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Zarubin M, Murugova T, Ryzhykau Y, Ivankov O, Uversky VN, Kravchenko E. Structural study of the intrinsically disordered tardigrade damage suppressor protein (Dsup) and its complex with DNA. Sci Rep 2024; 14:22910. [PMID: 39358423 DOI: 10.1038/s41598-024-74335-2] [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: 03/06/2024] [Accepted: 09/25/2024] [Indexed: 10/04/2024] Open
Abstract
Studies of proteins, found in one of the most stress-resistant animals tardigrade Ramazzottius varieornatus, aim to reveal molecular principles of extreme tolerance to various types of stress and developing applications based on them for medicine, biotechnology, pharmacy, and space research. Tardigrade DNA/RNA-binding damage suppressor protein (Dsup) reduces DNA damage caused by reactive oxygen spices (ROS) produced upon irradiation and oxidative stresses in Dsup-expressing transgenic organisms. This work is focused on the determination of structural features of Dsup protein and Dsup-DNA complex, which refines details of protective mechanism. For the first time, intrinsically disordered nature of Dsup protein with highly flexible structure was experimentally proven and characterized by the combination of small angle X-ray scattering (SAXS) technique, circular dichroism spectroscopy, and computational methods. Low resolution models of Dsup protein and an ensemble of conformations were presented. In addition, we have shown that Dsup forms fuzzy complex with DNA.
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Affiliation(s)
- Mikhail Zarubin
- Dzhelepov Laboratory of Nuclear Problems, Joint Institute for Nuclear Research, Dubna, Russia
| | - Tatiana Murugova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Yury Ryzhykau
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleksandr Ivankov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, USA
| | - Elena Kravchenko
- Dzhelepov Laboratory of Nuclear Problems, Joint Institute for Nuclear Research, Dubna, Russia.
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2
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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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3
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Mohammed ASA, Soloviov D, Jeffries CM. Perspectives on solution-based small angle X-ray scattering for protein and biological macromolecule structural biology. Phys Chem Chem Phys 2024. [PMID: 39323216 DOI: 10.1039/d4cp02001d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Small-angle X-ray scattering (SAXS) is used to extract structural information from a wide variety of non-crystalline samples in different fields (e.g., materials science, physics, chemistry, and biology). This review provides an overview of SAXS as applied to structural biology, specifically for proteins and other biomacromolecules in solution with an emphasis on extracting key structural parameters and the interpretation of SAXS data using a diverse array of techniques. These techniques cover aspects of building and assessing models to describe data measured from monodispersed and ideal dilute samples through to more complicated structurally polydisperse systems. Ab initio modelling, rigid body modelling as well as normal-mode analysis, molecular dynamics, mixed component and structural ensemble modelling are discussed. Dealing with polydispersity both physically in terms of component separation as well as approaching the analysis and modelling of data of mixtures and evolving systems are described, including methods for data decomposition such as single value decomposition/principle component analysis and evolving factor analysis. This review aims to highlight that solution SAXS, with the cohort of developments in data analysis and modelling, is well positioned to build upon the traditional 'single particle view' foundation of structural biology to take the field into new areas for interpreting the structures of proteins and biomacromolecules as population-states and dynamic structural systems.
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Affiliation(s)
- Ahmed S A Mohammed
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, co/DESY, Notkestrasse 85, D-22607 Hamburg, Germany.
- Physics Department, Faculty of Science, Fayoum University, 63514 Fayoum, Egypt
- Department of Biomedical Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Dmytro Soloviov
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, co/DESY, Notkestrasse 85, D-22607 Hamburg, Germany.
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, co/DESY, Notkestrasse 85, D-22607 Hamburg, Germany.
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4
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Koduru T, Hantman N, Peters EV, Jaworek MW, Wang J, Zhang S, McCallum SA, Gillilan RE, Fossat MJ, Roumestand C, Sagar A, Winter R, Bernadó P, Cherfils J, Royer CA. A molten globule ensemble primes Arf1-GDP for the nucleotide switch. Proc Natl Acad Sci U S A 2024; 121:e2413100121. [PMID: 39292747 PMCID: PMC11441498 DOI: 10.1073/pnas.2413100121] [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: 07/03/2024] [Accepted: 07/31/2024] [Indexed: 09/20/2024] Open
Abstract
The adenosine di-phosphate (ADP) ribosylation factor (Arf) small guanosine tri-phosphate (GTP)ases function as molecular switches to activate signaling cascades that control membrane organization in eukaryotic cells. In Arf1, the GDP/GTP switch does not occur spontaneously but requires guanine nucleotide exchange factors (GEFs) and membranes. Exchange involves massive conformational changes, including disruption of the core β-sheet. The mechanisms by which this energetically costly switch occurs remain to be elucidated. To probe the switch mechanism, we coupled pressure perturbation with nuclear magnetic resonance (NMR), Fourier Transform infra-red spectroscopy (FTIR), small-angle X-ray scattering (SAXS), fluorescence, and computation. Pressure induced the formation of a classical molten globule (MG) ensemble. Pressure also favored the GDP to GTP transition, providing strong support for the notion that the MG ensemble plays a functional role in the nucleotide switch. We propose that the MG ensemble allows for switching without the requirement for complete unfolding and may be recognized by GEFs. An MG-based switching mechanism could constitute a pervasive feature in Arfs and Arf-like GTPases, and more generally, the evolutionarily related (Ras-like small GTPases) Rags and Gα GTPases.
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Affiliation(s)
- Tejaswi Koduru
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Noam Hantman
- Graduate Program in Biochemistry and Biophysics, School of Science, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Edgar V. Peters
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Michel W. Jaworek
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, Technical University of Dortmund University, DortmundD-44227, Germany
| | - Jinqiu Wang
- Graduate Program in Biochemistry and Biophysics, School of Science, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Siwen Zhang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Scott A. McCallum
- Shirley Ann Jackson, PhD. Center for Biotechnology and Interdisciplinary Science, Rensselaer Polytechnic Institute, Troy, NY12180
| | | | - Martin J. Fossat
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetic, FreiburgD-79108, Germany
| | - Christian Roumestand
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier34090, France
| | - Amin Sagar
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier34090, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, Technical University of Dortmund University, DortmundD-44227, Germany
| | - Pau Bernadó
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier34090, France
| | - Jacqueline Cherfils
- Université Paris-Saclay, Ecole Normale Supérieure Paris-Saclay, CNRS, Gif-sur-Yvette91190, France
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY12180
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5
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Wang T, Coshic K, Badiee M, McDonald MR, Aksimentiev A, Pollack L, Leung AKL. Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose). Nat Commun 2024; 15:7901. [PMID: 39256374 PMCID: PMC11387394 DOI: 10.1038/s41467-024-51972-9] [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: 02/14/2024] [Accepted: 08/22/2024] [Indexed: 09/12/2024] Open
Abstract
Poly(ADP-ribose) (PAR), a non-canonical nucleic acid, is essential for DNA/RNA metabolism and protein condensation, and its dysregulation is linked to cancer and neurodegeneration. However, key structural insights into PAR's functions remain largely uncharacterized, hindered by the challenges in synthesizing and characterizing PAR, which are attributed to its length heterogeneity. A central issue is how PAR, comprised solely of ADP-ribose units, attains specificity in its binding and condensing proteins based on chain length. Here, we integrate molecular dynamics simulations with small-angle X-ray scattering to analyze PAR structures. We identify diverse structural ensembles of PAR that fall into distinct subclasses and reveal distinct compaction of two different lengths of PAR upon the addition of small amounts of Mg2+ ions. Unlike PAR15, PAR22 forms ADP-ribose bundles via local intramolecular coil-to-globule transitions. Understanding these length-dependent structural changes could be central to deciphering the specific biological functions of PAR.
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Affiliation(s)
- Tong Wang
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA
| | - Kush Coshic
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana Champaign, Urbana, IL, 61801, USA
| | - Mohsen Badiee
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Maranda R McDonald
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
- Chemistry-Biology Interface Graduate Program, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana Champaign, Urbana, IL, 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana Champaign, Urbana, IL, 61801, USA.
- Department of Physics, University of Illinois Urbana Champaign, Urbana, IL, 61801, USA.
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA.
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Chemistry-Biology Interface Graduate Program, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
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6
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Monsen RC, Sabo TM, Gray R, Hopkins JB, Chaires JB. Early Events in G-quadruplex Folding Captured by Time-Resolved Small-Angle X-Ray Scattering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.05.611539. [PMID: 39282441 PMCID: PMC11398465 DOI: 10.1101/2024.09.05.611539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Time-resolved small-angle X-ray experiments (TR-SAXS) are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in G4 folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 20.6 to 12.6 Å. The collapse is monophasic and is complete in less than 600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, to show that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method (EOM) analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.
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Affiliation(s)
- Robert C Monsen
- Department of Medicine, UofL Health Brown Cancer Center, University of Louisville, Louisville KY, 505 S Hancock St, Louisville, KY 40202
| | - T Michael Sabo
- Department of Medicine, UofL Health Brown Cancer Center, University of Louisville, Louisville KY, 505 S Hancock St, Louisville, KY 40202
| | - Robert Gray
- Department of Medicine, UofL Health Brown Cancer Center, University of Louisville, Louisville KY, 505 S Hancock St, Louisville, KY 40202
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT) Department of Physics, Illinois Institute of Technology, Chicago, IL 60616
| | - Jonathan B Chaires
- Department of Medicine, UofL Health Brown Cancer Center, University of Louisville, Louisville KY, 505 S Hancock St, Louisville, KY 40202
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7
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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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8
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Cortone G, Graewert MA, Kanade M, Longo A, Hegde R, González‐Magaña A, Chaves‐Arquero B, Blanco FJ, Napolitano LMR, Onesti S. Structural and biochemical characterization of the C-terminal region of the human RTEL1 helicase. Protein Sci 2024; 33:e5093. [PMID: 39180489 PMCID: PMC11344278 DOI: 10.1002/pro.5093] [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: 03/14/2024] [Revised: 06/03/2024] [Accepted: 06/16/2024] [Indexed: 08/26/2024]
Abstract
RTEL1 is an essential DNA helicase which plays an important role in various aspects of genome stability, from telomere metabolism to DNA replication, repair and recombination. RTEL1 has been implicated in a number of genetic diseases and cancer development, including glioma, breast, lung and gastrointestinal tumors. RTEL1 is a FeS helicase but, in addition to the helicase core, it comprises a long C-terminal region which includes a number of folded domains connected by intrinsically disordered loops and mediates RTEL1 interaction with factors involved in pivotal cellular pathways. However, information on the architecture and the function of this region is still limited. We expressed and purified a variety of fragments encompassing the folded domains and the unstructured regions. We determined the crystal structure of the second repeat, confirming that it has a fold similar to the harmonin homology domains. SAXS data provide low-resolution information on all the fragments and suggest that the presence of the RING domain affects the overall architecture of the C-terminal region, making the structure significantly more compact. NMR data provide experimental information on the interaction between PCNA and the RTEL1 C-terminal region, revealing a putative low-affinity additional site of interaction. A biochemical analysis shows that the C-terminal region, in addition to a preference for telomeric RNA and DNA G-quadruplexes, has a high affinity for R-loops and D-loops, consistent with the role played by the RTEL1 helicase in homologous recombination, telomere maintenance and preventing replication-transcription conflicts. We further dissected the contribution of each domain in binding different substrates.
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Affiliation(s)
- Giuseppe Cortone
- Structural Biology LaboratoryElettra‐Sincrotrone TriesteTriesteItaly
- International School for Advanced Studies (SISSA)TriesteItaly
| | | | - Manil Kanade
- Structural Biology LaboratoryElettra‐Sincrotrone TriesteTriesteItaly
| | - Antonio Longo
- Structural Biology LaboratoryElettra‐Sincrotrone TriesteTriesteItaly
- Department of ChemistryUniversità degli Studi di TriesteTriesteItaly
| | - Raghurama Hegde
- Structural Biology LaboratoryElettra‐Sincrotrone TriesteTriesteItaly
| | - Amaia González‐Magaña
- Instituto Biofisika and Departamento de Bioquímica y Biología Molecular (CSIC, UPV/EHU)University of the Basque CountryLeioaSpain
| | | | | | | | - Silvia Onesti
- Structural Biology LaboratoryElettra‐Sincrotrone TriesteTriesteItaly
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9
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Sun X, Yu Y, Saleh ASM, Akhtar KH, Li W, Zhang D, Wang Z. Conformational changes induced by selected flavor compounds from spices regulate the binding ability of myofibrillar proteins to aldehyde compounds. Food Chem 2024; 451:139455. [PMID: 38678659 DOI: 10.1016/j.foodchem.2024.139455] [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: 01/08/2024] [Revised: 03/08/2024] [Accepted: 04/21/2024] [Indexed: 05/01/2024]
Abstract
Interactions among flavor compounds from spices (FCS) and myofibrillar proteins (MP) were investigated. Fluorescence and Fourier transform infrared spectroscopy showed that hydrogen bonding and hydrophobic interactions were the main binding forces between FCS and MP. The FCS increased the particle size and SH content of MP and caused a reduction of zeta potential from -5.23 to -6.50 mV. Furthermore, FCS could modify the binding ability of MP and aldehydes. Eugenol reduced the ability of MP to bond with aldehydes by 22.70-47.87 %. Molecular dynamics simulations demonstrated that eugenol may combat nonanal to attain binding site of amino acid residue (PHE165) and induce protein conformational changes. Electrostatic interactions and van der Waals forces within myosin-nonanal may be disrupted by these alterations, which could reduce stability of complex and cause release of nonanal. This study could provide new insights into regulating the ability of proteins to release and hold flavors.
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Affiliation(s)
- Xiangxiang Sun
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China; College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Yumei Yu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Ahmed S M Saleh
- Department of Food Science and Technology, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
| | - Kumayl Hassan Akhtar
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Wenhao Li
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Zhenyu Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
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10
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Nelson AD, Wang L, Laffey KG, Becher LRE, Parks CA, Hoffmann MM, Galeano BK, Mangalam A, Teixeiro E, White TA, Schrum AG, Cannon JF, Gil D. Rigid crosslinking of the CD3 complex leads to superior T cell stimulation. Front Immunol 2024; 15:1434463. [PMID: 39281668 PMCID: PMC11392757 DOI: 10.3389/fimmu.2024.1434463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/07/2024] [Indexed: 09/18/2024] Open
Abstract
Functionally bivalent non-covalent Fab dimers (Bi-Fabs) specific for the TCR/CD3 complex promote CD3 signaling on T cells. While comparing functional responses to stimulation with Bi-Fab, F(ab')2 or mAb specific for the same CD3 epitope, we observed fratricide requiring anti-CD3 bridging of adjacent T cells. Surprisingly, anti-CD3 Bi-Fab ranked first in fratricide potency, followed by anti-CD3 F(ab')2 and anti-CD3 mAb. Low resolution structural studies revealed anti-CD3 Bi-Fabs and F(ab')2 adopt similar global shapes with CD3-binding sites oriented outward. However, under molecular dynamic simulations, anti-CD3 Bi-Fabs crosslinked CD3 more rigidly than F(ab')2. Furthermore, molecular modelling of Bi-Fab and F(ab')2 binding to CD3 predicted crosslinking of T cell antigen receptors located in opposing plasma membrane domains, a feature fitting with T cell fratricide observed. Thus, increasing rigidity of Fab-CD3 crosslinking between opposing effector-target pairs may result in stronger T cell effector function. These findings could guide improving clinical performance of bi-specific anti-CD3 drugs.
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Affiliation(s)
- Alfreda D Nelson
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
| | - Liangyu Wang
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Kimberly G Laffey
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Laura R E Becher
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Christopher A Parks
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Michele M Hoffmann
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Belinda K Galeano
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Ashutosh Mangalam
- Department of Pathology, University of Iowa, Iowa City, IA, United States
| | - Emma Teixeiro
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Tommi A White
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Adam G Schrum
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- Department of Biomedical, Biological and Medical Engineering, College of Engineering, University of Missouri, Columbia, MO, United States
| | - John F Cannon
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Diana Gil
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- Department of Biomedical, Biological and Medical Engineering, College of Engineering, University of Missouri, Columbia, MO, United States
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11
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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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12
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Pesce G, Gondelaud F, Ptchelkine D, Bignon C, Fourquet P, Longhi S. Dissecting Henipavirus W proteins conformational and fibrillation properties: contribution of their N- and C-terminal constituent domains. FEBS J 2024. [PMID: 39180270 DOI: 10.1111/febs.17239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/07/2024] [Accepted: 07/23/2024] [Indexed: 08/26/2024]
Abstract
The Nipah and Hendra viruses are severe human pathogens. In addition to the P protein, their P gene also encodes the V and W proteins that share with P their N-terminal intrinsically disordered domain (NTD) and possess distinct C-terminal domains (CTDs). The W protein is a key player in the evasion of the host innate immune response. We previously showed that the W proteins are intrinsically disordered and can form amyloid-like fibrils. However, structural information on W CTD (CTDW) and its potential contribution to the fibrillation process is lacking. In this study, we demonstrate that CTDWS are disordered and able to form dimers mediated by disulfide bridges. We also show that the NTD and the CTDW interact with each other and that this interaction triggers both a gain of secondary structure and a chain compaction within the NTD. Finally, despite the lack of intrinsic fibrillogenic properties, we show that the CTDW favors the formation of fibrils by the NTD both in cis and in trans. Altogether, the results herein presented shed light on the molecular mechanisms underlying Henipavirus pathogenesis and may thus contribute to the development of targeted therapies.
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Affiliation(s)
- Giulia Pesce
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS) and Aix Marseille University, France
| | - Frank Gondelaud
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS) and Aix Marseille University, France
| | - Denis Ptchelkine
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS) and Aix Marseille University, France
| | - Christophe Bignon
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS) and Aix Marseille University, France
| | - Patrick Fourquet
- INSERM, Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS), Marseille Protéomique, Institut Paoli-Calmettes, Aix Marseille University, France
| | - Sonia Longhi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS) and Aix Marseille University, France
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13
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Mazzone F, Hoeppner A, Reiners J, Gertzen CG, Applegate V, Abdullaziz MA, Gottstein J, Degrandi D, Wesemann M, Kurz T, Smits SH, Pfeffer K. 1-Deoxy-d-xylulose 5-phosphate reductoisomerase as target for anti Toxoplasma gondii agents: crystal structure, biochemical characterization and biological evaluation of inhibitors. Biochem J 2024; 481:1075-1096. [PMID: 39105673 PMCID: PMC11346426 DOI: 10.1042/bcj20240110] [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: 03/08/2024] [Revised: 07/27/2024] [Accepted: 08/06/2024] [Indexed: 08/07/2024]
Abstract
Toxoplasma gondii is a widely distributed apicomplexan parasite causing toxoplasmosis, a critical health issue for immunocompromised individuals and for congenitally infected foetuses. Current treatment options are limited in number and associated with severe side effects. Thus, novel anti-toxoplasma agents need to be identified and developed. 1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) is considered the rate-limiting enzyme in the non-mevalonate pathway for the biosynthesis of the isoprenoid precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate in the parasite, and has been previously investigated for its key role as a novel drug target in some species, encompassing Plasmodia, Mycobacteria and Escherichia coli. In this study, we present the first crystal structure of T. gondii DXR (TgDXR) in a tertiary complex with the inhibitor fosmidomycin and the cofactor NADPH in dimeric conformation at 2.5 Å resolution revealing the inhibitor binding mode. In addition, we biologically characterize reverse α-phenyl-β-thia and β-oxa fosmidomycin analogues and show that some derivatives are strong inhibitors of TgDXR which also, in contrast with fosmidomycin, inhibit the growth of T. gondii in vitro. Here, ((3,4-dichlorophenyl)((2-(hydroxy(methyl)amino)-2-oxoethyl)thio)methyl)phosphonic acid was identified as the most potent anti T. gondii compound. These findings will enable the future design and development of more potent anti-toxoplasma DXR inhibitors.
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Affiliation(s)
- Flaminia Mazzone
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, Düsseldorf, Germany
- University Hospital Düsseldorf, Düsseldorf, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Jens Reiners
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Christoph G.W. Gertzen
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Violetta Applegate
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Mona A. Abdullaziz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
- National Research Centre (NRC), Dokki, Cairo, Egypt
| | - Julia Gottstein
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Degrandi
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, Düsseldorf, Germany
- University Hospital Düsseldorf, Düsseldorf, Germany
| | - Martina Wesemann
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Thomas Kurz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Sander H.J. Smits
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, Düsseldorf, Germany
- University Hospital Düsseldorf, Düsseldorf, Germany
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14
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Aupič J, Pokorná P, Ruthstein S, Magistrato A. Predicting Conformational Ensembles of Intrinsically Disordered Proteins: From Molecular Dynamics to Machine Learning. J Phys Chem Lett 2024; 15:8177-8186. [PMID: 39093570 DOI: 10.1021/acs.jpclett.4c01544] [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: 08/04/2024]
Abstract
Intrinsically disordered proteins and regions (IDP/IDRs) are ubiquitous across all domains of life. Characterized by a lack of a stable tertiary structure, IDP/IDRs populate a diverse set of transiently formed structural states that can promiscuously adapt upon binding with specific interaction partners and/or certain alterations in environmental conditions. This malleability is foundational for their role as tunable interaction hubs in core cellular processes such as signaling, transcription, and translation. Tracing the conformational ensemble of an IDP/IDR and its perturbation in response to regulatory cues is thus paramount for illuminating its function. However, the conformational heterogeneity of IDP/IDRs poses several challenges. Here, we review experimental and computational methods devised to disentangle the conformational landscape of IDP/IDRs, highlighting recent computational advances that permit proteome-wide scans of IDP/IDRs conformations. We briefly evaluate selected computational methods using the disordered N-terminal of the human copper transporter 1 as a test case and outline further challenges in IDP/IDRs ensemble prediction.
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Affiliation(s)
- Jana Aupič
- CNR-IOM at International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Pavlína Pokorná
- CNR-IOM at International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences and the Institute for Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Alessandra Magistrato
- CNR-IOM at International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
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15
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Balboni B, Marotta R, Rinaldi F, Milordini G, Varignani G, Girotto S, Cavalli A. An integrative structural study of the human full-length RAD52 at 2.2 Å resolution. Commun Biol 2024; 7:956. [PMID: 39112549 PMCID: PMC11306251 DOI: 10.1038/s42003-024-06644-1] [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: 02/11/2024] [Accepted: 07/27/2024] [Indexed: 08/10/2024] Open
Abstract
Human RAD52 (RAD52) is a DNA-binding protein involved in many DNA repair mechanisms and genomic stability maintenance. In the last few years, this protein was discovered to be a promising novel pharmacological target for anticancer strategies. Although the interest in RAD52 has exponentially grown in the previous decade, most information about its structure and mechanism still needs to be elucidated. Here, we report the 2.2 Å resolution cryo-EM reconstruction of the full-length RAD52 (FL-RAD52) protein. This allows us to describe the hydration shell of the N-terminal region of FL-RAD52, which is structured in an undecamer ring. Water molecules coordinate with protein residues to promote stabilization inside and among the protomers and within the inner DNA binding cleft to drive protein-DNA recognition. Additionally, through a multidisciplinary approach involving SEC-SAXS and computational methods, we comprehensively describe the highly flexible and dynamic organization of the C-terminal portion of FL-RAD52. This work discloses unprecedented structural details on the FL-RAD52, which will be critical for characterizing its mechanism of action and inhibitor development, particularly in the context of novel approaches to synthetic lethality and anticancer drug discovery.
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Affiliation(s)
- Beatrice Balboni
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Roberto Marotta
- Electron Microscopy Facility (EMF), Istituto Italiano di Tecnologia, Genoa, Italy
| | - Francesco Rinaldi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Milordini
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Giulia Varignani
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefania Girotto
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy.
- Structural Biophysics Facility, Istituto Italiano di Tecnologia, Genoa, Italy.
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Genoa, Italy.
- CECAM, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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16
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Ravala SK, Adame-Garcia SR, Li S, Chen CL, Cianfrocco MA, Silvio Gutkind J, Cash JN, Tesmer JJG. Structural and dynamic changes in P-Rex1 upon activation by PIP 3 and inhibition by IP 4. eLife 2024; 12:RP92822. [PMID: 39082940 PMCID: PMC11290822 DOI: 10.7554/elife.92822] [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] [Indexed: 08/02/2024] Open
Abstract
PIP3-dependent Rac exchanger 1 (P-Rex1) is abundantly expressed in neutrophils and plays central roles in chemotaxis and cancer metastasis by serving as a guanine-nucleotide exchange factor (GEF) for Rac. The enzyme is synergistically activated by PIP3 and heterotrimeric Gβγ subunits, but mechanistic details remain poorly understood. While investigating the regulation of P-Rex1 by PIP3, we discovered that Ins(1,3,4,5)P4 (IP4) inhibits P-Rex1 activity and induces large decreases in backbone dynamics in diverse regions of the protein. Cryo-electron microscopy analysis of the P-Rex1·IP4 complex revealed a conformation wherein the pleckstrin homology (PH) domain occludes the active site of the Dbl homology (DH) domain. This configuration is stabilized by interactions between the first DEP domain (DEP1) and the DH domain and between the PH domain and a 4-helix bundle (4HB) subdomain that extends from the C-terminal domain of P-Rex1. Disruption of the DH-DEP1 interface in a DH/PH-DEP1 fragment enhanced activity and led to a more extended conformation in solution, whereas mutations that constrain the occluded conformation led to decreased GEF activity. Variants of full-length P-Rex1 in which the DH-DEP1 and PH-4HB interfaces were disturbed exhibited enhanced activity during chemokine-induced cell migration, confirming that the observed structure represents the autoinhibited state in living cells. Interactions with PIP3-containing liposomes led to disruption of these interfaces and increased dynamics protein-wide. Our results further suggest that inositol phosphates such as IP4 help to inhibit basal P-Rex1 activity in neutrophils, similar to their inhibitory effects on phosphatidylinositol-3-kinase.
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Affiliation(s)
- Sandeep K Ravala
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue UniversityWest LafayetteUnited States
| | - Sendi Rafael Adame-Garcia
- Department of Pharmacology and Moores Cancer Center, University of California, San DiegoSan DiegoUnited States
| | - Sheng Li
- Department of Medicine, University of California, San DiegoLa JollaUnited States
| | - Chun-Liang Chen
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue UniversityWest LafayetteUnited States
| | - Michael A Cianfrocco
- Department of Biological Chemistry, University of MichiganAnn ArborUnited States
| | - J Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San DiegoSan DiegoUnited States
| | - Jennifer N Cash
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - John JG Tesmer
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue UniversityWest LafayetteUnited States
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17
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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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18
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Anila MM, Rogowski P, Różycki B. Scrutinising the Conformational Ensemble of the Intrinsically Mixed-Folded Protein Galectin-3. Molecules 2024; 29:2768. [PMID: 38930833 PMCID: PMC11207097 DOI: 10.3390/molecules29122768] [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: 04/26/2024] [Revised: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Galectin-3 is a protein involved in many intra- and extra-cellular processes. It has been identified as a diagnostic or prognostic biomarker for certain types of heart disease, kidney disease and cancer. Galectin-3 comprises a carbohydrate recognition domain (CRD) and an N-terminal domain (NTD), which is unstructured and contains eight collagen-like Pro-Gly-rich tandem repeats. While the structure of the CRD has been solved using protein crystallography, current knowledge about conformations of full-length galectin-3 is limited. To fill in this knowledge gap, we performed molecular dynamics (MD) simulations of full-length galectin-3. We systematically re-scaled the solute-solvent interactions in the Martini 3 force field to obtain the best possible agreement between available data from SAXS experiments and the ensemble of conformations generated in the MD simulations. The simulation conformations were found to be very diverse, as reflected, e.g., by (i) large fluctuations in the radius of gyration, ranging from about 2 to 5 nm, and (ii) multiple transient contacts made by amino acid residues in the NTD. Consistent with evidence from NMR experiments, contacts between the CRD and NTD were observed to not involve the carbohydrate-binding site on the CRD surface. Contacts within the NTD were found to be made most frequently by aromatic residues. Formation of fuzzy complexes with unspecific stoichiometry was observed to be mediated mostly by the NTD. Taken together, we offer a detailed picture of the conformational ensemble of full-length galectin-3, which will be important for explaining the biological functions of this protein at the molecular level.
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Affiliation(s)
| | | | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland; (M.M.A.); (P.R.)
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19
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Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Baczynska M, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SBM, Kelly G, Lorenz CD, Fornili A, Cianciotto NP, Garnett JA. The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans. Nat Commun 2024; 15:4912. [PMID: 38851738 PMCID: PMC11162425 DOI: 10.1038/s41467-024-49255-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual trimer arrangement with a positively charged external surface and negatively charged solvent exposed internal cavity. Through molecular dynamics simulations, we show how the glycosaminoglycan chondroitin-4-sulphate associates with the Lcl-CTD surface via distinct binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate-binding mechanism.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Anna Katarina Antonovic
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ian E McIntire
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Huaixin Zheng
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Maria Baczynska
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Carlton O Adams
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Theo Portlock
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Katherine Richardson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rosie Shaw
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Alain Oregioni
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Giulia Mastroianni
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sara B-M Whittaker
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Christian D Lorenz
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Arianna Fornili
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK.
| | - Nicholas P Cianciotto
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
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20
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Kyriukha Y, Watkins MB, Redington JM, Dastvan R, Uversky VN, Hopkins JB, Pozzi N, Korolev S. The strand exchange domain of tumor suppressor PALB2 is intrinsically disordered and promotes oligomerization-dependent DNA compaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.01.543259. [PMID: 37333393 PMCID: PMC10274692 DOI: 10.1101/2023.06.01.543259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The Partner and Localizer of BRCA2 (PALB2) is a scaffold protein that links BRCA1 with BRCA2 to initiate homologous recombination (HR). PALB2 interaction with DNA strongly enhances HR efficiency in cells. The PALB2 DNA-binding domain (PALB2-DBD) supports strand exchange, a complex multistep reaction conducted by only a few proteins such as RecA-like recombinases and Rad52. Using bioinformatics analysis, small-angle X-ray scattering, circular dichroism, and electron paramagnetic spectroscopy, we determined that PALB2-DBD is an intrinsically disordered region (IDR) forming compact molten globule-like dimer. IDRs contribute to oligomerization synergistically with the coiled-coil interaction. Using confocal single-molecule FRET we demonstrated that PALB2-DBD compacts single-stranded DNA even in the absence of DNA secondary structures. The compaction is bimodal, oligomerization-dependent, and is driven by IDRs, suggesting a novel strand exchange mechanism. Intrinsically disordered proteins (IDPs) are prevalent in the human proteome. Novel DNA binding properties of PALB2-DBD and the complexity of strand exchange mechanism significantly expands the functional repertoire of IDPs. Multivalent interactions and bioinformatics analysis suggest that PALB2 function is likely to depend on formation of protein-nucleic acids condensates. Similar intrinsically disordered DBDs may use chaperone-like mechanism to aid formation and resolution of DNA and RNA multichain intermediates during DNA replication, repair and recombination.
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Affiliation(s)
- Yevhenii Kyriukha
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Maxwell B Watkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL
| | - Jennifer M Redington
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Reza Dastvan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
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21
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Zühlke MK, Ficko-Blean E, Bartosik D, Terrapon N, Jeudy A, Jam M, Wang F, Welsch N, Dürwald A, Martin LT, Larocque R, Jouanneau D, Eisenack T, Thomas F, Trautwein-Schult A, Teeling H, Becher D, Schweder T, Czjzek M. Unveiling the role of novel carbohydrate-binding modules in laminarin interaction of multimodular proteins from marine Bacteroidota during phytoplankton blooms. Environ Microbiol 2024; 26:e16624. [PMID: 38757353 DOI: 10.1111/1462-2920.16624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Laminarin, a β(1,3)-glucan, serves as a storage polysaccharide in marine microalgae such as diatoms. Its abundance, water solubility and simple structure make it an appealing substrate for marine bacteria. Consequently, many marine bacteria have evolved strategies to scavenge and decompose laminarin, employing carbohydrate-binding modules (CBMs) as crucial components. In this study, we characterized two previously unassigned domains as laminarin-binding CBMs in multimodular proteins from the marine bacterium Christiangramia forsetii KT0803T, thereby introducing the new laminarin-binding CBM families CBM102 and CBM103. We identified four CBM102s in a surface glycan-binding protein (SGBP) and a single CBM103 linked to a glycoside hydrolase module from family 16 (GH16_3). Our analysis revealed that both modular proteins have an elongated shape, with GH16_3 exhibiting greater flexibility than SGBP. This flexibility may aid in the recognition and/or degradation of laminarin, while the constraints in SGBP could facilitate the docking of laminarin onto the bacterial surface. Exploration of bacterial metagenome-assembled genomes (MAGs) from phytoplankton blooms in the North Sea showed that both laminarin-binding CBM families are widespread among marine Bacteroidota. The high protein abundance of CBM102- and CBM103-containing proteins during phytoplankton blooms further emphasizes their significance in marine laminarin utilization.
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Affiliation(s)
- Marie-Katherin Zühlke
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Elizabeth Ficko-Blean
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Daniel Bartosik
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université (AMU, UMR7257), CNRS, Marseille, France
| | - Alexandra Jeudy
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Murielle Jam
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Fengqing Wang
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Norma Welsch
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Alexandra Dürwald
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Helmholtz Institute for One Health, Helmholtz Centre for Infection Research HZI, Greifswald, Germany
| | - Laura Torres Martin
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - Robert Larocque
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Diane Jouanneau
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Tom Eisenack
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - François Thomas
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
| | - Anke Trautwein-Schult
- Microbial Proteomics, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Mirjam Czjzek
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Roscoff, France
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22
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Ravala SK, Adame-Garcia SR, Li S, Chen CL, Cianfrocco MA, Gutkind JS, Cash JN, Tesmer JJG. Structural and dynamic changes in P-Rex1 upon activation by PIP 3 and inhibition by IP 4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.15.557836. [PMID: 37745379 PMCID: PMC10515948 DOI: 10.1101/2023.09.15.557836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
PIP3-dependent Rac exchanger 1 (P-Rex1) is abundantly expressed in neutrophils and plays central roles in chemotaxis and cancer metastasis by serving as a guanine-nucleotide exchange factor (GEF) for Rac. The enzyme is synergistically activated by PIP3 and the heterotrimeric Gβγ subunits, but mechanistic details remain poorly understood. While investigating the regulation of P-Rex1 by PIP3, we discovered that Ins(1,3,4,5)P4 (IP4) inhibits P-Rex1 activity and induces large decreases in backbone dynamics in diverse regions of the protein. Cryo-electron microscopy analysis of the P-Rex1·IP4 complex revealed a conformation wherein the pleckstrin homology (PH) domain occludes the active site of the Dbl homology (DH) domain. This configuration is stabilized by interactions between the first DEP domain (DEP1) and the DH domain and between the PH domain and a 4-helix bundle (4HB) subdomain that extends from the C-terminal domain of P-Rex1. Disruption of the DH-DEP1 interface in a DH/PH-DEP1 fragment enhanced activity and led to a more extended conformation in solution, whereas mutations that constrain the occluded conformation led to decreased GEF activity. Variants of full-length P-Rex1 in which the DH-DEP1 and PH-4HB interfaces were disturbed exhibited enhanced activity during chemokine-induced cell migration, confirming that the observed structure represents the autoinhibited state in living cells. Interactions with PIP3-containing liposomes led to disruption of these interfaces and increased dynamics protein-wide. Our results further suggest that inositol phosphates such as IP4 help to inhibit basal P-Rex1 activity in neutrophils, similar to their inhibitory effects on phosphatidylinositol-3-kinase.
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Affiliation(s)
- Sandeep K. Ravala
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sendi Rafael Adame-Garcia
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Chun-Liang Chen
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Michael A. Cianfrocco
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - J. Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Jennifer N. Cash
- Department of Molecular and Cellular Biology, University of California-Davis, Davis, CA, 95616, USA
| | - John J. G. Tesmer
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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23
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Sanchez‐Martinez S, Nguyen K, Biswas S, Nicholson V, Romanyuk AV, Ramirez J, Kc S, Akter A, Childs C, Meese EK, Usher ET, Ginell GM, Yu F, Gollub E, Malferrari M, Francia F, Venturoli G, Martin EW, Caporaletti F, Giubertoni G, Woutersen S, Sukenik S, Woolfson DN, Holehouse AS, Boothby TC. Labile assembly of a tardigrade protein induces biostasis. Protein Sci 2024; 33:e4941. [PMID: 38501490 PMCID: PMC10949331 DOI: 10.1002/pro.4941] [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: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self-assembly of labile CAHS gels.
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Affiliation(s)
| | - K. Nguyen
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Biswas
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - V. Nicholson
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. V. Romanyuk
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
| | - J. Ramirez
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Kc
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. Akter
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - C. Childs
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. K. Meese
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. T. Usher
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - G. M. Ginell
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - F. Yu
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
| | - E. Gollub
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - M. Malferrari
- Dipartimento di Chimica “Giacomo Ciamician”Università di BolognaBolognaItaly
| | - F. Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
| | - G. Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o Dipartimento di Fisica e Astronomia (DIFA)Università di BolognaBolognaItaly
| | - E. W. Martin
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - F. Caporaletti
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - G. Giubertoni
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Woutersen
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Sukenik
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - D. N. Woolfson
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
- School of BiochemistryUniversity of Bristol, Biomedical Sciences BuildingBristolUK
| | - A. S. Holehouse
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - T. C. Boothby
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
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24
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Tamburrini KC, Kodama S, Grisel S, Haon M, Nishiuchi T, Bissaro B, Kubo Y, Longhi S, Berrin JG. The disordered C-terminal tail of fungal LPMOs from phytopathogens mediates protein dimerization and impacts plant penetration. Proc Natl Acad Sci U S A 2024; 121:e2319998121. [PMID: 38513096 PMCID: PMC10990093 DOI: 10.1073/pnas.2319998121] [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: 11/20/2023] [Accepted: 02/13/2024] [Indexed: 03/23/2024] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes that oxidatively degrade various polysaccharides, such as cellulose. Despite extensive research on this class of enzymes, the role played by their C-terminal regions predicted to be intrinsically disordered (dCTR) has been overlooked. Here, we investigated the function of the dCTR of an LPMO, called CoAA9A, up-regulated during plant infection by Colletotrichum orbiculare, the causative agent of anthracnose. After recombinant production of the full-length protein, we found that the dCTR mediates CoAA9A dimerization in vitro, via a disulfide bridge, a hitherto-never-reported property that positively affects both binding and activity on cellulose. Using SAXS experiments, we show that the homodimer is in an extended conformation. In vivo, we demonstrate that gene deletion impairs formation of the infection-specialized cell called appressorium and delays penetration of the plant. Using immunochemistry, we show that the protein is a dimer not only in vitro but also in vivo when secreted by the appressorium. As these peculiar LPMOs are also found in other plant pathogens, our findings open up broad avenues for crop protection.
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Affiliation(s)
- Ketty C. Tamburrini
- CNRS Aix Marseille Université, CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille13009, France
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l'Environnement, Biodiversité et Biotechnologie Fongiques, UMR 1163, Aix Marseille Université, Marseille13009, France
| | - Sayo Kodama
- Faculty of Agriculture, Setsunan University, Osaka573-0101, Japan
| | - Sacha Grisel
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l'Environnement, Biodiversité et Biotechnologie Fongiques, UMR 1163, Aix Marseille Université, Marseille13009, France
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Aix Marseille Université, 3PE Platform, Marseille13009, France
| | - Mireille Haon
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l'Environnement, Biodiversité et Biotechnologie Fongiques, UMR 1163, Aix Marseille Université, Marseille13009, France
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Aix Marseille Université, 3PE Platform, Marseille13009, France
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa920-1164, Japan
| | - Bastien Bissaro
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l'Environnement, Biodiversité et Biotechnologie Fongiques, UMR 1163, Aix Marseille Université, Marseille13009, France
| | - Yasuyuki Kubo
- Faculty of Agriculture, Setsunan University, Osaka573-0101, Japan
| | - Sonia Longhi
- CNRS Aix Marseille Université, CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille13009, France
| | - Jean-Guy Berrin
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l'Environnement, Biodiversité et Biotechnologie Fongiques, UMR 1163, Aix Marseille Université, Marseille13009, France
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25
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Dudas EF, Tully MD, Foldes T, Kelly G, Tartaglia GG, Pastore A. The structural properties of full-length annexin A11. Front Mol Biosci 2024; 11:1347741. [PMID: 38516187 PMCID: PMC10955470 DOI: 10.3389/fmolb.2024.1347741] [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: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 03/23/2024] Open
Abstract
Annexin A11 (ANXA11) is a calcium-dependent phospholipid-binding protein belonging to the annexin protein family and implicated in the neurodegenerative amyotrophic lateral sclerosis. Structurally, ANXA11 contains a conserved calcium-binding C-terminal domain common to all annexins and a putative intrinsically unfolded N-terminus specific for ANXA11. Little is known about the structure and functions of this region of the protein. By analogy with annexin A1, it was suggested that residues 38 to 59 within the ANXA11 N-terminus could form a helical region that would be involved in interactions. Interestingly, this region contains residues that, when mutated, may lead to clinical manifestations. In the present study, we have studied the structural features of the full-length protein with special attention to the N-terminal region using a combination of biophysical techniques which include nuclear magnetic resonance and small angle X-ray scattering. We show that the N-terminus is intrinsically disordered and that the overall features of the protein are not markedly affected by the presence of calcium. We also analyzed the 38-59 helix hypothesis using synthetic peptides spanning both the wild-type sequence and clinically relevant mutations. We show that the peptides have a remarkable character typical of a native helix and that mutations do not alter the behaviour suggesting that they are required for interactions rather than being structurally important. Our work paves the way to a more thorough understanding of the ANXA11 functions.
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Affiliation(s)
- Erika F. Dudas
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
| | - Mark D. Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Tamas Foldes
- University College London, Department of Physics and Astronomy, University College London, London, United Kingdom
- Institut de Biologie Structurale (IBS), Institut Laue-Langevin, University Grenoble Alpes, Grenoble, France
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
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26
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Sievers K, Neumann P, Sušac L, Da Vela S, Graewert M, Trowitzsch S, Svergun D, Tampé R, Ficner R. Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase. Structure 2024; 32:316-327.e5. [PMID: 38181786 DOI: 10.1016/j.str.2023.12.006] [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: 04/14/2023] [Revised: 07/06/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAsAsp,Asn,His,Tyr for queuine, a hypermodified 7-deazaguanine derivative. Eukaryotic TGT is a heterodimer comprised of a catalytic and a non-catalytic subunit. While binding of the tRNA anticodon loop to the active site is structurally well understood, the contribution of the non-catalytic subunit to tRNA binding remained enigmatic, as no complex structure with a complete tRNA was available. Here, we report a cryo-EM structure of eukaryotic TGT in complex with a complete tRNA, revealing the crucial role of the non-catalytic subunit in tRNA binding. We decipher the functional significance of these additional tRNA-binding sites, analyze solution state conformation, flexibility, and disorder of apo TGT, and examine conformational transitions upon tRNA binding.
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Affiliation(s)
- Katharina Sievers
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany
| | - Lukas Sušac
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Stefano Da Vela
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, GZMB, University of Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany.
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27
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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28
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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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Kravikass M, Koren G, Saleh OA, Beck R. From isolated polyelectrolytes to star-like assemblies: the role of sequence heterogeneity on the statistical structure of the intrinsically disordered neurofilament-low tail domain. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:13. [PMID: 38358563 PMCID: PMC10869404 DOI: 10.1140/epje/s10189-024-00409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structure of IDPs. However, the amino-acid sequence heterogeneity and complex intermolecular interaction network have significantly impeded the ability to get proper approximations. One such case is the intrinsically disordered tail domain of neurofilament low (NFLt), which comprises a 50 residue-long uncharged domain followed by a 96 residue-long negatively charged domain. Here, we measure two NFLt variants to identify the impact of the NFLt two main subdomains on its complex interactions and statistical structure. Using synchrotron small-angle x-ray scattering, we find that the uncharged domain of the NFLt induces attractive interactions that cause it to self-assemble into star-like polymer brushes. On the other hand, when the uncharged domain is truncated, the remaining charged N-terminal domains remain isolated in solution with typical polyelectrolyte characteristics. We further discuss how competing long- and short-ranged interactions within the polymer brushes dominate their ensemble structure and, in turn, their implications on previously observed phenomena in NFL native and diseased states.
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Affiliation(s)
- Mathar Kravikass
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Gil Koren
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Omar A Saleh
- Materials Department, Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, USA
- Physics Department, University of California, Santa Barbara, USA
| | - Roy Beck
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel.
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30
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Li L, Wang J, Zhong X, Jiang Y, Pei G, Yang X, Zhang K, Shen S, Jin X, Sun G, Su C, Chen S, Yin H. ADP-Hep-Induced Liquid Phase Condensation of TIFA-TRAF6 Activates ALPK1/TIFA-Dependent Innate Immune Responses. RESEARCH (WASHINGTON, D.C.) 2024; 7:0315. [PMID: 38357697 PMCID: PMC10865109 DOI: 10.34133/research.0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
The ALPK1 (alpha-kinase 1)-TIFA (TRAF-interacting protein with fork head-associated domain)-TRAF6 signaling pathway plays a pivotal role in regulating inflammatory processes, with TIFA and TRAF6 serving as key molecules in this cascade. Despite its significance, the functional mechanism of TIFA-TRAF6 remains incompletely understood. In this study, we unveil that TIFA undergoes liquid-liquid phase separation (LLPS) induced by ALPK1 in response to adenosine diphosphate (ADP)-β-D-manno-heptose (ADP-Hep) recognition. The phase separation of TIFA is primarily driven by ALPK1, the pT9-FHA domain, and the intrinsically disordered region segment. Simultaneously, TRAF6 exhibits phase separation during ADP-Hep-induced inflammation, a phenomenon observed consistently across various inflammatory signal pathways. Moreover, TRAF6 is recruited within the TIFA condensates, facilitating lysine (K) 63-linked polyubiquitin chain synthesis. The subsequent recruitment, enrichment, and activation of downstream effectors within these condensates contribute to robust inflammatory signal transduction. Utilizing a novel chemical probe (compound 22), our analysis demonstrates that the activation of the ALPK1-TIFA-TRAF6 signaling pathway in response to small molecules necessitates the phase separation of TIFA. In summary, our findings reveal TIFA as a sensor for upstream signals, initiating the LLPS of itself and downstream proteins. This process results in the formation of membraneless condensates within the ALPK1-TIFA-TRAF6 pathway, suggesting potential applications in therapeutic biotechnology development.
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Affiliation(s)
- Liping Li
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- Department of Cancer Research, Institute of Medicinal Biotechnology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, College of Future Technology,
Peking University, Beijing, China
| | - Xincheng Zhong
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yaoyao Jiang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- School of Life Sciences,
Tsinghua University, Beijing, 100084, China
| | - Xikang Yang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Kaixiang Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Siqi Shen
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Xue Jin
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Gaoge Sun
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Chaofei Su
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Shuzhen Chen
- Department of Cancer Research, Institute of Medicinal Biotechnology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hang Yin
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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31
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Yang K, Chen G, Yu F, Fang X, Zhang J, Zhang Z, Shi Y, Zhang L. Molecular mechanism of specific HLA-A mRNA recognition by the RNA-binding-protein hMEX3B to promote tumor immune escape. Commun Biol 2024; 7:158. [PMID: 38326406 PMCID: PMC10850505 DOI: 10.1038/s42003-024-05845-y] [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: 07/07/2023] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
Immunotherapy, including immune checkpoint inhibitors and adoptive cell transfer, has obtained great progress, but their efficiencies vary among patients due to the genetic and epigenetic differences. Human MEX3B (hMEX3B) protein is an RNA-binding protein that contains two KH domains at the N-terminus and a RING domain at its C-terminus, which has the activity of E3 ubiquitin ligase and is essential for RNA degradation. Current evidence suggests that hMEX3B is involved in many important biological processes, including tumor immune evasion and HLA-A regulation, but the sequence of substrate RNA recognized by hMEX3B and the functional molecular mechanisms are unclear. Here, we first screened the optimized hMEX3B binding sequence on the HLA-A mRNA and reported that the two tandem KH domains can bind with their substrate one hundred times more than the individual KH domains. We systematically investigated the binding characteristics between the two KH domains and their RNA substrates by nuclear magnetic resonance (NMR). Based on this information and the small-angle X-ray scattering (SAXS) data, we used molecular dynamics simulations to obtain structural models of KH domains in complex with their corresponding RNAs. By analyzing the models, we noticed that on the KH domains' variable loops, there were two pairs of threonines and arginines that can disrupt the recognition of the RNA completely, and this influence had also been verified both in vitro and in vivo. Finally, we presented a functional model of the hMEX3B protein, which indicated that hMEX3B regulated the degradation of its substrate mRNAs in many biological processes. Taken together, our research illustrated how the hMEX3B protein played a key role in translation inhibition during the immune response to tumor cells and provided an idea and a lead for the study of the molecular mechanism and function of other MEX3 family proteins.
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Affiliation(s)
- Kanglong Yang
- Hefei National Research Center for Cross disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, PR China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science & Technology of China, Hefei, Anhui, PR China
| | - Guanglin Chen
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Fan Yu
- Hefei National Research Center for Cross disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, PR China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science & Technology of China, Hefei, Anhui, PR China
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, PR China
| | - Jiahai Zhang
- Hefei National Research Center for Cross disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, PR China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science & Technology of China, Hefei, Anhui, PR China
| | - Zhiyong Zhang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, PR China.
| | - Yunyu Shi
- Hefei National Research Center for Cross disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, PR China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science & Technology of China, Hefei, Anhui, PR China.
| | - Liang Zhang
- Hefei National Research Center for Cross disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, PR China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science & Technology of China, Hefei, Anhui, PR China.
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32
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Mukhopadhyay S, Subedi S, Hopkins JB, Ugrinov A, Chakravarthy S, Colbert CL, Sinha SC. Invariant BECN1 CXXC motifs bind Zn 2+ and regulate structure and function of the BECN1 intrinsically disordered region. Autophagy 2024; 20:380-396. [PMID: 37791766 PMCID: PMC10813572 DOI: 10.1080/15548627.2023.2259707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
ABBREVIATIONS AFM: aromatic finger mutant; BH3D: BCL2 homology 3 domain; CCD: coiled-coil domain; CD: circular dichroism spectroscopy; [CysDM1]: C18S and C21S double mutant; [CysDM2]: C137S, and C140S double mutant; [CysTM], C18S, C21S, C137S, and C140S tetrad mutant; Dmax: maximum particle diameter; dRI, differential refractive index; EFA: evolving factor analysis; FHD: flexible helical domain; FL: full length; GFP: green fluorescent protein; HDX-MS: hydrogen/deuterium exchange mass spectrometry; ICP-MS: inductively coupled plasma mass spectrometry; IDR: intrinsically disordered region; ITC, isothermal titration calorimetry; MALS, multi angle light scattering; MBP: maltose-binding protein; MoRFs: molecular recognition features; P(r): pairwise-distance distribution; PtdIns3K: class III phosphatidylinositol 3-kinase; Rg: radius of gyration; SASBDB: small angle scattering biological data bank; SEC: size-exclusion chromatography; SEC-SAXS: size-exclusion chromatography in tandem with small angle X-ray scattering; TEV: tobacco-etch virus; TFE: 2,2,2-trifluoroethanol; TPEN: N,N,N,N-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine; Vc: volume of correlation; WT: wild-type.
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Affiliation(s)
- Shreya Mukhopadhyay
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Subeksha Subedi
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Jesse B. Hopkins
- The Biophysics Collaborative Access Team, Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team, Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL, USA
| | | | - Sangita C. Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
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33
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Sun X, Alfermann J, Li H, Watkins MB, Chen YT, Morrell TE, Mayerthaler F, Wang CY, Komatsuzaki T, Chu JW, Ando N, Mootz HD, Yang H. Subdomain dynamics enable chemical chain reactions in non-ribosomal peptide synthetases. Nat Chem 2024; 16:259-268. [PMID: 38049653 PMCID: PMC11227371 DOI: 10.1038/s41557-023-01361-4] [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: 06/06/2022] [Accepted: 10/03/2023] [Indexed: 12/06/2023]
Abstract
Many peptide-derived natural products are produced by non-ribosomal peptide synthetases (NRPSs) in an assembly-line fashion. Each amino acid is coupled to a designated peptidyl carrier protein (PCP) through two distinct reactions catalysed sequentially by the single active site of the adenylation domain (A-domain). Accumulating evidence suggests that large-amplitude structural changes occur in different NRPS states; yet how these molecular machines orchestrate such biochemical sequences has remained elusive. Here, using single-molecule Förster resonance energy transfer, we show that the A-domain of gramicidin S synthetase I adopts structurally extended and functionally obligatory conformations for alternating between adenylation and thioester-formation structures during enzymatic cycles. Complementary biochemical, computational and small-angle X-ray scattering studies reveal interconversion among these three conformations as intrinsic and hierarchical where intra-A-domain organizations propagate to remodel inter-A-PCP didomain configurations during catalysis. The tight kinetic coupling between structural transitions and enzymatic transformations is quantified, and how the gramicidin S synthetase I A-domain utilizes its inherent conformational dynamics to drive directional biosynthesis with a flexibly linked PCP domain is revealed.
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Affiliation(s)
- Xun Sun
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonas Alfermann
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Hao Li
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology; Institute of Molecular Medicine and Bioengineering; Department of Biological Science and Technology; Centre for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Thomas E Morrell
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | | | - Chia-Ying Wang
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tamiki Komatsuzaki
- Research Centre of Mathematics for Social Creativity, Research Institute for Electronic Science; The Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Japan
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology; Institute of Molecular Medicine and Bioengineering; Department of Biological Science and Technology; Centre for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Henning D Mootz
- Institute of Biochemistry, University of Münster, Münster, Germany.
| | - Haw Yang
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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34
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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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35
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Theisen FF, Prestel A, Elkjær S, Leurs YHA, Morffy N, Strader LC, O'Shea C, Teilum K, Kragelund BB, Skriver K. Molecular switching in transcription through splicing and proline-isomerization regulates stress responses in plants. Nat Commun 2024; 15:592. [PMID: 38238333 PMCID: PMC10796322 DOI: 10.1038/s41467-024-44859-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
The Arabidopsis thaliana DREB2A transcription factor interacts with the negative regulator RCD1 and the ACID domain of subunit 25 of the transcriptional co-regulator mediator (Med25) to integrate stress signals for gene expression, with elusive molecular interplay. Using biophysical and structural analyses together with high-throughput screening, we reveal a bivalent binding switch in DREB2A containing an ACID-binding motif (ABS) and the known RCD1-binding motif (RIM). The RIM is lacking in a stress-induced DREB2A splice variant with retained transcriptional activity. ABS and RIM bind to separate sites on Med25-ACID, and NMR analyses show a structurally heterogeneous complex deriving from a DREB2A-ABS proline residue populating cis- and trans-isomers with remote impact on the RIM. The cis-isomer stabilizes an α-helix, while the trans-isomer may introduce energetic frustration facilitating rapid exchange between activators and repressors. Thus, DREB2A uses a post-transcriptionally and post-translationally modulated switch for transcriptional regulation.
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Affiliation(s)
- Frederik Friis Theisen
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Steffie Elkjær
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yannick H A Leurs
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Charlotte O'Shea
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Karen Skriver
- The REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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36
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Taneja I, Lasker K. Machine-learning-based methods to generate conformational ensembles of disordered proteins. Biophys J 2024; 123:101-113. [PMID: 38053335 PMCID: PMC10808026 DOI: 10.1016/j.bpj.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/24/2023] [Accepted: 12/01/2023] [Indexed: 12/07/2023] Open
Abstract
Intrinsically disordered proteins are characterized by a conformational ensemble. While computational approaches such as molecular dynamics simulations have been used to generate such ensembles, their computational costs can be prohibitive. An alternative approach is to learn from data and train machine-learning models to generate conformational ensembles of disordered proteins. This has been a relatively unexplored approach, and in this work we demonstrate a proof-of-principle approach to do so. Specifically, we devised a two-stage computational pipeline: in the first stage, we employed supervised machine-learning models to predict ensemble-derived two-dimensional (2D) properties of a sequence, given the conformational ensemble of a closely related sequence. In the second stage, we used denoising diffusion models to generate three-dimensional (3D) coarse-grained conformational ensembles, given the two-dimensional predictions outputted by the first stage. We trained our models on a data set of coarse-grained molecular dynamics simulations of thousands of rationally designed synthetic sequences. The accuracy of our 2D and 3D predictions was validated across multiple metrics, and our work demonstrates the applicability of machine-learning techniques to predicting higher-dimensional properties of disordered proteins.
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Affiliation(s)
- Ishan Taneja
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California
| | - Keren Lasker
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California.
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37
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Bárria C, Athayde D, Hernandez G, Fonseca L, Casinhas J, Cordeiro TN, Archer M, Arraiano CM, Brito JA, Matos RG. Structure and function of Campylobacter jejuni polynucleotide phosphorylase (PNPase): Insights into the role of this RNase in pathogenicity. Biochimie 2024; 216:56-70. [PMID: 37806617 DOI: 10.1016/j.biochi.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/10/2023]
Abstract
Ribonucleases are in charge of the processing, degradation and quality control of all cellular transcripts, which makes them crucial factors in RNA regulation. This post-transcriptional regulation allows bacteria to promptly react to different stress conditions and growth phase transitions, and also to produce the required virulence factors in pathogenic bacteria. Campylobacter jejuni is the main responsible for human gastroenteritis in the world. In this foodborne pathogen, exoribonuclease PNPase (CjPNP) is essential for low-temperature cell survival, affects the synthesis of proteins involved in virulence and has an important role in swimming, cell adhesion/invasion ability, and chick colonization. Here we report the crystallographic structure of CjPNP, complemented with SAXS, which confirms the characteristic doughnut-shaped trimeric arrangement and evaluates domain arrangement and flexibility. Mutations in highly conserved residues were constructed to access their role in RNA degradation and polymerization. Surprisingly, we found two mutations that altered CjPNP into a protein that is only capable of degrading RNA even in conditions that favour polymerization. These findings will be important to develop new strategies to combat C. jejuni infections.
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Affiliation(s)
- Cátia Bárria
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Diogo Athayde
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Guillem Hernandez
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Leonor Fonseca
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Jorge Casinhas
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Tiago N Cordeiro
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Margarida Archer
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Cecília M Arraiano
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - José A Brito
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Rute G Matos
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
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38
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Sun X, Saleh ASM, Wang Z, Yu Y, Li W, Zhang D. Insights into the interactions between etheric compounds and myofibrillar proteins using multi-spectroscopy, molecular docking, and molecular dynamics simulation. Food Res Int 2024; 175:113787. [PMID: 38129009 DOI: 10.1016/j.foodres.2023.113787] [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: 10/26/2023] [Revised: 11/26/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
This study aimed to examine how the addition of etheric compounds (EC) affects the characteristics of myofibrillar proteins (MP) and to understand underlying interaction mechanisms. Fourier transform infrared spectroscopy confirmed that the EC-MP complex was formed through hydrogen bonding. The addition of EC resulted in an increase in the α-helix content and a decrease in the β-sheet content of MP, which would promote the protein unfolding. The unfolding of MP led to aggregation and formation of larger and non-uniform particles. As a result, the exposure of negative charge on the MP surface was enhanced, and zeta potential was decreased from -5.33 mV to -7.45 mV. Moreover, the EC-induced modification of MP conformation resulted in a less rigid three-dimensional network structure of MP gel and enhanced the discharge of aldehyde compounds (C > 6). Moreover, the rheological characteristics of MP were enhanced by the suppression of protein-protein interactions due to the MP unfolding. Molecular dynamics simulations revealed that anethole reduced the binding capacity of myosin to decanal by raising its binding energy from -22.22 kcal/mol to -19.38 kcal/mol. In the meantime, anethole competed for the amino acid residue (PHE165) where myosin connects to decanal. This caused the hydrogen bonds and hydrophobic contacts between the two molecules to dissolve, altering myosin's conformation and releasing decanal. The results might be useful in predicting and controlling the ability of proteins to release and hold onto flavors.
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Affiliation(s)
- Xiangxiang Sun
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Ahmed S M Saleh
- Department of Food Science and Technology, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
| | - Zhenyu Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Yumei Yu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Wenhao Li
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Integrated Laboratory of Processing Technology for Chinese Meat and Dish Products, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
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39
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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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40
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Rinaldi F, Schipani F, Balboni B, Catalano F, Marotta R, Myers SH, Previtali V, Veronesi M, Scietti L, Cecatiello V, Pasqualato S, Ortega JA, Girotto S, Cavalli A. Isolation and Characterization of Monomeric Human RAD51: A Novel Tool for Investigating Homologous Recombination in Cancer. Angew Chem Int Ed Engl 2023; 62:e202312517. [PMID: 37924230 DOI: 10.1002/anie.202312517] [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: 08/25/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/06/2023]
Abstract
DNA repair protein RAD51 is a key player in the homologous recombination pathway. Upon DNA damage, RAD51 is transported into the nucleus by BRCA2, where it can repair DNA double-strand breaks. Due to the structural complexity and dynamics, researchers have not yet clarified the mechanistic details of every step of RAD51 recruitment and DNA repair. RAD51 possesses an intrinsic tendency to form oligomeric structures, which make it challenging to conduct biochemical and biophysical investigations. Here, for the first time, we report on the isolation and characterization of a human monomeric RAD51 recombinant form, obtained through a double mutation, which preserves the protein's integrity and functionality. We investigated different buffers to identify the most suitable condition needed to definitively stabilize the monomer. The monomer of human RAD51 provides the community with a unique biological tool for investigating RAD51-mediated homologous recombination, and paves the way for more reliable structural, mechanistic, and drug discovery studies.
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Affiliation(s)
- Francesco Rinaldi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Fabrizio Schipani
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Beatrice Balboni
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Federico Catalano
- Electron Microscopy Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Roberto Marotta
- Electron Microscopy Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Samuel H Myers
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Viola Previtali
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marina Veronesi
- Structural Biophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Luigi Scietti
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Valentina Cecatiello
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Current address: Structural Biology Research Centre, Human Technopole Milan, Italy Palazzo Italia Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Sebastiano Pasqualato
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IRCCS European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Current address: Structural Biology Research Centre, Human Technopole Milan, Italy Palazzo Italia Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Jose Antonio Ortega
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Stefania Girotto
- Structural Biophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
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41
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Ferrero DS, Tomás Gilabert O, Verdaguer N. Structural insights on the nucleoprotein C-terminal domain of Měnglà virus. Microbiol Spectr 2023; 11:e0237323. [PMID: 37888996 PMCID: PMC10714759 DOI: 10.1128/spectrum.02373-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Filoviruses are the causative agents of severe and often fatal hemorrhagic disease in humans. Měnglà virus (MLAV) is a recently reported filovirus, isolated from fruit bats that is capable to replicate in human cells, representing a potential risk for human health. An in-depth structural and functional knowledge of MLAV proteins is an essential step for antiviral research on this virus that can also be extended to other emerging filoviruses. In this study, we determined the first crystal structures of the C-terminal domain (CTD) of the MLAV nucleoprotein (NP), showing important similarities to the equivalent domain in MARV. The structural data also show that the NP CTD has the ability to form large helical oligomers that may participate in the control of cytoplasmic inclusion body formation during viral replication.
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Affiliation(s)
| | | | - Nuria Verdaguer
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
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42
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Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SBM, Kelly G, Fornili A, Cianciotto NP, Garnett JA. The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570962. [PMID: 38106198 PMCID: PMC10723406 DOI: 10.1101/2023.12.10.570962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans (GAGs) on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual dynamic trimer arrangement with a positively charged external surface and a negatively charged solvent exposed internal cavity. Through Molecular Dynamics (MD) simulations, we show how the GAG chondroitin-4-sulphate associates with the Lcl-CTD surface via unique binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate binding mechanism.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Anna K. Antonovic
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ian E. McIntire
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Huaixin Zheng
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Carlton O. Adams
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Theo Portlock
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Katherine Richardson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rosie Shaw
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Alain Oregioni
- The Medical Research Council Biomedical NMR Centre, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Giulia Mastroianni
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sara B-M. Whittaker
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Arianna Fornili
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Nicholas P. Cianciotto
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
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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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44
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Kieslich B, Weiße RH, Brendler J, Ricken A, Schöneberg T, Sträter N. The dimerized pentraxin-like domain of the adhesion G protein-coupled receptor 112 (ADGRG4) suggests function in sensing mechanical forces. J Biol Chem 2023; 299:105356. [PMID: 37863265 PMCID: PMC10687090 DOI: 10.1016/j.jbc.2023.105356] [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: 10/14/2022] [Revised: 09/12/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Adhesion G protein-coupled receptors (aGPCRs) feature large extracellular regions with modular domains that often resemble protein classes of various function. The pentraxin (PTX) domain, which is predicted by sequence homology within the extracellular region of four different aGPCR members, is well known to form pentamers and other oligomers. Oligomerization of GPCRs is frequently reported and mainly driven by interactions of the seven-transmembrane region and N or C termini. While the functional importance of dimers is well-established for some class C GPCRs, relatively little is known about aGPCR multimerization. Here, we showcase the example of ADGRG4, an orphan aGPCR that possesses a PTX-like domain at its very N-terminal tip, followed by an extremely long stalk containing serine-threonine repeats. Using X-ray crystallography and biophysical methods, we determined the structure of this unusual PTX-like domain and provide experimental evidence for a homodimer equilibrium of this domain which is Ca2+-independent and driven by intermolecular contacts that differ vastly from the known soluble PTXs. The formation of this dimer seems to be conserved in mammalian ADGRG4 indicating functional relevance. Our data alongside of theoretical considerations lead to the hypothesis that ADGRG4 acts as an in vivo sensor for shear forces in enterochromaffin and Paneth cells of the small intestine.
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Affiliation(s)
- Björn Kieslich
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany; Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany.
| | - Renato H Weiße
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
| | - Jana Brendler
- Institute of Anatomy, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Albert Ricken
- Institute of Anatomy, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany.
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany.
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45
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Guillien M, Mouhand A, Sagar A, Fournet A, Allemand F, Pereira GAN, Thureau A, Bernadó P, Banères JL, Sibille N. Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction. Structure 2023; 31:1394-1406.e7. [PMID: 37669668 DOI: 10.1016/j.str.2023.08.011] [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: 03/21/2023] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 09/07/2023]
Abstract
Arrestin-dependent G protein-coupled receptor (GPCR) signaling pathway is regulated by the phosphorylation state of GPCR's C-terminal domain, but the molecular bases of arrestin:receptor interaction are to be further illuminated. Here we investigated the impact of phosphorylation on the conformational features of the C-terminal region from three rhodopsin-like GPCRs, the vasopressin V2 receptor (V2R), the growth hormone secretagogue or ghrelin receptor type 1a (GHSR), and the β2-adernergic receptor (β2AR). Using phosphomimetic variants, we identified pre-formed secondary structure elements, or short linear motifs (SLiMs), that undergo specific conformational transitions upon phosphorylation. Of importance, such conformational transitions appear to favor arrestin-2 binding. Hence, our results suggest a model in which the phosphorylation-dependent structuration of the GPCR C-terminal regions would modulate arrestin binding and therefore signaling outcomes in arrestin-dependent pathways.
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Affiliation(s)
- Myriam Guillien
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Assia Mouhand
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Amin Sagar
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Glaécia A N Pereira
- Institut des Biomolécules Max Mousseron (IBMM), UMR-5247, University Montpellier, CNRS, ENSCM, Montpellier, France
| | - Aurélien Thureau
- HélioBio Section, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, 91190 Gif-sur-Yvette, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR-5247, University Montpellier, CNRS, ENSCM, Montpellier, France
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France.
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Gonzalez JP, Frandsen KEH, Kesten C. The role of intrinsic disorder in binding of plant microtubule-associated proteins to the cytoskeleton. Cytoskeleton (Hoboken) 2023; 80:404-436. [PMID: 37578201 DOI: 10.1002/cm.21773] [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: 05/02/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/15/2023]
Abstract
Microtubules (MTs) represent one of the main components of the eukaryotic cytoskeleton and support numerous critical cellular functions. MTs are in principle tube-like structures that can grow and shrink in a highly dynamic manner; a process largely controlled by microtubule-associated proteins (MAPs). Plant MAPs are a phylogenetically diverse group of proteins that nonetheless share many common biophysical characteristics and often contain large stretches of intrinsic protein disorder. These intrinsically disordered regions are determinants of many MAP-MT interactions, in which structural flexibility enables low-affinity protein-protein interactions that enable a fine-tuned regulation of MT cytoskeleton dynamics. Notably, intrinsic disorder is one of the major obstacles in functional and structural studies of MAPs and represents the principal present-day challenge to decipher how MAPs interact with MTs. Here, we review plant MAPs from an intrinsic protein disorder perspective, by providing a complete and up-to-date summary of all currently known members, and address the current and future challenges in functional and structural characterization of MAPs.
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Affiliation(s)
- Jordy Perez Gonzalez
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Kristian E H Frandsen
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Christopher Kesten
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Chen R, Song Y, Wang Z, Ji H, Du Z, Ma Q, Yang Y, Liu X, Li N, Sun Y. Developments in small-angle X-ray scattering (SAXS) for characterizing the structure of surfactant-macromolecule interactions and their complex. Int J Biol Macromol 2023; 251:126288. [PMID: 37582436 DOI: 10.1016/j.ijbiomac.2023.126288] [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: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023]
Abstract
The surfactant-macromolecule interactions (SMI) are one of the most critical topics for scientific research and industrial application. Small-angle X-ray scattering (SAXS) is a powerful tool for comprehensively studying the structural and conformational features of macromolecules at a size ranging from Angstroms to hundreds of nanometers with a time-resolve in milliseconds scale. The SAXS integrative techniques have emerged for comprehensively analyzing the SMI and the structure of their complex in solution. Here, the various types of emerging interactions of surfactant with macromolecules, such as protein, lipid, nuclear acid, polysaccharide and virus, etc. have been systematically reviewed. Additionally, the principle of SAXS and theoretical models of SAXS for describing the structure of SMI as well as their complex has been summarized. Moreover, the recent developments in the applications of SAXS for charactering the structure of SMI have been also highlighted. Prospectively, the capacity to complement artificial intelligence (AI) in the structure prediction of biological macromolecules and the high-throughput bioinformatics sequencing data make SAXS integrative structural techniques expected to be the primary methodology for illuminating the self-assembling dynamics and nanoscale structure of SMI. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.
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Affiliation(s)
- Ruixin Chen
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Yang Song
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Zhichun Wang
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Hang Ji
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Zhongyao Du
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Qingwen Ma
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Ying Yang
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Xingxun Liu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Na Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, CAS, Shanghai, China.
| | - Yang Sun
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China.
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Ogbu CP, Kapoor S, Vecchio AJ. Structural Basis of Clostridium perfringens Enterotoxin Activation and Oligomerization by Trypsin. Toxins (Basel) 2023; 15:637. [PMID: 37999500 PMCID: PMC10674488 DOI: 10.3390/toxins15110637] [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: 09/15/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
Clostridium perfringens enterotoxin (CpE) is a β-pore forming toxin that disrupts gastrointestinal homeostasis in mammals by binding membrane protein receptors called claudins. Although structures of CpE fragments bound to claudins have been determined, the mechanisms that trigger CpE activation and oligomerization that lead to the formation of cytotoxic β-pores remain undetermined. Proteolysis of CpE in the gut by trypsin has been shown to play a role in this and subsequent cytotoxicity processes. Here, we report solution structures of full-length and trypsinized CpE using small-angle X-ray scattering (SAXS) and crystal structures of trypsinized CpE and its C-terminal claudin-binding domain (cCpE) using X-ray crystallography. Mass spectrometry and SAXS uncover that removal of the CpE N-terminus by trypsin alters the CpE structure to expose areas that are normally unexposed. Crystal structures of trypsinized CpE and cCpE reveal unique dimer interfaces that could serve as oligomerization sites. Moreover, comparisons of these structures to existing ones predict the functional implications of oligomerization in the contexts of cell receptor binding and β-pore formation. This study sheds light on trypsin's role in altering CpE structure to activate its function via inducing oligomerization on its path toward cytotoxic β-pore formation. Its findings can incite new approaches to inhibit CpE-based cytotoxicity with oligomer-disrupting therapeutics.
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Affiliation(s)
| | | | - Alex J. Vecchio
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, NY 14203, USA; (C.P.O.); (S.K.)
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Wang T, Coshic K, Badiee M, Aksimentiev A, Pollack L, Leung AKL. Length-dependent Intramolecular Coil-to-Globule Transition in Poly(ADP-ribose) Induced by Cations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564012. [PMID: 37961637 PMCID: PMC10634823 DOI: 10.1101/2023.10.25.564012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Poly(ADP-ribose) (PAR), as part of a post-translational modification, serves as a flexible scaffold for noncovalent protein binding. Such binding is influenced by PAR chain length through a mechanism yet to be elucidated. Structural insights have been elusive, partly due to the difficulties associated with synthesizing PAR chains of defined lengths. Here, we employ an integrated approach combining molecular dynamics (MD) simulations with small-angle X-ray scattering (SAXS) experiments, enabling us to identify highly heterogeneous ensembles of PAR conformers at two different, physiologically relevant lengths: PAR 15 and PAR 22 . Our findings reveal that numerous factors including backbone conformation, base stacking, and chain length contribute to determining the structural ensembles. We also observe length-dependent compaction of PAR upon the addition of small amounts of Mg 2+ ions, with the 22-mer exhibiting ADP-ribose bundles formed through local intramolecular coil-to-globule transitions. This study illuminates how such bundling could be instrumental in deciphering the length-dependent action of PAR. GRAPHICAL ABSTRACT
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50
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Kind L, Driver M, Raasakka A, Onck PR, Njølstad PR, Arnesen T, Kursula P. Structural properties of the HNF-1A transactivation domain. Front Mol Biosci 2023; 10:1249939. [PMID: 37908230 PMCID: PMC10613711 DOI: 10.3389/fmolb.2023.1249939] [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: 06/29/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
Hepatocyte nuclear factor 1α (HNF-1A) is a transcription factor with important gene regulatory roles in pancreatic β-cells. HNF1A gene variants are associated with a monogenic form of diabetes (HNF1A-MODY) or an increased risk for type 2 diabetes. While several pancreatic target genes of HNF-1A have been described, a lack of knowledge regarding the structure-function relationships in HNF-1A prohibits a detailed understanding of HNF-1A-mediated gene transcription, which is important for precision medicine and improved patient care. Therefore, we aimed to characterize the understudied transactivation domain (TAD) of HNF-1A in vitro. We present a bioinformatic approach to dissect the TAD sequence, analyzing protein structure, sequence composition, sequence conservation, and the existence of protein interaction motifs. Moreover, we developed the first protocol for the recombinant expression and purification of the HNF-1A TAD. Small-angle X-ray scattering and synchrotron radiation circular dichroism suggested a disordered conformation for the TAD. Furthermore, we present functional data on HNF-1A undergoing liquid-liquid phase separation, which is in line with in silico predictions and may be of biological relevance for gene transcriptional processes in pancreatic β-cells.
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Affiliation(s)
- Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Mark Driver
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section of Endocrinology and Metabolism, Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - 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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