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Hata K, Kobayashi N, Sugimura K, Qin W, Haxholli D, Chiba Y, Yoshimi S, Hayashi G, Onoda H, Ikegami T, Mulholland C, Nishiyama A, Nakanishi M, Leonhardt H, Konuma T, Arita K. Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger. Nucleic Acids Res 2022; 50:12527-12542. [PMID: 36420895 PMCID: PMC9757060 DOI: 10.1093/nar/gkac1082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/20/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022] Open
Abstract
Ubiquitin-like with PHD and RING finger domain-containing protein 1 (UHRF1)-dependent DNA methylation is essential for maintaining cell fate during cell proliferation. Developmental pluripotency-associated 3 (DPPA3) is an intrinsically disordered protein that specifically interacts with UHRF1 and promotes passive DNA demethylation by inhibiting UHRF1 chromatin localization. However, the molecular basis of how DPPA3 interacts with and inhibits UHRF1 remains unclear. We aimed to determine the structure of the mouse UHRF1 plant homeodomain (PHD) complexed with DPPA3 using nuclear magnetic resonance. Induced α-helices in DPPA3 upon binding of UHRF1 PHD contribute to stable complex formation with multifaceted interactions, unlike canonical ligand proteins of the PHD domain. Mutations in the binding interface and unfolding of the DPPA3 helical structure inhibited binding to UHRF1 and its chromatin localization. Our results provide structural insights into the mechanism and specificity underlying the inhibition of UHRF1 by DPPA3.
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Affiliation(s)
| | | | - Keita Sugimura
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Deis Haxholli
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Sae Yoshimi
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroki Onoda
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takahisa Ikegami
- Structural Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tsuyoshi Konuma
- Correspondence may also be addressed to Tsuyoshi Konuma. Tel: +81 45 508 7218; Fax: +81 45 508 7362;
| | - Kyohei Arita
- To whom correspondence should be addressed. Tel: +81 45 508 7225; Fax: +81 45 508 7365;
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2
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Sasamoto K, Himiyama T, Moriyoshi K, Ohmoto T, Uegaki K, Nakamura T, Nishiya Y. Functional analysis of the N-terminal region of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis. FEBS Open Bio 2022; 12:1875-1885. [PMID: 36054591 PMCID: PMC9527590 DOI: 10.1002/2211-5463.13476] [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: 06/27/2022] [Revised: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 12/14/2022] Open
Abstract
Acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866) has an N-terminal region (NTR; residues 23-135) between the signal sequence (residues 1-22) and the catalytic domain (residues 136-324), which is of unknown function. Our previous study revealed the crystal structure of the wild-type (WT) enzyme containing the NTR and the catalytic domain. Although the structure of the catalytic domain was successfully determined, that of the NTR was undetermined, as its electron density was unclear. In this study, we investigated the role of the NTR through functional and structural analyses of NTR truncation mutants. Based on sequence and secondary structure analyses, NTR was confirmed to be an intrinsically disordered region. The truncation of NTR significantly decreased the solubility of the proteins at low salt concentrations compared with that of the WT. The NTR-truncated mutant easily crystallized in a conventional buffer solution. The crystal exhibited crystallographic properties comparable with those of the WT crystals suitable for structural determination. These results suggest that NTR plays a role in maintaining the solubility and inhibiting the crystallization of the catalytic domain.
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Affiliation(s)
- Kohei Sasamoto
- Division of Life Science, Graduate School of Science and EngineeringSetsunan UniversityOsakaJapan,Biomedical Research InstituteNational Institute of Advanced Industrial Science and TechnologyOsakaJapan
| | - Tomoki Himiyama
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and TechnologyOsakaJapan
| | | | - Takashi Ohmoto
- Osaka Research Institute of Industrial Science and TechnologyJapan
| | - Koichi Uegaki
- Department of Applied Biological Chemistry, Faculty of AgricultureKindai UniversityNaraJapan,Agricultural Technology and Innovation Research InstituteKindai UniversityNaraJapan
| | - Tsutomu Nakamura
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and TechnologyOsakaJapan
| | - Yoshiaki Nishiya
- Division of Life Science, Graduate School of Science and EngineeringSetsunan UniversityOsakaJapan
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3
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Matsuo N, Goda N, Tenno T, Hiroaki H. Cryoprotective activities of FK20, a human genome-derived intrinsically disordered peptide against cryosensitive enzymes without a stereospecific molecular interaction. PEERJ PHYSICAL CHEMISTRY 2021. [DOI: 10.7717/peerj-pchem.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background
Intrinsically disordered proteins (IDPs) have been shown to exhibit cryoprotective activity toward other cellular enzymes without any obvious conserved sequence motifs. This study investigated relationships between the physical properties of several human genome-derived IDPs and their cryoprotective activities.
Methods
Cryoprotective activity of three human-genome derived IDPs and their truncated peptides toward lactate dehydrogenase (LDH) and glutathione S-transferase (GST) was examined. After the shortest cryoprotective peptide was defined (named FK20), cryoprotective activity of all-D-enantiomeric isoform of FK20 (FK20-D) as well as a racemic mixture of FK20 and FK20-D was examined. In order to examine the lack of increase of thermal stability of the target enzyme, the CD spectra of GST and LDH in the presence of a racemic mixture of FK20 and FK20-D at varying temperatures were measured and used to estimate Tm.
Results
Cryoprotective activity of IDPs longer than 20 amino acids was nearly independent of the amino acid length. The shortest IDP-derived 20 amino acid length peptide with sufficient cryoprotective activity was developed from a series of TNFRSF11B fragments (named FK20). FK20, FK20-D, and an equimolar mixture of FK20 and FK20-D also showed similar cryoprotective activity toward LDH and GST. Tm of GST in the presence and absence of an equimolar mixture of FK20 and FK20-D are similar, suggesting that IDPs’ cryoprotection mechanism seems partly from a molecular shielding effect rather than a direct interaction with the target enzymes.
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Affiliation(s)
- Naoki Matsuo
- Graduate School of Pharmaceutical Sciences, Laboratory of Structural and Molecular Pharmacology, Nagoya University, Nagoya, AICHI, JAPAN
| | - Natsuko Goda
- Graduate School of Pharmaceutical Sciences, Laboratory of Structural and Molecular Pharmacology, Nagoya University, Nagoya, AICHI, JAPAN
| | - Takeshi Tenno
- Graduate School of Pharmaceutical Sciences, Laboratory of Structural and Molecular Pharmacology, Nagoya University, Nagoya, AICHI, JAPAN
- BeCellBar, LLC., Nagoya, Aichi, Japan
| | - Hidekazu Hiroaki
- Graduate School of Pharmaceutical Sciences, Laboratory of Structural and Molecular Pharmacology, Nagoya University, Nagoya, AICHI, JAPAN
- BeCellBar, LLC., Nagoya, Aichi, Japan
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Presence of intrinsically disordered proteins can inhibit the nucleation phase of amyloid fibril formation of Aβ(1-42) in amino acid sequence independent manner. Sci Rep 2020; 10:12334. [PMID: 32703978 PMCID: PMC7378830 DOI: 10.1038/s41598-020-69129-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/19/2020] [Indexed: 11/27/2022] Open
Abstract
The molecular shield effect was studied for intrinsically disordered proteins (IDPs) that do not adopt compact and stable protein folds. IDPs are found among many stress-responsive gene products and cryoprotective- and drought-protective proteins. We recently reported that some fragments of human genome-derived IDPs are cryoprotective for cellular enzymes, despite a lack of relevant amino acid sequence motifs. This sequence-independent IDP function may reflect their molecular shield effect. This study examined the inhibitory activity of IDPs against fibril formation in an amyloid beta peptide (Aβ(1–42)) model system. Four of five human genome-derived IDPs (size range 20 to 44 amino acids) showed concentration-dependent inhibition of amyloid formation (IC50 range between 60 and 130 μM against 20 μM Aβ(1–42)). The IC50 value was two orders of magnitude lower than that of polyethylene-glycol and dextran, used as neutral hydrophilic polymer controls. Nuclear magnetic resonance with 15 N-labeled Aβ(1–42) revealed no relevant molecular interactions between Aβ(1–42) and IDPs. The inhibitory activities were abolished by adding external amyloid-formation seeds. Therefore, IDPs seemed to act only at the amyloid nucleation phase but not at the elongation phase. These results suggest that IDPs (0.1 mM or less) have a molecular shield effect that prevents aggregation of susceptible molecules.
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Nishiyama A, Mulholland CB, Bultmann S, Kori S, Endo A, Saeki Y, Qin W, Trummer C, Chiba Y, Yokoyama H, Kumamoto S, Kawakami T, Hojo H, Nagae G, Aburatani H, Tanaka K, Arita K, Leonhardt H, Nakanishi M. Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation. Nat Commun 2020; 11:1222. [PMID: 32144273 PMCID: PMC7060239 DOI: 10.1038/s41467-020-15006-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 02/10/2020] [Indexed: 12/31/2022] Open
Abstract
Stable inheritance of DNA methylation is critical for maintaining differentiated phenotypes in multicellular organisms. We have recently identified dual mono-ubiquitylation of histone H3 (H3Ub2) by UHRF1 as an essential mechanism to recruit DNMT1 to chromatin. Here, we show that PCNA-associated factor 15 (PAF15) undergoes UHRF1-dependent dual mono-ubiquitylation (PAF15Ub2) on chromatin in a DNA replication-coupled manner. This event will, in turn, recruit DNMT1. During early S-phase, UHRF1 preferentially ubiquitylates PAF15, whereas H3Ub2 predominates during late S-phase. H3Ub2 is enhanced under PAF15 compromised conditions, suggesting that H3Ub2 serves as a backup for PAF15Ub2. In mouse ES cells, loss of PAF15Ub2 results in DNA hypomethylation at early replicating domains. Together, our results suggest that there are two distinct mechanisms underlying replication timing-dependent recruitment of DNMT1 through PAF15Ub2 and H3Ub2, both of which are prerequisite for high fidelity DNA methylation inheritance. Ubiquitylation of histone H3 (H3Ub2) by UHRF1 recruits DNMT1 to chromatin, which is essential for DNA methylation inheritance. Here, the authors provide evidence that there are two distinct mechanisms underlying replication timing-dependent recruitment of DNMT1 through PAF15Ub2 and H3Ub2, both of which are required for high fidelity DNA methylation inheritance.
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Affiliation(s)
- Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan.
| | - Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Satomi Kori
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Akinori Endo
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Haruka Yokoyama
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Soichiro Kumamoto
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Toru Kawakami
- Laboratory of Protein Organic Chemistry, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Hironobu Hojo
- Laboratory of Protein Organic Chemistry, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Genta Nagae
- The Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Hiroyuki Aburatani
- The Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Kyohei Arita
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan.
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6
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Ki MR, Pack SP. Fusion tags to enhance heterologous protein expression. Appl Microbiol Biotechnol 2020; 104:2411-2425. [DOI: 10.1007/s00253-020-10402-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022]
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7
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Efficient and robust preparation of tyrosine phosphorylated intrinsically disordered proteins. Biotechniques 2019; 67:16-22. [PMID: 31092000 DOI: 10.2144/btn-2019-0033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are subject to post-translational modifications. This allows the same polypeptide to be involved in different interaction networks with different consequences, ranging from regulatory signalling networks to the formation of membrane-less organelles. We report a robust method for co-expression of modification enzyme and SUMO-tagged IDPs with a subsequent purification procedure that allows for the production of modified IDP. The robustness of our protocol is demonstrated using a challenging system: RNA polymerase II C-terminal domain (CTD); that is, a low-complexity repetitive region with multiple phosphorylation sites. In vitro phosphorylation approaches fail to yield multiple-site phosphorylated CTD, whereas our in vivo protocol allows the rapid production of near homogeneous phosphorylated CTD at a low cost. These samples can be used in functional and structural studies.
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8
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Graether SP. Troubleshooting Guide to Expressing Intrinsically Disordered Proteins for Use in NMR Experiments. Front Mol Biosci 2019; 5:118. [PMID: 30713842 PMCID: PMC6345686 DOI: 10.3389/fmolb.2018.00118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/23/2018] [Indexed: 12/17/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) represent a structural class of proteins that do not have a well-defined, 3D fold in solution, and often have little secondary structure. To characterize their function and molecular mechanism, it is helpful to examine their structure using nuclear magnetic resonance (NMR), which can report on properties, such as residual structure (at both the secondary and tertiary levels), ligand binding affinity, and the effect of ligand binding on IDP structure, all on a per residue basis. This brief review reports on the common problems and decisions that are involved when preparing a disordered protein for NMR studies. The paper covers gene design, expression host choice, protein purification, and the initial NMR experiments that are performed. While many of these steps are essentially identical to those for ordered proteins, a few key differences are highlighted, including the extreme sensitivity of IDPs to proteolytic cleavage, the ability to use denaturing conditions without having to refold the protein, the optimal chromatographic system choice, and the challenges of quantifying an IDP. After successful purification, characterization by NMR can be done using the standard 15N-heteronuclear single quantum coherence (15N-HSQC) experiment, or the newer CON series of experiments that are superior for disordered proteins.
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Affiliation(s)
- Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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9
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Okazaki H, Matsuo N, Tenno T, Goda N, Shigemitsu Y, Ota M, Hiroaki H. Using 1 H N amide temperature coefficients to define intrinsically disordered regions: An alternative NMR method. Protein Sci 2018; 27:1821-1830. [PMID: 30098073 DOI: 10.1002/pro.3485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/20/2018] [Accepted: 07/21/2018] [Indexed: 02/02/2023]
Abstract
This report describes a cost-effective experimental method for determining an intrinsically disordered protein (IDP) region in a given protein sample. In this area, the most popular (and conventional) means is using the amide (1 HN ) NMR signal chemical shift distributed in the range of 7.5-8.5 ppm. For this study, we applied an additional step: analysis of 1 HN chemical shift temperature coefficients (1 HN -CSTCs) of the signals. We measured 1 H-15 N two-dimensional NMR spectra of model IDP samples and ordered samples at four temperatures (288, 293, 298, and 303 K). We derived the 1 HN -CSTC threshold deviation, which gives the best correlation of ordered and disordered regions among the proteins examined (below -3.6 ppb/K). By combining these criteria with the newly optimized chemical shift range (7.8-8.5 ppm), the ratios of both true positive and true negative were improved by approximately 19% (62-81%) compared with the conventional "chemical shift-only" method.
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Affiliation(s)
- Hiroki Okazaki
- Department of Complex Systems Science, Graduate School of Information Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Naoki Matsuo
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Takeshi Tenno
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan.,BeCellBar LLC, Business Incubation Center, Nagoya University, Nagoya, 464-8601, Aichi, Japan
| | - Natsuko Goda
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Yoshiki Shigemitsu
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Motonori Ota
- Department of Complex Systems Science, Graduate School of Information Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan.,BeCellBar LLC, Business Incubation Center, Nagoya University, Nagoya, 464-8601, Aichi, Japan.,The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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Matsuo N, Goda N, Shimizu K, Fukuchi S, Ota M, Hiroaki H. Discovery of Cryoprotective Activity in Human Genome-Derived Intrinsically Disordered Proteins. Int J Mol Sci 2018; 19:ijms19020401. [PMID: 29385704 PMCID: PMC5855623 DOI: 10.3390/ijms19020401] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/17/2018] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are an emerging phenomenon. They may have a high degree of flexibility in their polypeptide chains, which lack a stable 3D structure. Although several biological functions of IDPs have been proposed, their general function is not known. The only finding related to their function is the genetically conserved YSK2 motif present in plant dehydrins. These proteins were shown to be IDPs with the YSK2 motif serving as a core region for the dehydrins’ cryoprotective activity. Here we examined the cryoprotective activity of randomly selected IDPs toward the model enzyme lactate dehydrogenase (LDH). All five IDPs that were examined were in the range of 35–45 amino acid residues in length and were equally potent at a concentration of 50 μg/mL, whereas folded proteins, the PSD-95/Dlg/ZO-1 (PDZ) domain, and lysozymes had no potency. We further examined their cryoprotective activity toward glutathione S-transferase as an example of the other enzyme, and toward enhanced green fluorescent protein as a non-enzyme protein example. We further examined the lyophilization protective activity of the peptides toward LDH, which revealed that some IDPs showed a higher activity than that of bovine serum albumin (BSA). Based on these observations, we propose that cryoprotection is a general feature of IDPs. Our findings may become a clue to various industrial applications of IDPs in the future.
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Affiliation(s)
- Naoki Matsuo
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Natsuko Goda
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Kana Shimizu
- Department of Computer Science and Communications Engineering, Waseda University, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.
| | - Satoshi Fukuchi
- Faculty of Engineering, Maebashi Institute of Technology, Maebashi 371-0816, Japan.
| | - Motonori Ota
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
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11
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Zhao Q, Xu W, Xing L, Lin Z. Recombinant production of medium- to large-sized peptides in Escherichia coli using a cleavable self-aggregating tag. Microb Cell Fact 2016; 15:136. [PMID: 27495238 PMCID: PMC4975908 DOI: 10.1186/s12934-016-0534-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 07/28/2016] [Indexed: 12/29/2022] Open
Abstract
Background Peptides have recently become attractive for therapeutic applications. However, efficient production of medium- to large-sized peptides (30–100 amino acids [aa]) remains challenging both by recombinant and chemical synthesis. We previously reported the formation of active enzyme aggregates in Escherichia coli cells induced by the short β-structured peptide ELK16 (LELELKLKLELELKLK) and developed a streamlined protein expression and purification approach. In this approach, a cleavable self-aggregating tag (cSAT) consisting of an intein molecule and ELK16 was used to release the recombinant peptides with reasonable purity from active aggregates. Results In this work, we extended the cSAT approach to a generalized expression and purification solution for a set of medium- to large-sized peptides with important therapeutic uses, including human glucagon-like peptide 1 (31 aa), B-type natriuretic peptide (32 aa), exendin 4 (39 aa), chemokine (C–C motif) ligand 5 (also known as RANTES, 66 aa), stromal cell-derived factor 1α (67 aa), insulin-like growth factor 1 (70 aa), and leptin (146 aa). After intein-mediated cleavage, the soluble peptides were released directly into the supernatant while insoluble peptides could be refolded and purified by reverse phase high-performance liquid chromatography. Additionally, an N-terminal thioredoxin tag was added upstream of the target peptides, which can be removed by enterokinase cleavage, generating native N-terminus for target peptides. Final yields of the peptides ranged from 0.1 to 1.8 μg/mg wet cell weight at laboratory scale. Conclusions The approach described in this study provides a fast and efficient route to express and purify peptides that are difficult or expensive to produce by chemical synthesis or by ordinary recombinant methods. It is particularly well suited for large peptides, peptides likely to be degraded, and peptides that have toxic effects on the host. It can greatly reduce the cost and time of downstream processing, and thus may be useful for both industrial manufacture and laboratory applications. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0534-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qing Zhao
- Department of Chemical Engineering, Tsinghua University, One Tsinghua Garden Road, Beijing, 100084, China
| | - Wanghui Xu
- Department of Chemical Engineering, Tsinghua University, One Tsinghua Garden Road, Beijing, 100084, China.,, Novozymes, China Headquarters, 14 Xinxi Road, Shangdi Zone, Haidian District, Beijing, 100085, China
| | - Lei Xing
- Department of Chemical Engineering, Tsinghua University, One Tsinghua Garden Road, Beijing, 100084, China.,China National Petroleum & Chemical Planning Institute, 16th Floor, 7 Block, Hepingli Zone, Beijing, 100013, China
| | - Zhanglin Lin
- Department of Chemical Engineering, Tsinghua University, One Tsinghua Garden Road, Beijing, 100084, China.
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Goda N, Shimizu K, Kuwahara Y, Tenno T, Noguchi T, Ikegami T, Ota M, Hiroaki H. A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR. Int J Mol Sci 2015; 16:15743-60. [PMID: 26184172 PMCID: PMC4519922 DOI: 10.3390/ijms160715743] [Citation(s) in RCA: 7] [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: 03/30/2015] [Revised: 06/17/2015] [Accepted: 07/01/2015] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) that lack stable conformations and are highly flexible have attracted the attention of biologists. Therefore, the development of a systematic method to identify polypeptide regions that are unstructured in solution is important. We have designed an "indirect/reflected" detection system for evaluating the physicochemical properties of IDPs using nuclear magnetic resonance (NMR). This approach employs a "chimeric membrane protein"-based method using the thermostable membrane protein PH0471. This protein contains two domains, a transmembrane helical region and a C-terminal OB (oligonucleotide/oligosaccharide binding)-fold domain (named NfeDC domain), connected by a flexible linker. NMR signals of the OB-fold domain of detergent-solubilized PH0471 are observed because of the flexibility of the linker region. In this study, the linker region was substituted with target IDPs. Fifty-three candidates were selected using the prediction tool POODLE and 35 expression vectors were constructed. Subsequently, we obtained 15N-labeled chimeric PH0471 proteins with 25 IDPs as linkers. The NMR spectra allowed us to classify IDPs into three categories: flexible, moderately flexible, and inflexible. The inflexible IDPs contain membrane-associating or aggregation-prone sequences. This is the first attempt to use an indirect/reflected NMR method to evaluate IDPs and can verify the predictions derived from our computational tools.
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Affiliation(s)
- Natsuko Goda
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Kana Shimizu
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building 2-4-7 Aomi, Koto-ku, Tokyo 135-0046, Japan.
| | - Yohta Kuwahara
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, 7-5-1, Chuo-ku, Kobe 650-0017, Japan.
| | - Takeshi Tenno
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Tamotsu Noguchi
- Pharmaceutical Education Research Center, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan.
| | - Takahisa Ikegami
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Motonori Ota
- Graduate School of Information Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Hidekazu Hiroaki
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, 7-5-1, Chuo-ku, Kobe 650-0017, Japan.
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
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