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PTX3 structure determination using a hybrid cryoelectron microscopy and AlphaFold approach offers insights into ligand binding and complement activation. Proc Natl Acad Sci U S A 2022; 119:e2208144119. [PMID: 35939690 PMCID: PMC9388099 DOI: 10.1073/pnas.2208144119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pattern recognition molecules (PRMs) form an important part of innate immunity, where they facilitate the response to infections and damage by triggering processes such as inflammation. The pentraxin family of soluble PRMs comprises long and short pentraxins, with the former containing unique N-terminal regions unrelated to other proteins or each other. No complete high-resolution structural information exists about long pentraxins, unlike the short pentraxins, where there is an abundance of both X-ray and cryoelectron microscopy (cryo-EM)-derived structures. This study presents a high-resolution structure of the prototypical long pentraxin, PTX3. Cryo-EM yielded a 2.5-Å map of the C-terminal pentraxin domains that revealed a radically different quaternary structure compared to other pentraxins, comprising a glycosylated D4 symmetrical octameric complex stabilized by an extensive disulfide network. The cryo-EM map indicated α-helices that extended N terminal of the pentraxin domains that were not fully resolved. AlphaFold was used to predict the remaining N-terminal structure of the octameric PTX3 complex, revealing two long tetrameric coiled coils with two hinge regions, which was validated using classification of cryo-EM two-dimensional averages. The resulting hybrid cryo-EM/AlphaFold structure allowed mapping of ligand binding sites, such as C1q and fibroblast growth factor-2, as well as rationalization of previous biochemical data. Given the relevance of PTX3 in conditions ranging from COVID-19 prognosis, cancer progression, and female infertility, this structure could be used to inform the understanding and rational design of therapies for these disorders and processes.
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2
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Vaidyanathan VV, Binz T. Ability of human SNAP-23 to generate high molecular weight SDS-resistant ternary SNARE complexes is influenced by C-terminal coil content. Biochem Biophys Rep 2021; 28:101150. [PMID: 34703905 PMCID: PMC8524102 DOI: 10.1016/j.bbrep.2021.101150] [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: 09/07/2020] [Revised: 08/23/2021] [Accepted: 09/21/2021] [Indexed: 11/26/2022] Open
Abstract
Using in vitro protein complex formation assay, ability of SNAP-25 isoforms to generate SDS-resistant ternary SNARE complexes with Syntaxin-1 and VAMP-2 was investigated. Major SNAP-25 family proteins were found to generate heat-resistant ternary complexes with varying efficiency. Compared to human SNAP-25, its non-neuronal counterparts SNAP-23 and SNAP-29 formed lower amounts of ternary complexes. Changing Pro182 in human SNAP-23 to Arg182 (SNAP-23 P182R) improved its ability to bind partners and form complexes. In silico analysis of C-terminal helical content in various SNAP-25 family members showed that except human SNAP-23, all others displayed secondary α-helical conformation. We also report that human SNAP-29 is resistant to the proteolytic action of botulinum neurotoxin A even when applied at large concentration. Human SNAP-23 forms reduced amounts of ternary SNARE complexes than human SNAP-25. SNAP-25 family proteins show varying levels of secondary structure at the C-terminus. C-terminal coil content influences neurotoxin sensitivity and ability to form stable ternary SNARE complexes.
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Affiliation(s)
| | - Thomas Binz
- Institute of Cellular Biochemistry, Hannover Medical School, Hannover, 30625, Germany
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3
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An Interaction Network of the Human SEPT9 Established by Quantitative Mass Spectrometry. G3-GENES GENOMES GENETICS 2019; 9:1869-1880. [PMID: 30975701 PMCID: PMC6553528 DOI: 10.1534/g3.119.400197] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Septins regulate the organization of the actin cytoskeleton, vesicle transport and fusion, chromosome alignment and segregation, and cytokinesis in mammalian cells. SEPT9 is part of the core septin hetero-octamer in human cells which is composed of SEPT2, SEPT6, SEPT7, and SEPT9. SEPT9 has been linked to a variety of intracellular functions as well as to diseases and diverse types of cancer. A targeted high-throughput approach to systematically identify the interaction partners of SEPT9 has not yet been performed. We applied a quantitative proteomics approach to establish an interactome of SEPT9 in human fibroblast cells. Among the newly identified interaction partners were members of the myosin family and LIM domain containing proteins. Fluorescence microscopy of SEPT9 and its interaction partners provides additional evidence that SEPT9 might participate in vesicle transport from and to the plasma membrane as well as in the attachment of actin stress fibers to cellular adhesions.
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Molecular Docking and Dynamics Simulation Studies Predict Munc18b as a Target of Mycolactone: A Plausible Mechanism for Granule Exocytosis Impairment in Buruli Ulcer Pathogenesis. Toxins (Basel) 2019; 11:toxins11030181. [PMID: 30934618 PMCID: PMC6468854 DOI: 10.3390/toxins11030181] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 12/18/2022] Open
Abstract
Ulcers due to infections with Mycobacterium ulcerans are characterized by complete lack of wound healing processes, painless, an underlying bed of host dead cells and undermined edges due to necrosis. Mycolactone, a macrolide produced by the mycobacterium, is believed to be the toxin responsible. Of interest and relevance is the knowledge that Buruli ulcer (BU) patients remember experiencing trauma previously at the site of the ulcers, suggesting an impairment of wound healing processes, the plausible effect due to the toxin. Wound healing processes involve activation of the blood platelets to release the contents of the dense granules mainly serotonin, calcium ions, and ADP/ATP by exocytosis into the bloodstream. The serotonin release results in attracting more platelets and mast cells to the wound site, with the mast cells also undergoing degranulation, releasing compounds into the bloodstream by exocytosis. Recent work has identified interference in the co-translational translocation of many secreted proteins via the endoplasmic reticulum and cell death involving Wiskott-Aldrich syndrome protein (WASP), Sec61, and angiotensin II receptors (AT2R). We hypothesized that mycolactone by being lipophilic, passively crosses cell membranes and binds to key proteins that are involved in exocytosis by platelets and mast cells, thus inhibiting the initiation of wound healing processes. Based on this, molecular docking studies were performed with mycolactone against key soluble n-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins and regulators, namely Vesicle-associated membrane protein (VAMP8), Synaptosomal-associated protein (SNAP23, syntaxin 11, Munc13-4 (its isoform Munc13-1 was used), and Munc18b; and also against known mycolactone targets (Sec61, AT2R, and WASP). Munc18b was shown to be a plausible mycolactone target after the molecular docking studies with binding affinity of -8.5 kcal/mol. Structural studies and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding energy calculations of the mycolactone and Munc18b complex was done with 100 ns molecular dynamics simulations using GROMACS. Mycolactone binds strongly to Munc18b with an average binding energy of -247.571 ± 37.471 kJ/mol, and its presence elicits changes in the structural conformation of the protein. Analysis of the binding interactions also shows that mycolactone interacts with Arg405, which is an important residue of Munc18b, whose mutation could result in impaired granule exocytosis. These findings consolidate the possibility that Munc18b could be a target of mycolactone. The implication of the interaction can be experimentally evaluated to further understand its role in granule exocytosis impairment in Buruli ulcer.
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5
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Morey C, Kienle CN, Klöpper TH, Burkhardt P, Fasshauer D. Evidence for a conserved inhibitory binding mode between the membrane fusion assembly factors Munc18 and syntaxin in animals. J Biol Chem 2017; 292:20449-20460. [PMID: 29046354 DOI: 10.1074/jbc.m117.811182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/10/2017] [Indexed: 12/30/2022] Open
Abstract
The membrane fusion necessary for vesicle trafficking is driven by the assembly of heterologous SNARE proteins orchestrated by the binding of Sec1/Munc18 (SM) proteins to specific syntaxin SNARE proteins. However, the precise mode of interaction between SM proteins and SNAREs is debated, as contrasting binding modes have been found for different members of the SM protein family, including the three vertebrate Munc18 isoforms. While different binding modes could be necessary, given their roles in different secretory processes in different tissues, the structural similarity of the three isoforms makes this divergence perplexing. Although the neuronal isoform Munc18a is well-established to bind tightly to both the closed conformation and the N-peptide of syntaxin 1a, thereby inhibiting SNARE complex formation, Munc18b and -c, which have a more widespread distribution, are reported to mainly interact with the N-peptide of their partnering syntaxins and are thought to instead promote SNARE complex formation. We have reinvestigated the interaction between Munc18c and syntaxin 4 (Syx4). Using isothermal titration calorimetry, we found that Munc18c, like Munc18a, binds to both the closed conformation and the N-peptide of Syx4. Furthermore, using a novel kinetic approach, we found that Munc18c, like Munc18a, slows down SNARE complex formation through high-affinity binding to syntaxin. This strongly suggests that secretory Munc18s in general control the accessibility of the bound syntaxin, probably preparing it for SNARE complex assembly.
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Affiliation(s)
- Czuee Morey
- From the Département des neurosciences fondamentales, Université de Lausanne, Rue du Bugnon 9, CH-1005 Lausanne, Switzerland
| | - C Nickias Kienle
- From the Département des neurosciences fondamentales, Université de Lausanne, Rue du Bugnon 9, CH-1005 Lausanne, Switzerland
| | - Tobias H Klöpper
- Whitehat Life Sciences Ltd., 20 Wenlock Road, N1 7GU London, United Kingdom, and
| | - Pawel Burkhardt
- the Marine Biological Association, Citadel Hill Marine Laboratory, Plymouth PL1 2PB, United Kingdom
| | - Dirk Fasshauer
- From the Département des neurosciences fondamentales, Université de Lausanne, Rue du Bugnon 9, CH-1005 Lausanne, Switzerland,
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Negahdaripour M, Golkar N, Hajighahramani N, Kianpour S, Nezafat N, Ghasemi Y. Harnessing self-assembled peptide nanoparticles in epitope vaccine design. Biotechnol Adv 2017; 35:575-596. [PMID: 28522213 PMCID: PMC7127164 DOI: 10.1016/j.biotechadv.2017.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/23/2017] [Accepted: 05/11/2017] [Indexed: 12/11/2022]
Abstract
Vaccination has been one of the most successful breakthroughs in medical history. In recent years, epitope-based subunit vaccines have been introduced as a safer alternative to traditional vaccines. However, they suffer from limited immunogenicity. Nanotechnology has shown value in solving this issue. Different kinds of nanovaccines have been employed, among which virus-like nanoparticles (VLPs) and self-assembled peptide nanoparticles (SAPNs) seem very promising. Recently, SAPNs have attracted special interest due to their unique properties, including molecular specificity, biodegradability, and biocompatibility. They also resemble pathogens in terms of their size. Their multivalency allows an orderly repetitive display of antigens on their surface, which induces a stronger immune response than single immunogens. In vaccine design, SAPN self-adjuvanticity is regarded an outstanding advantage, since the use of toxic adjuvants is no longer required. SAPNs are usually composed of helical or β-sheet secondary structures and are tailored from natural peptides or de novo structures. Flexibility in subunit selection opens the door to a wide variety of molecules with different characteristics. SAPN engineering is an emerging area, and more novel structures are expected to be generated in the future, particularly with the rapid progress in related computational tools. The aim of this review is to provide a state-of-the-art overview of self-assembled peptide nanoparticles and their use in vaccine design in recent studies. Additionally, principles for their design and the application of computational approaches to vaccine design are summarized.
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Affiliation(s)
- Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasim Golkar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutics Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasim Hajighahramani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sedigheh Kianpour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Dewangan PS, Sonawane PJ, Chouksey AR, Chauhan R. The Nup62 Coiled-Coil Motif Provides Plasticity for Triple-Helix Bundle Formation. Biochemistry 2017; 56:2803-2811. [PMID: 28406021 DOI: 10.1021/acs.biochem.6b01050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The central transport channel of the vertebrate nuclear pore complex (NPC) consists of nucleoporins: Nup62, Nup54, and Nup58. The coiled-coil domains in α-helical regions of these nucleoporins are thought to be crucial for several protein-protein interactions in the NPC subcomplexes. In this study, we determined the crystal structure of the coiled-coil domain of rat Nup62 fragment (residues 362-425) to 2.4 Å resolution. The crystal structure shows the conserved coiled-coil domain as a parallel three-helix bundle for the Nup62(362-425) fragment. On the basis of our size exclusion chromatography coupled to multiangle light scattering analysis and glutaraldehyde cross-linking experiments, we conclude that the Nup62(362-425) fragment displays dynamic behavior in solution and can also exist in either homodimeric or homotrimeric states. Our comparative analysis of the rat Nup62(362-425) homotrimeric structure with previously reported heterotrimeric structures [rat Nup62(362-425)·Nup54(346-407) and Xenopus Nup62(358-485)·Nup54(315-450)·Nup58(283-406) complexes] demonstrates the structural basis for parallel triple-helix bundle formation for Nup62 with different partners. Moreover, we show that the coiled-coil domain of Nup62 is sufficient for interaction with the coiled-coil domain of rat Exo70, a protein in an exocyst complex. On the basis of these observations, we suggest the plausible chain replacement mechanism that yields to diverse protein assemblies with Nup62. In summary, the coiled-coil motif present in Nup62 imparts the ability to form a homotrimer and heterotrimers either with Nup54 or with Nup54-Nup58 within the NPCs as well as with Exo70 beyond the NPCs. These complexes of Nup62 suggest the crucial role of the coiled-coil motifs in providing plasticity to various modular assemblies.
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Affiliation(s)
- Pravin S Dewangan
- National Centre for Cell Science , S. P. Pune University Campus, Ganeshkhind, Pune 411007, India
| | - Parshuram J Sonawane
- National Centre for Cell Science , S. P. Pune University Campus, Ganeshkhind, Pune 411007, India
| | - Ankita R Chouksey
- National Centre for Cell Science , S. P. Pune University Campus, Ganeshkhind, Pune 411007, India
| | - Radha Chauhan
- National Centre for Cell Science , S. P. Pune University Campus, Ganeshkhind, Pune 411007, India
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Kim BW, Jung YO, Kim MK, Kwon DH, Park SH, Kim JH, Kuk YB, Oh SJ, Kim L, Kim BH, Yang WS, Song HK. ACCORD: an assessment tool to determine the orientation of homodimeric coiled-coils. Sci Rep 2017; 7:43318. [PMID: 28266564 PMCID: PMC5339707 DOI: 10.1038/srep43318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/23/2017] [Indexed: 12/21/2022] Open
Abstract
The coiled-coil (CC) domain is a very important structural unit of proteins that plays critical roles in various biological functions. The major oligomeric state of CCs is a dimer, which can be either parallel or antiparallel. The orientation of each α-helix in a CC domain is critical for the molecular function of CC-containing proteins, but cannot be determined easily by sequence-based prediction. We developed a biochemical method for assessing differences between parallel and antiparallel CC homodimers and named it ACCORD (Assessment tool for homodimeric Coiled-Coil ORientation Decision). To validate this technique, we applied it to 15 different CC proteins with known structures, and the ACCORD results identified these proteins well, especially with long CCs. Furthermore, ACCORD was able to accurately determine the orientation of a CC domain of unknown directionality that was subsequently confirmed by X-ray crystallography and small angle X-ray scattering. Thus, ACCORD can be used as a tool to determine CC directionality to supplement the results of in silico prediction.
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Affiliation(s)
- Byeong-Won Kim
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Yang Ouk Jung
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Min Kyung Kim
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Do Hoon Kwon
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Si Hoon Park
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Jun Hoe Kim
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Yong-Boo Kuk
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Sun-Joo Oh
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Leehyeon Kim
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Bong Heon Kim
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Woo Seok Yang
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Hyun Kyu Song
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
- Center for Molecular Dynamics and Spectroscopy, Institute of Basic Science, Seoul 02841, Korea
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Kunii M, Ohara-Imaizumi M, Takahashi N, Kobayashi M, Kawakami R, Kondoh Y, Shimizu T, Simizu S, Lin B, Nunomura K, Aoyagi K, Ohno M, Ohmuraya M, Sato T, Yoshimura SI, Sato K, Harada R, Kim YJ, Osada H, Nemoto T, Kasai H, Kitamura T, Nagamatsu S, Harada A. Opposing roles for SNAP23 in secretion in exocrine and endocrine pancreatic cells. J Cell Biol 2016; 215:121-138. [PMID: 27697926 PMCID: PMC5057288 DOI: 10.1083/jcb.201604030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/26/2016] [Indexed: 12/17/2022] Open
Abstract
Kunii et al. reveal that the SNARE protein SNAP23 plays distinct roles in the secretion of amylase in exocrine cells and of insulin in endocrine cells the pancreas and show that MF286, a novel inhibitor of SNAP23, may be a new drug candidate for diabetes. The membrane fusion of secretory granules with plasma membranes is crucial for the exocytosis of hormones and enzymes. Secretion disorders can cause various diseases such as diabetes or pancreatitis. Synaptosomal-associated protein 23 (SNAP23), a soluble N-ethyl-maleimide sensitive fusion protein attachment protein receptor (SNARE) molecule, is essential for secretory granule fusion in several cell lines. However, the in vivo functions of SNAP23 in endocrine and exocrine tissues remain unclear. In this study, we show opposing roles for SNAP23 in secretion in pancreatic exocrine and endocrine cells. The loss of SNAP23 in the exocrine and endocrine pancreas resulted in decreased and increased fusion of granules to the plasma membrane after stimulation, respectively. Furthermore, we identified a low molecular weight compound, MF286, that binds specifically to SNAP23 and promotes insulin secretion in mice. Our results demonstrate opposing roles for SNAP23 in the secretion mechanisms of the endocrine and exocrine pancreas and reveal that the SNAP23-binding compound MF286 may be a promising drug for diabetes treatment.
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Affiliation(s)
- Masataka Kunii
- Laboratory of Molecular Traffic, Department of Molecular and Cellular Biology, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan Department of Cell Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Mica Ohara-Imaizumi
- Department of Biochemistry, Kyorin University School of Medicine, Tokyo 181-8611, Japan
| | - Noriko Takahashi
- Laboratory of Structural Physiology, Graduate School of Medicine, Center for Disease Biology and Integrative Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masaki Kobayashi
- Metabolic Signal Research Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Ryosuke Kawakami
- Laboratory of Molecular and Cellular Biophysics, Research Institute for Electronic Science, Hokkaido University, Hokkaido 001-0020, Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Takeshi Shimizu
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Kanagawa 223-8522, Japan
| | - Bangzhong Lin
- Drug Discovery Team, Office for University-Industry Collaboration Planning and Promotion, Osaka University, Osaka 565-0871, Japan
| | - Kazuto Nunomura
- Drug Discovery Team, Office for University-Industry Collaboration Planning and Promotion, Osaka University, Osaka 565-0871, Japan
| | - Kyota Aoyagi
- Department of Biochemistry, Kyorin University School of Medicine, Tokyo 181-8611, Japan
| | - Mitsuyo Ohno
- Laboratory of Structural Physiology, Graduate School of Medicine, Center for Disease Biology and Integrative Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masaki Ohmuraya
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-0811, Japan
| | - Takashi Sato
- Laboratory of Molecular Traffic, Department of Molecular and Cellular Biology, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Shin-Ichiro Yoshimura
- Department of Cell Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Ken Sato
- Laboratory of Molecular Traffic, Department of Molecular and Cellular Biology, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Reiko Harada
- Department of Cell Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan Department of Judo Therapy, Takarazuka University of Medical and Health Care, Hyogo 666-0152, Japan
| | - Yoon-Jeong Kim
- Drug Discovery Team, Office for University-Industry Collaboration Planning and Promotion, Osaka University, Osaka 565-0871, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Tomomi Nemoto
- Laboratory of Molecular and Cellular Biophysics, Research Institute for Electronic Science, Hokkaido University, Hokkaido 001-0020, Japan
| | - Haruo Kasai
- Laboratory of Structural Physiology, Graduate School of Medicine, Center for Disease Biology and Integrative Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tadahiro Kitamura
- Metabolic Signal Research Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
| | - Shinya Nagamatsu
- Department of Biochemistry, Kyorin University School of Medicine, Tokyo 181-8611, Japan
| | - Akihiro Harada
- Laboratory of Molecular Traffic, Department of Molecular and Cellular Biology, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan Department of Cell Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
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10
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Tu D, Li Y, Song HK, Toms AV, Gould CJ, Ficarro SB, Marto JA, Goode BL, Eck MJ. Crystal structure of a coiled-coil domain from human ROCK I. PLoS One 2011; 6:e18080. [PMID: 21445309 PMCID: PMC3061879 DOI: 10.1371/journal.pone.0018080] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 02/21/2011] [Indexed: 11/19/2022] Open
Abstract
The small GTPase Rho and one of its targets, Rho-associated kinase (ROCK), participate in a variety of actin-based cellular processes including smooth muscle contraction, cell migration, and stress fiber formation. The ROCK protein consists of an N-terminal kinase domain, a central coiled-coil domain containing a Rho binding site, and a C-terminal pleckstrin homology domain. Here we present the crystal structure of a large section of the central coiled-coil domain of human ROCK I (amino acids 535-700). The structure forms a parallel α-helical coiled-coil dimer that is structurally similar to tropomyosin, an actin filament binding protein. There is an unusual discontinuity in the coiled-coil; three charged residues (E613, R617 and D620) are positioned at what is normally the hydrophobic core of coiled-coil packing. We speculate that this conserved irregularity could function as a hinge that allows ROCK to adopt its autoinhibited conformation.
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Affiliation(s)
- Daqi Tu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Yiqun Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Hyun Kyu Song
- School of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Angela V. Toms
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Christopher J. Gould
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Scott B. Ficarro
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Jarrod A. Marto
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Bruce L. Goode
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Michael J. Eck
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- * E-mail:
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11
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Structural insight into the mechanisms of enveloped virus tethering by tetherin. Proc Natl Acad Sci U S A 2010; 107:18428-32. [PMID: 20940320 DOI: 10.1073/pnas.1011485107] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Tetherin/BST2 is a type-II membrane protein that inhibits the release of a range of enveloped viruses, including HIV-1. Here we report three crystal structures of human tetherin, including the full-length ectodomain, a triple cysteine mutant and an ectodomain truncation. These structures show that tetherin forms a continuous alpha helix encompassing almost the entire ectodomain. Tetherin helices dimerize into parallel coiled coils via interactions throughout the C-terminal portion of the ectodomain. A comparison of the multiple structures of the tetherin dimer reveals inherent constrained flexibility at two hinges positioned at residues A88 and G109. In the crystals, two tetherin ectodomain dimers associate into a tetramer by forming an antiparallel four-helix bundle at their N termini. However, mutagenesis studies suggest that the tetrametric form of tetherin, although potentially contributing to, is not essential for its antiviral activity. Nonetheless, the structural and chemical properties of the N terminus of the ectodomain are important for optimal tethering function. This study provides detailed insight into the mechanisms by which this broad-spectrum antiviral restriction factor can function.
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Halemani ND, Bethani I, Rizzoli SO, Lang T. Structure and Dynamics of a Two-Helix SNARE Complex in Live Cells. Traffic 2010; 11:394-404. [DOI: 10.1111/j.1600-0854.2009.01020.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Apostolovic B, Danial M, Klok HA. Coiled coils: attractive protein folding motifs for the fabrication of self-assembled, responsive and bioactive materials. Chem Soc Rev 2010; 39:3541-75. [DOI: 10.1039/b914339b] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Sharma AK, Zhou GP, Kupferman J, Surks HK, Christensen EN, Chou JJ, Mendelsohn ME, Rigby AC. Probing the interaction between the coiled coil leucine zipper of cGMP-dependent protein kinase Ialpha and the C terminus of the myosin binding subunit of the myosin light chain phosphatase. J Biol Chem 2008; 283:32860-9. [PMID: 18782776 DOI: 10.1074/jbc.m804916200] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitric oxide and nitrovasodilators induce vascular smooth muscle cell relaxation in part by cGMP-dependent protein kinase I (PKG-Ialpha)-mediated activation of myosin phosphatase (MLCP). Mechanistically it has been proposed that protein-protein interactions between the N-terminal leucine zipper (LZ) domain of PKG-Ialpha ((PKG-Ialpha(1-59)) and the LZ and/or coiled coil (CC) domain of the myosin binding subunit (MBS) of MLCP are localized in the C terminus of MBS. Although recent studies have supported these interactions, the critical amino acids responsible for these interactions have not been identified. Here we present structural and biophysical data identifying that the LZ domain of PKG-Ialpha(1-59) interacts with a well defined 42-residue CC motif (MBS(CT42)) within the C terminus of MBS. Using glutathione S-transferase pulldown experiments, chemical cross-linking, size exclusion chromatography, circular dichroism, and isothermal titration calorimetry we identified a weak dimer-dimer interaction between PKG-Ialpha(1-59) and this C-terminal CC domain of MBS. The K(d) of this non-covalent complex is 178.0+/-1.5 microm. Furthermore our (1)H-(15)N heteronuclear single quantum correlation NMR data illustrate that this interaction is mediated by several PKG-Ialpha residues that are on the a, d, e, and g hydrophobic and electrostatic interface of the C-terminal heptad layers 2, 4, and 5 of PKG-Ialpha. Taken together these data support a role for the LZ domain of PKG-Ialpha and the CC domain of MBS in this requisite contractile complex.
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Affiliation(s)
- Alok K Sharma
- Divison of Molecular and Vascular Medicine, Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
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Sieber JJ, Willig KI, Heintzmann R, Hell SW, Lang T. The SNARE motif is essential for the formation of syntaxin clusters in the plasma membrane. Biophys J 2006; 90:2843-51. [PMID: 16443657 PMCID: PMC1414554 DOI: 10.1529/biophysj.105.079574] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In the plasma membrane, syntaxin 1 and syntaxin 4 clusters define sites at which secretory granules and caveolae fuse, respectively. It is widely believed that lipid phases are mandatory for cluster formation, as cluster integrity depends on cholesterol. Here we report that the native lipid environment is not sufficient for correct syntaxin 1 clustering and that additional cytoplasmic protein-protein interactions, primarily involving the SNARE motif, are required. Apparently no specific cofactors are needed because i), clusters form equally well in nonneuronal cells, and ii), as revealed by nanoscale subdiffraction resolution provided by STED microscopy, the number of clusters directly depends on the syntaxin 1 concentration. For syntaxin 4 clustering the N-terminal domain and the linker region are also dispensable. Moreover, clustering is specific because in both cluster types syntaxins mutually exclude one another at endogenous levels. We suggest that the SNARE motifs of syntaxin 1 and 4 mediate specific syntaxin clustering by homooligomerization, thereby spatially separating sites for different biological activities. Thus, syntaxin clustering represents a mechanism of membrane patterning that is based on protein-protein interactions.
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Affiliation(s)
- Jochen J Sieber
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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