1
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Kuroda Y. Biophysical studies of amorphous protein aggregation and in vivo immunogenicity. Biophys Rev 2022; 14:1495-1501. [PMID: 36465085 PMCID: PMC9684872 DOI: 10.1007/s12551-022-01011-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/26/2022] [Indexed: 11/27/2022] Open
Abstract
Amorphous protein aggregates are oligomers that lack specific, high-order structures. Soluble amorphous aggregates are smaller than ~1 µm. Despite their lack of high-order structure, amorphous protein aggregates exhibit specific biophysical properties such as reversibility of formation, density, conformation, and biochemical stability. Our mutational analysis using a Solubility Controlling Peptide (SCP) tag strongly suggests that amorphous aggregation of small globular proteins can significantly increase in vivo immune response and that the magnitude of enhanced immune responses depends on the aggregates' biophysical and biochemical properties. We propose that SCP tags might help develop subunit (protein) adjuvant-free (immunostimulant-free) vaccines by controlling the aggregation propensity of target proteins.
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Affiliation(s)
- Yutaka Kuroda
- Department of Biotechnology and Life Sciences, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-Shi, Tokyo, 184-8588 Japan
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2
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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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3
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Reverse Engineering Analysis of the High-Temperature Reversible Oligomerization and Amyloidogenicity of PSD95-PDZ3. Molecules 2022; 27:molecules27092813. [PMID: 35566161 PMCID: PMC9103278 DOI: 10.3390/molecules27092813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/09/2022] [Accepted: 04/18/2022] [Indexed: 02/01/2023] Open
Abstract
PSD95-PDZ3, the third PDZ domain of the post-synaptic density-95 protein (MW 11 kDa), undergoes a peculiar three-state thermal denaturation (N ↔ In ↔ D) and is amyloidogenic. PSD95-PDZ3 in the intermediate state (I) is reversibly oligomerized (RO: Reversible oligomerization). We previously reported a point mutation (F340A) that inhibits both ROs and amyloidogenesis and constructed the PDZ3-F340A variant. Here, we “reverse engineered” PDZ3-F340A for inducing high-temperature RO and amyloidogenesis. We produced three variants (R309L, E310L, and N326L), where we individually mutated hydrophilic residues exposed at the surface of the monomeric PDZ3-F340A but buried in the tetrameric crystal structure to a hydrophobic leucine. Differential scanning calorimetry indicated that two of the designed variants (PDZ3-F340A/R309L and E310L) denatured according to the two-state model. On the other hand, PDZ3-F340A/N326L denatured according to a three-state model and produced high-temperature ROs. The secondary structures of PDZ3-F340A/N326L and PDZ3-wt in the RO state were unfolded according to circular dichroism and differential scanning calorimetry. Furthermore, PDZ3-F340A/N326L was amyloidogenic as assessed by Thioflavin T fluorescence. Altogether, these results demonstrate that a single amino acid mutation can trigger the formation of high-temperature RO and concurrent amyloidogenesis.
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4
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Saotome T, Onchaiya S, Subbaian B, Mezaki T, Unzai S, Noguchi K, Martinez JC, Kidokoro SI, Kuroda Y. Blocking PSD95-PDZ3's amyloidogenesis through point mutations that inhibit high-temperature reversible oligomerization (RO). FEBS J 2021; 289:3205-3216. [PMID: 34967499 DOI: 10.1111/febs.16339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/05/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Abstract
The third PDZ domain of postsynaptic density protein 95 (PSD95-PDZ3; 11 kDa, 103 residues) has a propensity to form amyloid fibrils at high temperatures. At neutral pH, wild type PDZ3 is natively folded, but it exhibits a peculiar three-state thermal unfolding with a reversible oligomerization (RO) equilibrium at high temperatures, which is uncharacteristic in the unfolding of small globular protein as PDZ3 is. Here, we examined RO's role in PDZ3's amyloidogenesis at high-temperature using two variants (F340A and L342A) that suppress the high-temperature RO and five single-alanine-mutated variants, where we mutated surface-exposed hydrophobic residues to alanine. Circular Dichroism (CD), Analytical Ultracentrifuge (AUC), and other spectroscopic measurements confirmed the retention of the native structure at ambient temperature. Differential Scanning Calorimetry (DSC) was used to assess the presence or absence of the high-temperature RO, and the amyloidogenicity of the variants was measured by Thioflavin T (ThT) fluorescence and Transmission Electron Microscopy (TEM). By comparing the fraction of RO and the ThT signal, we found that mutations that suppressed the high-temperature RO strongly inhibited amyloidogenesis. On the other hand, all variants forming RO also formed amyloids under the same conditions as the wild type PDZ3.
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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.,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1, Harumi-cho, Fuchu, Tokyo, 183-8538, Japan.,Department of Bioengineering, Nagaoka University of Technology, Kamitomioka-cho, Nagaoka, Niigata, 940-2188, Japan
| | - Sawaros Onchaiya
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei, Tokyo, 184-8588, Japan
| | - Brindha Subbaian
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei, Tokyo, 184-8588, Japan
| | - Taichi Mezaki
- Department of Bioengineering, Nagaoka University of Technology, Kamitomioka-cho, Nagaoka, Niigata, 940-2188, Japan
| | - Satoru Unzai
- Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Kajino-cho, Koganei, Tokyo, 185-8584, Japan.,Research Center for Micro-Nano Technology, Hosei University, Midori-cho, Koganei, Tokyo, 184-0003, Japan
| | - Keiichi Noguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei, Tokyo, 184-8588, Japan
| | - Jose C Martinez
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071, Granada, Spain
| | - Shun-Ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology, Kamitomioka-cho, Nagaoka, Niigata, 940-2188, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei, Tokyo, 184-8588, Japan.,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1, Harumi-cho, Fuchu, Tokyo, 183-8538, Japan
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5
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Rahman N, Miura S, Okawa M, Kibria MG, Islam MM, Kuroda Y. Solubility Controlling Peptide Tags of Opposite Charges Generate a Bivalent Immune Response Against Dengue ED3 Serotypes 3 and 4. Front Immunol 2021; 12:671590. [PMID: 34177912 PMCID: PMC8226127 DOI: 10.3389/fimmu.2021.671590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/04/2021] [Indexed: 11/24/2022] Open
Abstract
We previously demonstrated that a protein’s immunogenicity could be substantially increased by attaching a hydrophobic solubility controlling peptide tag (SCP-tag) producing small sub-visible aggregates. Here, we report the oligomerization of Dengue envelop protein domain 3 (ED3), and consequently, its immunogenicity increase by mixing ED3s attached with SCP-tags of opposite charges at equimolar concentration. We used ED3 of serotype 3 (D3ED3) and serotype 4 (D4ED3), which are, respectively, moderately and poorly immunogenic, and their SCP tagged variants constructed by attaching either a C-termini 5-Aspartic acid (C5D) or a 5-Lysine (C5K) tag. Light scattering indicated that the isolated tagged ED3s remained monomeric, but mixing the C5D and C5K tagged ED3s at equimolar concentration generated sub-visible aggregates or oligomers of ~500 nm through electrostatic interaction. In addition, the oligomerized ED3s remained in a native-like state, as assessed by fluorescence spectroscopy and circular dichroism. The in vivo immunogenicity of the D3ED3 and D4ED3 oligomers generated by the charged tags increased by 5 and 16 fold, respectively. Furthermore, injection of heterotypic ED3 oligomers (D3C5D+D4C5K) induced an immune response against both D3ED3 and D4ED3 in 3 of 4 responsive mice, and the IgG titer of the bivalent anti-D3C5D-D4C5K sera was over 100 times higher than that generated by co-injecting the untagged D3ED3 and D4ED3 (D3+D4). Altogether, these observations suggest that SCP-tags could be used as a platform for producing a long-sought tetravalent dengue vaccine.
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Affiliation(s)
- Nafsoon Rahman
- Department of Biotechnology and Life Sciences, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shiho Miura
- Department of Biotechnology and Life Sciences, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Mami Okawa
- Department of Biotechnology and Life Sciences, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Md Golam Kibria
- Department of Biotechnology and Life Sciences, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Mohammad Monirul Islam
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong, Bangladesh
| | - Yutaka Kuroda
- Department of Biotechnology and Life Sciences, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
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6
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Saotome T, Mezaki T, Brindha S, Unzai S, Martinez JC, Kidokoro SI, Kuroda Y. Thermodynamic Analysis of Point Mutations Inhibiting High-Temperature Reversible Oligomerization of PDZ3. Biophys J 2020; 119:1391-1401. [PMID: 32961107 DOI: 10.1016/j.bpj.2020.08.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/12/2020] [Accepted: 08/20/2020] [Indexed: 12/27/2022] Open
Abstract
Differential scanning calorimetry (DSC) indicated that PDZ3 undergoes a peculiar thermal denaturation, exhibiting two endothermic peaks because of the formation of reversible oligomers at high temperature (N↔I6↔D). This contrasts sharply with the standard two-state denaturation model observed for small, globular proteins. We performed an alanine scanning analysis by individually mutating three hydrophobic residues at the crystallographic oligomeric interface (Phe340, Leu342, and Ile389) and one away from the interface (Leu349, as a control). DSC analysis indicated that PDZ3-F340A and PDZ3-L342A exhibited a single endothermic peak. Furthermore, PDZ3-L342A underwent a perfect two-state denaturation, as evidenced by the single endothermic peak and confirmed by detailed DSC analysis, including global fitting of data measured at different protein concentrations. Reversible oligomerization (RO) at high temperatures by small globular proteins is a rare event. Furthermore, our present study showing that a point mutation, L342A, designed based on the crystal structure inhibited RO is surprising because RO occurs at a high-temperature. Future studies will determine how and why mutations designed using crystal structures determined at ambient temperatures influence the formation of RO at high temperatures, and whether high-temperature ROs are related to the propensity of proteins to aggregate or precipitate at lower temperatures, which would provide a novel and unique way of controlling protein solubility and aggregation.
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Affiliation(s)
- Tomonori Saotome
- Department of Biotechnology and Life Science; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Taichi Mezaki
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
| | | | - Satoru Unzai
- Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Tokyo, Japan
| | - Jose C Martinez
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Shun-Ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
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7
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Nakamura S, Kibria MG, Unzai S, Kuroda Y, Kidokoro SI. Reversible Oligomerization and Reverse Hydrophobic Effect Induced by Isoleucine Tags Attached at the C-Terminus of a Simplified BPTI Variant. Biochemistry 2020; 59:3660-3668. [PMID: 32924442 DOI: 10.1021/acs.biochem.0c00436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein amorphous aggregation has become the focus of great attention, as it can impair the ability of cells to function properly. Here, we evaluated the effects of three peptide tags, consisting of one, three, and five consecutive isoleucines attached at the C-terminus end of a simplified bovine pancreatic trypsin inhibitor (BPTI) variant, BPTI-19A, on the thermal stability and oligomerization by circular dichroism spectrometry and differential scanning calorimetry in detail. All of the BPTI-19A variants exhibited a reversible and apparently two-state thermal transition like BPTI-19A at pH 4.7. The thermal transition of the five-isoleucine-tagged variant showed clear protein-concentration dependence, where the apparent denaturation temperature decreased as the protein concentration increased. Quantitative analysis indicated that this phenomenon originated from the presence of reversibly oligomerized (RO) states at high temperatures. The results also illustrated that the thermodynamic stability difference between the native and the monomeric denatured state in all the proteins was destabilized by the hydrophobic tags and was well explained by the reverse hydrophobic effect due to the tags. The existence of the RO states was confirmed by both analytical ultracentrifugation and dynamic light scattering. This indicated that the five-isoleucine hydrophobic tag is strong enough to induce intermolecular hydrophobic contact among the denatured molecules leading to oligomerization, and even one- or three-isoleucine tags are effective enough to generate intramolecular hydrophobic contact, thus provoking denaturation through the reverse hydrophobic effect.
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Affiliation(s)
- Shigeyoshi Nakamura
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.,Department of General Education, National Institute of Technology, Ube College, 2-14-1 Tokiwadai, Ube, Yamaguchi 755-8555, Japan
| | - Md Golam Kibria
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-15 Nakamachi, Koganei, Tokyo 184-8588, Japan
| | - Satoru Unzai
- Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-15 Nakamachi, Koganei, Tokyo 184-8588, Japan
| | - Shun-Ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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8
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Islam MM, Miura S, Hasan MN, Rahman N, Kuroda Y. Anti-Dengue ED3 Long-Term Immune Response With T-Cell Memory Generated Using Solubility Controlling Peptide Tags. Front Immunol 2020; 11:333. [PMID: 32256488 PMCID: PMC7089932 DOI: 10.3389/fimmu.2020.00333] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 02/10/2020] [Indexed: 12/23/2022] Open
Abstract
Recombinant proteins are an attractive choice as a safe alternative to traditional live attenuated vaccines. However, most small-size proteins are poorly immunogenic, and adjuvants, whose mode of action remain to be fully clarified, are needed for increasing their immunogenicity. Here, we report the effects of short solubility controlling peptide tags (SCP-tags) on the immunogenicity of DENV3 envelope protein domain 3 (3ED3; 103 residues, 11.46 kDa) in ICR and Swiss albino model mice. The attachment of a 4-Ile SCP-tag (C4I-tag) increased the hydrodynamic radius of 3ED3 from 2.2 ± 0.09 to 111 ± 146 nm as assessed by dynamic light scattering in phosphate buffered saline at 37°C, indicating that the C4I-tag oligomerized 3ED3. Immunization at 30 μg/dose showed that the untagged 3ED3 was not or poorly immunogenic, whereas the C4I-tag increased its immunogenicity by up to 39-fold as assessed by the IgG level measured using ELISA. Moreover, the increased antibody level was sustained for over 6 months after immunization and a high number of effector and central memory T cells were generated. These observations provide solid and quantitative evidence for the hypothesis that subvisible aggregates with hydrodynamic radii of 100 nm can increase immunogenicity and that SCP-tag can establish a long-term, target-specific immune response in a way adequate for the development of a peptide/protein-based DENV vaccine.
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Affiliation(s)
- Mohammad M Islam
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong, Bangladesh
| | - Shiho Miura
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Mohammad N Hasan
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong, Bangladesh
| | - Nafsoon Rahman
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
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9
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Saotome T, Yamazaki T, Kuroda Y. Misfolding of a Single Disulfide Bonded Globular Protein into a Low-Solubility Species Conformationally and Biophysically Distinct from the Native One. Biomolecules 2019; 9:biom9060250. [PMID: 31242697 PMCID: PMC6627273 DOI: 10.3390/biom9060250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 11/16/2022] Open
Abstract
In practice and despite Anfinsen’s dogma, the refolding of recombinant multiple SS-bonded proteins is famously difficult because misfolded species with non-native SS-bonds appear upon the oxidization of their cysteine residues. On the other hand, single SS-bond proteins are thought to be simple to refold because their cysteines have only one SS-bond partner. Here, we report that dengue 4 envelope protein domain 3 (DEN4 ED3), a single SS-bonded protein can be irreversibly trapped into a misfolded species through the formation of its sole intramolecular SS-bond. The misfolded species had a much lower solubility than the native one at pHs higher than about 7, and circular dichroism measurements clearly indicated that its secondary structure content was different from the native species. Furthermore, the peaks in the Heteronuclear Single Quantum Correlation spectroscopy (HSQC) spectrum of DEN4 ED3 from the supernatant fraction were sharp and well dispersed, reflecting the beta-sheeted native structure, whereas the spectrum of the precipitated fraction showed broad signals clustered near its center suggesting no or little structure and a strong tendency to aggregate. The two species had distinct biophysical properties and could interconvert into each other only by cleaving and reforming the SS-bond, strongly suggesting that they are topologically different. This phenomenon can potentially happen with any single SS-bonded protein, and our observation emphasizes the need for assessing the conformation and biophysical properties of bacterially produced therapeutic proteins in addition to their chemical purities.
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Affiliation(s)
- Tomonori Saotome
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology (TUAT), Tokyo 184-8588, Japan
| | - Toshio Yamazaki
- NMR Facility, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology (TUAT), Tokyo 184-8588, Japan.
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10
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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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11
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Auerswald H, Klepsch L, Schreiber S, Hülsemann J, Franzke K, Kann S, Y B, Duong V, Buchy P, Schreiber M. The Dengue ED3 Dot Assay, a Novel Serological Test for the Detection of Denguevirus Type-Specific Antibodies and Its Application in a Retrospective Seroprevalence Study. Viruses 2019; 11:v11040304. [PMID: 30934772 PMCID: PMC6521013 DOI: 10.3390/v11040304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 02/08/2023] Open
Abstract
There are four distinct antigenic serotypes of dengue viruses (DENV-1-4). Sequential infections with different serotypes lead to cross-reactive but also serotype-specific neutralizing antibody responses. Neutralization assays are considered as gold standard for serotype-specific antibody detection. However, for retrospective seroprevalence studies, access to large serum quantities is limited making neutralization assays well-nigh impossible. Therefore, a serological test, wasting only 10 µL serum, was developed using fusion proteins of maltose binding protein and E protein domain 3 (MBP-ED3) as antigens. Twelve MBP-ED3 antigens for DENV-1-4, three MBP-ED3 antigens for WNV, JEV, and TBEV, and MBP were dotted onto a single nitrocellulose strip. ED3 dot assay results were compared to virus neutralization and ED3 ELISA test results, showing a >90% accordance for DENV-1 and a 100% accordance for DENV-2, making the test specifically useful for DENV-1/-2 serotype-specific antibody detection. Since 2010, DENV-1 has replaced DENV-2 as the dominant serotype in Cambodia. In a retrospective cohort analysis, sera collected during the DENV-1/-2 endemic period showed a shift to DENV-2-specific antibody responses in 2012 paralleled by the decline of DENV-2 infections. Altogether, the ED3 dot assay is a serum-, time- and money-saving diagnostic tool for serotype-specific antibody detection, especially when serum samples are limited.
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Affiliation(s)
- Heidi Auerswald
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
| | - Leonard Klepsch
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
| | - Sebastian Schreiber
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
| | - Janne Hülsemann
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
| | - Kati Franzke
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
| | - Simone Kann
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
| | - Bunthin Y
- Virology Unit, Institut Pasteur in Cambodia, 5 Monivong Boulevard, 12201 Phnom Penh, Cambodia.
| | - Veasna Duong
- Virology Unit, Institut Pasteur in Cambodia, 5 Monivong Boulevard, 12201 Phnom Penh, Cambodia.
| | - Philippe Buchy
- Virology Unit, Institut Pasteur in Cambodia, 5 Monivong Boulevard, 12201 Phnom Penh, Cambodia.
- GlaxoSmithKline, Vaccines R&D, 23 Rochester Park, Singapore 139234, Singapore.
| | - Michael Schreiber
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
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12
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Nautiyal K, Kuroda Y. A SEP tag enhances the expression, solubility and yield of recombinant TEV protease without altering its activity. N Biotechnol 2018; 42:77-84. [DOI: 10.1016/j.nbt.2018.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/16/2018] [Accepted: 02/09/2018] [Indexed: 10/18/2022]
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Hall D, Takagi J, Nakamura H. Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday. Biophys Rev 2018; 10:105-129. [PMID: 29500796 PMCID: PMC5899743 DOI: 10.1007/s12551-018-0401-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 01/29/2018] [Indexed: 02/08/2023] Open
Abstract
This issue of Biophysical Reviews, titled 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', is a collection of articles dedicated in honour of Professor Fumio Arisaka's 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.
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Affiliation(s)
- Damien Hall
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
- Research School of Chemistry, Australian National University, Acton, ACT 2601 Australia
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
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Kabir MG, Islam MM, Kuroda Y. Reversible association of proteins into sub-visible amorphous aggregates using short solubility controlling peptide tags. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:366-372. [PMID: 28951312 DOI: 10.1016/j.bbapap.2017.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 09/01/2017] [Accepted: 09/21/2017] [Indexed: 01/04/2023]
Abstract
Careful analysis of sub-visible amorphous aggregates, where proteins associate non-covalently in either native or denatured states without forming a specific quaternary structure, may shed insight into the mechanisms of protein aggregation and solubility. Here we report a biophysical and biochemical analysis of our model protein, a bovine pancreatic trypsin inhibitor variant (BPTI-19A), whose oligomerization were controlled by attaching solubility controlling peptide tags (SCP tags) to its C terminus, which are short peptides composed of a single type of amino acid that modulate protein solubility. The dynamic light scattering and static light scattering at 25°C indicated that 11 out of 15 SCP tags merely affected the hydrodynamic radius and light scattering intensity of our reference variants BPTI-19A and BPTI-C2G. On the other hand, hydrophobic SCP tags composed of 5 Ile (C5I) or 5 Leu (C5L) were associated into sub-visible aggregates. Circular dichroism indicated that all tagged BPTI variants had the same secondary structure contents as the reference BPTI-19A at 25°C, suggesting that BPTI-C5I and C5L kept their native structure upon association. Furthermore, the thermal denaturation of all of the BPTI variants was fully reversible and typical of natively folded small globular proteins, as monitored by CD at 222 nm. However, the thermal stability of BPTI-19A tagged with hydrophobic residues decreased with increasing protein concentration and tag's hydrophobicity, and BPTI-C5I and C5L were partially denatured at 37°C. Biochemical stability assessed by limited proteolysis with pepsin correlated with the extent of the variants' aggregation, and the large sub-visible aggregates formed by BPTI-C5I and C5L significantly increased their resistance to pepsin proteolysis. Altogether, these observations indicated that hydrophobic SCP tags led to the reversible association of native-like proteins into sub-visible soluble amorphous aggregates resistant to pepsin digestion.
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Affiliation(s)
- Md Golam Kabir
- Department of Biotechnology and Life Sciences, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Mohammad Monirul Islam
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh
| | - Yutaka Kuroda
- Department of Biotechnology and Life Sciences, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan.
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Nakamura S, Saotome T, Nakazawa A, Fukuda M, Kuroda Y, Kidokoro SI. Thermodynamics of the Thermal Denaturation of Acid Molten Globule State of Cytochrome c Indicate a Reversible High-Temperature Oligomerization Process. Biochemistry 2017; 56:2372-2378. [DOI: 10.1021/acs.biochem.6b01225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shigeyoshi Nakamura
- Department
of General Education, National Institute of Technology, Ube College, 2-14-1 Tokiwadai, Ube 755-8555, Japan
- Department
of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
| | - Tomonori Saotome
- Department
of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-15 Nakamachi, Koganei 184-8588, Japan
| | - Akiko Nakazawa
- Department
of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
| | - Masao Fukuda
- Department
of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
| | - Yutaka Kuroda
- Department
of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-15 Nakamachi, Koganei 184-8588, Japan
| | - Shun-ichi Kidokoro
- Department
of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
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Islam MM, Yohda M, Kidokoro SI, Kuroda Y. Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy. Sci Rep 2017; 7:41205. [PMID: 28266637 PMCID: PMC5339861 DOI: 10.1038/srep41205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 12/16/2016] [Indexed: 11/15/2022] Open
Abstract
We report a thermodynamic and structural analysis of six extensively simplified bovine pancreatic trypsin inhibitor (BPTI) variants containing 19–24 alanines out of 58 residues. Differential scanning calorimetry indicated a two-state thermal unfolding, typical of a native protein with densely packed interior. Surprisingly, increasing the number of alanines induced enthalpy stabilization, which was however over-compensated by entropy destabilization. X-ray crystallography indicated that the alanine substitutions caused the recruitment of novel water molecules facilitating the formation of protein–water hydrogen bonds and improving the hydration shells around the alanine’s methyl groups, both of which presumably contributed to enthalpy stabilization. There was a strong correlation between the number of water molecules and the thermodynamic parameters. Overall, our results demonstrate that, in contrast to our initial expectation, a protein sequence in which over 40% of the residues are alanines can retain a densely packed structure and undergo thermal denaturation with a large enthalpy change, mainly contributed by hydration.
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Affiliation(s)
- Mohammad Monirul Islam
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan.,Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong-4331, Bangladesh
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Shun-Ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology, Kamitomioka-cho, Nagaoka, Niigata 940-2188, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
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