1
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Krokengen OC, Touma C, Mularski A, Sutinen A, Dunkel R, Ytterdal M, Raasakka A, Mertens HDT, Simonsen AC, Kursula P. The cytoplasmic tail of myelin protein zero induces morphological changes in lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184368. [PMID: 38971517 DOI: 10.1016/j.bbamem.2024.184368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
The major myelin protein expressed by the peripheral nervous system Schwann cells is protein zero (P0), which represents 50% of the total protein content in myelin. This 30-kDa integral membrane protein consists of an immunoglobulin (Ig)-like domain, a transmembrane helix, and a 69-residue C-terminal cytoplasmic tail (P0ct). The basic residues in P0ct contribute to the tight packing of myelin lipid bilayers, and alterations in the tail affect how P0 functions as an adhesion molecule necessary for the stability of compact myelin. Several neurodegenerative neuropathies are related to P0, including the more common Charcot-Marie-Tooth disease (CMT) and Dejerine-Sottas syndrome (DSS) as well as rare cases of motor and sensory polyneuropathy. We found that high P0ct concentrations affected the membrane properties of bicelles and induced a lamellar-to-inverted hexagonal phase transition, which caused bicelles to fuse into long, protein-containing filament-like structures. These structures likely reflect the formation of semicrystalline lipid domains with potential relevance for myelination. Not only is P0ct important for stacking lipid membranes, but time-lapse fluorescence microscopy also shows that it might affect membrane properties during myelination. We further describe recombinant production and low-resolution structural characterization of full-length human P0. Our findings shed light on P0ct effects on membrane properties, and with the successful purification of full-length P0, we have new tools to study the role of P0 in myelin formation and maintenance in vitro.
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Affiliation(s)
- Oda C Krokengen
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Christine Touma
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anna Mularski
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ryan Dunkel
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Marie Ytterdal
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY, Hamburg, Germany
| | - Adam Cohen Simonsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway; Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
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2
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Bagchi A, Stayrook SE, Xenaki KT, Starbird CA, Doulkeridou S, El Khoulati R, Roovers RC, Schmitz KR, van Bergen En Henegouwen PMP, Ferguson KM. Structural insights into the role and targeting of EGFRvIII. Structure 2024; 32:1367-1380.e6. [PMID: 38908376 PMCID: PMC11380598 DOI: 10.1016/j.str.2024.05.018] [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: 11/03/2023] [Revised: 04/06/2024] [Accepted: 05/28/2024] [Indexed: 06/24/2024]
Abstract
The epidermal growth factor receptor (EGFR) is a well-known oncogenic driver in lung and other cancers. In glioblastoma multiforme (GBM), the EGFR deletion variant III (EGFRvIII) is frequently found alongside EGFR amplification. Agents targeting the EGFR axis have shown limited clinical benefits in GBM and the role of EGFRvIII in GBM is poorly understood. To shed light on the role of EGFRvIII and its potential as a therapeutic target, we determined X-ray crystal structures of a monomeric EGFRvIII extracellular region (ECR). The EGFRvIII ECR resembles the unliganded conformation of EGFR, including the orientation of the C-terminal region of domain II. Domain II is mostly disordered, but the ECR structure is compact. We selected a nanobody with preferential binding to EGFRvIII relative to EGFR and structurally defined an epitope on domain IV that is occluded in the unliganded intact EGFR. These findings suggest new avenues for EGFRvIII targeting in GBM.
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Affiliation(s)
- Atrish Bagchi
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven E Stayrook
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Katerina T Xenaki
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Chrystal A Starbird
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Sofia Doulkeridou
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Rachid El Khoulati
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Rob C Roovers
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Karl R Schmitz
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Paul M P van Bergen En Henegouwen
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Kathryn M Ferguson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA.
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3
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Wang H, Xie C, Deng B, Ding J, Li N, Kou Z, Jin M, He J, Wang Q, Wen H, Zhang J, Zhou Q, Chen S, Chen X, Yuan TF, Zhu S. Structural basis for antibody-mediated NMDA receptor clustering and endocytosis in autoimmune encephalitis. Nat Struct Mol Biol 2024:10.1038/s41594-024-01387-3. [PMID: 39227720 DOI: 10.1038/s41594-024-01387-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 08/07/2024] [Indexed: 09/05/2024]
Abstract
Antibodies against N-methyl-D-aspartate receptors (NMDARs) are most frequently detected in persons with autoimmune encephalitis (AE) and used as diagnostic biomarkers. Elucidating the structural basis of monoclonal antibody (mAb) binding to NMDARs would facilitate the development of targeted therapy for AE. Here, we reconstructed nanodiscs containing green fluorescent protein-fused NMDARs to label and sort individual immune B cells from persons with AE and further cloned and identified mAbs against NMDARs. This allowed cryo-electron microscopy analysis of NMDAR-Fab complexes, revealing that autoantibodies bind to the R1 lobe of the N-terminal domain of the GluN1 subunit. Small-angle X-ray scattering studies demonstrated NMDAR-mAb stoichiometry of 2:1 or 1:2, structurally suitable for mAb-induced clustering and endocytosis of NMDARs. Importantly, these mAbs reduced the surface NMDARs and NMDAR-mediated currents, without tonically affecting NMDAR channel gating. These structural and functional findings imply that the design of neutralizing antibody binding to the R1 lobe of NMDARs represents a potential therapy for AE treatment.
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Affiliation(s)
- Han Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun Xie
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Bo Deng
- Department of Neurology, Huashan Hospital and Institute of Neurology, National Center for Neurological Disorders, Fudan University, Shanghai, China
| | - Jingjun Ding
- Shanghai Key Laboratory of Psychotic Disorders, Brain Health Institute, National Center for Mental Disorders, Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine and School of Psychology, Shanghai, China
| | - Na Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Zengwei Kou
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Mengmeng Jin
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie He
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Han Wen
- DP Technology, Beijing, China
| | - Jinbao Zhang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Qinming Zhou
- Department of Neurology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Sheng Chen
- Department of Neurology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Xiangjun Chen
- Department of Neurology, Huashan Hospital and Institute of Neurology, National Center for Neurological Disorders, Fudan University, Shanghai, China.
| | - Ti-Fei Yuan
- Shanghai Key Laboratory of Psychotic Disorders, Brain Health Institute, National Center for Mental Disorders, Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine and School of Psychology, Shanghai, China.
| | - Shujia Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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4
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Wang J, Dong Z, Zhang Y, Hua W, Wang Z, Guo H, Yang Y, Bi X. StreamSAXS: a Python-based workflow platform for processing streaming SAXS/WAXS data. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:1249-1256. [PMID: 39007823 PMCID: PMC11371052 DOI: 10.1107/s1600577524005149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/30/2024] [Indexed: 07/16/2024]
Abstract
StreamSAXS is a Python-based small- and wide-angle X-ray scattering (SAXS/WAXS) data analysis workflow platform with graphical user interface (GUI). It aims to provide an interactive and user-friendly tool for analysis of both batch data files and real-time data streams. Users can easily create customizable workflows through the GUI to meet their specific needs. One characteristic of StreamSAXS is its plug-in framework, which enables developers to extend the built-in workflow tasks. Another feature is the support for both already acquired and real-time data sources, allowing StreamSAXS to function as an offline analysis platform or be integrated into large-scale acquisition systems for end-to-end data management. This paper presents the core design of StreamSAXS and provides user cases demonstrating its utilization for SAXS/WAXS data analysis in offline and online scenarios.
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Affiliation(s)
- Jiayi Wang
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of SciencesBeijing100049People’s Republic of China
| | - Zheng Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of SciencesBeijing100049People’s Republic of China
- Spallation Neutron Source Science Center, Dongguan523803, People’s Republic of China
| | - Yi Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of SciencesBeijing100049People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
| | - Wenqiang Hua
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research InstituteChinese Academy of SciencesShanghai201204People’s Republic of China
| | - Zudeng Wang
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of SciencesBeijing100049People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
| | - Huilong Guo
- Global Energy Interconnection Group Co. Ltd, Beijing100031, People’s Republic of China
| | - Yiming Yang
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of SciencesBeijing100049People’s Republic of China
| | - Xiaoxue Bi
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of SciencesBeijing100049People’s Republic of China
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5
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Struble LR, Lovelace JJ, Borgstahl GEO. A glimpse into the hidden world of the flexible C-terminal protein binding domains of human RAD52. J Struct Biol 2024; 216:108115. [PMID: 39117045 DOI: 10.1016/j.jsb.2024.108115] [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: 03/01/2024] [Revised: 07/25/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024]
Abstract
Human RAD52 protein binds DNA and is involved in genomic stability maintenance and several forms of DNA repair, including homologous recombination and single-strand annealing. Despite its importance, there are very few structural details about the variability of the RAD52 ring size and the RAD52 C-terminal protein-protein interaction domains. Even recent attempts to employ cryogenic electron microscopy (cryoEM) methods on full-length yeast and human RAD52 do not reveal interpretable structures for the C-terminal half that contains the replication protein A (RPA) and RAD51 binding domains. In this study, we employed the monodisperse purification of two RAD52 deletion constructs and small angle X-ray scattering (SAXS) to construct a structural model that includes RAD52's RPA binding domain. This model is of interest to DNA repair specialists as well as for drug development against HR-deficient cancers.
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Affiliation(s)
- Lucas R Struble
- The Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - Jeffrey J Lovelace
- The Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
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6
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Kocher F, Applegate V, Reiners J, Port A, Spona D, Hänsch S, Mirzaiebadizi A, Ahmadian MR, Smits SHJ, Hegemann JH, Mölleken K. The Chlamydia pneumoniae effector SemD exploits its host's endocytic machinery by structural and functional mimicry. Nat Commun 2024; 15:7294. [PMID: 39181890 PMCID: PMC11344771 DOI: 10.1038/s41467-024-51681-3] [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: 02/12/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
To enter epithelial cells, the obligate intracellular pathogen Chlamydia pneumoniae secretes early effector proteins, which bind to and modulate the host-cell's plasma membrane and recruit several pivotal endocytic host proteins. Here, we present the high-resolution structure of an entry-related chlamydial effector protein, SemD. Co-crystallisation of SemD with its host binding partners demonstrates that SemD co-opts the Cdc42 binding site to activate the actin cytoskeleton regulator N-WASP, making active, GTP-bound Cdc42 superfluous. While SemD binds N-WASP much more strongly than Cdc42 does, it does not bind the Cdc42 effector protein FMNL2, indicating effector protein specificity. Furthermore, by identifying flexible and structured domains, we show that SemD can simultaneously interact with the membrane, the endocytic protein SNX9, and N-WASP. Here, we show at the structural level how a single effector protein can hijack central components of the host's endocytic system for efficient internalization.
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Affiliation(s)
- Fabienne Kocher
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Functional Microbial Genomics, Düsseldorf, Germany
| | - Violetta Applegate
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Center for Structural Studies, Düsseldorf, Germany
| | - Jens Reiners
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Center for Structural Studies, Düsseldorf, Germany
| | - Astrid Port
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Center for Structural Studies, Düsseldorf, Germany
| | - Dominik Spona
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Functional Microbial Genomics, Düsseldorf, Germany
| | - Sebastian Hänsch
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Center for Advanced Imaging, Düsseldorf, Germany
| | - Amin Mirzaiebadizi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Center for Structural Studies, Düsseldorf, Germany
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Düsseldorf, Germany
| | - Johannes H Hegemann
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Functional Microbial Genomics, Düsseldorf, Germany.
| | - Katja Mölleken
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Functional Microbial Genomics, Düsseldorf, Germany
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7
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Mota C, Webster M, Saidi M, Kapp U, Zubieta C, Giachin G, Manso JA, de Sanctis D. Metal ion activation and DNA recognition by the Deinococcus radiodurans manganese sensor DR2539. FEBS J 2024; 291:3384-3402. [PMID: 38652591 DOI: 10.1111/febs.17140] [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: 02/15/2024] [Revised: 03/14/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024]
Abstract
The accumulation of manganese ions is crucial for scavenging reactive oxygen species and protecting the proteome of Deinococcus radiodurans (Dr). However, metal homeostasis still needs to be tightly regulated to avoid toxicity. DR2539, a dimeric transcription regulator, plays a key role in Dr manganese homeostasis. Despite comprising three well-conserved domains - a DNA-binding domain, a dimerisation domain, and an ancillary domain - the mechanisms underlying both, metal ion activation and DNA recognition remain elusive. In this study, we present biophysical analyses and the structure of the dimerisation and DNA-binding domains of DR2539 in its holo-form and in complex with the 21 base pair pseudo-palindromic repeat of the dr1709 promoter region, shedding light on these activation and recognition mechanisms. The dimer presents eight manganese binding sites that induce structural conformations essential for DNA binding. The analysis of the protein-DNA interfaces elucidates the significance of Tyr59 and helix α3 sequence in the interaction with the DNA. Finally, the structure in solution as determined by small-angle X-ray scattering experiments and supported by AlphaFold modeling provides a model illustrating the conformational changes induced upon metal binding.
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Affiliation(s)
- Cristiano Mota
- ESRF - The European Synchrotron, Grenoble, France
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | | | | | - Ulrike Kapp
- ESRF - The European Synchrotron, Grenoble, France
| | | | | | - José Antonio Manso
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
- I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
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8
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Aschenbrenner I, Böckler M, Franke F, Liebl K, Catici DAM, Brandl M, Behnke J, Feige MJ. Development of an enabling platform biotechnology for the production of proteins. Biol Chem 2024; 405:471-483. [PMID: 38916991 DOI: 10.1515/hsz-2023-0376] [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: 12/25/2023] [Accepted: 03/27/2024] [Indexed: 06/27/2024]
Abstract
Protein-based drugs are a mainstay of modern medicine. In contrast to antibodies, most of these need highly individualized production processes which often limits their development. Here, we develop an immunoglobulin domain tag (i-Tag), which can be fused to any protein of interest. This tag is made of a linear arrangement of antibody light chain constant domains. It enhances expression as well as secretion of the fusion partner and allows for simple purification of several structurally and functionally distinct fusion proteins. Furthermore, it improves the biophysical characteristics of most fusion proteins tested, is inert, and does not compromise the fusion partners' functionality. Taken together, the i-Tag should facilitate the development of biopharmaceuticals and diagnostic proteins otherwise lacking a common structural element.
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Affiliation(s)
- Isabel Aschenbrenner
- TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), 9184 Technical University of Munich , D-85748 Garching, Germany
| | - Maximilian Böckler
- TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), 9184 Technical University of Munich , D-85748 Garching, Germany
| | - Fabian Franke
- TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), 9184 Technical University of Munich , D-85748 Garching, Germany
| | - Korbinian Liebl
- TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), 9184 Technical University of Munich , D-85748 Garching, Germany
| | - Dragana A M Catici
- TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), 9184 Technical University of Munich , D-85748 Garching, Germany
| | - Matthias Brandl
- TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center (BNMRZ), 9184 Technical University of Munich , D-85748 Garching, Germany
| | - Julia Behnke
- TUM School of Medicine, Department of Surgery, Klinikum Rechts der Isar München, 9184 Technical University of Munich , D-81675 Munich, Germany
| | - Matthias J Feige
- TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), 9184 Technical University of Munich , D-85748 Garching, Germany
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9
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Fiorucci L, Schiavina M, Felli IC, Pierattelli R, Ravera E. Are Protein Conformational Ensembles in Agreement with Experimental Data? A Geometrical Interpretation of the Problem. J Chem Inf Model 2024; 64:5392-5401. [PMID: 38959217 DOI: 10.1021/acs.jcim.4c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The conformational variability of biological macromolecules can play an important role in their biological function. Therefore, understanding conformational variability is expected to be key for predicting the behavior of a particular molecule in the context of organism-wide studies. Several experimental methods have been developed and deployed for accessing this information, and computational methods are continuously updated for the profitable integration of different experimental sources. The outcome of this endeavor is conformational ensembles, which may vary significantly in properties and composition when different ensemble reconstruction methods are used, and this raises the issue of comparing the predicted ensembles against experimental data. In this article, we discuss a geometrical formulation to provide a framework for understanding the agreement of an ensemble prediction to the experimental observations.
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Affiliation(s)
- Letizia Fiorucci
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Marco Schiavina
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Enrico Ravera
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Florence Data Science, University of Florence, Viale G.B. Morgagni 59, 50134 Florence, Italy
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10
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Shweta H, Gupta K, Zhou Y, Cui X, Li S, Lu Z, Goldman YE, Dantzig JA. Characterization and structural basis for the brightness of mCLIFY: a novel monomeric and circularly permuted bright yellow fluorescent protein. RESEARCH SQUARE 2024:rs.3.rs-4638282. [PMID: 39070629 PMCID: PMC11276004 DOI: 10.21203/rs.3.rs-4638282/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
We present mCLIFY: a monomeric, bright, yellow, and long-lived fluorescent protein (FP) created by circular permutation of YPet, the brightest yellow FP from Aequorea Victoria for use in cellular and in vitro single molecule studies. mCLIFY retains the enhanced photophysical properties of YPET as a monomer at concentrations ≤ 40 μM. In contrast, we determined that YPet has a dimerization dissociation constant (K D 1-2) of 3.4 μM. Dimerization of YPet can cause homo-FRET, which underlies quantitative errors due to dimerization and homo-FRET. We determined the atomic structure of mCLIFY at 1.57 Å resolution and used its similarity with Venus for guided chromophore-targeted substitution studies to provide insights into its enhanced photophysical properties. The mutation V58L within the chromophore pocket improved quantum yield and extinction coefficient, making mCLIFY ~30% brighter than Venus. The extensive characterization of the photophysical and structural properties of YPet and mCLIFY presented here allowed us to reveal the basis of their long lifetimes and enhanced brightness and the basis of YPet's dimerization.
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Affiliation(s)
- Him Shweta
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Center for Engineering Mechanobiology (CEMB), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Present address: Departments of Pharmacology and Cellular and Molecular Biology, University of California, Davis, CA-95616
| | - Kushol Gupta
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Yufeng Zhou
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Xiaonan Cui
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Selene Li
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Zhe Lu
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Yale E. Goldman
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Center for Engineering Mechanobiology (CEMB), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Present address: Departments of Pharmacology and Cellular and Molecular Biology, University of California, Davis, CA-95616
| | - Jody A. Dantzig
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
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11
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Apostol AJ, Bragagnolo NJ, Rodriguez CS, Audette GF. Structural insights into the disulfide isomerase and chaperone activity of TrbB of the F plasmid type IV secretion system. Curr Res Struct Biol 2024; 8:100156. [PMID: 39131116 PMCID: PMC11315126 DOI: 10.1016/j.crstbi.2024.100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/07/2024] [Accepted: 07/10/2024] [Indexed: 08/13/2024] Open
Abstract
Bacteria have evolved elaborate mechanisms to thrive in stressful environments. F-like plasmids in gram-negative bacteria encode for a multi-protein Type IV Secretion System (T4SSF) that is functional for bacterial proliferation and adaptation through the process of conjugation. The periplasmic protein TrbB is believed to have a stabilizing chaperone role in the T4SSF assembly, with TrbB exhibiting disulfide isomerase (DI) activity. In the current report, we demonstrate that the deletion of the disordered N-terminus of TrbBWT, resulting in a truncation construct TrbB37-161, does not affect its catalytic in vitro activity compared to the wild-type protein (p = 0.76). Residues W37-K161, which include the active thioredoxin motif, are sufficient for DI activity. The N-terminus of TrbBWT is disordered as indicated by a structural model of GST-TrbBWT based on ColabFold-AlphaFold2 and Small Angle X-Ray Scattering data and 1H-15N Heteronuclear Single Quantum Correlation (HSQC) spectroscopy of the untagged protein. This disordered region likely contributes to the protein's dynamicity; removal of this region results in a more stable protein based on 1H-15N HSQC and Circular Dichroism Spectroscopies. Lastly, size exclusion chromatography analysis of TrbBWT in the presence of TraW, a T4SSF assembly protein predicted to interact with TrbBWT, does not support the inference of a stable complex forming in vitro. This work advances our understanding of TrbB's structure and function, explores the role of structural disorder in protein dynamics in the context of a T4SSF accessory protein, and highlights the importance of redox-assisted protein folding in the T4SSF.
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Affiliation(s)
- Arnold J. Apostol
- Department of Chemistry, York University, 4700 Keele St, Toronto, ON, Canada, M3J 1P3
- Centre for Research on Biomolecular Interactions, York University, Canada
| | - Nicholas J. Bragagnolo
- Department of Chemistry, York University, 4700 Keele St, Toronto, ON, Canada, M3J 1P3
- Centre for Research on Biomolecular Interactions, York University, Canada
| | - Christina S. Rodriguez
- Department of Chemistry, York University, 4700 Keele St, Toronto, ON, Canada, M3J 1P3
- Centre for Research on Biomolecular Interactions, York University, Canada
| | - Gerald F. Audette
- Department of Chemistry, York University, 4700 Keele St, Toronto, ON, Canada, M3J 1P3
- Centre for Research on Biomolecular Interactions, York University, Canada
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12
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Chen G, Wang Y, Zheng Z, Jiang W, Leppert A, Zhong X, Belorusova A, Siegal G, Jegerschöld C, Koeck PJB, Abelein A, Hebert H, Knight SD, Johansson J. Molecular basis for different substrate-binding sites and chaperone functions of the BRICHOS domain. Protein Sci 2024; 33:e5063. [PMID: 38864729 PMCID: PMC11168071 DOI: 10.1002/pro.5063] [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: 02/06/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Proteins can misfold into fibrillar or amorphous aggregates and molecular chaperones act as crucial guardians against these undesirable processes. The BRICHOS chaperone domain, found in several otherwise unrelated proproteins that contain amyloidogenic regions, effectively inhibits amyloid formation and toxicity but can in some cases also prevent non-fibrillar, amorphous protein aggregation. Here, we elucidate the molecular basis behind the multifaceted chaperone activities of the BRICHOS domain from the Bri2 proprotein. High-confidence AlphaFold2 and RoseTTAFold predictions suggest that the intramolecular amyloidogenic region (Bri23) is part of the hydrophobic core of the proprotein, where it occupies the proposed amyloid binding site, explaining the markedly reduced ability of the proprotein to prevent an exogenous amyloidogenic peptide from aggregating. However, the BRICHOS-Bri23 complex maintains its ability to form large polydisperse oligomers that prevent amorphous protein aggregation. A cryo-EM-derived model of the Bri2 BRICHOS oligomer is compatible with surface-exposed hydrophobic motifs that get exposed and come together during oligomerization, explaining its effects against amorphous aggregation. These findings provide a molecular basis for the BRICHOS chaperone domain function, where distinct surfaces are employed against different forms of protein aggregation.
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Affiliation(s)
- Gefei Chen
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden
| | - Yu Wang
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- College of Wildlife and Protected Area, Northeast Forestry UniversityHarbinChina
| | - Zihan Zheng
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of PharmacologyXi'an Jiaotong UniversityXi'anChina
| | - Wangshu Jiang
- Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden
| | - Axel Leppert
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Present address:
Department of Microbiology, Tumour and Cell BiologyKarolinska InstitutetSolnaSweden
| | - Xueying Zhong
- Department of Biomedical Engineering and Health Systems, School of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyHuddingeSweden
| | | | | | - Caroline Jegerschöld
- Department of Biomedical Engineering and Health Systems, School of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyHuddingeSweden
| | - Philip J. B. Koeck
- Department of Biomedical Engineering and Health Systems, School of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyHuddingeSweden
| | - Axel Abelein
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Hans Hebert
- Department of Biomedical Engineering and Health Systems, School of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyHuddingeSweden
| | - Stefan D. Knight
- Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden
| | - Jan Johansson
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
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13
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Paoletti F. ATP binding to Nerve Growth Factor (NGF) and pro-Nerve Growth Factor (proNGF): an endogenous molecular switch modulating neurotrophins activity. Biochem Soc Trans 2024; 52:1293-1304. [PMID: 38716884 DOI: 10.1042/bst20231089] [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: 02/28/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/27/2024]
Abstract
ATP has recently been reconsidered as a molecule with functional properties which go beyond its recognized role of the energetic driver of the cell. ATP has been described as an allosteric modulator as well as a biological hydrotrope with anti-aggregation properties in the crowded cellular environment. The role of ATP as a modulator of the homeostasis of the neurotrophins (NTs), a growth factor protein family whose most known member is the nerve growth factor (NGF), has been investigated. The modulation of NTs by small endogenous ligands is still a scarcely described area, with few papers reporting on the topic, and very few reports on the molecular determinants of these interactions. However, a detailed atomistic description of the NTs interaction landscape is of urgent need, aiming at the identification of novel molecules as potential therapeutics and considering the wide range of potential pharmacological applications for NGF and its family members. This mini-review will focus on the unique cartography casting the interactions of the endogenous ligand ATP, in the interaction with NGF as well as with its precursor proNGF. These interactions revealed interesting features of the ATP binding and distinct differences in the binding mode between the highly structured mature NGF and its precursor, proNGF, which is characterized by an intrinsically unstructured domain. The overview on the recent available data will be presented, together with the future perspectives on the field.
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Affiliation(s)
- Francesca Paoletti
- Institute of Crystallography - C.N.R. - Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy
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14
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Xiao W, Liu G, Chen T, Zhang Y, Lu C. Bifidobacterium bifidum SAM-VI Riboswitch Conformation Change Requires Peripheral Helix Formation. Biomolecules 2024; 14:742. [PMID: 39062457 PMCID: PMC11274715 DOI: 10.3390/biom14070742] [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: 05/11/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
The Bifidobacterium bifidum SAM-VI riboswitch undergoes dynamic conformational changes that modulate downstream gene expression. Traditional structural methods such as crystallography capture the bound conformation at high resolution, and additional efforts would reveal details from the dynamic transition. Here, we revealed a transcription-dependent conformation model for Bifidobacterium bifidum SAM-VI riboswitch. In this study, we combine small-angle X-ray scattering, chemical probing, and isothermal titration calorimetry to unveil the ligand-binding properties and conformational changes of the Bifidobacterium bifidum SAM-VI riboswitch and its variants. Our results suggest that the SAM-VI riboswitch contains a pre-organized ligand-binding pocket and stabilizes into the bound conformation upon binding to SAM. Whether the P1 stem formed and variations in length critically influence the conformational dynamics of the SAM-VI riboswitch. Our study provides the basis for artificially engineering the riboswitch by manipulating its peripheral sequences without modifying the SAM-binding core.
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Affiliation(s)
- Wenwen Xiao
- College of Biological and Medical Engineering, Donghua University, Shanghai 201620, China; (W.X.); (T.C.); (Y.Z.)
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China;
| | - Ting Chen
- College of Biological and Medical Engineering, Donghua University, Shanghai 201620, China; (W.X.); (T.C.); (Y.Z.)
| | - Yunlong Zhang
- College of Biological and Medical Engineering, Donghua University, Shanghai 201620, China; (W.X.); (T.C.); (Y.Z.)
| | - Changrui Lu
- College of Biological and Medical Engineering, Donghua University, Shanghai 201620, China; (W.X.); (T.C.); (Y.Z.)
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15
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Goradia N, Werner S, Mullapudi E, Greimeier S, Bergmann L, Lang A, Mertens H, Węglarz A, Sander S, Chojnowski G, Wikman H, Ohlenschläger O, von Amsberg G, Pantel K, Wilmanns M. Master corepressor inactivation through multivalent SLiM-induced polymerization mediated by the oncogene suppressor RAI2. Nat Commun 2024; 15:5241. [PMID: 38898011 PMCID: PMC11187106 DOI: 10.1038/s41467-024-49488-3] [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: 11/19/2023] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
While the elucidation of regulatory mechanisms of folded proteins is facilitated due to their amenability to high-resolution structural characterization, investigation of these mechanisms in disordered proteins is more challenging due to their structural heterogeneity, which can be captured by a variety of biophysical approaches. Here, we used the transcriptional master corepressor CtBP, which binds the putative metastasis suppressor RAI2 through repetitive SLiMs, as a model system. Using cryo-electron microscopy embedded in an integrative structural biology approach, we show that RAI2 unexpectedly induces CtBP polymerization through filaments of stacked tetrameric CtBP layers. These filaments lead to RAI2-mediated CtBP nuclear foci and relieve its corepressor function in RAI2-expressing cancer cells. The impact of RAI2-mediated CtBP loss-of-function is illustrated by the analysis of a diverse cohort of prostate cancer patients, which reveals a substantial decrease in RAI2 in advanced treatment-resistant cancer subtypes. As RAI2-like SLiM motifs are found in a wide range of organisms, including pathogenic viruses, our findings serve as a paradigm for diverse functional effects through multivalent interaction-mediated polymerization by disordered proteins in healthy and diseased conditions.
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Affiliation(s)
- Nishit Goradia
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Stefan Werner
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Mildred Scheel Cancer Career Center HaTriCS4, Martinistrasse 52, 20246, Hamburg, Germany
| | - Edukondalu Mullapudi
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sarah Greimeier
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Lina Bergmann
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Andras Lang
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstraße 11, 07745, Jena, Germany
| | - Haydyn Mertens
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aleksandra Węglarz
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Simon Sander
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstraße 11, 07745, Jena, Germany
| | - Gunhild von Amsberg
- Martini Clinic, Martinistrasse 52, 20246, Hamburg, Germany
- Department of Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany.
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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16
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Busby JN, Trevelyan S, Pegg CL, Kerr ED, Schulz BL, Chassagnon I, Landsberg MJ, Weston MK, Hurst MRH, Lott JS. The ABC toxin complex from Yersinia entomophaga can package three different cytotoxic components expressed from distinct genetic loci in an unfolded state: the structures of both shell and cargo. IUCRJ 2024; 11:299-308. [PMID: 38512773 PMCID: PMC11067744 DOI: 10.1107/s2052252524001969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
Bacterial ABC toxin complexes (Tcs) comprise three core proteins: TcA, TcB and TcC. The TcA protein forms a pentameric assembly that attaches to the surface of target cells and penetrates the cell membrane. The TcB and TcC proteins assemble as a heterodimeric TcB-TcC subcomplex that makes a hollow shell. This TcB-TcC subcomplex self-cleaves and encapsulates within the shell a cytotoxic `cargo' encoded by the C-terminal region of the TcC protein. Here, we describe the structure of a previously uncharacterized TcC protein from Yersinia entomophaga, encoded by a gene at a distant genomic location from the genes encoding the rest of the toxin complex, in complex with the TcB protein. When encapsulated within the TcB-TcC shell, the C-terminal toxin adopts an unfolded and disordered state, with limited areas of local order stabilized by the chaperone-like inner surface of the shell. We also determined the structure of the toxin cargo alone and show that when not encapsulated within the shell, it adopts an ADP-ribosyltransferase fold most similar to the catalytic domain of the SpvB toxin from Salmonella typhimurium. Our structural analysis points to a likely mechanism whereby the toxin acts directly on actin, modifying it in a way that prevents normal polymerization.
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Affiliation(s)
- Jason N. Busby
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Sarah Trevelyan
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Cassandra L. Pegg
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Edward D. Kerr
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Irene Chassagnon
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Michael J. Landsberg
- School of Chemistry and Molecular Biosciences, University of Central Queensland, Brisbane, Queensland 4072, Australia
| | - Mitchell K. Weston
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - Mark R. H. Hurst
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - J. Shaun Lott
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
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17
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Gogou C, Beugelink JW, Frias CP, Kresik L, Jaroszynska N, Drescher U, Janssen BJC, Hindges R, Meijer DH. Alternative splicing controls teneurin-3 compact dimer formation for neuronal recognition. Nat Commun 2024; 15:3648. [PMID: 38684645 PMCID: PMC11058771 DOI: 10.1038/s41467-024-47763-x] [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: 11/16/2023] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Neuronal network formation is facilitated by recognition between synaptic cell adhesion molecules at the cell surface. Alternative splicing of cell adhesion molecules provides additional specificity in forming neuronal connections. For the teneurin family of cell adhesion molecules, alternative splicing of the EGF-repeats and NHL domain controls synaptic protein-protein interactions. Here we present cryo-EM structures of the compact dimeric ectodomain of two teneurin-3 isoforms that harbour the splice insert in the EGF-repeats. This dimer is stabilised by an EGF8-ABD contact between subunits. Cryo-EM reconstructions of all four splice variants, together with SAXS and negative stain EM, reveal compacted dimers for each, with variant-specific dimeric arrangements. This results in specific trans-cellular interactions, as tested in cell clustering and stripe assays. The compact conformations provide a structural basis for teneurin homo- and heterophilic interactions. Altogether, our findings demonstrate how alternative splicing results in rearrangements of the dimeric subunits, influencing neuronal recognition and likely circuit wiring.
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Affiliation(s)
- Christos Gogou
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, van der Maasweg 9, Delft, the Netherlands
| | - J Wouter Beugelink
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht, the Netherlands
| | - Cátia P Frias
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, van der Maasweg 9, Delft, the Netherlands
| | - Leanid Kresik
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, van der Maasweg 9, Delft, the Netherlands
| | - Natalia Jaroszynska
- Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, UK
| | - Uwe Drescher
- Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Bert J C Janssen
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht, the Netherlands
| | - Robert Hindges
- Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Dimphna H Meijer
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, van der Maasweg 9, Delft, the Netherlands.
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18
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Mikkelsen JH, Stødkilde K, Jensen MP, Hansen AG, Wu Q, Lorentzen J, Graversen JH, Andersen GR, Fenton RA, Etzerodt A, Thiel S, Andersen CBF. Trypanosoma brucei Invariant Surface Glycoprotein 75 Is an Immunoglobulin Fc Receptor Inhibiting Complement Activation and Antibody-Mediated Cellular Phagocytosis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1334-1344. [PMID: 38391367 DOI: 10.4049/jimmunol.2300862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Various subspecies of the unicellular parasite Trypanosoma brucei cause sleeping sickness, a neglected tropical disease affecting millions of individuals and domestic animals. Immune evasion mechanisms play a pivotal role in parasite survival within the host and enable the parasite to establish a chronic infection. In particular, the rapid switching of variant surface glycoproteins covering a large proportion of the parasite's surface enables the parasite to avoid clearance by the adaptive immune system of the host. In this article, we present the crystal structure and discover an immune-evasive function of the extracellular region of the T. brucei invariant surface gp75 (ISG75). Structural analysis determined that the ISG75 ectodomain is organized as a globular head domain and a long slender coiled-coil domain. Subsequent ligand screening and binding analysis determined that the head domain of ISG75 confers interaction with the Fc region of all subclasses of human IgG. Importantly, the ISG75-IgG interaction strongly inhibits both activation of the classical complement pathway and Ab-dependent cellular phagocytosis by competing with C1q and host cell FcγR CD32. Our data reveal a novel immune evasion mechanism of T. brucei, with ISG75 able to inactivate the activities of Abs recognizing the parasite surface proteins.
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Affiliation(s)
| | | | | | | | - Qi Wu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Josefine Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jonas Heilskov Graversen
- Department of Cancer and Inflammation, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Gregers Rom Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Anders Etzerodt
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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19
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Hadži S, Živič Z, Kovačič M, Zavrtanik U, Haesaerts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R. Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Nat Commun 2024; 15:3105. [PMID: 38600130 PMCID: PMC11006873 DOI: 10.1038/s41467-024-47296-3] [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: 05/21/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disordered protein sequences can exhibit different binding modes, ranging from well-ordered folding-upon-binding to highly dynamic fuzzy binding. The primary function of the intrinsically disordered region of the antitoxin HigA2 from Vibrio cholerae is to neutralize HigB2 toxin through ultra-high-affinity folding-upon-binding interaction. Here, we show that the same intrinsically disordered region can also mediate fuzzy interactions with its operator DNA and, through interplay with the folded helix-turn-helix domain, regulates transcription from the higBA2 operon. NMR, SAXS, ITC and in vivo experiments converge towards a consistent picture where a specific set of residues in the intrinsically disordered region mediate electrostatic and hydrophobic interactions while "hovering" over the DNA operator. Sensitivity of the intrinsically disordered region to scrambling the sequence, position-specific contacts and absence of redundant, multivalent interactions, point towards a more specific type of fuzzy binding. Our work demonstrates how a bacterial regulator achieves dual functionality by utilizing two distinct interaction modes within the same disordered sequence.
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Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Zala Živič
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Daniel Charlier
- Research group of Microbiology, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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20
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Matsui T, Rajkovic I, Mooers BHM, Liu P, Weiss TM. Adaptable SEC-SAXS data collection for higher quality structure analysis in solution. Protein Sci 2024; 33:e4946. [PMID: 38501481 PMCID: PMC10949327 DOI: 10.1002/pro.4946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/31/2024] [Accepted: 02/10/2024] [Indexed: 03/20/2024]
Abstract
The two major challenges in synchrotron size-exclusion chromatography coupled in-line with small-angle x-ray scattering (SEC-SAXS) experiments are the overlapping peaks in the elution profile and the fouling of radiation-damaged materials on the walls of the sample cell. In recent years, many post-experimental analyses techniques have been developed and applied to extract scattering profiles from these problematic SEC-SAXS data. Here, we present three modes of data collection at the BioSAXS Beamline 4-2 of the Stanford Synchrotron Radiation Lightsource (SSRL BL4-2). The first mode, the High-Resolution mode, enables SEC-SAXS data collection with excellent sample separation and virtually no additional peak broadening from the UHPLC UV detector to the x-ray position by taking advantage of the low system dispersion of the UHPLC. The small bed volume of the analytical SEC column minimizes sample dilution in the column and facilitates data collection at higher sample concentrations with excellent sample economy equal to or even less than that of the conventional equilibrium SAXS method. Radiation damage problems during SEC-SAXS data collection are evaded by additional cleaning of the sample cell after buffer data collection and avoidance of unnecessary exposures through the use of the x-ray shutter control options, allowing sample data collection with a clean sample cell. Therefore, accurate background subtraction can be performed at a level equivalent to the conventional equilibrium SAXS method without requiring baseline correction, thereby leading to more reliable downstream structural analysis and quicker access to new science. The two other data collection modes, the High-Throughput mode and the Co-Flow mode, add agility to the planning and execution of experiments to efficiently achieve the user's scientific objectives at the SSRL BL4-2.
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Affiliation(s)
- Tsutomu Matsui
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Ivan Rajkovic
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Blaine H. M. Mooers
- Department of Biochemistry and PhysiologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
- Stephenson Cancer CenterUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
- Laboratory of Biomolecular Structure and FunctionUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
| | - Ping Liu
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
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21
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Doğru EK, Sakallı T, Liu G, Sayers Z, Surmeli NB. Small angle X-ray scattering analysis of thermophilic cytochrome P450 CYP119 and the effects of the N-terminal histidine tag. Int J Biol Macromol 2024; 265:131026. [PMID: 38522710 DOI: 10.1016/j.ijbiomac.2024.131026] [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: 01/11/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Combining size exclusion chromatography-small angle X-ray scattering (SEC-SAXS) and molecular dynamics (MD) analysis is a promising approach to investigate protein behavior in solution, particularly for understanding conformational changes due to substrate binding in cytochrome P450s (CYPs). This study investigates conformational changes in CYP119, a thermophilic CYP from Sulfolobus acidocaldarius that exhibits structural flexibility similar to mammalian CYPs. Although the crystal structure of ligand-free (open state) and ligand-bound (closed state) forms of CYP119 is known, the overall structure of the enzyme in solution has not been explored until now. It was found that theoretical scattering profiles from the crystal structures of CYP119 did not align with the SAXS data, but conformers from MD simulations, particularly starting from the open state (46 % of all frames), agreed well. Interestingly, a small percentage of closed-state conformers also fit the data (9 %), suggesting ligand-free CYP119 samples ligand-bound conformations. Ab initio SAXS models for N-His tagged CYP119 revealed a tail-like unfolded structure impacting protein flexibility, which was confirmed by in silico modeling. SEC-SAXS analysis of N-His CYP119 indicated pentameric structures in addition to monomers in solution, affecting the stability and activity of the enzyme. This study adds insights into the conformational dynamics of CYP119 in solution.
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Affiliation(s)
- Ekin Kestevur Doğru
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye
| | - Tuğçe Sakallı
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye
| | - Goksin Liu
- Sabancı University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla 34956, Istanbul, Türkiye
| | - Zehra Sayers
- Sabancı University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla 34956, Istanbul, Türkiye
| | - Nur Basak Surmeli
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye.
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22
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Meloni M, Fanti S, Tedesco D, Gurrieri L, Trost P, Fermani S, Lemaire SD, Zaffagnini M, Henri J. Characterization of chloroplast ribulose-5-phosphate-3-epimerase from the microalga Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2024; 194:2263-2277. [PMID: 38134324 DOI: 10.1093/plphys/kiad680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/09/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
Carbon fixation relies on Rubisco and 10 additional enzymes in the Calvin-Benson-Bassham cycle. Epimerization of xylulose-5-phosphate (Xu5P) into ribulose-5-phosphate (Ru5P) contributes to the regeneration of ribulose-1,5-bisphosphate, the substrate of Rubisco. Ribulose-5-phosphate-3-epimerase (RPE, EC 5.1.3.1) catalyzes the formation of Ru5P, but it can also operate in the pentose-phosphate pathway by catalyzing the reverse reaction. Here, we describe the structural and biochemical properties of the recombinant RPE isoform 1 from Chlamydomonas (Chlamydomonas reinhardtii) (CrRPE1). The enzyme is a homo-hexamer that contains a zinc ion in the active site and exposes a catalytic pocket on the top of an α8β8 triose isomerase-type barrel as observed in structurally solved RPE isoforms from both plant and non-plant sources. By optimizing and developing enzyme assays to monitor the reversible epimerization of Ru5P to Xu5P and vice versa, we determined the catalytic parameters that differ from those of other plant paralogs. Despite being identified as a putative target of multiple thiol-based redox modifications, CrRPE1 activity is not affected by both reductive and oxidative treatments, indicating that enzyme catalysis is insensitive to possible redox alterations of cysteine residues. We mapped phosphorylation sites on the crystal structure, and the specific location at the entrance of the catalytic cleft supports a phosphorylation-based regulatory mechanism. This work provides an accurate description of the structural features of CrRPE1 and an in-depth examination of its catalytic and regulatory properties highlighting the physiological relevance of this enzyme in the context of photosynthetic carbon fixation.
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Affiliation(s)
- Maria Meloni
- Laboratory of Molecular Plant Physiology, Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
- Sorbonne Université, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, 4 Place Jussieu, 75005, Paris, France
| | - Silvia Fanti
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Daniele Tedesco
- Institute for Organic Synthesis and Photoreactivity, National Research Council (ISOF-CNR), Via Gobetti 101, 40129, Bologna, Italy
| | - Libero Gurrieri
- Laboratory of Molecular Plant Physiology, Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Paolo Trost
- Laboratory of Molecular Plant Physiology, Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Simona Fermani
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Stéphane D Lemaire
- Sorbonne Université, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, 4 Place Jussieu, 75005, Paris, France
| | - Mirko Zaffagnini
- Laboratory of Molecular Plant Physiology, Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Julien Henri
- Sorbonne Université, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, 4 Place Jussieu, 75005, Paris, France
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23
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Zhang S, Jeffreys LN, Poddar H, Yu Y, Liu C, Patel K, Johannissen LO, Zhu L, Cliff MJ, Yan C, Schirò G, Weik M, Sakuma M, Levy CW, Leys D, Heyes DJ, Scrutton NS. Photocobilins integrate B 12 and bilin photochemistry for enzyme control. Nat Commun 2024; 15:2740. [PMID: 38548733 PMCID: PMC10979010 DOI: 10.1038/s41467-024-46995-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 03/17/2024] [Indexed: 04/01/2024] Open
Abstract
Photoreceptor proteins utilise chromophores to sense light and trigger a biological response. The discovery that adenosylcobalamin (or coenzyme B12) can act as a light-sensing chromophore heralded a new field of B12-photobiology. Although microbial genome analysis indicates that photoactive B12-binding domains form part of more complex protein architectures, regulating a range of molecular-cellular functions in response to light, experimental evidence is lacking. Here we identify and characterise a sub-family of multi-centre photoreceptors, termed photocobilins, that use B12 and biliverdin (BV) to sense light across the visible spectrum. Crystal structures reveal close juxtaposition of the B12 and BV chromophores, an arrangement that facilitates optical coupling. Light-triggered conversion of the B12 affects quaternary structure, in turn leading to light-activation of associated enzyme domains. The apparent widespread nature of photocobilins implies involvement in light regulation of a wider array of biochemical processes, and thus expands the scope for B12 photobiology. Their characterisation provides inspiration for the design of broad-spectrum optogenetic tools and next generation bio-photocatalysts.
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Affiliation(s)
- Shaowei Zhang
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China.
| | - Laura N Jeffreys
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Harshwardhan Poddar
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yuqi Yu
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Chuanyang Liu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Kaylee Patel
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Cunyu Yan
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Colin W Levy
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - David Leys
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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24
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Shtykova EV, Dubrovin EV, Ksenofontov AL, Gifer PK, Petoukhov MV, Tokhtar VK, Sapozhnikova IM, Stavrianidi AN, Kordyukova LV, Batishchev OV. Structural Insights into Plant Viruses Revealed by Small-Angle X-ray Scattering and Atomic Force Microscopy. Viruses 2024; 16:427. [PMID: 38543792 PMCID: PMC10975137 DOI: 10.3390/v16030427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 05/23/2024] Open
Abstract
The structural study of plant viruses is of great importance to reduce the damage caused by these agricultural pathogens and to support their biotechnological applications. Nowadays, X-ray crystallography, NMR spectroscopy and cryo-electron microscopy are well accepted methods to obtain the 3D protein structure with the best resolution. However, for large and complex supramolecular structures such as plant viruses, especially flexible filamentous ones, there are a number of technical limitations to resolving their native structure in solution. In addition, they do not allow us to obtain structural information about dynamics and interactions with physiological partners. For these purposes, small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM) are well established. In this review, we have outlined the main principles of these two methods and demonstrated their advantages for structural studies of plant viruses of different shapes with relatively high spatial resolution. In addition, we have demonstrated the ability of AFM to obtain information on the mechanical properties of the virus particles that are inaccessible to other experimental techniques. We believe that these under-appreciated approaches, especially when used in combination, are valuable tools for studying a wide variety of helical plant viruses, many of which cannot be resolved by classical structural methods.
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Affiliation(s)
- Eleonora V. Shtykova
- National Research Centre, “Kurchatov Institute”, Moscow 123098, Russia; (E.V.S.)
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Evgeniy V. Dubrovin
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Polina K. Gifer
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Maxim V. Petoukhov
- National Research Centre, “Kurchatov Institute”, Moscow 123098, Russia; (E.V.S.)
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
| | - Valeriy K. Tokhtar
- Scientific and Educational Center, Botanical Garden of the National Research University “BelSU”, Belgorod 308033, Russia;
| | - Irina M. Sapozhnikova
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Ekaterinburg 620002, Russia;
| | - Andrey N. Stavrianidi
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Larisa V. Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Oleg V. Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia; (E.V.D.); (P.K.G.); (A.N.S.)
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25
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Belviso BD, Shen Y, Carrozzini B, Morishita M, di Luccio E, Caliandro R. Structural insights into the C-terminus of the histone-lysine N-methyltransferase NSD3 by small-angle X-ray scattering. Front Mol Biosci 2024; 11:1191246. [PMID: 38516186 PMCID: PMC10955146 DOI: 10.3389/fmolb.2024.1191246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
NSD3 is a member of six H3K36-specific histone lysine methyltransferases in metazoans. Its overexpression or mutation is implicated in developmental defects and oncogenesis. Aside from the well-characterized catalytic SET domain, NSD3 has multiple clinically relevant potential chromatin-binding motifs, such as the proline-tryptophan-tryptophan-proline (PWWP), the plant homeodomain (PHD), and the adjacent Cys-His-rich domain located at the C-terminus. The crystal structure of the individual domains is available, and this structural knowledge has allowed the designing of potential inhibitors, but the intrinsic flexibility of larger constructs has hindered the characterization of mutual domain conformations. Here, we report the first structural characterization of the NSD3 C-terminal region comprising the PWWP2, SET, and PHD4 domains, which has been achieved at a low resolution in solution by small-angle X-ray scattering (SAXS) data on two multiple-domain NSD3 constructs complemented with size-exclusion chromatography and advanced computational modeling. Structural models predicted by machine learning have been validated in direct space, by comparison with the SAXS-derived molecular envelope, and in reciprocal space, by reproducing the experimental SAXS profile. Selected models have been refined by SAXS-restrained molecular dynamics. This study shows how SAXS data can be used with advanced computational modeling techniques to achieve a detailed structural characterization and sheds light on how NSD3 domains are interconnected in the C-terminus.
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Affiliation(s)
| | - Yunpeng Shen
- Department of Biotechnology, School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan, China
| | | | - Masayo Morishita
- Department of Genetic Engineering, School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Eric di Luccio
- Department of Genetic Engineering, School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
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26
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Hu Q, Botuyan MV, Mer G. Identification of a conserved α-helical domain at the N terminus of human DNA methyltransferase 1. J Biol Chem 2024; 300:105775. [PMID: 38382673 PMCID: PMC10950863 DOI: 10.1016/j.jbc.2024.105775] [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: 01/12/2024] [Revised: 02/03/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024] Open
Abstract
In vertebrates, DNA methyltransferase 1 (DNMT1) contributes to preserving DNA methylation patterns, ensuring the stability and heritability of epigenetic marks important for gene expression regulation and the maintenance of cellular identity. Previous structural studies have elucidated the catalytic mechanism of DNMT1 and its specific recognition of hemimethylated DNA. Here, using solution nuclear magnetic resonance spectroscopy and small-angle X-ray scattering, we demonstrate that the N-terminal region of human DNMT1, while flexible, encompasses a conserved globular domain with a novel α-helical bundle-like fold. This work expands our understanding of the structure and dynamics of DNMT1 and provides a structural framework for future functional studies in relation with this new domain.
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Affiliation(s)
- Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Department of Cancer Biology, Mayo Clinic, Rochester, Minnesota, USA.
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27
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Mao YQ, Seraphim TV, Wan Y, Wu R, Coyaud E, Bin Munim M, Mollica A, Laurent E, Babu M, Mennella V, Raught B, Houry WA. DPCD is a regulator of R2TP in ciliogenesis initiation through Akt signaling. Cell Rep 2024; 43:113713. [PMID: 38306274 DOI: 10.1016/j.celrep.2024.113713] [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: 02/23/2023] [Revised: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024] Open
Abstract
R2TP is a chaperone complex consisting of the AAA+ ATPases RUVBL1 and RUVBL2, as well as RPAP3 and PIH1D1 proteins. R2TP is responsible for the assembly of macromolecular complexes mainly acting through different adaptors. Using proximity-labeling mass spectrometry, we identified deleted in primary ciliary dyskinesia (DPCD) as an adaptor of R2TP. Here, we demonstrate that R2TP-DPCD influences ciliogenesis initiation through a unique mechanism by interaction with Akt kinase to regulate its phosphorylation levels rather than its stability. We further show that DPCD is a heart-shaped monomeric protein with two domains. A highly conserved region in the cysteine- and histidine-rich domains-containing proteins and SGT1 (CS) domain of DPCD interacts with the RUVBL2 DII domain with high affinity to form a stable R2TP-DPCD complex both in cellulo and in vitro. Considering that DPCD is one among several CS-domain-containing proteins found to associate with RUVBL1/2, we propose that RUVBL1/2 are CS-domain-binding proteins that regulate complex assembly and downstream signaling.
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Affiliation(s)
- Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yimei Wan
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ruikai Wu
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Muhammad Bin Munim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Antonio Mollica
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Vito Mennella
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; MRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QR, UK; Department of Pathology, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QP, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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28
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Sun S, Zhu R, Zhu M, Wang Q, Li N, Yang B. Visualization of conformational transition of GRP94 in solution. Life Sci Alliance 2024; 7:e202302051. [PMID: 37949474 PMCID: PMC10638095 DOI: 10.26508/lsa.202302051] [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: 03/21/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
GRP94, an ER paralog of the heat-shock protein 90 family, binds and hydrolyses ATP to chaperone the folding and maturation of its selected clients. Compared with other hsp90 proteins, the in-solution conformational dynamics of GRP94 along the ATP hydrolysis cycle are less understood, hindering our understanding of its chaperoning mechanism. Leveraging small-angle X-ray scattering, negative-staining EM, and hydrogen-deuterium exchange coupled mass-spec, here we show that in its apo form, ∼60% of mouse GRP94 (mGRP94) populates an "extended" conformation, whereas the rest exist in either "close V" or "twist V" like "compact" conformations. Different from other hsp90 proteins, the presence of AMPPNP only impacts the relative abundance of the two compact conformations, rather than shifting the equilibrium between the "extended" and "compact" conformations of mGRP94. HDX-MS study of apo, AMPPNP-bound, and ADP-bound mGRP94 suggests a conformational transition from "twist V" to "close V" upon ATP binding and a back transition from "close V" to "twist V" upon ATP hydrolysis. These results illustrate the dissimilarities of GRP94 in conformation transition during ATP hydrolysis from other hsp90 paralogs.
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Affiliation(s)
- Shangwu Sun
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Rui Zhu
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mengyao Zhu
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qi Wang
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Na Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), Chinese Academy of Sciences, Shanghai, China
| | - Bei Yang
- https://ror.org/030bhh786 Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- https://ror.org/030bhh786 Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
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29
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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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30
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Saini M, Upadhyay N, Dhiman K, Manjhi SK, Kattuparambil AA, Ghoshal A, Arya R, Dey SK, Sharma A, Aduri R, Thelma BK, Ashish F, Kundu S. ARL15, a GTPase implicated in rheumatoid arthritis, potentially repositions its truncated N-terminus as a function of guanine nucleotide binding. Int J Biol Macromol 2024; 254:127898. [PMID: 37939768 DOI: 10.1016/j.ijbiomac.2023.127898] [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: 04/21/2023] [Revised: 10/21/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
The ADP ribosylation factor like protein 15 (ARL15) gene encodes for an uncharacterized GTPase associated with rheumatoid arthritis (RA) and other metabolic disorders. Investigation of the structural and functional attributes of ARL15 is important to position the protein as a potential drug target. Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively. The equilibrium dissociation constant (Kd) of GTP binding with ARL15 was estimated to be about eight-fold higher than that of GDP. Small Angle X-ray Scattering (SAXS) data indicated that in solution, the apo state of monomeric ARL15 adopts a shape characterized by a globe of maximum linear dimension (Dmax) of 6.1 nm, and upon binding to GTP or GDP, the vector distribution profile changes to peak-n-tail shoulder with Dmax extended to 7.6 and 7.7 nm, respectively. Structure restoration using a sequence-based template and experimental SAXS data provided the first visual insight revealing that the folded N-terminal in the unbound state of the protein may toggle open upon binding to guanine nucleotides. The conformational dynamics observed in the N-terminal region offer a scope to develop drugs that target this unique GTPase, potentially providing treatments for a range of metabolic disorders.
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Affiliation(s)
- Manisha Saini
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Neelam Upadhyay
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Kanika Dhiman
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Satish Kumar Manjhi
- Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India
| | - Aman Achutan Kattuparambil
- Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India
| | - Antara Ghoshal
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Richa Arya
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Sanjay Kumar Dey
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Aditya Sharma
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | - Raviprasad Aduri
- Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | - Fnu Ashish
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India; Department of Biological Sciences, Birla Institute of Technology and Science, K K Birla Goa Campus, Goa 403726, India.
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Yadav P, Gupta M, Wazahat R, Islam Z, Tsutakawa SE, Kamthan M, Kumar P. Structural basis for the role of C-terminus acidic tail of Saccharomyces cerevisiae ubiquitin-conjugating enzyme (Rad6) in E3 ligase (Bre1) mediated recognition of histones. Int J Biol Macromol 2024; 254:127717. [PMID: 37923031 DOI: 10.1016/j.ijbiomac.2023.127717] [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: 08/15/2023] [Revised: 10/07/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Ubiquitination of histone H2B on chromatin is key to gene regulation. E3 ligase Bre1 and E2 Rad6 in Saccharomyces cerevisiae associate together to catalyze mono-ubiquitination at histone H2BK123. Prior studies identified the role of a highly dynamic C-terminal acidic tail of Rad6 indispensable for H2BK123 mono-ubiquitination. However, the mechanistic basis for the Rad6-acidic tail role remained elusive. Using different structural and biophysical approaches, this study for the first time uncovers the direct role of Rad6-acidic tail in interaction with the Bre1 Rad6-Binding Domain (RBD) and recognition of histones surface to facilitate histone H2B mono-ubiquitination. A combination of NMR, SAXS, ITC, site-directed mutagenesis and molecular dynamics studies reveal that RBD domain of Bre1 interacts with Rad6 to stabilize the dynamics of acidic tail. This Bre1-RBD mediated stability in acidic tail of Rad6 could be one of the key factors for facilitating correct recognition of histone surface and ubiquitin-transfer at H2BK123. We provide biophysical evidence that Rad6-acidic tail and a positivity charged surface on histone H2B are involved in recognition of E2:Histones. Taken together, this study uncovers the mechanistic basis for the role of Rad6-acidic in Bre1-RBD mediated recognition of histone surface that ensure the histone H2B mono-ubiquitination.
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Affiliation(s)
- Pawan Yadav
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India
| | - Manish Gupta
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Rushna Wazahat
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India
| | - Zeyaul Islam
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mohan Kamthan
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India
| | - Pankaj Kumar
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India.
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Sudarev VV, Gette MS, Bazhenov SV, Tilinova OM, Zinovev EV, Manukhov IV, Kuklin AI, Ryzhykau YL, Vlasov AV. Ferritin-based fusion protein shows octameric deadlock state of self-assembly. Biochem Biophys Res Commun 2024; 690:149276. [PMID: 38007906 DOI: 10.1016/j.bbrc.2023.149276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/28/2023]
Abstract
Ferritin is a universal protein complex responsible for iron perception in almost all living organisms and has applications from fundamental biophysics to drug delivery and structure-based immunogen design. Different platforms based on ferritin share similar technological challenges limiting their development - control of self-assembling processes of ferritin itself as well as ferritin-based chimeric recombinant protein complexes. In our research, we studied self-assembly processes of ferritin-based protein complexes under different expression conditions. We fused a ferritin subunit with a SMT3 protein tag, a homolog of human Small Ubiquitin-like Modifier (SUMO-tag), which was taken to destabilize ferritin 3-fold channel contacts and increase ferritin-SUMO subunits solubility. We first obtained the octameric protein complex of ferritin-SUMO (8xFer-SUMO) and studied its structural organization by small-angle X-ray scattering (SAXS). Obtained SAXS data correspond well with the high-resolution models predicted by AlphaFold and CORAL software of an octameric assembly around the 4-fold channel of ferritin without formation of 3-fold channels. Interestingly, three copies of 8xFer-SUMO do not assemble into 24-meric globules. Thus, we first obtained and structurally characterized ferritin-based self-assembling oligomers in a deadlock state. Deadlock oligomeric states of ferritin extend the known scheme of its self-assembly process, being new potential tools for a number of applications. Finally, our results might open new directions for various biotechnological platforms utilizing ferritin-based tools.
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Affiliation(s)
- V V Sudarev
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - M S Gette
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - S V Bazhenov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - O M Tilinova
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - E V Zinovev
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - I V Manukhov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - A I Kuklin
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980, Russian Federation
| | - Yu L Ryzhykau
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980, Russian Federation.
| | - A V Vlasov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980, Russian Federation.
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Coto ALDS, Pereira AA, Oliveira SD, Moritz MNDO, Franco da Rocha AM, Dores-Silva PR, da Silva NSM, de Araújo Nogueira AR, Gava LM, Seraphim TV, Borges JC. Structural characterization of the human DjC20/HscB cochaperone in solution. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140970. [PMID: 37871810 DOI: 10.1016/j.bbapap.2023.140970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/27/2023] [Accepted: 10/14/2023] [Indexed: 10/25/2023]
Abstract
J-domain proteins (JDPs) form a very large molecular chaperone family involved in proteostasis processes, such as protein folding, trafficking through membranes and degradation/disaggregation. JDPs are Hsp70 co-chaperones capable of stimulating ATPase activity as well as selecting and presenting client proteins to Hsp70. In mitochondria, human DjC20/HscB (a type III JDP that possesses only the conserved J-domain in some region of the protein) is involved in [FeS] protein biogenesis and assists human mitochondrial Hsp70 (HSPA9). Human DjC20 possesses a zinc-finger domain in its N-terminus, which closely contacts the J-domain and appears to be essential for its function. Here, we investigated the hDjC20 structure in solution as well as the importance of Zn+2 for its stability. The recombinant hDjC20 was pure, folded and capable of stimulating HSPA9 ATPase activity. It behaved as a slightly elongated monomer, as attested by small-angle X-ray scattering and SEC-MALS. The presence of Zn2+ in the hDjC20 samples was verified, a stoichiometry of 1:1 was observed, and its removal by high concentrations of EDTA and DTPA was unfeasible. However, thermal and chemical denaturation in the presence of EDTA led to a reduction in protein stability, suggesting a synergistic action between the chelating agent and denaturators that facilitate protein unfolding depending on metal removal. These data suggest that the affinity of Zn+2 for the protein is very high, evidencing its importance for the hDjC20 structure.
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Affiliation(s)
| | - Arthur Alexandre Pereira
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | - Sabrina Dorta Oliveira
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | | | | | | | | | | | | | - Thiago Vagas Seraphim
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | - Júlio César Borges
- São Carlos Institute of Chemistry, University of São Paulo - USP, 13560-970 São Carlos, SP, Brazil.
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34
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Hutin S, Tully MD, Brennich M. Small-Angle X-Ray Scattering for Macromolecular Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:163-172. [PMID: 38507206 DOI: 10.1007/978-3-031-52193-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Small angle X-ray scattering (SAXS) is a versatile technique that can provide unique insights in the solution structure of macromolecules and their complexes, covering the size range from small peptides to complete viral assemblies. Technological and conceptual advances in the last two decades have tremendously improved the accessibility of the technique and transformed it into an indispensable tool for structural biology. In this chapter we introduce and discuss several approaches to collecting SAXS data on macromolecular complexes, including several approaches to online chromatography. We include practical advice on experimental design and point out common pitfalls of the technique.
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Affiliation(s)
- Stephanie Hutin
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, Grenoble, France
| | - Mark D Tully
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, Grenoble, France
| | - Martha Brennich
- European Molecular Biology Laboratory, Grenoble, Grenoble, France.
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35
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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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36
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Sahoo PK, Sheenu, Jain D. REC domain stabilizes the active heptamer of σ 54-dependent transcription factor, FleR from Pseudomonas aeruginosa. iScience 2023; 26:108397. [PMID: 38058307 PMCID: PMC10696123 DOI: 10.1016/j.isci.2023.108397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 09/12/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023] Open
Abstract
Motility in Pseudomonas aeruginosa is mediated through a single, polar flagellum, which is essential for virulence, colonization, and biofilm formation. FleSR, a two-component system (TCS), serves as a critical checkpoint in flagellar assembly. FleR is a σ54-dependent response regulator that undergoes phosphorylation via cognate sensor kinase FleS for the assembly of the functionally active form. The active form remodels the σ54-RNAP complex to initiate transcription. Small-angle X-ray scattering, crystallography, and negative staining electron microscopy reconstructions of FleR revealed that it exists predominantly as a dimer in the inactive form with low ATPase activity and assembles into heptamers upon phosphorylation with amplified ATPase activity. We establish that receiver (REC) domain stabilizes the heptamers and is indispensable for assembly of the functional phosphorylated form of FleR. The structural, biochemical, and in vivo complementation assays provide details of the phosphorylation-mediated assembly of FleR to regulate the expression of flagellar genes.
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Affiliation(s)
- Pankaj Kumar Sahoo
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India
| | - Sheenu
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India
| | - Deepti Jain
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India
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37
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Sun Y, Yang XN, Yang SS, Lyu YZ, Zhang B, Liu KW, Li N, Cui JC, Huang GX, Liu CL, Xu J, Mi JQ, Chen Z, Fan XH, Chen SJ, Chen S. Antigen-induced chimeric antigen receptor multimerization amplifies on-tumor cytotoxicity. Signal Transduct Target Ther 2023; 8:445. [PMID: 38062078 PMCID: PMC10703879 DOI: 10.1038/s41392-023-01686-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 12/18/2023] Open
Abstract
Ligand-induced receptor dimerization or oligomerization is a widespread mechanism for ensuring communication specificity, safeguarding receptor activation, and facilitating amplification of signal transduction across the cellular membrane. However, cell-surface antigen-induced multimerization (dubbed AIM herein) has not yet been consciously leveraged in chimeric antigen receptor (CAR) engineering for enriching T cell-based therapies. We co-developed ciltacabtagene autoleucel (cilta-cel), whose CAR incorporates two B-cell maturation antigen (BCMA)-targeted nanobodies in tandem, for treating multiple myeloma. Here we elucidated a structural and functional model in which BCMA-induced cilta-cel CAR multimerization amplifies myeloma-targeted T cell-mediated cytotoxicity. Crystallographic analysis of BCMA-nanobody complexes revealed atomic details of antigen-antibody hetero-multimerization whilst analytical ultracentrifugation and small-angle X-ray scattering characterized interdependent BCMA apposition and CAR juxtaposition in solution. BCMA-induced nanobody CAR multimerization enhanced cytotoxicity, alongside elevated immune synapse formation and cytotoxicity-mediating cytokine release, towards myeloma-derived cells. Our results provide a framework for contemplating the AIM approach in designing next-generation CARs.
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Affiliation(s)
- Yan Sun
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiu-Na Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shuang-Shuang Yang
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yi-Zhu Lyu
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Department of Hematology, Second Hospital of Dalian Medical University, Dalian, 116023, China
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Kai-Wen Liu
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Na Li
- National Facility for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Jia-Chen Cui
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guang-Xiang Huang
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Cheng-Lin Liu
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jie Xu
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jian-Qing Mi
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiao-Hu Fan
- Legend Biotech China, Nanjing, 211112, China.
- Wondercel Biotechnology, Shenzhen, 518052, China.
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Shuo Chen
- Shanghai Institute of Hematology, National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Immune Therapy Institute, Shanghai Cancer Institute, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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38
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EswarKumar N, Yang CH, Tewary S, Peng WH, Chen GC, Yeh YQ, Yang HC, Ho MC. An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation. Structure 2023; 31:1567-1577.e5. [PMID: 37794594 DOI: 10.1016/j.str.2023.09.004] [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: 06/13/2022] [Revised: 07/10/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023]
Abstract
The structure determination of protein tyrosine phosphatase (PTP): phospho-protein complexes, which is essential to understand how specificity is achieved at the amino acid level, remains a significant challenge for protein crystallography and cryoEM due to the transient nature of binding interactions. Using rPTPεD1 and phospho-SrcKD as a model system, we have established an integrative workflow to address this problem, by means of which we generate a protein:phospho-protein complex model using predetermined protein structures, SAXS and pTyr-tailored MD simulations. Our model reveals transient protein-protein interactions between rPTPεD1 and phospho-SrcKD and is supported by three independent experimental validations. Measurements of the association rate between rPTPεD1 and phospho-SrcKD showed that mutations on the rPTPεD1: SrcKD complex interface disrupts these transient interactions, resulting in a reduction in protein-protein association rate and, eventually, phosphatase activity. This integrative approach is applicable to other PTP: phospho-protein complexes and the characterization of transient protein-protein interface interactions.
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Affiliation(s)
- Nadendla EswarKumar
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Sunilkumar Tewary
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wen-Hsin Peng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsin-Chu 300, Taiwan
| | - Hsiao-Ching Yang
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan.
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.
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39
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Bolding JE, Nielsen AL, Jensen I, Hansen TN, Ryberg LA, Jameson ST, Harris P, Peters GHJ, Denu JM, Rogers JM, Olsen CA. Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7. Angew Chem Int Ed Engl 2023; 62:e202314597. [PMID: 37873919 DOI: 10.1002/anie.202314597] [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: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
The sirtuins are NAD+ -dependent lysine deacylases, comprising seven isoforms (SIRT1-7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.
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Affiliation(s)
- Julie E Bolding
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Alexander L Nielsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
- Current address: Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Iben Jensen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Line A Ryberg
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Current address: Department of Immunology and Microbiology, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Samuel T Jameson
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Current address: Department of Chemistry, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Joseph M Rogers
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
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40
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Ptak CP, Peterson TA, Hopkins JB, Ahern CA, Shy ME, Piper RC. Homomeric interactions of the MPZ Ig domain and their relation to Charcot-Marie-Tooth disease. Brain 2023; 146:5110-5123. [PMID: 37542466 PMCID: PMC10690024 DOI: 10.1093/brain/awad258] [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: 04/04/2023] [Revised: 06/28/2023] [Accepted: 07/17/2023] [Indexed: 08/07/2023] Open
Abstract
Mutations in MPZ (myelin protein zero) can cause demyelinating early-onset Charcot-Marie-Tooth type 1B disease or later onset type 2I/J disease characterized by axonal degeneration, reflecting the diverse roles of MPZ in Schwann cells. MPZ holds apposing membranes of the myelin sheath together, with the adhesion role fulfilled by its extracellular immunoglobulin-like domain (IgMPZ), which oligomerizes. Models for how the IgMPZ might form oligomeric assemblies has been extrapolated from a protein crystal structure in which individual rat IgMPZ subunits are packed together under artificial conditions, forming three weak interfaces. One interface organizes the IgMPZ into tetramers, a second 'dimer' interface links tetramers together across the intraperiod line, and a third hydrophobic interface that mediates binding to lipid bilayers or the same hydrophobic surface on another IgMPZ domain. Presently, there are no data confirming whether the proposed IgMPZ interfaces actually mediate oligomerization in solution, whether they are required for the adhesion activity of MPZ, whether they are important for myelination, or whether their loss results in disease. We performed nuclear magnetic resonance spectroscopy and small angle X-ray scattering analysis of wild-type IgMPZ as well as mutant forms with amino acid substitutions designed to interrupt its presumptive oligomerization interfaces. Here, we confirm the interface that mediates IgMPZ tetramerization, but find that dimerization is mediated by a distinct interface that has yet to be identified. We next correlated different types of Charcot-Marie-Tooth disease symptoms to subregions within IgMPZ tetramers. Variants causing axonal late-onset disease (CMT2I/J) map to surface residues of IgMPZ proximal to the transmembrane domain. Variants causing early-onset demyelinating disease (CMT1B) segregate into two groups: one is described by variants that disrupt the stability of the Ig-fold itself and are largely located within the core of the IgMPZ domain; whereas another describes a region on the surface of IgMPZ tetramers, accessible to protein interactions. Computational docking studies predict that this latter disease-relevant subregion may potentially mediate dimerization of IgMPZ tetramers.
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Affiliation(s)
- Christopher P Ptak
- Biomolecular Nuclear Magnetic Resonance Facility, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Tabitha A Peterson
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Jesse B Hopkins
- BioCAT, Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Michael E Shy
- Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
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41
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Seetaha S, Kamonsutthipaijit N, Yagi-Utsumi M, Seako Y, Yamaguchi T, Hannongbua S, Kato K, Choowongkomon K. Biophysical Characterization of p51 and p66 Monomers of HIV-1 Reverse Transcriptase with Their Inhibitors. Protein J 2023; 42:741-752. [PMID: 37728788 DOI: 10.1007/s10930-023-10156-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2023] [Indexed: 09/21/2023]
Abstract
Human immunodeficiency virus (HIV)-1 reverse transcriptase (HIV-1 RT) is responsible for the transcription of viral RNA genomes into DNA genomes and has become an important target for the treatment of acquired immune deficiency syndrome (AIDS). This study used biophysical techniques to characterize the HIV-1 RT structure, monomer forms, and the non-nucleoside reverse transcriptase inhibitors (NNRTIs) bound forms. Inactive p66W401A and p51W401A were selected as models to study the HIV-1 RT monomer structures. Nuclear magnetic resonance (NMR) spectroscopy revealed that the unliganded forms of p66W401A protein and p51W401A protein had similar conformation to each other in solution. The complexes of p66W401A or p51W401A with inhibitors showed similar conformations to p66 in the RT heterodimer bound to the NNRTIs. Furthermore, the results of paramagnetic relaxation enhancement (PRE)-assisted NMR revealed that the unliganded forms of the p66W401A and p51W401A conformations were different from the unliganded heterodimer, characterized by a greater distance between the fingers and thumb subdomains. Small-angle X-ray scattering (SAXS) experiments confirmed that p66W401A and p51W401A can bind with inhibitors, similar to the p66/p51 heterodimer. The findings of this study increase the structural knowledge base of HIV-1 RT monomers, which may be helpful in the future design of potent viral inhibitors.
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Affiliation(s)
- Supaphorn Seetaha
- KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Nuntaporn Kamonsutthipaijit
- Synchrotron Light Research Institute, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems, Okazaki, Aichi, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Yanaka Seako
- Exploratory Research Center on Life and Living Systems, Okazaki, Aichi, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Takumi Yamaguchi
- Exploratory Research Center on Life and Living Systems, Okazaki, Aichi, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems, Okazaki, Aichi, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Kiattawee Choowongkomon
- KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand.
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.
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42
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Raviv U, Asor R, Shemesh A, Ginsburg A, Ben-Nun T, Schilt Y, Levartovsky Y, Ringel I. Insight into structural biophysics from solution X-ray scattering. J Struct Biol 2023; 215:108029. [PMID: 37741561 DOI: 10.1016/j.jsb.2023.108029] [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: 04/29/2023] [Revised: 08/09/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.
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Affiliation(s)
- Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yaelle Schilt
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
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43
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Golub M, Pieper J. Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods. Molecules 2023; 28:7414. [PMID: 37959833 PMCID: PMC10650700 DOI: 10.3390/molecules28217414] [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: 09/30/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Utilized for gaining structural insights, small-angle neutron and X-ray scattering techniques (SANS and SAXS, respectively) enable an examination of biomolecules, including photosynthetic pigment-protein complexes, in solution at physiological temperatures. These methods can be seen as instrumental bridges between the high-resolution structural information achieved by crystallography or cryo-electron microscopy and functional explorations conducted in a solution state. The review starts with a comprehensive overview about the fundamental principles and applications of SANS and SAXS, with a particular focus on the recent advancements permitting to enhance the efficiency of these techniques in photosynthesis research. Among the recent developments discussed are: (i) the advent of novel modeling tools whereby a direct connection between SANS and SAXS data and high-resolution structures is created; (ii) the employment of selective deuteration, which is utilized to enhance spatial selectivity and contrast matching; (iii) the potential symbioses with molecular dynamics simulations; and (iv) the amalgamations with functional studies that are conducted to unearth structure-function relationships. Finally, reference is made to time-resolved SANS/SAXS experiments, which enable the monitoring of large-scale structural transformations of proteins in a real-time framework.
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Affiliation(s)
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald Str. 1, 50411 Tartu, Estonia;
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44
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Nakasone Y, Murakami H, Tokonami S, Oda T, Terazima M. Time-resolved study on signaling pathway of photoactivated adenylate cyclase and its nonlinear optical response. J Biol Chem 2023; 299:105285. [PMID: 37742920 PMCID: PMC10634658 DOI: 10.1016/j.jbc.2023.105285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
Photoactivated adenylate cyclases (PACs) are multidomain BLUF proteins that regulate the cellular levels of cAMP in a light-dependent manner. The signaling route and dynamics of PAC from Oscillatoria acuminata (OaPAC), which consists of a light sensor BLUF domain, an adenylate cyclase domain, and a connector helix (α3-helix), were studied by detecting conformational changes in the protein moiety. Although circular dichroism and small-angle X-ray scattering measurements did not show significant changes upon light illumination, the transient grating method successfully detected light-induced changes in the diffusion coefficient (diffusion-sensitive conformational change (DSCC)) of full-length OaPAC and the BLUF domain with the α3-helix. DSCC of full-length OaPAC was observed only when both protomers in a dimer were photoconverted. This light intensity dependence suggests that OaPAC is a cyclase with a nonlinear light intensity response. The enzymatic activity indeed nonlinearly depends on light intensity, that is, OaPAC is activated under strong light conditions. It was also found that both DSCC and enzymatic activity were suppressed by a mutation in the W90 residue, indicating the importance of the highly conserved Trp in many BLUF domains for the function. Based on these findings, a reaction scheme was proposed together with the reaction dynamics.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroto Murakami
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shunrou Tokonami
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Takashi Oda
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.
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45
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Ettich J, Wittich C, Moll JM, Behnke K, Floss DM, Reiners J, Christmann A, Lang PA, Smits SHJ, Kolmar H, Scheller J. Respiratory syncytial virus-approved mAb Palivizumab as ligand for anti-idiotype nanobody-based synthetic cytokine receptors. J Biol Chem 2023; 299:105270. [PMID: 37734558 PMCID: PMC10630626 DOI: 10.1016/j.jbc.2023.105270] [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: 04/26/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Synthetic cytokine receptors can modulate cellular functions based on an artificial ligand to avoid off-target and/or unspecific effects. However, ligands that can modulate receptor activity so far have not been used clinically because of unknown toxicity and immunity against the ligands. Here, we developed a fully synthetic cytokine/cytokine receptor pair based on the antigen-binding domain of the respiratory syncytial virus-approved mAb Palivizumab as a synthetic cytokine and a set of anti-idiotype nanobodies (AIPVHH) as synthetic receptors. Importantly, Palivizumab is neither cross-reactive with human proteins nor immunogenic. For the synthetic receptors, AIPVHH were fused to the activating interleukin-6 cytokine receptor gp130 and the apoptosis-inducing receptor Fas. We found that the synthetic cytokine receptor AIPVHHgp130 was efficiently activated by dimeric Palivizumab single-chain variable fragments. In summary, we created an in vitro nonimmunogenic full-synthetic cytokine/cytokine receptor pair as a proof of concept for future in vivo therapeutic strategies utilizing nonphysiological targets during immunotherapy.
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Affiliation(s)
- Julia Ettich
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Christoph Wittich
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jens M Moll
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany; PROvendis GmbH, Muelheim an der Ruhr, Germany
| | - Kristina Behnke
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Doreen M Floss
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jens Reiners
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Christmann
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Philipp A Lang
- Institute of Molecular Medicine II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Center for Structural Studies, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany; Centre of Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Jürgen Scheller
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
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46
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Blanchet CE, Round A, Mertens HDT, Ayyer K, Graewert M, Awel S, Franke D, Dörner K, Bajt S, Bean R, Custódio TF, de Wijn R, Juncheng E, Henkel A, Gruzinov A, Jeffries CM, Kim Y, Kirkwood H, Kloos M, Knoška J, Koliyadu J, Letrun R, Löw C, Makroczyova J, Mall A, Meijers R, Pena Murillo GE, Oberthür D, Round E, Seuring C, Sikorski M, Vagovic P, Valerio J, Wollweber T, Zhuang Y, Schulz J, Haas H, Chapman HN, Mancuso AP, Svergun D. Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS). Commun Biol 2023; 6:1057. [PMID: 37853181 PMCID: PMC10585004 DOI: 10.1038/s42003-023-05416-7] [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: 01/30/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
Free-electron lasers (FEL) are revolutionizing X-ray-based structural biology methods. While protein crystallography is already routinely performed at FELs, Small Angle X-ray Scattering (SAXS) studies of biological macromolecules are not as prevalent. SAXS allows the study of the shape and overall structure of proteins and nucleic acids in solution, in a quasi-native environment. In solution, chemical and biophysical parameters that have an influence on the structure and dynamics of molecules can be varied and their effect on conformational changes can be monitored in time-resolved XFEL and SAXS experiments. We report here the collection of scattering form factors of proteins in solution using FEL X-rays. The form factors correspond to the scattering signal of the protein ensemble alone; the scattering contributions from the solvent and the instrument are separately measured and accurately subtracted. The experiment was done using a liquid jet for sample delivery. These results pave the way for time-resolved studies and measurements from dilute samples, capitalizing on the intense and short FEL X-ray pulses.
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Affiliation(s)
- Clement E Blanchet
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Kartik Ayyer
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Saša Bajt
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - E Juncheng
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | | | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Christian Löw
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | | | - Abhishek Mall
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Rob Meijers
- Institute for Protein Innovation (IPI), 4 Blackfan Circle, Boston, MA, 02115, USA
| | - Gisel Esperanza Pena Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Ekaterina Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Patrik Vagovic
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Joana Valerio
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tamme Wollweber
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yulong Zhuang
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Dmitri Svergun
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany.
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47
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Cuesta-Hernández HN, Contreras J, Soriano-Maldonado P, Sánchez-Wandelmer J, Yeung W, Martín-Hurtado A, Muñoz IG, Kannan N, Llimargas M, Muñoz J, Plaza-Menacho I. An allosteric switch between the activation loop and a c-terminal palindromic phospho-motif controls c-Src function. Nat Commun 2023; 14:6548. [PMID: 37848415 PMCID: PMC10582172 DOI: 10.1038/s41467-023-41890-7] [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: 09/27/2022] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
Autophosphorylation controls the transition between discrete functional and conformational states in protein kinases, yet the structural and molecular determinants underlying this fundamental process remain unclear. Here we show that c-terminal Tyr 530 is a de facto c-Src autophosphorylation site with slow time-resolution kinetics and a strong intermolecular component. On the contrary, activation-loop Tyr 419 undergoes faster kinetics and a cis-to-trans phosphorylation switch that controls c-terminal Tyr 530 autophosphorylation, enzyme specificity, and strikingly, c-Src non-catalytic function as a substrate. In line with this, we visualize by X-ray crystallography a snapshot of Tyr 530 intermolecular autophosphorylation. In an asymmetric arrangement of both catalytic domains, a c-terminal palindromic phospho-motif flanking Tyr 530 on the substrate molecule engages the G-loop of the active kinase adopting a position ready for entry into the catalytic cleft. Perturbation of the phospho-motif accounts for c-Src dysfunction as indicated by viral and colorectal cancer (CRC)-associated c-terminal deleted variants. We show that c-terminal residues 531 to 536 are required for c-Src Tyr 530 autophosphorylation, and such a detrimental effect is caused by the substrate molecule inhibiting allosterically the active kinase. Our work reveals a crosstalk between the activation and c-terminal segments that control the allosteric interplay between substrate- and enzyme-acting kinases during autophosphorylation.
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Affiliation(s)
- Hipólito Nicolás Cuesta-Hernández
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Julia Contreras
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Pablo Soriano-Maldonado
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria (UFV), 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Jana Sánchez-Wandelmer
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Wayland Yeung
- Institute of Bioinformatics, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Ana Martín-Hurtado
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Inés G Muñoz
- Protein Crystallography Unit, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Natarajan Kannan
- Institute of Bioinformatics, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Marta Llimargas
- Institute of Molecular Biology of Barcelona (IMBB) CSIC, 08028, Barcelona, Spain
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, IIS Biocruces Bizkaia, Building Biocruces Bizkaia 1, 48903, Cruces, Bizkaia, Spain
| | - Iván Plaza-Menacho
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain.
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48
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Pierson E, De Pol F, Fillet M, Wouters J. A morpheein equilibrium regulates catalysis in phosphoserine phosphatase SerB2 from Mycobacterium tuberculosis. Commun Biol 2023; 6:1024. [PMID: 37817000 PMCID: PMC10564941 DOI: 10.1038/s42003-023-05402-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: 02/13/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
Mycobacterium tuberculosis phosphoserine phosphatase MtSerB2 is of interest as a new antituberculosis target due to its essential metabolic role in L-serine biosynthesis and effector functions in infected cells. Previous works indicated that MtSerB2 is regulated through an oligomeric transition induced by L-Ser that could serve as a basis for the design of selective allosteric inhibitors. However, the mechanism underlying this transition remains highly elusive due to the lack of experimental structural data. Here we describe a structural, biophysical, and enzymological characterisation of MtSerB2 oligomerisation in the presence and absence of L-Ser. We show that MtSerB2 coexists in dimeric, trimeric, and tetrameric forms of different activity levels interconverting through a conformationally flexible monomeric state, which is not observed in two near-identical mycobacterial orthologs. This morpheein behaviour exhibited by MtSerB2 lays the foundation for future allosteric drug discovery and provides a starting point to the understanding of its peculiar multifunctional moonlighting properties.
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Affiliation(s)
- Elise Pierson
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000, Namur, Belgium
| | - Florian De Pol
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000, Namur, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines (LAM), Center for Interdisciplinary Research on Medicines (CIRM), University of Liège (ULiège), 4000, Liège, Belgium
| | - Johan Wouters
- Laboratoire de Chimie Biologique Structurale (CBS), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000, Namur, Belgium.
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49
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Štih V, Amenitsch H, Plavec J, Podbevšek P. Spatial arrangement of functional domains in OxyS stress response sRNA. RNA (NEW YORK, N.Y.) 2023; 29:1520-1534. [PMID: 37380360 PMCID: PMC10578473 DOI: 10.1261/rna.079618.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/18/2023] [Indexed: 06/30/2023]
Abstract
Small noncoding RNAs are an important class of regulatory RNAs in bacteria, often regulating responses to changes in environmental conditions. OxyS is a 110 nt, stable, trans-encoded small RNA found in Escherichia coli and is induced by an increased concentration of hydrogen peroxide. OxyS has an important regulatory role in cell stress response, affecting the expression of multiple genes. In this work, we investigated the structure of OxyS and the interaction with fhlA mRNA using nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and unbiased molecular dynamics simulations. We determined the secondary structures of isolated stem-loops and confirmed their structural integrity in OxyS. Unexpectedly, stem-loop SL4 was identified in the region that was predicted to be unstructured. Three-dimensional models of OxyS demonstrate that OxyS adopts an extended structure with four solvent-exposed stem-loops, which are available for interaction with other RNAs and proteins. Furthermore, we provide evidence of base-pairing between OxyS and fhlA mRNA.
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Affiliation(s)
- Vesna Štih
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Peter Podbevšek
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
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50
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Vicente-Ruiz S, Armiñán A, Maso K, Gallon E, Zagorodko O, Movellan J, Rodríguez-Otormín F, Baues M, May JN, De Lorenzi F, Lammers T, Vicent MJ. Poly-l-glutamic acid modification modulates the bio-nano interface of a therapeutic anti-IGF-1R antibody in prostate cancer. Biomaterials 2023; 301:122280. [PMID: 37598440 DOI: 10.1016/j.biomaterials.2023.122280] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 08/04/2023] [Accepted: 08/12/2023] [Indexed: 08/22/2023]
Abstract
Modifying biological agents with polymers such as polyethylene glycol (PEG) has demonstrated clinical benefits; however, post-market surveillance of PEGylated derivatives has revealed PEG-associated toxicity issues, prompting the search for alternatives. We explore how conjugating a poly-l-glutamic acid (PGA) to an anti-insulin growth factor 1 receptor antibody (AVE1642) modulates the bio-nano interface and anti-tumor activity in preclinical prostate cancer models. Native and PGA-modified AVE1642 display similar anti-tumor activity in vitro; however, AVE1642 prompts IGF-1R internalization while PGA conjugation prompts higher affinity IGF-1R binding, thereby inhibiting IGF-1R internalization and altering cell trafficking. AVE1642 attenuates phosphoinositide 3-kinase signaling, while PGA-AVE1642 inhibits phosphoinositide 3-kinase and mitogen-activated protein kinase signaling. PGA conjugation also enhances AVE1642's anti-tumor activity in an orthotopic prostate cancer mouse model, while PGA-AVE1642 induces more significant suppression of cancer cell proliferation/angiogenesis than AVE1642. These findings demonstrate that PGA conjugation modulates an antibody's bio-nano interface, mechanism of action, and therapeutic activity.
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Affiliation(s)
- Sonia Vicente-Ruiz
- Polymer Therapeutics Laboratory, Prince Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Ana Armiñán
- Polymer Therapeutics Laboratory, Prince Felipe Research Center (CIPF), 46012, Valencia, Spain; CIBERONC, Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Katia Maso
- Polymer Therapeutics Laboratory, Prince Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Elena Gallon
- Polymer Therapeutics Laboratory, Prince Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Oleksandr Zagorodko
- Polymer Therapeutics Laboratory, Prince Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Julie Movellan
- Polymer Therapeutics Laboratory, Prince Felipe Research Center (CIPF), 46012, Valencia, Spain; Current address: CIDETEC, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Gipuzkoa, Donostia-San Sebastián, Spain
| | | | - Maike Baues
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular Imaging (ExMI), RWTH Aachen University Clinic, Aachen, 52074, Germany
| | - Jan-Niklas May
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular Imaging (ExMI), RWTH Aachen University Clinic, Aachen, 52074, Germany
| | - Federica De Lorenzi
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular Imaging (ExMI), RWTH Aachen University Clinic, Aachen, 52074, Germany
| | - Twan Lammers
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular Imaging (ExMI), RWTH Aachen University Clinic, Aachen, 52074, Germany
| | - María J Vicent
- Polymer Therapeutics Laboratory, Prince Felipe Research Center (CIPF), 46012, Valencia, Spain; CIBERONC, Instituto de Salud Carlos III, 28029, Madrid, Spain.
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