific.
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Affiliation(s)
- Jannatul Aklima
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh
| | - Sawaros Onchaiya
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Tomonori Saotome
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
- Department of Bioengineering, Nagaoka University of Technology, Niigata 940-2188, Japan
| | - Punitha Velmurugan
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Taihei Motoichi
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Jannatul Naima
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Yutaka Kuroda
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Yoshihiro Ohta
- Division of Biotechnology and Life Sciences, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
- Correspondence:
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Dias RS, Teixeira MD, Xisto MF, Prates JWO, Silva JDD, Mello IO, Silva CCD, De Paula SO. DENV-3 precursor membrane (prM) glycoprotein enhances E protein immunogenicity and confers protection against DENV-2 infections in a murine model. Hum Vaccin Immunother 2021; 17:1271-1277. [PMID: 33121347 DOI: 10.1080/21645515.2020.1826798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
To improve a DNA vaccine containing the truncated dengue virus serotype 2 (DENV-2) envelope (E) protein and evaluate the influence of precursor membrane (prM) glycoprotein polymorphism on E protein immunogenicity, two vaccine candidates have been constructed by upstream insertion of the DENV-2 and DENV-3 prM genes into the DENV-2 E gene, named pCID2EtD2prM and pCID2EtD3prM, respectively. Both constructs were able to induce antibody production, which were neutralizing against DENV-2 in a murine model. Splenocytes of immunized groups, when challenged with virus, demonstrated Th1 cytokine pattern and proliferation, in addition to the increase of specific T cells. Vaccine candidates pCID2EtD2prM and pCID2EtD3prM confer 70% and 90% protection against DENV-2, respectively. The pCID2EtD3prM plasmid conferred only 40% protection in the lethal challenge with DENV-2. The results demonstrate that DENV-3 prM has a greater influence on the immunogenicity of the E protein and, probably due to its role as a chaperone, these results may be related to the correct folding and, consequently, an increase in the presentation efficiency of produced transcripts.
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Affiliation(s)
- Roberto S Dias
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa (MG), Brazil
| | - Michelle D Teixeira
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa (MG), Brazil
| | - Mariana F Xisto
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa (MG), Brazil
| | - John W O Prates
- Department of Microbiology, Federal University of Viçosa, Viçosa (MG), Brazil
| | - Jessica D Da Silva
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa (MG), Brazil
| | - Iago O Mello
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa (MG), Brazil
| | - Cynthia C Da Silva
- Department of Microbiology, Federal University of Viçosa, Viçosa (MG), Brazil
| | - Sérgio O De Paula
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa (MG), Brazil
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Saotome T, Doret M, Kulkarni M, Yang YS, Barthe P, Kuroda Y, Roumestand C. Folding of the Ig-Like Domain of the Dengue Virus Envelope Protein Analyzed by High-Hydrostatic-Pressure NMR at a Residue-Level Resolution. Biomolecules 2019; 9:biom9080309. [PMID: 31357538 PMCID: PMC6723665 DOI: 10.3390/biom9080309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/15/2022] Open
Abstract
Dengue fever is a mosquito-borne endemic disease in tropical and subtropical regions, causing a significant public health problem in Southeast Asia. Domain III (ED3) of the viral envelope protein contains the two dominant putative epitopes and part of the heparin sulfate receptor binding region that drives the dengue virus (DENV)’s fusion with the host cell. Here, we used high-hydrostatic-pressure nuclear magnetic resonance (HHP-NMR) to obtain residue-specific information on the folding process of domain III from serotype 4 dengue virus (DEN4-ED3), which adopts the classical three-dimensional (3D) ß-sandwich structure known as the Ig-like fold. Interestingly, the folding pathway of DEN4-ED3 shares similarities with that of the Titin I27 module, which also adopts an Ig-like fold, but is functionally unrelated to ED3. For both proteins, the unfolding process starts by the disruption of the N- and C-terminal strands on one edge of the ß-sandwich, yielding a folding intermediate stable over a substantial pressure range (from 600 to 1000 bar). In contrast to this similarity, pressure-jump kinetics indicated that the folding transition state is considerably more hydrated in DEN4-ED3 than in Titin I27.
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Affiliation(s)
- Tomonori Saotome
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei, Tokyo 184-8588, Japan
| | - Maxime Doret
- Centre de Biochimie Structurale, CNRS UMR 5048, University of Montpellier-INSERM U 1054, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Manjiri Kulkarni
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei, Tokyo 184-8588, Japan
| | - Yin-Shan Yang
- Centre de Biochimie Structurale, CNRS UMR 5048, University of Montpellier-INSERM U 1054, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Philippe Barthe
- Centre de Biochimie Structurale, CNRS UMR 5048, University of Montpellier-INSERM U 1054, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei, Tokyo 184-8588, Japan
| | - Christian Roumestand
- Centre de Biochimie Structurale, CNRS UMR 5048, University of Montpellier-INSERM U 1054, 29 Rue de Navacelles, 34090 Montpellier, France.
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Sobhia ME, Ghosh K, Singh A, Sul K, Singh M, Kumar R, Sandeep, Merugu S, Donempudi S. A Multi-Perspective Review on Dengue Research. Curr Drug Targets 2019; 20:1550-1562. [PMID: 31339068 DOI: 10.2174/1389450120666190724145937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/03/2019] [Accepted: 07/17/2019] [Indexed: 11/22/2022]
Abstract
Dengue fever is a disease which is caused by a family of viruses named Flaviviridae which are transmitted by female Aedes mosquitoes. Today, this is endemic in more than 100 nations in the World Health Organization's African, Americas, Eastern Mediterranean, South-East Asia and Western Pacific locales. The treatment of typical dengue is focused on relieving the symptoms and signs. Carica papaya is a very common plant whose leaf extract is used in the treatment of this disease. Despite extensive research on Dengue, not a single vaccine or anti-viral drug was available until 2016 (a partially effective Chimeric Yellow fever virus treated by DENV-Tetravalent Dengue Vaccine for dengue fever made by Sanofi Pasteur). This review highlights dengue fever's current situation and explains the importance of Natural chemical moieties like methionine-proline anilides, tetrapeptide aldehyde uncovered via Structure Activity Relationship studies. Also, we have reviewed the drug candidates currently in the clinical trials that have the potential to solve these issues. Important patents in the past 20 years have been outlined in this review. An in depth Protein Data Bank analysis of the different possible target proteins that can potentially have a major role in curing Dengue fever has been conducted.
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Affiliation(s)
- M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Ketan Ghosh
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Ajeet Singh
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Komal Sul
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Monica Singh
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Ravi Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Sandeep
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Satti Merugu
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Sunilchand Donempudi
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
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Islam MM, Kobayashi K, Kidokoro S, Kuroda Y. Hydrophobic surface residues can stabilize a protein through improved water–protein interactions. FEBS J 2019; 286:4122-4134. [DOI: 10.1111/febs.14941] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/19/2019] [Accepted: 05/28/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Mohammad M. Islam
- Department of Biochemistry and Molecular Biology University of Chittagong Chittagong Bangladesh
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Tokyo Japan
| | - Kei Kobayashi
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Tokyo Japan
| | - Shun‐Ichi Kidokoro
- Department of Bioengineering Nagaoka University of Technology Niigata Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Tokyo Japan
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Baykov IK, Emelyanova LA, Sokolova LM, Karelina EM, Matveev AL, Babkin IV, Khlusevich YА, Podgornyy VF, Tikunova NV. ANALYSIS OF DOMAIN SPECIFICITY OF THE PROTECTIVE CHIMERIC ANTIBODY ch14D5a AGAINST GLYCOPROTEIN E OF TICK-BORNE ENCEPHALITIS VIRUS. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A drug for the prevention and therapy of tick-borne encephalitis virus is being developed on the basis of the protective chimeric antibody ch14D5a. At the same time, the epitope recognized by this antibody on the surface of glycoprotein E has not been localized yet. The aim of this work was to identify the domain of glycoprotein E, to which the protective antibody ch14D5a binds. As a result, four recombinant variants of glycoprotein E were generated using the bacterial expression system: (1) the rE protein containing the domains D1, D2, and D3 of glycoprotein E; (2) the rED1+2 protein containing domains D1 and D2; (3) the rED3_301 protein, which is domain D3 of glycoprotein E, and (4) the rED3_294 protein comprising domain D3 and a hinge region connecting domains D1 and D3. The rED3_294 and rED3_301 proteins were obtained in soluble monomeric form. The rE and rED1+2 proteins were extracted from the inclusion bodies of Escherichia coli. Using Western blot analysis and surface plasmon resonance analysis, it was demonstrated that the protective chimeric antibody ch14D5a and its Fab fragment bound specifically to domain D3 of glycoprotein E. Since the antibodies recognizing epitopes on the surface of domain D3 do not tend to cause antibody-dependent enhancement of the infection as compared to antibodies directed to domains D1 and D2, the data obtained confirm the promise of using the antibody ch14D5a in the development of a therapeutic preparation against the tick-borne encephalitis virus.
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Saotome T, Nakamura S, Islam MM, Nakazawa A, Dellarole M, Arisaka F, Kidokoro SI, Kuroda Y. Unusual Reversible Oligomerization of Unfolded Dengue Envelope Protein Domain 3 at High Temperatures and Its Abolition by a Point Mutation. Biochemistry 2016; 55:4469-75. [PMID: 27433922 DOI: 10.1021/acs.biochem.6b00431] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report differential scanning calorimetry (DSC) experiments between 10 and 120 °C of Dengue 4 envelope protein domain 3 (DEN4 ED3), a small 107-residue monomeric globular protein domain. The thermal unfolding of DEN4 ED3 was fully reversible and exhibited two peculiar endothermic peaks. AUC (analytical ultracentrifugation) experiments at 25 °C indicated that DEN4 ED3 was monomeric. Detailed thermodynamic analysis indicated that the two endothermic peaks separated with an increasing protein concentration, and global fitting of the DSC curves strongly suggested the presence of unfolded tetramers at temperatures around 80-90 °C, which dissociated to unfolded monomers at even higher temperatures. To further characterize this rare thermal unfolding process, we designed and constructed a DEN4 ED3 variant that would unfold according to a two-state model, typical of globular proteins. We thus substituted Val 380, the most buried residue at the dimeric interface in the protein crystal, with less hydrophobic amino acids (Ala, Ser, Thr, Asn, and Lys). All variants showed a single heat absorption peak, typical of small globular proteins. In particular, the DSC thermogram of DEN4 V380K indicated a two-state reversible thermal unfolding independent of protein concentration, indicating that the high-temperature oligomeric state was successfully abolished by a single mutation. These observations confirmed the standard view that small monomeric globular proteins undergo a two-state unfolding. However, the reversible formation of unfolded oligomers at high temperatures is a truly new phenomenon, which was fully inhibited by an accurately designed single mutation.
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Affiliation(s)
- Tomonori Saotome
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , Tokyo 184-8588, Japan
| | - Shigeyoshi Nakamura
- Department of Bioengineering, Nagaoka University of Technology , Niigata 940-2188, Japan.,Department of Creative Engineering, National Institute of Technology, Kitakyushu College , Kitakyushu 802-0985, Japan
| | - Mohammad M Islam
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , Tokyo 184-8588, Japan
| | - Akiko Nakazawa
- Department of Bioengineering, Nagaoka University of Technology , Niigata 940-2188, Japan
| | - Mariano Dellarole
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université de Montpellier , 34090 Montpellier, France
| | - Fumio Arisaka
- College of Bioresource Science, Nihon University , Fujisawa, Kanagawa 252-0880, Japan
| | - Shun-Ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology , Niigata 940-2188, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , Tokyo 184-8588, Japan
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