1
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Inaba H, Shisaka Y, Ariyasu S, Sakakibara E, Ueda G, Aiba Y, Shimizu N, Sugimoto H, Shoji O. Heme-substituted protein assembly bridged by synthetic porphyrin: achieving controlled configuration while maintaining rotational freedom. RSC Adv 2024; 14:8829-8836. [PMID: 38495978 PMCID: PMC10941265 DOI: 10.1039/d4ra01042f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
The use of biological host-guest interactions, specifically the binding of hemoprotein to heme, has attracted significant research interest in the design of artificial protein assemblies. However, because of the inherent flexibility of the propionic acid group of heme, it is difficult to control the positioning and orientation of the protein unit and to construct well-ordered structures. Herein, we report a heme-substituted protein dimer composed of the native hemoprotein HasA, which accommodates a tetraphenylporphyrin bearing an additional metal coordination site. The specific binding of the tetraphenylporphyrin with an additional metal coordination site that protrudes in a fixed direction confines the configuration of the dimer structure to a defined bent form. The small-angle X-ray scattering profile shows the dimer structure with a bent form and suggests dynamic rotational behavior while keeping its bent-core structure, resembling a bevel gear. This unique dimer structure demonstrates that the design of heme-substituted protein assemblies can be expanded to protein assemblies while maintaining the rotational freedom of the individual protein units.
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Affiliation(s)
- Hiroaki Inaba
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Yuma Shisaka
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Shinya Ariyasu
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Erika Sakakibara
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Garyo Ueda
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Yuichiro Aiba
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) 1-1 Oho Tsukuba Ibaraki 305-0801 Japan
- RIKEN SPring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | | | - Osami Shoji
- Department of Chemistry, School of Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-0802 Japan
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2
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Monge N, Deschamps A, Amini MR. Automated selection of nanoparticle models for small-angle X-ray scattering data analysis using machine learning. Acta Crystallogr A Found Adv 2024; 80:202-212. [PMID: 38420992 PMCID: PMC10913671 DOI: 10.1107/s2053273324000950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Small-angle X-ray scattering (SAXS) is widely used to analyze the shape and size of nanoparticles in solution. A multitude of models, describing the SAXS intensity resulting from nanoparticles of various shapes, have been developed by the scientific community and are used for data analysis. Choosing the optimal model is a crucial step in data analysis, which can be difficult and time-consuming, especially for non-expert users. An algorithm is proposed, based on machine learning, representation learning and SAXS-specific preprocessing methods, which instantly selects the nanoparticle model best suited to describe SAXS data. The different algorithms compared are trained and evaluated on a simulated database. This database includes 75 000 scattering spectra from nine nanoparticle models, and realistically simulates two distinct device configurations. It will be made freely available to serve as a basis of comparison for future work. Deploying a universal solution for automatic nanoparticle model selection is a challenge made more difficult by the diversity of SAXS instruments and their flexible settings. The poor transferability of classification rules learned on one device configuration to another is highlighted. It is shown that training on several device configurations enables the algorithm to be generalized, without degrading performance compared with configuration-specific training. Finally, the classification algorithm is evaluated on a real data set obtained by performing SAXS experiments on nanoparticles for each of the instrumental configurations, which have been characterized by transmission electron microscopy. This data set, although very limited, allows estimation of the transferability of the classification rules learned on simulated data to real data.
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Affiliation(s)
- Nicolas Monge
- Xenocs, Grenoble, France
- SIMaP, University of Grenoble Alpes, CNRS, Grenoble INP, Grenoble, France
- LIG, University of Grenoble Alpes, CNRS, Grenoble, France
| | - Alexis Deschamps
- SIMaP, University of Grenoble Alpes, CNRS, Grenoble INP, Grenoble, France
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3
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Hopkins JB. BioXTAS RAW 2: new developments for a free open-source program for small-angle scattering data reduction and analysis. J Appl Crystallogr 2024; 57:194-208. [PMID: 38322719 PMCID: PMC10840314 DOI: 10.1107/s1600576723011019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/21/2023] [Indexed: 02/08/2024] Open
Abstract
BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI; updated automated Guinier fitting and D max finding algorithms; automated series (e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares (REGALS); creation of electron-density reconstructions using electron density via solution scattering (DENSS); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.
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Affiliation(s)
- Jesse B. Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
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4
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Düring J, Wolter M, Toplak JJ, Torres C, Dybkov O, Fokkens TJ, Bohnsack KE, Urlaub H, Steinchen W, Dienemann C, Lorenz S. Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1. Nat Struct Mol Biol 2024; 31:364-377. [PMID: 38332367 PMCID: PMC10873202 DOI: 10.1038/s41594-023-01203-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/07/2023] [Indexed: 02/10/2024]
Abstract
Ubiquitin ligases (E3s) are pivotal specificity determinants in the ubiquitin system by selecting substrates and decorating them with distinct ubiquitin signals. However, structure determination of the underlying, specific E3-substrate complexes has proven challenging owing to their transient nature. In particular, it is incompletely understood how members of the catalytic cysteine-driven class of HECT-type ligases (HECTs) position substrate proteins for modification. Here, we report a cryogenic electron microscopy (cryo-EM) structure of the full-length human HECT HACE1, along with solution-based conformational analyses by small-angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry. Structure-based functional analyses in vitro and in cells reveal that the activity of HACE1 is stringently regulated by dimerization-induced autoinhibition. The inhibition occurs at the first step of the catalytic cycle and is thus substrate-independent. We use mechanism-based chemical crosslinking to reconstitute a complex of activated, monomeric HACE1 with its major substrate, RAC1, determine its structure by cryo-EM and validate the binding mode by solution-based analyses. Our findings explain how HACE1 achieves selectivity in ubiquitinating the active, GTP-loaded state of RAC1 and establish a framework for interpreting mutational alterations of the HACE1-RAC1 interplay in disease. More broadly, this work illuminates central unexplored aspects in the architecture, conformational dynamics, regulation and specificity of full-length HECTs.
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Affiliation(s)
- Jonas Düring
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Madita Wolter
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Julia J Toplak
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Camilo Torres
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Olexandr Dybkov
- Research Group 'Bioanalytical Mass Spectrometry', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Thornton J Fokkens
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Research Group 'Bioanalytical Mass Spectrometry', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- 'Bioanalytics', Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
- 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells', University of Göttingen, Göttingen, Germany
| | - Wieland Steinchen
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sonja Lorenz
- Research Group 'Ubiquitin Signaling Specificity', Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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5
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Hopkins JB. BioXTAS RAW 2: new developments for a free open-source program for small angle scattering data reduction and analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559353. [PMID: 37808703 PMCID: PMC10557611 DOI: 10.1101/2023.09.25.559353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
BioXTAS RAW is a free, open-source program for reduction, analysis and modelling of biological small angle scattering data. Here, the new developments in RAW version 2 are described. These include: improved data reduction using pyFAI; updated automated Guinier fitting and Dmax finding algorithms; automated series (e.g. SEC-SAXS) buffer and sample region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using REGALS; creation of electron density reconstructions via DENSS; a comparison window showing residuals, ratios, and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. In addition, there is now a RAW API, which can be used without the GUI, providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.
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Affiliation(s)
- Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
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6
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Ferrero DS, Tomás Gilabert O, Verdaguer N. Structural insights on the nucleoprotein C-terminal domain of Měnglà virus. Microbiol Spectr 2023; 11:e0237323. [PMID: 37888996 PMCID: PMC10714759 DOI: 10.1128/spectrum.02373-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Filoviruses are the causative agents of severe and often fatal hemorrhagic disease in humans. Měnglà virus (MLAV) is a recently reported filovirus, isolated from fruit bats that is capable to replicate in human cells, representing a potential risk for human health. An in-depth structural and functional knowledge of MLAV proteins is an essential step for antiviral research on this virus that can also be extended to other emerging filoviruses. In this study, we determined the first crystal structures of the C-terminal domain (CTD) of the MLAV nucleoprotein (NP), showing important similarities to the equivalent domain in MARV. The structural data also show that the NP CTD has the ability to form large helical oligomers that may participate in the control of cytoplasmic inclusion body formation during viral replication.
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Affiliation(s)
| | | | - Nuria Verdaguer
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
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7
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Jiang X, Ogawa T, Yonezawa K, Shimizu N, Ichinose S, Uchihashi T, Nagaike W, Moriya T, Adachi N, Kawasaki M, Dohmae N, Senda T, Hirokawa N. The two-step cargo recognition mechanism of heterotrimeric kinesin. EMBO Rep 2023; 24:e56864. [PMID: 37575008 PMCID: PMC10626431 DOI: 10.15252/embr.202356864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 08/15/2023] Open
Abstract
Kinesin-driven intracellular transport is essential for various cell biological events and thus plays a crucial role in many pathological processes. However, little is known about the molecular basis of the specific and dynamic cargo-binding mechanism of kinesins. Here, an integrated structural analysis of the KIF3/KAP3 and KIF3/KAP3-APC complexes unveils the mechanism by which KIF3/KAP3 can dynamically grasp APC in a two-step manner, which suggests kinesin-cargo recognition dynamics composed of cargo loading, locking, and release. Our finding is the first demonstration of the two-step cargo recognition and stabilization mechanism of kinesins, which provides novel insights into the intracellular trafficking machinery.
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Affiliation(s)
- Xuguang Jiang
- Department of Cell Biology and Anatomy, Graduate School of MedicineThe University of TokyoTokyoJapan
- Tsinghua‐Peking Center for Life Sciences, School of Life SciencesTsinghua UniversityBeijingChina
| | - Tadayuki Ogawa
- Department of Cell Biology and Anatomy, Graduate School of MedicineThe University of TokyoTokyoJapan
- Research Center for Advanced Medical ScienceDokkyo Medical UniversityTochigiJapan
- Biomolecular Characterization UnitRIKEN Center for Sustainable Resource ScienceWakoJapan
| | - Kento Yonezawa
- Structural Biology Research Center, Photon FactoryInstitute of Materials Structure Science, High Energy Accelerator Research Organization (KEK)TsukubaJapan
- Center for Digital Green‐InnovationNara Institute of Science and TechnologyNaraJapan
| | - Nobutaka Shimizu
- Structural Biology Research Center, Photon FactoryInstitute of Materials Structure Science, High Energy Accelerator Research Organization (KEK)TsukubaJapan
| | - Sotaro Ichinose
- Department of Cell Biology and Anatomy, Graduate School of MedicineThe University of TokyoTokyoJapan
- Department of Anatomy, Graduate School of MedicineGunma UniversityGunmaJapan
| | - Takayuki Uchihashi
- Department of PhysicsNagoya UniversityNagoyaJapan
- Exploratory Research Center on Life and Living Systems (ExCELLS)National Institutes of Natural SciencesOkazakiJapan
| | | | - Toshio Moriya
- Structural Biology Research Center, Photon FactoryInstitute of Materials Structure Science, High Energy Accelerator Research Organization (KEK)TsukubaJapan
| | - Naruhiko Adachi
- Structural Biology Research Center, Photon FactoryInstitute of Materials Structure Science, High Energy Accelerator Research Organization (KEK)TsukubaJapan
| | - Masato Kawasaki
- Structural Biology Research Center, Photon FactoryInstitute of Materials Structure Science, High Energy Accelerator Research Organization (KEK)TsukubaJapan
| | - Naoshi Dohmae
- Biomolecular Characterization UnitRIKEN Center for Sustainable Resource ScienceWakoJapan
| | - Toshiya Senda
- Structural Biology Research Center, Photon FactoryInstitute of Materials Structure Science, High Energy Accelerator Research Organization (KEK)TsukubaJapan
| | - Nobutaka Hirokawa
- Department of Cell Biology and Anatomy, Graduate School of MedicineThe University of TokyoTokyoJapan
- Juntendo Advanced Research Institute for Health ScienceJuntendo UniversityTokyoJapan
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8
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Dorn G, Gmeiner C, de Vries T, Dedic E, Novakovic M, Damberger FF, Maris C, Finol E, Sarnowski CP, Kohlbrecher J, Welsh TJ, Bolisetty S, Mezzenga R, Aebersold R, Leitner A, Yulikov M, Jeschke G, Allain FHT. Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility. Nat Commun 2023; 14:6429. [PMID: 37833274 PMCID: PMC10576089 DOI: 10.1038/s41467-023-42012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.
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Affiliation(s)
- Georg Dorn
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christoph Gmeiner
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tebbe de Vries
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Mihajlo Novakovic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Fred F Damberger
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christophe Maris
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Esteban Finol
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Joachim Kohlbrecher
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, Villigen, Switzerland
| | - Timothy J Welsh
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Sreenath Bolisetty
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Raffaele Mezzenga
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Frédéric H-T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
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9
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Warden M, DeRose E, Tamayo J, Mueller G, Gavis E, Hall T. The translational repressor Glorund uses interchangeable RNA recognition domains to recognize Drosophila nanos. Nucleic Acids Res 2023; 51:8836-8849. [PMID: 37427795 PMCID: PMC10484662 DOI: 10.1093/nar/gkad586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/01/2023] [Accepted: 06/30/2023] [Indexed: 07/11/2023] Open
Abstract
The Drosophila melanogaster protein Glorund (Glo) represses nanos (nos) translation and uses its quasi-RNA recognition motifs (qRRMs) to recognize both G-tract and structured UA-rich motifs within the nos translational control element (TCE). We showed previously that each of the three qRRMs is multifunctional, capable of binding to G-tract and UA-rich motifs, yet if and how the qRRMs combine to recognize the nos TCE remained unclear. Here we determined solution structures of a nos TCEI_III RNA containing the G-tract and UA-rich motifs. The RNA structure demonstrated that a single qRRM is physically incapable of recognizing both RNA elements simultaneously. In vivo experiments further indicated that any two qRRMs are sufficient to repress nos translation. We probed interactions of Glo qRRMs with TCEI_III RNA using NMR paramagnetic relaxation experiments. Our in vitro and in vivo data support a model whereby tandem Glo qRRMs are indeed multifunctional and interchangeable for recognition of TCE G-tract or UA-rich motifs. This study illustrates how multiple RNA recognition modules within an RNA-binding protein may combine to diversify the RNAs that are recognized and regulated.
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Affiliation(s)
- Meghan S Warden
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Eugene F DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Joel V Tamayo
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Geoffrey A Mueller
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Elizabeth R Gavis
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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10
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Qin XY, Furutani Y, Yonezawa K, Shimizu N, Kato-Murayama M, Shirouzu M, Xu Y, Yamano Y, Wada A, Gailhouste L, Shrestha R, Takahashi M, Keillor JW, Su T, Yu W, Fujii S, Kagechika H, Dohmae N, Shirakami Y, Shimizu M, Masaki T, Matsuura T, Suzuki H, Kojima S. Targeting transglutaminase 2 mediated exostosin glycosyltransferase 1 signaling in liver cancer stem cells with acyclic retinoid. Cell Death Dis 2023; 14:358. [PMID: 37308486 DOI: 10.1038/s41419-023-05847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 06/14/2023]
Abstract
Transglutaminase 2 (TG2) is a multifunctional protein that promotes or suppresses tumorigenesis, depending on intracellular location and conformational structure. Acyclic retinoid (ACR) is an orally administered vitamin A derivative that prevents hepatocellular carcinoma (HCC) recurrence by targeting liver cancer stem cells (CSCs). In this study, we examined the subcellular location-dependent effects of ACR on TG2 activity at a structural level and characterized the functional role of TG2 and its downstream molecular mechanism in the selective depletion of liver CSCs. A binding assay with high-performance magnetic nanobeads and structural dynamic analysis with native gel electrophoresis and size-exclusion chromatography-coupled multi-angle light scattering or small-angle X-ray scattering showed that ACR binds directly to TG2, induces oligomer formation of TG2, and inhibits the transamidase activity of cytoplasmic TG2 in HCC cells. The loss-of-function of TG2 suppressed the expression of stemness-related genes, spheroid proliferation and selectively induced cell death in an EpCAM+ liver CSC subpopulation in HCC cells. Proteome analysis revealed that TG2 inhibition suppressed the gene and protein expression of exostosin glycosyltransferase 1 (EXT1) and heparan sulfate biosynthesis in HCC cells. In contrast, high levels of ACR increased intracellular Ca2+ concentrations along with an increase in apoptotic cells, which probably contributed to the enhanced transamidase activity of nuclear TG2. This study demonstrates that ACR could act as a novel TG2 inhibitor; TG2-mediated EXT1 signaling is a promising therapeutic target in the prevention of HCC by disrupting liver CSCs.
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Affiliation(s)
- Xian-Yang Qin
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
| | - Yutaka Furutani
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Kento Yonezawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Miyuki Kato-Murayama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Yali Xu
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Yumiko Yamano
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe, Hyogo, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe, Hyogo, Japan
| | - Luc Gailhouste
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Brain Development and Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Rajan Shrestha
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Pharmacy, Kathmandu University, Dhulikhel, Kavre, Nepal
| | - Masataka Takahashi
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jeffrey W Keillor
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Ting Su
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Wenkui Yu
- School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Shinya Fujii
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Yohei Shirakami
- Department of Gastroenterology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Masahito Shimizu
- Department of Gastroenterology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Takahiro Masaki
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Tomokazu Matsuura
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Harukazu Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Soichi Kojima
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
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11
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Garcia NK, Kephart SM, Benhaim MA, Matsui T, Mileant A, Guttman M, Lee KK. Structural dynamics reveal subtype-specific activation and inhibition of influenza virus hemagglutinin. J Biol Chem 2023; 299:104765. [PMID: 37121546 PMCID: PMC10220487 DOI: 10.1016/j.jbc.2023.104765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/25/2023] [Accepted: 04/24/2023] [Indexed: 05/02/2023] Open
Abstract
Influenza hemagglutinin (HA) is a prototypical class 1 viral entry glycoprotein, responsible for mediating receptor binding and membrane fusion. Structures of its prefusion and postfusion forms, embodying the beginning and endpoints of the fusion pathway, have been extensively characterized. Studies probing HA dynamics during fusion have begun to identify intermediate states along the pathway, enhancing our understanding of how HA becomes activated and traverses its conformational pathway to complete fusion. HA is also the most variable, rapidly evolving part of influenza virus, and it is not known whether mechanisms of its activation and fusion are conserved across divergent viral subtypes. Here, we apply hydrogen-deuterium exchange mass spectrometry to compare fusion activation in two subtypes of HA, H1 and H3. Our data reveal subtype-specific behavior in the regions of HA that undergo structural rearrangement during fusion, including the fusion peptide and HA1/HA2 interface. In the presence of an antibody that inhibits the conformational change (FI6v3), we observe that acid-induced dynamic changes near the epitope are dampened, but the degree of protection at the fusion peptide is different for the two subtypes investigated. These results thus provide new insights into variation in the mechanisms of influenza HA's dynamic activation and its inhibition.
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Affiliation(s)
- Natalie K Garcia
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Sally M Kephart
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Mark A Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Laboratory, SLAC, Menlo Park, California, USA
| | - Alexander Mileant
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
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12
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Montaño SP, Rowland SJ, Fuller JR, Burke ME, MacDonald A, Boocock M, Stark W, Rice P. Structural basis for topological regulation of Tn3 resolvase. Nucleic Acids Res 2023; 51:1001-1018. [PMID: 36100255 PMCID: PMC9943657 DOI: 10.1093/nar/gkac733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/02/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Site-specific DNA recombinases play a variety of biological roles, often related to the dissemination of antibiotic resistance, and are also useful synthetic biology tools. The simplest site-specific recombination systems will recombine any two cognate sites regardless of context. Other systems have evolved elaborate mechanisms, often sensing DNA topology, to ensure that only one of multiple possible recombination products is produced. The closely related resolvases from the Tn3 and γδ transposons have historically served as paradigms for the regulation of recombinase activity by DNA topology. However, despite many proposals, models of the multi-subunit protein-DNA complex (termed the synaptosome) that enforces this regulation have been unsatisfying due to a lack of experimental constraints and incomplete concordance with experimental data. Here, we present new structural and biochemical data that lead to a new, detailed model of the Tn3 synaptosome, and discuss how it harnesses DNA topology to regulate the enzymatic activity of the recombinase.
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Affiliation(s)
- Sherwin P Montaño
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sally-J Rowland
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, Scotland, UK
| | - James R Fuller
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Mary E Burke
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, Scotland, UK
| | - Alasdair I MacDonald
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, Scotland, UK
| | - Martin R Boocock
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, Scotland, UK
| | - W Marshall Stark
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, Scotland, UK
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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13
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De Silva NIU, Fargason T, Zhang Z, Wang T, Zhang J. Inter-domain Flexibility of Human Ser/Arg-Rich Splicing Factor 1 Allows Variable Spacer Length in Cognate RNA’s Bipartite Motifs. Biochemistry 2022; 61:2922-2932. [DOI: 10.1021/acs.biochem.2c00565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Naiduwadura Ivon Upekala De Silva
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Talia Fargason
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Zihan Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Ting Wang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Jun Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
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14
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Bobde RC, Kumar A, Vasudevan D. Plant-specific HDT family histone deacetylases are nucleoplasmins. THE PLANT CELL 2022; 34:4760-4777. [PMID: 36069647 PMCID: PMC9709999 DOI: 10.1093/plcell/koac275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Histone acetyltransferase (HAT)- and histone deacetylase (HDAC)-mediated histone acetylation and deacetylation regulate nucleosome dynamics and gene expression. HDACs are classified into different families, with HD-tuins or HDTs being specific to plants. HDTs show some sequence similarity to nucleoplasmins, the histone chaperones that aid in binding, storing, and loading H2A/H2B dimers to assemble nucleosomes. Here, we solved the crystal structure of the N-terminal domain (NTD) of all four HDTs (HDT1, HDT2, HDT3, and HDT4) from Arabidopsis (Arabidopsis thaliana). The NTDs form a nucleoplasmin fold, exist as pentamers in solution, and are resistant to protease treatment, high temperature, salt, and urea conditions. Structurally, HDTs do not form a decamer, unlike certain classical nucleoplasmins. The HDT-NTD requires an additional A2 acidic tract C-terminal to the nucleoplasmin domain for interaction with histone H3/H4 and H2A/H2B oligomers. We also report the in-solution structures of HDT2 pentamers in complex with histone oligomers. Our study provides a detailed structural and in vitro functional characterization of HDTs, revealing them to be nucleoplasmin family histone chaperones. The experimental confirmation that HDTs are nucleoplasmins may spark new interest in this enigmatic family of proteins.
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Affiliation(s)
- Ruchir C Bobde
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Ashish Kumar
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
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15
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Expanding the Toolbox for Bicelle-Forming Surfactant–Lipid Mixtures. Molecules 2022; 27:molecules27217628. [PMID: 36364455 PMCID: PMC9658636 DOI: 10.3390/molecules27217628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022] Open
Abstract
Bicelles are disk-shaped models of cellular membranes used to study lipid–protein interactions, as well as for structural and functional studies on transmembrane proteins. One challenge for the incorporation of transmembrane proteins in bicelles is the limited range of detergent and lipid combinations available for the successful reconstitution of proteins in model membranes. This is important, as the function and stability of transmembrane proteins are very closely linked to the detergents used for their purification and to the lipids that the proteins are embedded in. Here, we expand the toolkit of lipid and detergent combinations that allow the formation of stable bicelles. We use a combination of dynamic light scattering, small-angle X-ray scattering and cryogenic electron microscopy to perform a systematic sample characterization, thus providing a set of conditions under which bicelles can be successfully formed.
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16
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Mertens HDT. Computational methods for the analysis of solution small-angle X-ray scattering of biomolecules: ATSAS. Methods Enzymol 2022; 678:193-236. [PMID: 36641208 DOI: 10.1016/bs.mie.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ATSAS software suite provides a comprehensive set of programs for the processing, analysis and modeling of small-angle scattering data, tailored for but not limited to data acquired on biological macromolecules. In this review the major components and developments in the ATSAS package are described, with a focus on user driven application. Data reduction, analysis and modeling approaches and strategies will be introduced and discussed. At the time of writing the latest package, ATSAS 3.1, is freely available for academic users at: https://www.embl-hamburg.de/biosaxs/software.html.
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17
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Kieffer J, Brennich M, Florial JB, Oscarsson M, De Maria Antolinos A, Tully M, Pernot P. New data analysis for BioSAXS at the ESRF. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:1318-1328. [PMID: 36073892 PMCID: PMC9455220 DOI: 10.1107/s1600577522007238] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 05/09/2023]
Abstract
The second phase of the ESRF upgrade program did not only provide a new storage ring (Extremely Brilliant Source, EBS) but also allowed several beamlines to be refurbished. The BioSAXS beamline (located on port BM29) was upgraded with a new wiggler source and a larger detector. All analysis software has been rewritten to cope with the increased data flux and continues to provide beamline users with reduced and pre-processed data in real time. This article describes FreeSAS, an open-source collection of various small-angle scattering analysis algorithms needed to reduce and analyze BioSAXS data, and Dahu, the tool used to interface data analysis with beamline control. It further presents the data-processing pipelines for the different data acquisitions modes of the beamline, using either a sample changer for individual homogeneous samples or an inline size-exclusion chromatography setup.
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Affiliation(s)
- Jérôme Kieffer
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
- Correspondence e-mail:
| | - Martha Brennich
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Jean-Baptiste Florial
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Marcus Oscarsson
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | - Mark Tully
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Petra Pernot
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
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18
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Bhat B, Pahari S, Liu S, Lin YT, Kwon J, Akbulut M. Nanostructural and Rheological Transitions of pH-Responsive Supramolecular Systems Involving a Zwitterionic Amphiphile and a Triamine. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.130067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Takahashi D, Yonezawa K, Okizaki Y, Caaveiro JMM, Ueda T, Shimada A, Sakane F, Shimizu N. Ca 2+ -induced structural changes and intramolecular interactions in N-terminal region of diacylglycerol kinase alpha. Protein Sci 2022; 31:e4365. [PMID: 35762720 DOI: 10.1002/pro.4365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/09/2022] [Accepted: 05/27/2022] [Indexed: 11/05/2022]
Abstract
Diacylglycerol kinases (DGKs) are multi-domain lipid kinases that modulate the levels of lipid messengers, diacylglycerol, and phosphatidic acid. Recently, increasing attention has been paid to its α isozyme (DGKα) as a potential target for cancer immunotherapy. However, little progress has been made on the structural biology of DGKs, and a detailed understanding of the Ca2+ -triggered activation of DGKα, for which the N-terminal domains likely play a critical role, remains unclear. We have recently shown that Ca2+ binding to DGKα-EF induces conformational changes from a protease-susceptible "open" conformation in the apo state to a well-folded one in its holo state. Here, we further studied the structural properties of DGKα N-terminal (RVH and EF) domains using a series of biophysical techniques. We first revealed that the N-terminal RVH domain is a novel Ca2+ -binding domain, but the Ca2+ -induced conformational changes mainly occur in the EF domain. This was corroborated by NMR experiments showing that the EF domain adopts a molten-globule like structure in the apo state. Further analyses using SEC-SAXS and NMR indicate that the partially unfolded EF domain interacts with RVH domain, likely via hydrophobic interactions in the absence of Ca2+ , and this interaction is modified in the presence of Ca2+ . Taken together, these results present novel insights into the structural rearrangement of DGKα N-terminal domains upon binding to Ca2+ , which is essential for the activation of the enzyme.
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Affiliation(s)
- Daisuke Takahashi
- Department of Protein Structure, Function, and Design, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan
| | - Kento Yonezawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan.,Center for Digital Green-Innovation (CDG), Nara Institute of Science and Technology (NAIST), Ikoma, Japan
| | - Yuki Okizaki
- Department of Protein Structure, Function, and Design, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan
| | - Jose M M Caaveiro
- Department of Global Healthcare, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan
| | - Tadashi Ueda
- Department of Protein Structure, Function, and Design, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan
| | - Atsushi Shimada
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
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20
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Bon C, Cabantous S, Julien S, Guillet V, Chalut C, Rima J, Brison Y, Malaga W, Sanchez-Dafun A, Gavalda S, Quémard A, Marcoux J, Waldo GS, Guilhot C, Mourey L. Solution structure of the type I polyketide synthase Pks13 from Mycobacterium tuberculosis. BMC Biol 2022; 20:147. [PMID: 35729566 PMCID: PMC9210659 DOI: 10.1186/s12915-022-01337-9] [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: 04/02/2021] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Type I polyketide synthases (PKSs) are multifunctional enzymes responsible for the biosynthesis of a group of diverse natural compounds with biotechnological and pharmaceutical interest called polyketides. The diversity of polyketides is impressive despite the limited set of catalytic domains used by PKSs for biosynthesis, leading to considerable interest in deciphering their structure-function relationships, which is challenging due to high intrinsic flexibility. Among nineteen polyketide synthases encoded by the genome of Mycobacterium tuberculosis, Pks13 is the condensase required for the final condensation step of two long acyl chains in the biosynthetic pathway of mycolic acids, essential components of the cell envelope of Corynebacterineae species. It has been validated as a promising druggable target and knowledge of its structure is essential to speed up drug discovery to fight against tuberculosis. RESULTS We report here a quasi-atomic model of Pks13 obtained using small-angle X-ray scattering of the entire protein and various molecular subspecies combined with known high-resolution structures of Pks13 domains or structural homologues. As a comparison, the low-resolution structures of two other mycobacterial polyketide synthases, Mas and PpsA from Mycobacterium bovis BCG, are also presented. This study highlights a monomeric and elongated state of the enzyme with the apo- and holo-forms being identical at the resolution probed. Catalytic domains are segregated into two parts, which correspond to the condensation reaction per se and to the release of the product, a pivot for the enzyme flexibility being at the interface. The two acyl carrier protein domains are found at opposite sides of the ketosynthase domain and display distinct characteristics in terms of flexibility. CONCLUSIONS The Pks13 model reported here provides the first structural information on the molecular mechanism of this complex enzyme and opens up new perspectives to develop inhibitors that target the interactions with its enzymatic partners or between catalytic domains within Pks13 itself.
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Affiliation(s)
- Cécile Bon
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Stéphanie Cabantous
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Los Alamos National Laboratory, Bioscience Division B-N2, Los Alamos, NM, 87545, USA.,Present address: Centre de Recherche en Cancérologie de Toulouse (CRCT), Inserm, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sylviane Julien
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Valérie Guillet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julie Rima
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yoann Brison
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Present address: Toulouse White Biotechnology, 31400, Toulouse, France
| | - Wladimir Malaga
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Angelique Sanchez-Dafun
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sabine Gavalda
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Present address: Carbios, Biopole Clermont Limagne, 63360, Saint-Beauzire, France
| | - Annaïk Quémard
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Geoffrey S Waldo
- Los Alamos National Laboratory, Bioscience Division B-N2, Los Alamos, NM, 87545, USA
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
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21
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Small-angle X-ray scattering data of a guanine-rich DNA derived from the promoter region of c-MYC gene in solution. Data Brief 2022; 42:108285. [PMID: 35647231 PMCID: PMC9133745 DOI: 10.1016/j.dib.2022.108285] [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: 03/26/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 11/20/2022] Open
Abstract
This article presented the small-angle X-ray scattering (SAXS) data of a guanine-rich DNA derived from the promoter region of c-MYC gene (Pu22) in solution. The data is collected under the condition, where the Pu22 takes a guanine quadruplex (GQ) structure. The SAXS curve was also measured and analyzed when 18-crown-6, a chelator of K+ ions, was added to the Pu22 solution.
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22
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Levina A, Fleming KD, Burke JE, Leonard TA. Activation of the essential kinase PDK1 by phosphoinositide-driven trans-autophosphorylation. Nat Commun 2022; 13:1874. [PMID: 35387990 PMCID: PMC8986801 DOI: 10.1038/s41467-022-29368-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/08/2022] [Indexed: 12/18/2022] Open
Abstract
3-phosphoinositide-dependent kinase 1 (PDK1) is an essential serine/threonine protein kinase, which plays a crucial role in cell growth and proliferation. It is often referred to as a 'master' kinase due to its ability to activate at least 23 downstream protein kinases implicated in various signaling pathways. In this study, we have elucidated the mechanism of phosphoinositide-driven PDK1 auto-activation. We show that PDK1 trans-autophosphorylation is mediated by a PIP3-mediated face-to-face dimer. We report regulatory motifs in the kinase-PH interdomain linker that allosterically activate PDK1 autophosphorylation via a linker-swapped dimer mechanism. Finally, we show that PDK1 is autoinhibited by its PH domain and that positive cooperativity of PIP3 binding drives switch-like activation of PDK1. These results imply that the PDK1-mediated activation of effector kinases, including Akt, PKC, Sgk, S6K and RSK, many of whom are not directly regulated by phosphoinositides, is also likely to be dependent on PIP3 or PI(3,4)P2.
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Affiliation(s)
- Aleksandra Levina
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, 1090, Vienna, Austria
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030, Vienna, Austria.
- Department of Medical Biochemistry, Medical University of Vienna, 1090, Vienna, Austria.
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23
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Thomasen FE, Pesce F, Roesgaard MA, Tesei G, Lindorff-Larsen K. Improving Martini 3 for Disordered and Multidomain Proteins. J Chem Theory Comput 2022; 18:2033-2041. [PMID: 35377637 DOI: 10.1021/acs.jctc.1c01042] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coarse-grained molecular dynamics simulations are a useful tool to determine conformational ensembles of proteins. Here, we show that the coarse-grained force field Martini 3 underestimates the global dimensions of intrinsically disordered proteins (IDPs) and multidomain proteins when compared with small-angle X-ray scattering (SAXS) data and that increasing the strength of protein-water interactions favors more expanded conformations. We find that increasing the strength of interactions between protein and water by ca. 10% results in improved agreement with the SAXS data for IDPs and multidomain proteins. We also show that this correction results in a more accurate description of self-association of IDPs and folded proteins and better agreement with paramagnetic relaxation enhancement data for most IDPs. While simulations with this revised force field still show deviations to experiments for some systems, our results suggest that it is overall a substantial improvement for coarse-grained simulations of soluble proteins.
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Affiliation(s)
- F Emil Thomasen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Francesco Pesce
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Mette Ahrensback Roesgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Giulio Tesei
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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24
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Molodenskiy DS, Svergun DI, Kikhney AG. Artificial neural networks for solution scattering data analysis. Structure 2022; 30:900-908.e2. [DOI: 10.1016/j.str.2022.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/24/2022] [Accepted: 03/16/2022] [Indexed: 11/27/2022]
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25
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Bleuler-Martinez S, Varrot A, Olieric V, Schubert M, Vogt E, Fetz C, Wohlschlager T, Plaza DF, Wälti M, Duport Y, Capitani G, Aebi M, Künzler M. Structure-function relationship of a novel fucoside-binding fruiting body lectin from Coprinopsis cinerea exhibiting nematotoxic activity. Glycobiology 2022; 32:600-615. [PMID: 35323921 PMCID: PMC9191617 DOI: 10.1093/glycob/cwac020] [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: 11/16/2021] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 11/14/2022] Open
Abstract
Lectins are non-immunoglobulin-type proteins that bind to specific carbohydrate epitopes and play important roles in intra- and inter-organismic interactions. Here, we describe a novel fucose-specific lectin, termed CML1, which we identified from fruiting body extracts of Coprinopsis cinerea. For further characterization, the coding sequence for CML1 was cloned and heterologously expressed in Escherichia coli. Feeding of CML1-producing bacteria inhibited larval development of the bacterivorous nematode Caenorhabditis tropicalis, but not of C. elegans. The crystal structure of the recombinant protein in its apo-form and in complex with H type I or Lewis A blood group antigens was determined by X-ray crystallography. The protein folds as a sandwich of 2 antiparallel β-sheets and forms hexamers resulting from a trimer of dimers. The hexameric arrangement was confirmed by small-angle X-ray scattering (SAXS). One carbohydrate-binding site per protomer was found at the dimer interface with both protomers contributing to ligand binding, resulting in a hexavalent lectin. In terms of lectin activity of recombinant CML1, substitution of the carbohydrate-interacting residues His54, Asn55, Trp94, and Arg114 by Ala abolished carbohydrate-binding and nematotoxicity. Although no similarities to any characterized lectin were found, sequence alignments identified many non-characterized agaricomycete proteins. These results suggest that CML1 is the founding member of a novel family of fucoside-binding lectins involved in the defense of agaricomycete fruiting bodies against predation by fungivorous nematodes.
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Affiliation(s)
- Silvia Bleuler-Martinez
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Annabelle Varrot
- University Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Vincent Olieric
- Swiss Light Source (SLS), Paul Scherrer Institute (PSI), Villigen, Switzerland
| | - Mario Schubert
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria
| | - Eva Vogt
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Céline Fetz
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Therese Wohlschlager
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - David Fernando Plaza
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.,Division of Infectious Diseases, Karolinska University Hospital, 171 64, Solna, Sweden
| | - Martin Wälti
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Yannick Duport
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Guido Capitani
- Swiss Light Source (SLS), Paul Scherrer Institute (PSI), Villigen, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
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26
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Barclay A, Tidemand Johansen N, Tidemand FG, Arleth L, Pedersen MC. Global fitting of multiple data frames from SEC–SAXS to investigate the structure of next-generation nanodiscs. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:483-493. [PMID: 35362471 PMCID: PMC8972807 DOI: 10.1107/s2059798322001838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022]
Abstract
The combination of online size-exclusion chromatography and small-angle X-ray scattering (SEC–SAXS) is rapidly becoming a key technique for structural investigations of elaborate biophysical samples in solution. Here, a novel model-refinement strategy centred around the technique is outlined and its utility is demonstrated by analysing data series from several SEC–SAXS experiments on phospholipid bilayer nanodiscs. Using this method, a single model was globally refined against many frames from the same data series, thereby capturing the frame-to-frame tendencies of the irradiated sample. These are compared with models refined in the traditional manner, in which refinement is based on the average profile of a set of consecutive frames from the same data series without an in-depth comparison of individual frames. This is considered to be an attractive model-refinement scheme as it considerably lowers the total number of parameters refined from the data series, produces tendencies that are automatically consistent between frames, and utilizes a considerably larger portion of the recorded data than is often performed in such experiments. Additionally, a method is outlined for correcting a measured UV absorption signal by accounting for potential peak broadening by the experimental setup.
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27
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Garcia AA, Mathews II, Horikoshi N, Matsui T, Kaur M, Wakatsuki S, Mochly-Rosen D. Stabilization of glucose-6-phosphate dehydrogenase oligomers enhances catalytic activity and stability of clinical variants. J Biol Chem 2022; 298:101610. [PMID: 35065072 PMCID: PMC8861134 DOI: 10.1016/j.jbc.2022.101610] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 11/30/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a genetic trait that can cause hemolytic anemia. To date, over 150 nonsynonymous mutations have been identified in G6PD, with pathogenic mutations clustering near the dimer and/or tetramer interface and the allosteric NADP+-binding site. Recently, our lab identified a small molecule that activates G6PD variants by stabilizing the allosteric NADP+ and dimer complex, suggesting therapeutics that target these regions may improve structural defects. Here, we elucidated the connection between allosteric NADP+ binding, oligomerization, and pathogenicity to determine whether oligomer stabilization can be used as a therapeutic strategy for G6PD deficiency (G6PDdef). We first solved the crystal structure for G6PDK403Q, a mutant that mimics the physiological acetylation of wild-type G6PD in erythrocytes and demonstrated that loss of allosteric NADP+ binding induces conformational changes in the dimer. These structural changes prevent tetramerization, are unique to Class I variants (the most severe form of G6PDdef), and cause the deactivation and destabilization of G6PD. We also introduced nonnative cysteines at the oligomer interfaces and found that the tetramer complex is more catalytically active and stable than the dimer. Furthermore, stabilizing the dimer and tetramer improved protein stability in clinical variants, regardless of clinical classification, with tetramerization also improving the activity of G6PDK403Q and Class I variants. These findings were validated using enzyme activity and thermostability assays, analytical size-exclusion chromatography (SEC), and SEC coupled with small-angle X-ray scattering (SEC-SAXS). Taken together, our findings suggest a potential therapeutic strategy for G6PDdef and provide a foundation for future drug discovery efforts.
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Affiliation(s)
- Adriana Ann Garcia
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, California, USA
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Naoki Horikoshi
- Life Science Center for Survival Dynamics, University of Tsukuba, Tsukuba, Ibaraki, Japan; Biological Sciences Division, SLAC National Accelerator Laboratory, Menlo Park, California, USA; Department of Structural Biology, School of Medicine, Stanford University, Stanford, California, USA
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Manat Kaur
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, California, USA
| | - Soichi Wakatsuki
- Biological Sciences Division, SLAC National Accelerator Laboratory, Menlo Park, California, USA; Department of Structural Biology, School of Medicine, Stanford University, Stanford, California, USA.
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, California, USA.
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28
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Kittilä T, Calero P, Fredslund F, Lowe PT, Tezé D, Nieto-Domínguez M, O'Hagan D, Nikel PI, Welner DH. Oligomerization engineering of the fluorinase enzyme leads to an active trimer that supports synthesis of fluorometabolites in vitro. Microb Biotechnol 2022; 15:1622-1632. [PMID: 35084776 PMCID: PMC9049626 DOI: 10.1111/1751-7915.14009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 12/15/2022] Open
Abstract
The fluorinase enzyme represents the only biological mechanism capable of forming stable C–F bonds characterized in nature thus far, offering a biotechnological route to the biosynthesis of value‐added organofluorines. The fluorinase is known to operate in a hexameric form, but the consequence(s) of the oligomerization status on the enzyme activity and its catalytic properties remain largely unknown. In this work, this aspect was explored by rationally engineering trimeric fluorinase variants that retained the same catalytic rate as the wild‐type enzyme. These results ruled out hexamerization as a requisite for the fluorination activity. The Michaelis constant (KM) for S‐adenosyl‐l‐methionine, one of the substrates of the fluorinase, increased by two orders of magnitude upon hexamer disruption. Such a shift in S‐adenosyl‐l‐methionine affinity points to a long‐range effect of hexamerization on substrate binding – likely decreasing substrate dissociation and release from the active site. A practical application of trimeric fluorinase is illustrated by establishing in vitro fluorometabolite synthesis in a bacterial cell‐free system.
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Affiliation(s)
- Tiia Kittilä
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Patricia Calero
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Folmer Fredslund
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Phillip T Lowe
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - David Tezé
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - David O'Hagan
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Ditte H Welner
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
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29
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Abe H, Nemoto F, Hiroi K, Ohishi K, Takata S. Spontaneous formations of nanoconfined water in ionic liquids by small-angle neutron scattering. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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The Structure and Function of Modular Escherichia coli O157:H7 Bacteriophage FTBEc1 endolysin, LysT84: Defining a New Endolysin Catalytic Subfamily. Biochem J 2021; 479:207-223. [PMID: 34935873 DOI: 10.1042/bcj20210701] [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: 10/06/2021] [Revised: 12/12/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022]
Abstract
Bacteriophage endolysins degrade peptidoglycan and have been identified as antibacterial candidates to combat antimicrobial resistance. Considering the catalytic and structural diversity of endolysins, there is a paucity of structural data to inform how these enzymes work at the molecular level-key data that is needed to realize the potential of endolysin-based antibacterial agents. Here, we determine the atomic structure and define the enzymatic function of Escherichia coli O157:H7 phage FTEBc1 endolysin, LysT84. Bioinformatic analysis reveals that LysT84 is a modular endolysin, which is unusual for Gram-negative endolysins, comprising a peptidoglycan binding domain and an enzymatic domain. The crystal structure of LysT84 (2.99 Å) revealed a mostly α-helical protein with two domains connected by a linker region but packed together. LysT84 was determined to be a monomer in solution using analytical ultracentrifugation. Small-angle X-ray scattering data revealed that LysT84 is a flexible protein but does not have the expected bimodal P(r) function of a multidomain protein, suggesting that the domains of LysT84 pack closely creating a globular protein as seen in the crystal structure. Structural analysis reveals two key glutamate residues positioned on either side of the active site cavity; mutagenesis demonstrating these residues are critical for peptidoglycan degradation. Molecular dynamic simulations suggest that the enzymatically active domain is dynamic, allowing the appropriate positioning of these catalytic residues for hydrolysis of the β(1-4) bond. Overall, our study defines the structural basis for peptidoglycan degradation by LysT84 which supports rational engineering of related endolysins into effective antibacterial agents.
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31
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Pohl C, Mahapatra S, Kulakova A, Streicher W, Peters GHJ, Nørgaard A, Harris P. Combination of high throughput and structural screening to assess protein stability - a screening perspective. Eur J Pharm Biopharm 2021; 171:1-10. [PMID: 34826593 DOI: 10.1016/j.ejpb.2021.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 11/04/2022]
Abstract
High throughput screening to measure the stability of industrially relevant proteins and their variants is necessary for quality assessment in the development process. Advances in automation, measurement time and sample consumption for many techniques allow rapid measurements with minimal amount of protein. However, many methods include automated data analysis, potentially neglecting important aspects of the proteińs behavior in certain conditions. In this study we implement small angle X-ray scattering (SAXS), typically not used to assess protein behavior in industrial screening, in a high throughput screening workflow to address problems of contradicting results and reproducibility among different high throughput methods. As a case study we use the lipases of Thermomyces lanuginosus and Rhizomucor miehei, widely used industrial biocatalysts. We show that even the initial analysis of the SAXS data without performing any time-consuming modelling provide valuable information on interparticle interactions. We conclude that recent advances in automation and data processing, have enabled SAXS to be used more widely as a tool to gain in-depth knowledge highly useful for protein formulation development. This is especially relevant in light of increasing accessibility to SAXS due to the commercial availability of benchtop instruments.
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Affiliation(s)
- Christin Pohl
- Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark; Technical University of Denmark, Department of Chemistry, Kemitorvet 207, 2800 Kongens Lyngby, Denmark.
| | - Sujata Mahapatra
- Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark; Technical University of Denmark, Department of Chemistry, Kemitorvet 207, 2800 Kongens Lyngby, Denmark
| | - Alina Kulakova
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen
| | | | - Günther H J Peters
- Technical University of Denmark, Department of Chemistry, Kemitorvet 207, 2800 Kongens Lyngby, Denmark
| | - Allan Nørgaard
- Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Pernille Harris
- Technical University of Denmark, Department of Chemistry, Kemitorvet 207, 2800 Kongens Lyngby, Denmark.
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32
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Strutzenberg TS, Zhu Y, Novick SJ, Garcia-Ordonez RD, Doebelin C, He Y, Chang MR, Kamenecka TM, Edwards DP, Griffin PR. Conformational Changes of RORγ During Response Element Recognition and Coregulator Engagement. J Mol Biol 2021; 433:167258. [PMID: 34547329 PMCID: PMC8556364 DOI: 10.1016/j.jmb.2021.167258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/09/2022]
Abstract
The retinoic acid receptor-related orphan receptor γ (RORγ) is a ligand-dependent transcription factor of the nuclear receptor super family that underpins metabolic activity, immune function, and cancer progression. Despite being a valuable drug target in health and disease, our understanding of the ligand-dependent activities of RORγ is far from complete. Like most nuclear receptors, RORγ must recruit coregulatory protein to enact the RORγ target gene program. To date, a majority of structural studies have been focused exclusively on the RORγ ligand-binding domain and the ligand-dependent recruitment of small peptide segments of coregulators. Herein, we examine the ligand-dependent assembly of full length RORγ:coregulator complexes on cognate DNA response elements using structural proteomics and small angle x-ray scattering. The results from our studies suggest that RORγ becomes elongated upon DNA recognition, preventing long range interdomain crosstalk. We also determined that the DNA binding domain adopts a sequence-specific conformation, and that coregulatory protein may be able to 'sense' the ligand- and DNA-bound status of RORγ. We propose a model where ligand-dependent coregulator recruitment may be influenced by the sequence of the DNA to which RORγ is bound. Overall, the efforts described herein will illuminate important aspects of full length RORγ and monomeric orphan nuclear receptor target gene regulation through DNA-dependent conformational changes.
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Affiliation(s)
| | - Yingmin Zhu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | | | - Christelle Doebelin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Yuanjun He
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Mi Ra Chang
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Theodore M Kamenecka
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Dean P Edwards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA.
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33
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Lyu C, Da Vela S, Al-Hilaly Y, Marshall KE, Thorogate R, Svergun D, Serpell LC, Pastore A, Hanger DP. The Disease Associated Tau35 Fragment has an Increased Propensity to Aggregate Compared to Full-Length Tau. Front Mol Biosci 2021; 8:779240. [PMID: 34778381 PMCID: PMC8581542 DOI: 10.3389/fmolb.2021.779240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Tau35 is a truncated form of tau found in human brain in a subset of tauopathies. Tau35 expression in mice recapitulates key features of human disease, including progressive increase in tau phosphorylation, along with cognitive and motor dysfunction. The appearance of aggregated tau suggests that Tau35 may have structural properties distinct from those of other tau species that could account for its pathological role in disease. To address this hypothesis, we performed a structural characterization of monomeric and aggregated Tau35 and compared the results to those of two longer isoforms, 2N3R and 2N4R tau. We used small angle X-ray scattering to show that Tau35, 2N3R and 2N4R tau all behave as disordered monomeric species but Tau35 exhibits higher rigidity. In the presence of the poly-anion heparin, Tau35 increases thioflavin T fluorescence significantly faster and to a greater extent than full-length tau, demonstrating a higher propensity to aggregate. By using atomic force microscopy, circular dichroism, transmission electron microscopy and X-ray fiber diffraction, we provide evidence that Tau35 aggregation is mechanistically and morphologically similar to previously reported tau fibrils but they are more densely packed. These data increase our understanding of the aggregation inducing properties of clinically relevant tau fragments and their potentially damaging role in the pathogenesis of human tauopathies.
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Affiliation(s)
- Chen Lyu
- Department of Basic and Clinical Neuroscience, King’s College London, London, United Kingdom
| | - Stefano Da Vela
- European Molecular Biology Laboratory, Hamburg Site, Hamburg, Germany
| | - Youssra Al-Hilaly
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Karen E. Marshall
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Richard Thorogate
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Site, Hamburg, Germany
| | - Louise C. Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Annalisa Pastore
- Department of Basic and Clinical Neuroscience, King’s College London, London, United Kingdom
| | - Diane P. Hanger
- Department of Basic and Clinical Neuroscience, King’s College London, London, United Kingdom
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34
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Shi F, Mendrola JM, Sheetz JB, Wu N, Sommer A, Speer KF, Noordermeer JN, Kan ZY, Perry K, Englander SW, Stayrook SE, Fradkin LG, Lemmon MA. ROR and RYK extracellular region structures suggest that receptor tyrosine kinases have distinct WNT-recognition modes. Cell Rep 2021; 37:109834. [PMID: 34686333 PMCID: PMC8650758 DOI: 10.1016/j.celrep.2021.109834] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/06/2021] [Accepted: 09/22/2021] [Indexed: 01/08/2023] Open
Abstract
WNTs play key roles in development and disease, signaling through Frizzled (FZD) seven-pass transmembrane receptors and numerous co-receptors including ROR and RYK family receptor tyrosine kinases (RTKs). We describe crystal structures and WNT-binding characteristics of extracellular regions from the Drosophila ROR and RYK orthologs Nrk (neurospecific receptor tyrosine kinase) and Derailed-2 (Drl-2), which bind WNTs though a FZD-related cysteine-rich domain (CRD) and WNT-inhibitory factor (WIF) domain respectively. Our crystal structures suggest that neither Nrk nor Drl-2 can accommodate the acyl chain typically attached to WNTs. The Nrk CRD contains a deeply buried bound fatty acid, unlikely to be exchangeable. The Drl-2 WIF domain lacks the lipid-binding site seen in WIF-1. We also find that recombinant DWnt-5 can bind Drosophila ROR and RYK orthologs despite lacking an acyl chain. Alongside analyses of WNT/receptor interaction sites, our structures provide further insight into how WNTs may recruit RTK co-receptors into signaling complexes.
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Affiliation(s)
- Fumin Shi
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeannine M Mendrola
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Joshua B Sheetz
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Neo Wu
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Anselm Sommer
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Kelsey F Speer
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Medicine (Hematology-Oncology), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jasprina N Noordermeer
- Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Zhong-Yuan Kan
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kay Perry
- NE-CAT, Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439, USA
| | - S Walter Englander
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Steven E Stayrook
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Lee G Fradkin
- Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands; Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Mark A Lemmon
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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35
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Currie MJ, Manjunath L, Horne CR, Rendle PM, Subramanian R, Friemann R, Fairbanks AJ, Muscroft-Taylor AC, North RA, Dobson RCJ. N-acetylmannosamine-6-phosphate 2-epimerase uses a novel substrate-assisted mechanism to catalyze amino sugar epimerization. J Biol Chem 2021; 297:101113. [PMID: 34437902 PMCID: PMC8482478 DOI: 10.1016/j.jbc.2021.101113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/14/2022] Open
Abstract
There are five known general catalytic mechanisms used by enzymes to catalyze carbohydrate epimerization. The amino sugar epimerase N-acetylmannosamine-6-phosphate 2-epimerase (NanE) has been proposed to use a deprotonation-reprotonation mechanism, with an essential catalytic lysine required for both steps. However, the structural determinants of this mechanism are not clearly established. We characterized NanE from Staphylococcus aureus using a new coupled assay to monitor NanE catalysis in real time and found that it has kinetic constants comparable with other species. The crystal structure of NanE from Staphylococcus aureus, which comprises a triosephosphate isomerase barrel fold with an unusual dimeric architecture, was solved with both natural and modified substrates. Using these substrate-bound structures, we identified the following active-site residues lining the cleft at the C-terminal end of the β-strands: Gln11, Arg40, Lys63, Asp124, Glu180, and Arg208, which were individually substituted and assessed in relation to the mechanism. From this, we re-evaluated the central role of Glu180 in this mechanism alongside the catalytic lysine. We observed that the substrate is bound in a conformation that ideally positions the C5 hydroxyl group to be activated by Glu180 and donate a proton to the C2 carbon. Taken together, we propose that NanE uses a novel substrate-assisted proton displacement mechanism to invert the C2 stereocenter of N-acetylmannosamine-6-phosphate. Our data and mechanistic interpretation may be useful in the development of inhibitors of this enzyme or in enzyme engineering to produce biocatalysts capable of changing the stereochemistry of molecules that are not amenable to synthetic methods.
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Affiliation(s)
- Michael J Currie
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Lavanyaa Manjunath
- Institute of Stem Cell Science and Regenerative Medicine, NCBS, Bangalore, Karnataka, India
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Phillip M Rendle
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Ramaswamy Subramanian
- Institute of Stem Cell Science and Regenerative Medicine, NCBS, Bangalore, Karnataka, India
| | - Rosmarie Friemann
- Fujirebio Diagnostics, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Antony J Fairbanks
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andrew C Muscroft-Taylor
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
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Leysen S, Burnley RJ, Rodriguez E, Milroy LG, Soini L, Adamski CJ, Nitschke L, Davis R, Obsil T, Brunsveld L, Crabbe T, Zoghbi HY, Ottmann C, Davis JM. A Structural Study of the Cytoplasmic Chaperone Effect of 14-3-3 Proteins on Ataxin-1. J Mol Biol 2021; 433:167174. [PMID: 34302818 PMCID: PMC8505757 DOI: 10.1016/j.jmb.2021.167174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022]
Abstract
Expansion of the polyglutamine tract in the N terminus of Ataxin-1 is the main cause of the neurodegenerative disease, spinocerebellar ataxia type 1 (SCA1). However, the C-terminal part of the protein - including its AXH domain and a phosphorylation on residue serine 776 - also plays a crucial role in disease development. This phosphorylation event is known to be crucial for the interaction of Ataxin-1 with the 14-3-3 adaptor proteins and has been shown to indirectly contribute to Ataxin-1 stability. Here we show that 14-3-3 also has a direct anti-aggregation or "chaperone" effect on Ataxin-1. Furthermore, we provide structural and biophysical information revealing how phosphorylated S776 in the intrinsically disordered C terminus of Ataxin-1 mediates the cytoplasmic interaction with 14-3-3 proteins. Based on these findings, we propose that 14-3-3 exerts the observed chaperone effect by interfering with Ataxin-1 dimerization through its AXH domain, reducing further self-association. The chaperone effect is particularly important in the context of SCA1, as it was previously shown that a soluble form of mutant Ataxin-1 is the major driver of pathology.
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Affiliation(s)
- Seppe Leysen
- Global Chemistry, UCB Biopharma UK, Slough SL1 3WE, UK
| | | | | | - Lech-Gustav Milroy
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
| | - Lorenzo Soini
- Global Chemistry, UCB Biopharma UK, Slough SL1 3WE, UK; Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
| | - Carolyn J Adamski
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Larissa Nitschke
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Davis
- Global Chemistry, UCB Biopharma UK, Slough SL1 3WE, UK
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Lucas Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
| | - Tom Crabbe
- Immuno-Bone Discovery, UCB Biopharma UK, Slough SL1 3WE, UK
| | - Huda Yahya Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
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Yui A, Caaveiro JMM, Kuroda D, Nakakido M, Nagatoishi S, Goda S, Maruno T, Uchiyama S, Tsumoto K. Mechanism of dimerization and structural features of human LI-cadherin. J Biol Chem 2021; 297:101054. [PMID: 34364873 PMCID: PMC8427231 DOI: 10.1016/j.jbc.2021.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/02/2021] [Accepted: 08/04/2021] [Indexed: 11/24/2022] Open
Abstract
Liver intestine (LI)-cadherin is a member of the cadherin superfamily, which encompasses a group of Ca2+-dependent cell-adhesion proteins. The expression of LI-cadherin is observed on various types of cells in the human body, such as normal small intestine and colon cells, and gastric cancer cells. Because its expression is not observed on normal gastric cells, LI-cadherin is a promising target for gastric cancer imaging. However, because the cell adhesion mechanism of LI-cadherin has remained unknown, rational design of therapeutic molecules targeting this cadherin has been hampered. Here, we have studied the homodimerization mechanism of LI-cadherin. We report the crystal structure of the LI-cadherin homodimer containing its first four extracellular cadherin repeats (EC1-4). The EC1-4 homodimer exhibited a unique architecture different from that of other cadherins reported so far, driven by the interactions between EC2 of one protein chain and EC4 of the second protein chain. The crystal structure also revealed that LI-cadherin possesses a noncanonical calcium ion-free linker between the EC2 and EC3 domains. Various biochemical techniques and molecular dynamics simulations were employed to elucidate the mechanism of homodimerization. We also showed that the formation of the homodimer observed in the crystal structure is necessary for LI-cadherin-dependent cell adhesion by performing cell aggregation assays. Taken together, our data provide structural insights necessary to advance the use of LI-cadherin as a target for imaging gastric cancer.
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Affiliation(s)
- Anna Yui
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Shuichiro Goda
- Graduate School of Science and Engineering, Soka University, Tokyo, Japan
| | - Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
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Structural Features of a Full-Length Ubiquitin Ligase Responsible for the Formation of Patches at the Plasma Membrane. Int J Mol Sci 2021; 22:ijms22179455. [PMID: 34502365 PMCID: PMC8431560 DOI: 10.3390/ijms22179455] [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: 08/01/2021] [Revised: 08/22/2021] [Accepted: 08/27/2021] [Indexed: 11/28/2022] Open
Abstract
Plant U-box armadillo repeat (PUB-ARM) ubiquitin (Ub) ligases have important functions in plant defense through the ubiquitination of target proteins. Defense against pathogens involves vesicle trafficking and the formation of extracellular vesicles. The PUB-ARM protein SENESCENCE ASSOCIATED UBIQUITIN E3 LIGASE1 (SAUL1) can form patches at the plasma membrane related to tethering multi-vesicular bodies (MVBs) to the plasma membrane. We uncovered the structure of a full-length plant ubiquitin ligase and the structural requirements of SAUL1, which are crucial for its function in patch formation. We resolved the structure of SAUL1 monomers by small-angle X-ray scattering (SAXS). The SAUL1 model showed that SAUL1 consists of two domains: a domain containing the N-terminal U-box and armadillo (ARM) repeats and the C-terminal ARM repeat domain, which includes a positively charged groove. We showed that all C-terminal ARM repeats are essential for patch formation and that this function requires arginine residue at position 736. By applying SAXS to polydisperse SAUL1 systems, the oligomerization of SAUL1 is detectable, with SAUL1 tetramers being the most prominent oligomers at higher concentrations. The oligomerization domain consists of the N-terminal U-box and some N-terminal ARM repeats. Deleting the U-box resulted in the promotion of the SAUL1 tethering function. Our findings indicate that structural changes in SAUL1 may be fundamental to its function in forming patches at the plasma membrane.
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Truebestein L, Hornegger H, Anrather D, Hartl M, Fleming KD, Stariha JTB, Pardon E, Steyaert J, Burke JE, Leonard TA. Structure of autoinhibited Akt1 reveals mechanism of PIP 3-mediated activation. Proc Natl Acad Sci U S A 2021; 118:e2101496118. [PMID: 34385319 PMCID: PMC8379990 DOI: 10.1073/pnas.2101496118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The protein kinase Akt is one of the primary effectors of growth factor signaling in the cell. Akt responds specifically to the lipid second messengers phosphatidylinositol-3,4,5-trisphosphate [PI(3,4,5)P3] and phosphatidylinositol-3,4-bisphosphate [PI(3,4)P2] via its PH domain, leading to phosphorylation of its activation loop and the hydrophobic motif of its kinase domain, which are critical for activity. We have now determined the crystal structure of Akt1, revealing an autoinhibitory interface between the PH and kinase domains that is often mutated in cancer and overgrowth disorders. This interface persists even after stoichiometric phosphorylation, thereby restricting maximum Akt activity to PI(3,4,5)P3- or PI(3,4)P2-containing membranes. Our work helps to resolve the roles of lipids and phosphorylation in the activation of Akt and has wide implications for the spatiotemporal control of Akt and potentially lipid-activated kinase signaling in general.
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Affiliation(s)
- Linda Truebestein
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - Harald Hornegger
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - Dorothea Anrather
- Mass Spectrometry Core Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Core Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Jordan T B Stariha
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria;
- Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
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40
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Thapa C, Roivas P, Haataja T, Permi P, Pentikäinen U. Interaction mechanism of endogenous PP2A inhibitor protein ENSA with PP2A. FEBS J 2021; 289:519-534. [PMID: 34346186 DOI: 10.1111/febs.16150] [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: 04/29/2021] [Revised: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 01/09/2023]
Abstract
The vast diversity of protein phosphatase 2A (PP2A) holoenzyme composition ensures its multifaceted role in the regulation of cellular growth and signal transduction. In several pathological conditions, such as cancer, PP2A is inhibited by endogenous inhibitor proteins. Several PP2A inhibitor proteins have been identified, one of which is α-endosulfine (ENSA). ENSA inhibits PP2A activity when it is phosphorylated at Ser67 by Greatwall (Gwl) kinase. The role of ENSA in PP2A inhibition is rather well characterized, but knowledge of the mechanism of inhibition is scarce. In this study, we have performed comprehensive structural characterization of ENSA, and its interaction with PP2A A- and various B56-subunit isoforms by combining NMR spectroscopy, small-angle X-ray scattering (SAXS) and interaction assays. The results clearly indicate that ENSA is an intrinsically disordered protein containing three transient α-helical structures. ENSA was observed to interact PP2A mainly via A-subunit, as the affinity with the A-subunit is significantly stronger than with any of the B56 subunits. Based on our results, it seems that ENSA follows the dock-and-coalesce mechanism in associating with PP2A A-subunit. Taken together, our results provide an essential structural and molecular framework to understanding molecular bases of ENSA-mediated PP2A inhibition, which is crucial for the development of new therapies for diseases linked to PP2A inhibition.
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Affiliation(s)
- Chandan Thapa
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Finland.,Turku BioScience, University of Turku, Finland
| | - Pekka Roivas
- Institute of Biomedicine, University of Turku, Finland.,Turku BioScience, University of Turku, Finland
| | - Tatu Haataja
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Finland.,Department of Chemistry and Nanoscience Center, University of Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Institute of Biomedicine, University of Turku, Finland.,Turku BioScience, University of Turku, Finland
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Degli Esposti L, Adamiano A, Siliqi D, Giannini C, Iafisco M. The effect of chemical structure of carboxylate molecules on hydroxyapatite nanoparticles. A structural and morphological study. Bioact Mater 2021; 6:2360-2371. [PMID: 33553821 PMCID: PMC7844063 DOI: 10.1016/j.bioactmat.2021.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/07/2021] [Accepted: 01/09/2021] [Indexed: 12/30/2022] Open
Abstract
Being the most abundant non-macromolecular organic component of bone, the role of citrate (Cit) in hydroxyapatite (HA) crystallization is of high relevance. In this work we have investigated the influence of hydroxycitrate (CitOH) and glutarate (Glr) on HA crystallization in terms of particle growth, composition, and morphology in comparison to Cit. CitOH and Glr have been selected for this work because they share the same backbone structure of Cit but bear different functional groups in the central region. Our data has revealed that CitOH strongly inhibits HA crystallization more efficiently than Cit. CitOH-HA nanoparticles are composed of platy, elongated particles similar to those of Cit-HA but they are ca. twice smaller and have a lower crystal order. On the other hand, Glr does not inhibit HA crystallization as Cit, but leads to the formation of OCP platelets that convert with maturation time to HA nanorods with larger aspect ratio than Cit-HA. In comparison to Cit-HA samples, Glr-HA nanoparticles have bigger dimensions, and higher structural order. Overall, our data reveal that the central carboxyl group of Cit is involved in the selective binding with HA crystal surface and in regulating HA crystal growth. The results of this work highlight new possibilities to control the formation of HA for designing advanced bioactive materials and give new insights on the role of the structure of Cit in regulating the HA morphology.
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Affiliation(s)
- Lorenzo Degli Esposti
- Institute of Science and Technology for Ceramics (ISTEC), National Research Council (CNR), Via Granarolo 64, 48018, Faenza, Italy
| | - Alessio Adamiano
- Institute of Science and Technology for Ceramics (ISTEC), National Research Council (CNR), Via Granarolo 64, 48018, Faenza, Italy
| | - Dritan Siliqi
- Institute of Crystallography (IC), National Research Council (CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), National Research Council (CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Michele Iafisco
- Institute of Science and Technology for Ceramics (ISTEC), National Research Council (CNR), Via Granarolo 64, 48018, Faenza, Italy
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42
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Martin EW, Harmon TS, Hopkins JB, Chakravarthy S, Incicco JJ, Schuck P, Soranno A, Mittag T. A multi-step nucleation process determines the kinetics of prion-like domain phase separation. Nat Commun 2021; 12:4513. [PMID: 34301955 PMCID: PMC8302766 DOI: 10.1038/s41467-021-24727-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/30/2021] [Indexed: 11/08/2022] Open
Abstract
Compartmentalization by liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mechanism underlying the organization of biomolecules in space and time. Here, we combine rapid-mixing time-resolved small-angle X-ray scattering (SAXS) approaches to characterize the assembly kinetics of a prototypical prion-like domain with equilibrium techniques that characterize its phase boundaries and the size distribution of clusters prior to phase separation. We find two kinetic regimes on the micro- to millisecond timescale that are distinguished by the size distribution of clusters. At the nanoscale, small complexes are formed with low affinity. After initial unfavorable complex assembly, additional monomers are added with higher affinity. At the mesoscale, assembly resembles classical homogeneous nucleation. Careful multi-pronged characterization is required for the understanding of condensate assembly mechanisms and will promote understanding of how the kinetics of biological phase separation is encoded in biomolecules.
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Affiliation(s)
- Erik W Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Tyler S Harmon
- The Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - J Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
- Center for Science and Engineering of Living Cells (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
- Center for Science and Engineering of Living Cells (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Long-range structural defects by pathogenic mutations in most severe glucose-6-phosphate dehydrogenase deficiency. Proc Natl Acad Sci U S A 2021; 118:2022790118. [PMID: 33468660 PMCID: PMC7848525 DOI: 10.1073/pnas.2022790118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mechanism of the loss of activity of the most severe patient-derived mutants of glucose-6-phosphate dehydrogenase (G6PD) deficiency has remained elusive despite the availability of the G6PD structures for decades. Structural and biophysical investigations have revealed a common mechanism and dynamics of how these mutations hinder the substrate-binding site, reducing enzymatic activity. These are triggered by a long-distance propagation of structural defects at the dimer interface and the binding site of the noncatalytic cofactor. These structural distortions are found among all of the class I mutants investigated, providing critical clues for drug design to address G6PD deficiency by correcting the structural defects. Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common blood disorder, presenting multiple symptoms, including hemolytic anemia. It affects 400 million people worldwide, with more than 160 single mutations reported in G6PD. The most severe mutations (about 70) are classified as class I, leading to more than 90% loss of activity of the wild-type G6PD. The crystal structure of G6PD reveals these mutations are located away from the active site, concentrating around the noncatalytic NADP+-binding site and the dimer interface. However, the molecular mechanisms of class I mutant dysfunction have remained elusive, hindering the development of efficient therapies. To resolve this, we performed integral structural characterization of five G6PD mutants, including four class I mutants, associated with the noncatalytic NADP+ and dimerization, using crystallography, small-angle X-ray scattering (SAXS), cryogenic electron microscopy (cryo-EM), and biophysical analyses. Comparisons with the structure and properties of the wild-type enzyme, together with molecular dynamics simulations, bring forward a universal mechanism for this severe G6PD deficiency due to the class I mutations. We highlight the role of the noncatalytic NADP+-binding site that is crucial for stabilization and ordering two β-strands in the dimer interface, which together communicate these distant structural aberrations to the active site through a network of additional interactions. This understanding elucidates potential paths for drug development targeting G6PD deficiency.
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The Molecular Basis for Escherichia coli O157:H7 Phage FAHEc1 Endolysin Function and Protein Engineering to Increase Thermal Stability. Viruses 2021; 13:v13061101. [PMID: 34207694 PMCID: PMC8228626 DOI: 10.3390/v13061101] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 02/02/2023] Open
Abstract
Bacteriophage-encoded endolysins have been identified as antibacterial candidates. However, the development of endolysins as mainstream antibacterial agents first requires a comprehensive biochemical understanding. This study defines the atomic structure and enzymatic function of Escherichia coli O157:H7 phage FAHEc1 endolysin, LysF1. Bioinformatic analysis suggests this endolysin belongs to the T4 Lysozyme (T4L)-like family of proteins and contains a highly conserved catalytic triad. We then solved the structure of LysF1 with x-ray crystallography to 1.71 Å. LysF1 was confirmed to exist as a monomer in solution by sedimentation velocity experiments. The protein architecture of LysF1 is conserved between T4L and related endolysins. Comparative analysis with related endolysins shows that the spatial orientation of the catalytic triad is conserved, suggesting the catalytic mechanism of peptidoglycan degradation is the same as that of T4L. Differences in the sequence illustrate the role coevolution may have in the evolution of this fold. We also demonstrate that by mutating a single residue within the hydrophobic core, the thermal stability of LysF1 can be increased by 9.4 °C without compromising enzymatic activity. Overall, the characterization of LysF1 provides further insight into the T4L-like class of endolysins. Our study will help advance the development of related endolysins as antibacterial agents, as rational engineering will rely on understanding mutable positions within this protein fold.
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Johansen NT, Luchini A, Tidemand FG, Orioli S, Martel A, Porcar L, Arleth L, Pedersen MC. Structural and Biophysical Properties of Supercharged and Circularized Nanodiscs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:6681-6690. [PMID: 34038130 DOI: 10.1021/acs.langmuir.1c00560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nanodiscs based on membrane scaffold proteins (MSPs) and phospholipids are used as membrane mimics to stabilize membrane proteins in solution for structural and functional studies. Combining small-angle X-ray scattering (SAXS), differential scanning calorimetry (DSC), and time-resolved small-angle neutron scattering (TR-SANS), we characterized the structure and lipid bilayer properties of five different nanodiscs made with dimyristoylphosphatidylcholine and different MSPs varying in size, charge, and circularization. Our SAXS modeling showed that the structural parameters of the embedded lipids are all similar, irrespective of the MSP properties. DSC showed that the lipid packing is not homogeneous in the nanodiscs and that a 20 Å wide boundary layer of lipids with perturbed packing is located close to the MSP, while the packing of central lipids is tighter than in large unilamellar vesicles. Finally, TR-SANS showed that lipid exchange rates in nanodiscs decrease with increasing nanodisc size and are lower for the nanodiscs made with supercharged MSPs compared to conventional nanodiscs. Altogether, the results provide a thorough biophysical understanding of the nanodisc as a model membrane system, which is important in order to carry out and interpret experiments on membrane proteins embedded in such systems.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Structural Biophysics Group, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen E, Denmark
| | - Alessandra Luchini
- Structural Biophysics Group, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen E, Denmark
| | - Frederik Grønbæk Tidemand
- Structural Biophysics Group, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen E, Denmark
| | - Simone Orioli
- Structural Biophysics Group, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen E, Denmark
- Structural Biology and NMR Laboratory and Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Anne Martel
- Institut Laue Langevin, 38000 Grenoble, France
| | | | - Lise Arleth
- Structural Biophysics Group, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen E, Denmark
| | - Martin Cramer Pedersen
- Structural Biophysics Group, Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen E, Denmark
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46
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Afsar M, Shukla A, Kumar N, Ramachandran R. Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD +-dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:776-789. [PMID: 34076591 DOI: 10.1107/s2059798321003107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/24/2021] [Indexed: 11/10/2022]
Abstract
NAD+-dependent DNA ligase (LigA) is the principal bacterial ligase and catalyses a multistep ligation reaction. The adenylation (AdD) domain at the N-terminus consists of subdomains 1a and 1b, where subdomain 1a is unique to LigA. Small-angle X-ray scattering and X-ray diffraction studies were used to probe changes in the relative spatial dispositions of the two subdomains during the adenylation reaction. Structural analyses of the inter-subdomain interactions of the AdD domain suggest that salt bridges formed by Glu22, Glu26 and Glu87 of subdomain 1a with Arg144, Arg315 and His240 of subdomain 1b play an important role in stabilizing the intermediate conformations of the two subdomains. E22A, E26A and E87A mutations reduce the in vitro activity by 89%, 64% and 39%, respectively, on a nicked DNA substrate, while they show no activity loss on a pre-adenylated DNA substrate, thus suggesting that the salt bridges are important in the initial steps of the ligation reaction. Furthermore, the E22A, E26A and E87A mutants exhibited extremely delayed growth in complementation assays involving the Escherichia coli GR501 strain, which harbours its own temperature-sensitive LigA. The H236A and H236Y mutants, which involve the residue that stacks against the adenine moiety of AMP, severely impact the activity and the ability to complement the growth-defective E. coli GR501 strain. Analysis of the K123A and K123R mutations in the active site rationalizes their total loss of activity and inability to rescue the growth-defective E. coli GR501 strain.
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Affiliation(s)
- Mohammad Afsar
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Ankita Shukla
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Nelam Kumar
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
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47
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Mohammad Sadik, Mohammad Afsar, Ramachandran R, Habib S. [Fe-S] biogenesis and unusual assembly of the ISC scaffold complex in the Plasmodium falciparum mitochondrion. Mol Microbiol 2021; 116:606-623. [PMID: 34032321 DOI: 10.1111/mmi.14735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022]
Abstract
The malaria parasite harbors two [Fe-S] biogenesis pathways of prokaryotic origin-the SUF and ISC systems in the apicoplast and mitochondrion, respectively. While the SUF machinery has been delineated, there is little experimental evidence on the ISC pathway. We confirmed mitochondrial targeting of Plasmodium falciparum ISC proteins followed by analyses of cysteine desulfurase, scaffold, and [Fe-S]-carrier components. PfIscU functioned as the scaffold in complex with the PfIscS-PfIsd11 cysteine desulfurase and could directly assemble [4Fe-4S] without prior [2Fe-2S] formation seen in other homologs. Small angle X-ray scattering and spectral studies showed that PfIscU, a trimer, bound one [4Fe-4S]. In a deviation from reported complexes from other organisms, the P. falciparum desulfurase-scaffold complex assembled around a PfIscS tetramer instead of a dimer, resulting in a symmetric hetero-hexamer [2× (2PfIscS-2PfIsd11-2PfIscU)]. PfIscU directly transferred [4Fe-4S] to the apo-protein aconitase B thus abrogating the requirement of intermediary proteins for conversion of [2Fe-2S] to [4Fe-4S] before transfer to [4Fe-4S]-recipients. Among the putative cluster-carriers, PfIscA2 was more efficient than PfNifU-like protein; PfIscA1 primarily bound iron, suggesting its potential role as a Fe2+ carrier/donor. Our results identify the core P. falciparum ISC machinery and reveal unique features compared with those in bacteria or yeast and human mitochondria.
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Affiliation(s)
- Mohammad Sadik
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Afsar
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ravishankar Ramachandran
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
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48
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Bucher M, Niebling S, Han Y, Molodenskiy D, Hassani Nia F, Kreienkamp HJ, Svergun D, Kim E, Kostyukova AS, Kreutz MR, Mikhaylova M. Autism-associated SHANK3 missense point mutations impact conformational fluctuations and protein turnover at synapses. eLife 2021; 10:66165. [PMID: 33945465 PMCID: PMC8169116 DOI: 10.7554/elife.66165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/01/2021] [Indexed: 12/18/2022] Open
Abstract
Members of the SH3- and ankyrin repeat (SHANK) protein family are considered as master scaffolds of the postsynaptic density of glutamatergic synapses. Several missense mutations within the canonical SHANK3 isoform have been proposed as causative for the development of autism spectrum disorders (ASDs). However, there is a surprising paucity of data linking missense mutation-induced changes in protein structure and dynamics to the occurrence of ASD-related synaptic phenotypes. In this proof-of-principle study, we focus on two ASD-associated point mutations, both located within the same domain of SHANK3 and demonstrate that both mutant proteins indeed show distinct changes in secondary and tertiary structure as well as higher conformational fluctuations. Local and distal structural disturbances result in altered synaptic targeting and changes of protein turnover at synaptic sites in rat primary hippocampal neurons.
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Affiliation(s)
- Michael Bucher
- AG Optobiology, Institute of Biology, Humboldt-University, Berlin, Germany.,DFG Emmy Noether Guest Group 'Neuronal Protein Transport', Institute for Molecular Neurogenetics, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.,RG Neuroplasticity, Leibniz-Institute for Neurobiology (LIN), Magdeburg, Germany
| | - Stephan Niebling
- Molecular Biophysics and High-Throughput Crystallization, European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Yuhao Han
- DFG Emmy Noether Guest Group 'Neuronal Protein Transport', Institute for Molecular Neurogenetics, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.,Structural Cell Biology of Viruses, Centre for Structural Systems Biology (CSSB) and Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, DESY, Hamburg, Germany
| | - Fatemeh Hassani Nia
- Institute of Human Genetics, Center for Obstetrics and Pediatrics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Hans-Jürgen Kreienkamp
- Institute of Human Genetics, Center for Obstetrics and Pediatrics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, DESY, Hamburg, Germany
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS) and Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Alla S Kostyukova
- DFG Emmy Noether Guest Group 'Neuronal Protein Transport', Institute for Molecular Neurogenetics, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University (WSU), Pullman, United States
| | - Michael R Kreutz
- RG Neuroplasticity, Leibniz-Institute for Neurobiology (LIN), Magdeburg, Germany.,Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.,German Center for Neurodegenerative Diseases, Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Marina Mikhaylova
- AG Optobiology, Institute of Biology, Humboldt-University, Berlin, Germany.,DFG Emmy Noether Guest Group 'Neuronal Protein Transport', Institute for Molecular Neurogenetics, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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49
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Thapa C, Roivas P, Haataja T, Permi P, Pentikäinen U. The Interaction Mechanism of Intrinsically Disordered PP2A Inhibitor Proteins ARPP-16 and ARPP-19 With PP2A. Front Mol Biosci 2021; 8:650881. [PMID: 33842550 PMCID: PMC8032985 DOI: 10.3389/fmolb.2021.650881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/03/2021] [Indexed: 12/01/2022] Open
Abstract
Protein phosphatase 2A (PP2A) activity is critical for maintaining normal physiological cellular functions. PP2A is inhibited by endogenous inhibitor proteins in several pathological conditions including cancer. A PP2A inhibitor protein, ARPP-19, has recently been connected to several human cancer types. Accordingly, the knowledge about ARPP-19—PP2A inhibition mechanism is crucial for the understanding the disease development and the therapeutic targeting of ARPP-19—PP2A. Here, we show the first structural characterization of ARPP-19, and its splice variant ARPP-16 using NMR spectroscopy, and SAXS. The results reveal that both ARPP proteins are intrinsically disordered but contain transient secondary structure elements. The interaction mechanism of ARPP-16/19 with PP2A was investigated using microscale thermophoresis and NMR spectroscopy. Our results suggest that ARPP—PP2A A-subunit interaction is mediated by linear motif and has modest affinity whereas, the interaction of ARPPs with B56-subunit is weak and transient. Like many IDPs, ARPPs are promiscuous binders that transiently interact with PP2A A- and B56 subunits using multiple interaction motifs. In summary, our results provide a good starting point for future studies and development of therapeutics that block ARPP-PP2A interactions.
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Affiliation(s)
- Chandan Thapa
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Pekka Roivas
- Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Tatu Haataja
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Department of Chemistry and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
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50
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Manalastas-Cantos K, Konarev PV, Hajizadeh NR, Kikhney AG, Petoukhov MV, Molodenskiy DS, Panjkovich A, Mertens HDT, Gruzinov A, Borges C, Jeffries CM, Svergun DI, Franke D. ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. J Appl Crystallogr 2021; 54:343-355. [PMID: 33833657 PMCID: PMC7941305 DOI: 10.1107/s1600576720013412] [Citation(s) in RCA: 392] [Impact Index Per Article: 130.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/06/2020] [Indexed: 11/11/2022] Open
Abstract
The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy - a PyMOL plugin to run a subset of ATSAS tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.
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Affiliation(s)
- Karen Manalastas-Cantos
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Nelly R. Hajizadeh
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Maxim V. Petoukhov
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Dmitry S. Molodenskiy
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Alejandro Panjkovich
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Clemente Borges
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
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