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Micsonai A, Wien F, Bulyáki É, Kun J, Moussong É, Lee YH, Goto Y, Réfrégiers M, Kardos J. BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra. Nucleic Acids Res 2019; 46:W315-W322. [PMID: 29893907 PMCID: PMC6031044 DOI: 10.1093/nar/gky497] [Citation(s) in RCA: 671] [Impact Index Per Article: 134.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/22/2018] [Indexed: 12/31/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.
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Affiliation(s)
- András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Frank Wien
- Synchrotron SOLEIL, Gif-sur-Yvette 91192, France
| | - Éva Bulyáki
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Judit Kun
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Éva Moussong
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | | | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest H-1117, Hungary
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Bondarchuk TV, Lozhko DM, Shalak VF, Fatalska A, Szczepanowski RH, Dadlez M, Negrutskii BS, El'skaya AV. The protein-binding N-terminal domain of human translation elongation factor 1Bβ possesses a dynamic α-helical structural organization. Int J Biol Macromol 2019; 126:899-907. [PMID: 30590147 DOI: 10.1016/j.ijbiomac.2018.12.220] [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] [Received: 08/07/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 10/27/2022]
Abstract
Translation elongation factor 1Bβ (eEF1Bβ) is a metazoan-specific protein involved into the macromolecular eEF1B complex, containing also eEF1Bα and eEF1Bγ subunits. Both eEF1Bα and eEF1Bβ ensure the guanine nucleotide exchange on eEF1A while eEF1Bγ is thought to have a structural role. The structures of the eEF1Bβ catalytic C-terminal domain and neighboring central acidic region are known while the structure of the protein-binding N-terminal domain remains unidentified which prevents clear understanding of architecture of the eEF1B complex. Here we show that the N-terminal domain comprising initial 77 amino acids of eEF1Bβ, eEF1Bβ(1-77), is a monomer in solution with increased hydrodynamic volume. This domain binds eEF1Bγ in equimolar ratio. The CD spectra reveal that the secondary structure of eEF1Bβ(1-77) consists predominantly of α-helices and a portion of disordered region. Very rapid hydrogen/deuterium exchange for all eEF1Bβ(1-77) peptides favors a flexible tertiary organization of eEF1Bβ(1-77). Computational modeling of eEF1Bβ(1-77) suggests several conformation states each composed of three α-helices connected by flexible linkers. Altogether, the data imply that the protein-binding domain of eEF1Bβ shows flexible spatial organization which may be needed for interaction with eEF1Bγ or other protein partners.
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Affiliation(s)
- Tetiana V Bondarchuk
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150, Zabolotnogo St., 03680 Kyiv, Ukraine
| | - Dmytro M Lozhko
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150, Zabolotnogo St., 03680 Kyiv, Ukraine
| | - Vyacheslav F Shalak
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150, Zabolotnogo St., 03680 Kyiv, Ukraine.
| | - Agnieszka Fatalska
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego 5a, 02-109 Warsaw, Poland
| | - Roman H Szczepanowski
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego 5a, 02-109 Warsaw, Poland
| | - Boris S Negrutskii
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150, Zabolotnogo St., 03680 Kyiv, Ukraine
| | - Anna V El'skaya
- Institute of Molecular Biology and Genetics, NAS of Ukraine, 150, Zabolotnogo St., 03680 Kyiv, Ukraine
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3
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Qian H, Zou Y, Tang Y, Gong Y, Qian Z, Wei G, Zhang Q. Proline hydroxylation at different sites in hypoxia-inducible factor 1α modulates its interactions with the von Hippel–Lindau tumor suppressor protein. Phys Chem Chem Phys 2018; 20:18756-18765. [DOI: 10.1039/c8cp01964a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proline hydroxylation of HIF-1α affects the interaction affinity between pVHL and HIF-1α and allosterically induces the conformational change of pVHL.
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Affiliation(s)
- Hongsheng Qian
- College of Physical Education and Training
- Shanghai University of Sport
- Shanghai 200438
- China
| | - Yu Zou
- College of Physical Education and Training
- Shanghai University of Sport
- Shanghai 200438
- China
| | - Yiming Tang
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University
- Shanghai 200433
- China
| | - Yehong Gong
- College of Physical Education and Training
- Shanghai University of Sport
- Shanghai 200438
- China
| | - Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport
- Shanghai 200438
- China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University
- Shanghai 200433
- China
| | - Qingwen Zhang
- College of Physical Education and Training
- Shanghai University of Sport
- Shanghai 200438
- China
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Furukawa Y, Inoue Y, Sakaguchi A, Mori Y, Fukumura T, Miyata T, Namba K, Minamino T. Structural stability of flagellin subunit affects the rate of flagellin export in the absence of FliS chaperone. Mol Microbiol 2016; 102:405-416. [PMID: 27461872 DOI: 10.1111/mmi.13469] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2016] [Indexed: 12/17/2022]
Abstract
FliS chaperone binds to flagellin FliC in the cytoplasm and transfers FliC to a sorting platform of the flagellar type III export apparatus through the interaction between FliS and FlhA for rapid and efficient protein export during flagellar filament assembly. FliS also suppresses the secretion of an anti-σ factor, FlgM. Loss of FliS results in a short filament phenotype although the expression levels of FliC are increased considerably due to an increase in the secretion level of FlgM. Here to clarify the rate limiting step of FliC export in the absence of FliS, we isolated bypass mutants from a Salmonella ΔfliS mutant. All the bypass mutations were identified in FliC. These bypass mutations increased the export rate of FliC by ca. twofold, allowing the bypass mutant cells to produce longer filaments than the parental ΔfliS cells. Both far-UV CD measurements and limited proteolysis revealed that the bypass mutations significantly destabilize the folded structure of FliC monomer. These results suggest that an unfolding step of FliC limits the export rate of FliC in the ΔfliS mutant, thereby producing short filaments. We propose that FliS promotes FliC docking at the FlhA platform to facilitate subsequent unfolding of FliC.
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Affiliation(s)
- Yukio Furukawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yumi Inoue
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Aya Sakaguchi
- Department of Food Science and Nutrition, Faculty of Human Life and Science, Doshisha Women's College of Liberal Arts, Kyoto, 602-0893, Japan
| | - Yoko Mori
- Department of Food Science and Nutrition, Faculty of Human Life and Science, Doshisha Women's College of Liberal Arts, Kyoto, 602-0893, Japan
| | - Takuma Fukumura
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Quantitative Biology Center, RIKEN, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Quantitative Biology Center, RIKEN, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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Kinoshita M, Nakanishi Y, Furukawa Y, Namba K, Imada K, Minamino T. Rearrangements of α-helical structures of FlgN chaperone control the binding affinity for its cognate substrates during flagellar type III export. Mol Microbiol 2016; 101:656-70. [PMID: 27178222 DOI: 10.1111/mmi.13415] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2016] [Indexed: 11/29/2022]
Abstract
The bacterial flagellar type III export chaperones not only act as bodyguards to protect their cognate substrates from aggregation and proteolysis in the cytoplasm but also ensure the order of export through their interactions with an export gate protein FlhA. FlgN chaperone binds to FlgK and FlgL with nanomolar affinity and transfers them to FlhA for their efficient and rapid transport for the formation of the hook-filament junction zone. However, it remains unknown how FlgN releases FlgK and FlgL at the FlhA export gate platform in a timely manner. Here, we have solved the crystal structure of Salmonella FlgN at 2.3 Å resolution and carried out structure-based functional analyses. FlgN consists of three α helices, α1, α2 and α3. Helix α1 adopts two distinct, extended and bent conformations through the conformational change of N-loop between α1 and α2. The N-loop deletion not only increases the probability of FlgN dimer formation but also abolish the interaction between FlgN and FlgK. Highly conserved Asn-92, Asn-95 and Ile-103 residues in helix α3 are involved in the strong interaction with FlgK. We propose that the N-loop coordinates helical rearrangements of FlgN with the association and dissociation of its cognate substrates during their export.
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Affiliation(s)
- Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Yuki Nakanishi
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Yukio Furukawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Quantitative Biology Center, Riken, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
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