1
|
Mazzone F, Hoeppner A, Reiners J, Gertzen CGW, Applegate V, Abdullaziz MA, Gottstein J, Degrandi D, Wesemann M, Kurz T, Smits SHJ, 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 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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Das P, Saha S, Kumar Guha P, Kumar Bhunia A. Quantum dot-protein interface: Interaction of the CdS quantum dot with human hemoglobin for the study of the energy transfer process and binding mechanism along with detection of the unfolding of hemoglobin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 324:124937. [PMID: 39137709 DOI: 10.1016/j.saa.2024.124937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/12/2024] [Accepted: 08/04/2024] [Indexed: 08/15/2024]
Abstract
In this study, the interaction of the human hemoglobin with cost effective and chemically fabricated CdS quantum dots (QDs) (average sizes ≈3nm) has been investigated. The semiconductor QDs showed maximum visible absorption at 445 nm with excitonic formation and band gap of ≈ 2.88 eV along with hexagonal crystalline phase. The binding of QDs-Hb occurs through corona formation to the ground sate complex formation. The life time of the heme pocket binding and reorganization were found to be t1 = 43 min and t2 = 642 min, respectively. The emission quenching of the Hb has been indicated large energy transfer between CdS QDs and Hb with tertiary deformation of Hb. The binding thermodynamics showed highly exothermic nature. The ultrafast decay during corona formation was studied from TCSPC. The results showed that the energy transfer efficiency increases with the increase of the QDs concentration and maximum ≈71.5 % energy transfer occurs and average ultrafast lifetime varies from 5.45 ns to1.51 ns. The deformation and unfolding of the secondary structure of Hb with changes of the α-helix (≈74 % to ≈51.07 %) and β-sheets (≈8.63 % to ≈10.25 %) have been observed from circular dichroism spectrum. The SAXS spectrum showed that the radius of gyration of CdS QDs-Hb bioconjugate increased (up to 23 ± 0.45 nm) with the increase of the concentration of QDs compare with pure Hb (11 ± 0.23 nm) and Hb becoming more unfolded.
Collapse
Affiliation(s)
- Priyanka Das
- Department of Physics, Vidyasagar University, Paschim Medinipur 721102, West Bengal, India
| | - Satyajit Saha
- Department of Physics, Vidyasagar University, Paschim Medinipur 721102, West Bengal, India
| | - Prasanta Kumar Guha
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Paschim Medinipur, 721302, India; School of Nano Science and Technology, Indian Institute of Technology Kharagpur, Paschim Medinipur 721302, India
| | - Amit Kumar Bhunia
- Department of Physics, Government General Degree College Gopiballavpur-II, Jhargram 721517, India.
| |
Collapse
|
4
|
Fiorucci L, Schiavina M, Felli IC, Pierattelli R, Ravera E. Are Protein Conformational Ensembles in Agreement with Experimental Data? A Geometrical Interpretation of the Problem. J Chem Inf Model 2024; 64:5392-5401. [PMID: 38959217 DOI: 10.1021/acs.jcim.4c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The conformational variability of biological macromolecules can play an important role in their biological function. Therefore, understanding conformational variability is expected to be key for predicting the behavior of a particular molecule in the context of organism-wide studies. Several experimental methods have been developed and deployed for accessing this information, and computational methods are continuously updated for the profitable integration of different experimental sources. The outcome of this endeavor is conformational ensembles, which may vary significantly in properties and composition when different ensemble reconstruction methods are used, and this raises the issue of comparing the predicted ensembles against experimental data. In this article, we discuss a geometrical formulation to provide a framework for understanding the agreement of an ensemble prediction to the experimental observations.
Collapse
Affiliation(s)
- Letizia Fiorucci
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Marco Schiavina
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Enrico Ravera
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Florence Data Science, University of Florence, Viale G.B. Morgagni 59, 50134 Florence, Italy
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Diagouraga B, Tambones I, Carivenc C, Bechara C, Nadal M, de Massy B, le Maire A, Robert T. The TOPOVIBL meiotic DSB formation protein: new insights from its biochemical and structural characterization. Nucleic Acids Res 2024:gkae587. [PMID: 38966985 DOI: 10.1093/nar/gkae587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
The TOPOVIL complex catalyzes the formation of DNA double strand breaks (DSB) that initiate meiotic homologous recombination, an essential step for chromosome segregation and genetic diversity during gamete production. TOPOVIL is composed of two subunits (SPO11 and TOPOVIBL) and is evolutionarily related to the archaeal TopoVI topoisomerase complex. SPO11 is the TopoVIA subunit orthologue and carries the DSB formation catalytic activity. TOPOVIBL shares homology with the TopoVIB ATPase subunit. TOPOVIBL is essential for meiotic DSB formation, but its molecular function remains elusive, partly due to the lack of biochemical studies. Here, we purified TOPOVIBLΔC25 and characterized its structure and mode of action in vitro. Our structural analysis revealed that TOPOVIBLΔC25 adopts a dynamic conformation in solution and our biochemical study showed that the protein remains monomeric upon incubation with ATP, which correlates with the absence of ATP binding. Moreover, TOPOVIBLΔC25 interacted with DNA, with a preference for some geometries, suggesting that TOPOVIBL senses specific DNA architectures. Altogether, our study identified specific TOPOVIBL features that might help to explain how TOPOVIL function evolved toward a DSB formation activity in meiosis.
Collapse
Affiliation(s)
- Boubou Diagouraga
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Izabella Tambones
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Coralie Carivenc
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Chérine Bechara
- Institut de Génomique Fonctionnelle (IGF), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Marc Nadal
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Department of Life Sciences, Université Paris Cité, Paris, France
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Univ Montpellier, CNRS, 34090 Montpellier, France
| | - Albane le Maire
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Thomas Robert
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| |
Collapse
|
7
|
Mitra R, Usher ET, Dedeoğlu S, Crotteau MJ, Fraser OA, Yennawar NH, Gadkari VV, Ruotolo BT, Holehouse AS, Salmon L, Showalter SA, Bardwell JCA. Molecular insights into the interaction between a disordered protein and a folded RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598678. [PMID: 38915483 PMCID: PMC11195163 DOI: 10.1101/2024.06.12.598678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Intrinsically disordered protein regions (IDRs) are well-established as contributors to intermolecular interactions and the formation of biomolecular condensates. In particular, RNA-binding proteins (RBPs) often harbor IDRs in addition to folded RNA-binding domains that contribute to RBP function. To understand the dynamic interactions of an IDR-RNA complex, we characterized the RNA-binding features of a small (68 residues), positively charged IDR-containing protein, SERF. At high concentrations, SERF and RNA undergo charge-driven associative phase separation to form a protein- and RNA-rich dense phase. A key advantage of this model system is that this threshold for demixing is sufficiently high that we could use solution-state biophysical methods to interrogate the stoichiometric complexes of SERF with RNA in the one-phase regime. Herein, we describe our comprehensive characterization of SERF alone and in complex with a small fragment of the HIV-1 TAR RNA (TAR) with complementary biophysical methods and molecular simulations. We find that this binding event is not accompanied by the acquisition of structure by either molecule; however, we see evidence for a modest global compaction of the SERF ensemble when bound to RNA. This behavior likely reflects attenuated charge repulsion within SERF via binding to the polyanionic RNA and provides a rationale for the higher-order assembly of SERF in the context of RNA. We envision that the SERF-RNA system will lower the barrier to accessing the details that support IDR-RNA interactions and likewise deepen our understanding of the role of IDR-RNA contacts in complex formation and liquid-liquid phase separation.
Collapse
Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Selin Dedeoğlu
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, (CRMN), UMR 5082, CNRS, ENS Lyon, UCBL, Université de Lyon, 69100 Villeurbanne, France
| | - Matthew J. Crotteau
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olivia A. Fraser
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Neela H. Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Varun V. Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Loïc Salmon
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, (CRMN), UMR 5082, CNRS, ENS Lyon, UCBL, Université de Lyon, 69100 Villeurbanne, France
| | - Scott A. Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - James C. A. Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Chen X, Ostovan A, Arabi M, Wang Y, Chen L, Li J. Molecular Imprinting-Based SERS Detection Strategy for the Large-Size Protein Quantitation and Curbing Non-Specific Recognition. Anal Chem 2024; 96:6417-6425. [PMID: 38606984 DOI: 10.1021/acs.analchem.4c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Molecular imprinting-based surface-enhanced Raman scattering (MI-SERS) sensors have shown remarkable potential from an academic standpoint. However, their practical applications, especially in the detection of large-size protein (≥10 nm), face challenges due to the lack of versatile sensing strategies and nonspecific fouling of matrix species. Herein, we propose a Raman reporter inspector mechanism (RRIM) implemented on a protein-imprinted polydopamine (PDA) layer coated on the SERS active substrate. In the RRIM, after large-size protein recognition, the permeability of the PDA imprinted cavities undergoes changes that are scrutinized by Raman reporter molecules. Target proteins can specifically bind and fully occupy the imprinted cavities, whereas matrix species cannot. Then, Raman reporter molecules with suitable size are introduced to serve as both inspectors of the recognition status and inducers of the SERS signal, which can only penetrate through the vacant and nonspecifically filled cavities. Consequently, changes in the SERS signal exclusively originate from the specific binding of target proteins, while the nonspecific recognition of matrix species is curbed. The RRIM enables reproducible quantitation of the large-size cyanobacteria-specific protein model (≥10 nm), phycocyanin, at the level down to 2.6 × 10-3 μg L-1. Finally, the practical applicability of the RRIM is confirmed by accurately analyzing crude urban waterway samples over 21 min without any pretreatment.
Collapse
Affiliation(s)
- Xuan Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Abbas Ostovan
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Maryam Arabi
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yunqing Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Lingxin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Jinhua Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Vieira MFM, Hernandez G, Zhong Q, Arbesú M, Veloso T, Gomes T, Martins ML, Monteiro H, Frazão C, Frankel G, Zanzoni A, Cordeiro TN. The pathogen-encoded signalling receptor Tir exploits host-like intrinsic disorder for infection. Commun Biol 2024; 7:179. [PMID: 38351154 PMCID: PMC10864410 DOI: 10.1038/s42003-024-05856-9] [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: 11/23/2022] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
The translocated intimin receptor (Tir) is an essential type III secretion system (T3SS) effector of attaching and effacing pathogens contributing to the global foodborne disease burden. Tir acts as a cell-surface receptor in host cells, rewiring intracellular processes by targeting multiple host proteins. We investigated the molecular basis for Tir's binding diversity in signalling, finding that Tir is a disordered protein with host-like binding motifs. Unexpectedly, also are several other T3SS effectors. By an integrative approach, we reveal that Tir dimerises via an antiparallel OB-fold within a highly disordered N-terminal cytosolic domain. Also, it has a long disordered C-terminal cytosolic domain partially structured at host-like motifs that bind lipids. Membrane affinity depends on lipid composition and phosphorylation, highlighting a previously unrecognised host interaction impacting Tir-induced actin polymerisation and cell death. Furthermore, multi-site tyrosine phosphorylation enables Tir to engage host SH2 domains in a multivalent fuzzy complex, consistent with Tir's scaffolding role and binding promiscuity. Our findings provide insights into the intracellular Tir domains, highlighting the ability of T3SS effectors to exploit host-like protein disorder as a strategy for host evasion.
Collapse
Affiliation(s)
- Marta F M Vieira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Guillem Hernandez
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Qiyun Zhong
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Miguel Arbesú
- Department of NMR-supported Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
- InstaDeep Ltd, 5 Merchant Square, London, UK
| | - Tiago Veloso
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Tiago Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Maria L Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Hugo Monteiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Gad Frankel
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Andreas Zanzoni
- Aix-Marseille Université, Inserm, TAGC, UMR_S1090, Marseille, France
| | - Tiago N Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal.
| |
Collapse
|
14
|
Mantonico MV, De Leo F, Quilici G, Colley LS, De Marchis F, Crippa M, Mezzapelle R, Schulte T, Zucchelli C, Pastorello C, Carmeno C, Caprioglio F, Ricagno S, Giachin G, Ghitti M, Bianchi ME, Musco G. The acidic intrinsically disordered region of the inflammatory mediator HMGB1 mediates fuzzy interactions with CXCL12. Nat Commun 2024; 15:1201. [PMID: 38331917 PMCID: PMC10853541 DOI: 10.1038/s41467-024-45505-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Chemokine heterodimers activate or dampen their cognate receptors during inflammation. The CXCL12 chemokine forms with the fully reduced (fr) alarmin HMGB1 a physiologically relevant heterocomplex (frHMGB1•CXCL12) that synergically promotes the inflammatory response elicited by the G-protein coupled receptor CXCR4. The molecular details of complex formation were still elusive. Here we show by an integrated structural approach that frHMGB1•CXCL12 is a fuzzy heterocomplex. Unlike previous assumptions, frHMGB1 and CXCL12 form a dynamic equimolar assembly, with structured and unstructured frHMGB1 regions recognizing the CXCL12 dimerization surface. We uncover an unexpected role of the acidic intrinsically disordered region (IDR) of HMGB1 in heterocomplex formation and its binding to CXCR4 on the cell surface. Our work shows that the interaction of frHMGB1 with CXCL12 diverges from the classical rigid heterophilic chemokines dimerization. Simultaneous interference with multiple interactions within frHMGB1•CXCL12 might offer pharmacological strategies against inflammatory conditions.
Collapse
Affiliation(s)
- Malisa Vittoria Mantonico
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
| | - Federica De Leo
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- Experimental Therapeutics Program, IFOM ETS - The AIRC Institute of Molecular Oncology and AIRC, Fondazione AIRC per la Ricerca sul Cancro ETS, Milan, Italy
| | - Giacomo Quilici
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Liam Sean Colley
- HMGBiotech S.r.l., 20133, Milan, Italy
- School of Medicine and Surgery, Università Milano-Bicocca, 20126, Milan, Italy
| | - Francesco De Marchis
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Massimo Crippa
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Rosanna Mezzapelle
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Tim Schulte
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Milan, Italy
| | - Chiara Zucchelli
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Chiara Pastorello
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Camilla Carmeno
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Francesca Caprioglio
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Stefano Ricagno
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Milan, Italy
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Gabriele Giachin
- Department of Chemical Sciences (DiSC), University of Padua, 35131, Padova, Italy
| | - Michela Ghitti
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy.
| | - Marco Emilio Bianchi
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Giovanna Musco
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy.
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Condeminas M, Macias MJ. Overcoming challenges in structural biology with integrative approaches and nanobody-derived technologies. Curr Opin Struct Biol 2024; 84:102764. [PMID: 38215529 DOI: 10.1016/j.sbi.2023.102764] [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: 10/02/2023] [Revised: 11/24/2023] [Accepted: 12/11/2023] [Indexed: 01/14/2024]
Abstract
A full understanding of protein structure is key to unraveling how these systems work, how mutations affect their function, and discovering new hotspots for drug discovery. Research tackling this field began with the analysis of globular proteins. In recent years, as technology has improved, research efforts have broadened their focus to include the study of multidomain proteins and the analysis of conformational variability, flexibility, and dynamic systems. Here, we have selected five recent examples that integrate complementary structural methods to provide insight into the behavior of modular, flexible, and transient contacts. We also describe the structural application of domains derived from single-chain antibodies, which are instrumental in overcoming the size limitation of cryogenic electron microscopy (cryoEM) studies. As these methods are continuously developed, they will lead to the interrogation of more complex systems, revealing how large signaling and transcriptional machines are assembled in the context of health and disease.
Collapse
Affiliation(s)
- Miriam Condeminas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 10, Barcelona 08028, Spain; Department of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS-UPF), Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 10, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain.
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Chamberlain SR, Moore S, Grant TD. Fitting high-resolution electron density maps from atomic models to solution scattering data. Biophys J 2023; 122:4567-4581. [PMID: 37924208 PMCID: PMC10719074 DOI: 10.1016/j.bpj.2023.10.034] [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: 06/05/2023] [Revised: 08/29/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023] Open
Abstract
Solution scattering techniques, such as small- and wide-angle X-ray scattering (SWAXS), provide valuable insights into the structure and dynamics of biological macromolecules in solution. In this study, we present an approach to accurately predict solution X-ray scattering profiles at wide angles from atomic models by generating high-resolution electron density maps. Our method accounts for the excluded volume of bulk solvent by calculating unique adjusted atomic volumes directly from the atomic coordinates. This approach eliminates the need for one of the free fitting parameters commonly used in existing algorithms, resulting in improved accuracy of the calculated SWAXS profile. An implicit model of the hydration shell is generated that uses the form factor of water. Two parameters, namely the bulk solvent density and the mean hydration shell contrast, are adjusted to best fit the data. Results using eight publicly available SWAXS profiles show high-quality fits to the data. In each case, the optimized parameter values show small adjustments demonstrating that the default values are close to the true solution. Disabling parameter optimization produces significantly more accurate predicted scattering profiles compared to the leading software. The algorithm is computationally efficient, comparable to the leading software and up to 10 times faster for large molecules. The algorithm is encoded in a command line script called denss.pdb2mrc.py and is available open source as part of the DENSS v1.7.0 software package. In addition to improving the ability to compare atomic models to experimental SWAXS data, these developments pave the way for increasing the accuracy of modeling algorithms using SWAXS data and decreasing the risk of overfitting.
Collapse
Affiliation(s)
- Sarah R Chamberlain
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Stephen Moore
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York.
| |
Collapse
|
21
|
Fenton M, Gregory E, Daughdrill G. Protein disorder and autoinhibition: The role of multivalency and effective concentration. Curr Opin Struct Biol 2023; 83:102705. [PMID: 37778184 PMCID: PMC10841074 DOI: 10.1016/j.sbi.2023.102705] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Regulation of protein binding through autoinhibition commonly occurs via interactions involving intrinsically disordered regions (IDRs). These intramolecular interactions can directly or allosterically inhibit intermolecular protein or DNA binding, regulate enzymatic activity, and control the assembly of large macromolecular complexes. Autoinhibitory interactions mediated by protein disorder are inherently transient, making their identification and characterization challenging. In this review, we explore the structural and functional diversity of disorder-mediated autoinhibition for a variety of biological mechanisms, with a focus on the role of multivalency and effective concentration. We also discuss the evolution of disordered motifs that participate in autoinhibition using examples where sequence conservation varies from high to low. In some cases, identifiable motifs that are essential for autoinhibition remain intact within a rapidly evolving sequence, over long evolutionary distances. Finally, we examine the potential of AlphaFold2 to predict autoinhibitory intramolecular interactions involving IDRs.
Collapse
Affiliation(s)
- Malissa Fenton
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Emily Gregory
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Gary Daughdrill
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
Forsberg Z, Stepnov AA, Tesei G, Wang Y, Buchinger E, Kristiansen SK, Aachmann FL, Arleth L, Eijsink VGH, Lindorff-Larsen K, Courtade G. The effect of linker conformation on performance and stability of a two-domain lytic polysaccharide monooxygenase. J Biol Chem 2023; 299:105262. [PMID: 37734553 PMCID: PMC10598543 DOI: 10.1016/j.jbc.2023.105262] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/05/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
A considerable number of lytic polysaccharide monooxygenases (LPMOs) and other carbohydrate-active enzymes are modular, with catalytic domains being tethered to additional domains, such as carbohydrate-binding modules, by flexible linkers. While such linkers may affect the structure, function, and stability of the enzyme, their roles remain largely enigmatic, as do the reasons for natural variation in length and sequence. Here, we have explored linker functionality using the two-domain cellulose-active ScLPMO10C from Streptomyces coelicolor as a model system. In addition to investigating the WT enzyme, we engineered three linker variants to address the impact of both length and sequence and characterized these using small-angle X-ray scattering, NMR, molecular dynamics simulations, and functional assays. The resulting data revealed that, in the case of ScLPMO10C, linker length is the main determinant of linker conformation and enzyme performance. Both the WT and a serine-rich variant, which have the same linker length, demonstrated better performance compared with those with either a shorter linker or a longer linker. A highlight of our findings was the substantial thermostability observed in the serine-rich variant. Importantly, the linker affects thermal unfolding behavior and enzyme stability. In particular, unfolding studies show that the two domains unfold independently when mixed, whereas the full-length enzyme shows one cooperative unfolding transition, meaning that the impact of linkers in biomass-processing enzymes is more complex than mere structural tethering.
Collapse
Affiliation(s)
- Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Giulio Tesei
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Yong Wang
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark; College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Edith Buchinger
- Vectron Biosolutions AS, Trondheim, Norway; Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Sandra K Kristiansen
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Finn L Aachmann
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Lise Arleth
- X-ray and Neutron Science, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Gaston Courtade
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
| |
Collapse
|
25
|
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.
Collapse
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.)
| |
Collapse
|
26
|
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
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Vedel IM, Papagiannoula A, Naudi-Fabra S, Milles S. Nuclear magnetic resonance/single molecule fluorescence combinations to study dynamic protein systems. Curr Opin Struct Biol 2023; 82:102659. [PMID: 37499445 PMCID: PMC10565672 DOI: 10.1016/j.sbi.2023.102659] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/04/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Many proteins require different structural states or conformations for function, and intrinsically disordered proteins, i.e. proteins without stable three-dimensional structure, are certainly an extreme. Single molecule fluorescence and nuclear magnetic resonance (NMR) spectroscopy are both exceptionally well suited to decipher and describe these states and their interconversion. Different time scales, from picoseconds to several milliseconds, can be addressed by both techniques. The length scales probed and the sample requirements (e.g. concentration, molecular weight, sample complexity) are, however, vastly different, making NMR and single molecule fluorescence an excellent combination for integrated studies. Here, we review recently undertaken approaches for the combined use of NMR and single molecule fluorescence to study protein dynamics.
Collapse
Affiliation(s)
- Ida Marie Vedel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Andromachi Papagiannoula
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Samuel Naudi-Fabra
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sigrid Milles
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany.
| |
Collapse
|
29
|
Abdollahi H, Prestegard JH, Valafar H. Computational modeling multiple conformational states of proteins with residual dipolar coupling data. Curr Opin Struct Biol 2023; 82:102655. [PMID: 37454402 DOI: 10.1016/j.sbi.2023.102655] [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: 03/21/2023] [Revised: 06/06/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
Solution nuclear magnetic resonance spectroscopy provides unique opportunities to study the structure and dynamics of biomolecules in aqueous environments. While spin relaxation methods are well recognized for their ability to probe timescales of motion, residual dipolar couplings (RDCs) provide access to amplitudes and directions of motion, characteristics that are important to the function of these molecules. Although observed in the 1960s, the acquisition and computational analysis of RDCs has gained significant momentum in recent years, and particularly applications to motion in proteins have become more numerous. This trend may well continue as RDCs can easily leverage structures produced by new computational methods (e.g., AlphaFold) to produce functional descriptions. In this report, we provide examples and a summary of the ways that RDCs have been used to confirm the existence of internal dynamics, characterize the type of dynamics, and recover atomic-scale structural ensembles that define the full range of conformational sampling.
Collapse
Affiliation(s)
- Hamed Abdollahi
- Department of Computer Science and Engineering, University of South Carolina, 29201, Columbia, SC, USA.
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
| | - Homayoun Valafar
- Department of Computer Science and Engineering, University of South Carolina, 29201, Columbia, SC, USA.
| |
Collapse
|
30
|
Chen SH, Weiss KL, Stanley C, Bhowmik D. Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing. Protein Sci 2023; 32:e4772. [PMID: 37646172 PMCID: PMC10503416 DOI: 10.1002/pro.4772] [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: 04/28/2023] [Revised: 08/22/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure-function relationships. Due to the different neutron scattering lengths of hydrogen and deuterium, selective labeling and contrast matching in small-angle neutron scattering (SANS) becomes an effective tool to study dynamic structures of disordered systems. However, experimental timescales typically capture measurements averaged over multiple conformations, leaving complex SANS data for disentanglement. We hereby demonstrate an integrated method to elucidate the structural ensemble of a complex formed by two IDRs. We use data from both full contrast and contrast matching with residue-specific deuterium labeling SANS experiments, microsecond all-atom molecular dynamics (MD) simulations with four molecular mechanics force fields, and an autoencoder-based deep learning (DL) algorithm. From our combined approach, we show that selective deuteration provides additional information that helps characterize structural ensembles. We find that among the four force fields, a99SB-disp and CHARMM36m show the strongest agreement with SANS and NMR experiments. In addition, our DL algorithm not only complements conventional structural analysis methods but also successfully differentiates NMR and MD structures which are indistinguishable on the free energy surface. Lastly, we present an ensemble that describes experimental SANS and NMR data better than MD ensembles generated by one single force field and reveal three clusters of distinct conformations. Our results demonstrate a new integrated approach for characterizing structural ensembles of IDPs.
Collapse
Affiliation(s)
- Serena H. Chen
- Computational Sciences and Engineering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Kevin L. Weiss
- Neutron Scattering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Christopher Stanley
- Computational Sciences and Engineering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Debsindhu Bhowmik
- Computational Sciences and Engineering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| |
Collapse
|
31
|
Quek AJ, Cowieson NP, Caradoc-Davies TT, Conroy PJ, Whisstock JC, Law RHP. A High-Throughput Small-Angle X-ray Scattering Assay to Determine the Conformational Change of Plasminogen. Int J Mol Sci 2023; 24:14258. [PMID: 37762561 PMCID: PMC10531915 DOI: 10.3390/ijms241814258] [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: 08/12/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Plasminogen (Plg) is the inactive form of plasmin (Plm) that exists in two major glycoforms, referred to as glycoforms I and II (GI and GII). In the circulation, Plg assumes an activation-resistant "closed" conformation via interdomain interactions and is mediated by the lysine binding site (LBS) on the kringle (KR) domains. These inter-domain interactions can be readily disrupted when Plg binds to lysine/arginine residues on protein targets or free L-lysine and analogues. This causes Plg to convert into an "open" form, which is crucial for activation by host activators. In this study, we investigated how various ligands affect the kinetics of Plg conformational change using small-angle X-ray scattering (SAXS). We began by examining the open and closed conformations of Plg using size-exclusion chromatography (SEC) coupled with SAXS. Next, we developed a high-throughput (HTP) 96-well SAXS assay to study the conformational change of Plg. This method enables us to determine the Kopen value, which is used to directly compare the effect of different ligands on Plg conformation. Based on our analysis using Plg GII, we have found that the Kopen of ε-aminocaproic acid (EACA) is approximately three times greater than that of tranexamic acid (TXA), which is widely recognized as a highly effective ligand. We demonstrated further that Plg undergoes a conformational change when it binds to the C-terminal peptides of the inhibitor α2-antiplasmin (α2AP) and receptor Plg-RKT. Our findings suggest that in addition to the C-terminal lysine, internal lysine(s) are also necessary for the formation of open Plg. Finally, we compared the conformational changes of Plg GI and GII directly and found that the closed form of GI, which has an N-linked glycosylation, is less stable. To summarize, we have successfully determined the response of Plg to various ligand/receptor peptides by directly measuring the kinetics of its conformational changes.
Collapse
Affiliation(s)
- Adam J. Quek
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Nathan P. Cowieson
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Tom T. Caradoc-Davies
- Australian Synchrotron, ANSTO_Melbourne, 800 Blackburn Rd., Clayton, VIC 3168, Australia
| | - Paul J. Conroy
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
| | - James C. Whisstock
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Ruby H. P. Law
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
32
|
Masone A, Zucchelli C, Caruso E, Lavigna G, Eraña H, Giachin G, Tapella L, Comerio L, Restelli E, Raimondi I, Elezgarai SR, De Leo F, Quilici G, Taiarol L, Oldrati M, Lorenzo NL, García-Martínez S, Cagnotto A, Lucchetti J, Gobbi M, Vanni I, Nonno R, Di Bari MA, Tully MD, Cecatiello V, Ciossani G, Pasqualato S, Van Anken E, Salmona M, Castilla J, Requena JR, Banfi S, Musco G, Chiesa R. A tetracationic porphyrin with dual anti-prion activity. iScience 2023; 26:107480. [PMID: 37636075 PMCID: PMC10448035 DOI: 10.1016/j.isci.2023.107480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/09/2022] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Prions are deadly infectious agents made of PrPSc, a misfolded variant of the cellular prion protein (PrPC) which self-propagates by inducing misfolding of native PrPC. PrPSc can adopt different pathogenic conformations (prion strains), which can be resistant to potential drugs, or acquire drug resistance, hampering the development of effective therapies. We identified Zn(II)-BnPyP, a tetracationic porphyrin that binds to distinct domains of native PrPC, eliciting a dual anti-prion effect. Zn(II)-BnPyP binding to a C-terminal pocket destabilizes the native PrPC fold, hindering conversion to PrPSc; Zn(II)-BnPyP binding to the flexible N-terminal tail disrupts N- to C-terminal interactions, triggering PrPC endocytosis and lysosomal degradation, thus reducing the substrate for PrPSc generation. Zn(II)-BnPyP inhibits propagation of different prion strains in vitro, in neuronal cells and organotypic brain cultures. These results identify a PrPC-targeting compound with an unprecedented dual mechanism of action which might be exploited to achieve anti-prion effects without engendering drug resistance.
Collapse
Affiliation(s)
- Antonio Masone
- Laboratory of Prion Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Chiara Zucchelli
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Enrico Caruso
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Giada Lavigna
- Laboratory of Prion Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Hasier Eraña
- Centro de Investigación Cooperativa en Biociencias (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Carlos III National Health Institute, 28029 Madrid, Spain
| | - Gabriele Giachin
- Department of Chemical Sciences (DiSC), University of Padua, 35131 Padua, Italy
| | - Laura Tapella
- Laboratory of Prion Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Liliana Comerio
- Laboratory of Prion Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Elena Restelli
- Laboratory of Prion Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Ilaria Raimondi
- Laboratory of Prion Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Saioa R. Elezgarai
- Laboratory of Prion Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Federica De Leo
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Giacomo Quilici
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Lorenzo Taiarol
- Laboratory of Prion Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Marvin Oldrati
- Laboratory of Prion Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Nuria L. Lorenzo
- CIMUS Biomedical Research Institute and Department of Medical Sciences, University of Santiago de Compostela-IDIS, 15782 Santiago de Compostela, Spain
| | - Sandra García-Martínez
- Centro de Investigación Cooperativa en Biociencias (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Alfredo Cagnotto
- Laboratory of Biochemistry and Protein Chemistry, Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Jacopo Lucchetti
- Laboratory of Pharmacodynamics and Pharmacokinetics, Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Marco Gobbi
- Laboratory of Pharmacodynamics and Pharmacokinetics, Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Ilaria Vanni
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Romolo Nonno
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Michele A. Di Bari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Mark D. Tully
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38000 Grenoble, France
| | - Valentina Cecatiello
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
| | - Giuseppe Ciossani
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
| | - Sebastiano Pasqualato
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
| | - Eelco Van Anken
- Protein Transport and Secretion Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Mario Salmona
- Laboratory of Biochemistry and Protein Chemistry, Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Joaquín Castilla
- Centro de Investigación Cooperativa en Biociencias (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Carlos III National Health Institute, 28029 Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Bizkaia, Spain
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute and Department of Medical Sciences, University of Santiago de Compostela-IDIS, 15782 Santiago de Compostela, Spain
| | - Stefano Banfi
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Giovanna Musco
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Roberto Chiesa
- Laboratory of Prion Neurobiology, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| |
Collapse
|
33
|
Tants JN, Schlundt A. Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA. Chembiochem 2023; 24:e202300110. [PMID: 37466350 DOI: 10.1002/cbic.202300110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/22/2023] [Indexed: 07/20/2023]
Abstract
RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA-regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy can provide high-resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small-angle X-ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large-sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.
Collapse
Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| |
Collapse
|
34
|
Manso JA, Carabias A, Sárkány Z, de Pereda JM, Pereira PJB, Macedo-Ribeiro S. Pathogen-specific structural features of Candida albicans Ras1 activation complex: uncovering new antifungal drug targets. mBio 2023; 14:e0063823. [PMID: 37526476 PMCID: PMC10470544 DOI: 10.1128/mbio.00638-23] [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: 03/13/2023] [Accepted: 06/16/2023] [Indexed: 08/02/2023] Open
Abstract
An important feature associated with Candida albicans pathogenicity is its ability to switch between yeast and hyphal forms, a process in which CaRas1 plays a key role. CaRas1 is activated by the guanine nucleotide exchange factor (GEF) CaCdc25, triggering hyphal growth-related signaling pathways through its conserved GTP-binding (G)-domain. An important function in hyphal growth has also been proposed for the long hypervariable region downstream the G-domain, whose unusual content of polyglutamine stretches and Q/N repeats make CaRas1 unique within Ras proteins. Despite its biological importance, both the structure of CaRas1 and the molecular basis of its activation by CaCdc25 remain unexplored. Here, we show that CaRas1 has an elongated shape and limited conformational flexibility and that its hypervariable region contains helical structural elements, likely forming an intramolecular coiled-coil. Functional assays disclosed that CaRas1-activation by CaCdc25 is highly efficient, with activities up to 2,000-fold higher than reported for human GEFs. The crystal structure of the CaCdc25 catalytic region revealed an active conformation for the α-helical hairpin, critical for CaRas1-activation, unveiling a specific region exclusive to CTG-clade species. Structural studies on CaRas1/CaCdc25 complexes also revealed an interaction surface clearly distinct from that of homologous human complexes. Furthermore, we identified an inhibitory synthetic peptide, prompting the proposal of a key regulatory mechanism for CaCdc25. To our knowledge, this is the first report of specific inhibition of the CaRas1-activation via targeting its GEF. This, together with their unique pathogen-structural features, disclose a set of novel strategies to specifically block this important virulence-related mechanism. IMPORTANCE Candida albicans is the main causative agent of candidiasis, the commonest fungal infection in humans. The eukaryotic nature of C. albicans and the rapid emergence of antifungal resistance raise the challenge of identifying novel drug targets to battle this prevalent and life-threatening disease. CaRas1 and CaCdc25 are key players in the activation of signaling pathways triggering multiple virulence traits, including the yeast-to-hypha interconversion. The structural similarity of the conserved G-domain of CaRas1 to those of human homologs and the lack of structural information on CaCdc25 has impeded progress in targeting these proteins. The unique structural and functional features for CaRas1 and CaCdc25 presented here, together with the identification of a synthetic peptide capable of specifically inhibiting the GEF activity of CaCdc25, open new possibilities to uncover new antifungal drug targets against C. albicans virulence.
Collapse
Affiliation(s)
- José A. Manso
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Arturo Carabias
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas-University of Salamanca, Salamanca, Spain
| | - Zsuzsa Sárkány
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - José M. de Pereda
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas-University of Salamanca, Salamanca, Spain
| | - Pedro José Barbosa Pereira
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| |
Collapse
|
35
|
Mistry H, Kumari S, Aswal VK, Gupta GD. Structural characterization of transcription-coupled repair protein UVSSA and its interaction with TFIIH protein. Int J Biol Macromol 2023; 247:125792. [PMID: 37442507 DOI: 10.1016/j.ijbiomac.2023.125792] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/29/2023] [Accepted: 07/09/2023] [Indexed: 07/15/2023]
Abstract
UV-stimulated scaffold protein A (UVSSA) is a key protein in the Transcription-Coupled Nucleotide Excision Repair (TC-NER) pathway. UVSSA, an intrinsically disordered protein, interacts with multiple members of the pathway, tethering them into the complex. Several studies have reported that UVSSA recruits Transcription Factor IIH (TFIIH) via direct interaction, following which CSB is degraded and the lesion recognition TC-NER complex dissociates from the damage site to facilitate the DNA repair. Structural insights into these events remain largely unknown. Herein, we have investigated the interaction of human UVSSA with the Pleckstrin-Homology-domain of p62 subunit of TFIIH (p62-PHD) using biophysical techniques. We observed that UVSSA forms a stable complex with the p62-PHD in vitro. Small-angle scattering measurements using X-rays and neutrons revealed a significant change in pair-distance distribution function for UVSSA662/p62-PHD complex compared to UVSSA alone. Additionally, a significant decrease was observed in the radius of gyration of the complex. Our findings suggest that TFIIH binding to UVSSA causes significant conformational changes in UVSSA. We hypothesize that these conformational changes play an important role in the dissociation of the lesion recognition TC-NER complex.
Collapse
Affiliation(s)
- Hiral Mistry
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Shweta Kumari
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Gagan D Gupta
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India.
| |
Collapse
|
36
|
Pan Z, Mu J, Chen HF. Balanced Three-Point Water Model OPC3-B for Intrinsically Disordered and Ordered Proteins. J Chem Theory Comput 2023; 19:4837-4850. [PMID: 37452752 DOI: 10.1021/acs.jctc.3c00297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Intrinsically disordered proteins (IDPs) play a critical role in many biological processes. Due to the inherent structural flexibility of IDPs, experimental methods present significant challenges for sampling their conformational information at the atomic level. Therefore, molecular dynamics (MD) simulations have emerged as the primary tools for modeling IDPs whose accuracy depend on force field and water model. To enhance the accuracy of physical modeling of IDPs, several force fields have been developed. However, current water models lack precision and underestimate the interaction between water molecules and proteins. Here, we used Monte-Carlo re-weighting method to re-parameterize a three-point water model based on OPC3 for IDPs (named OPC3-B). We benchmarked the performance of OPC3-B compared with nine different water models for 10 IDPs and three ordered proteins. The results indicate that the performance of OPC3-B is better than other water models for both IDPs and ordered proteins. At the same time, OPC3-B possess the power of transferability with other force field to simulate IDPs. This newly developed water model can be used to insight into the research of sequence-disordered-function paradigm for IDPs.
Collapse
Affiliation(s)
- Zhengsong Pan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- 4+4 Medical Doctor Program, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Junxi Mu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Center for Bioinformation Technology, Shanghai 200235, China
| |
Collapse
|
37
|
Hamley IW, Castelletto V. Small-angle scattering techniques for peptide and peptide hybrid nanostructures and peptide-based biomaterials. Adv Colloid Interface Sci 2023; 318:102959. [PMID: 37473606 DOI: 10.1016/j.cis.2023.102959] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023]
Abstract
The use of small-angle scattering (SAS) in the study of the self-assembly of peptides and peptide conjugates (lipopeptides, polymer-peptide conjugates and others) is reviewed, highlighting selected research that illustrates different methods and analysis techniques. Both small-angle x-ray scattering (SAXS) and small-angle neutron scattering (SANS) are considered along with examples that exploit their unique capabilities. For SAXS, this includes the ability to perform rapid measurements enabling high throughput or fast kinetic studies and measurements under dilute conditions. For SANS, contrast variation using H2O/D2O mixtures enables the study of peptides interacting with lipids and TR-SANS (time-resolved SANS) studies of exchange kinetics and/or peptide-induced structural changes. Examples are provided of studies measuring form factors of different self-assembled structures (micelles, fibrils, nanotapes, nanotubes etc) as well as structure factors from ordered phases (lyotropic mesophases), peptide gels and hybrid materials such as membranes formed by mixing peptides with polysaccharides or peptide/liposome mixtures. SAXS/WAXS (WAXS: wide-angle x-ray scattering) on peptides and peptide hybrids is also discussed, and the review concludes with a perspective on potential future directions for research in the field.
Collapse
Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK.
| | - Valeria Castelletto
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| |
Collapse
|
38
|
Healey RD, Couillaud L, Hoh F, Mouhand A, Fouillen A, Couvineau P, Granier S, Leyrat C. Structure, dynamics and transferability of the metal-dependent polyhistidine tetramerization motif TetrHis for single-chain Fv antibodies. Commun Chem 2023; 6:160. [PMID: 37507458 PMCID: PMC10382482 DOI: 10.1038/s42004-023-00962-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
The polyhistidine (6XHis) motif is one of the most ubiquitous protein purification tags. The 6XHis motif enables the binding of tagged proteins to various metals, which can be advantageously used for purification with immobilized metal affinity chromatography. Despite its popularity, protein structures encompassing metal-bound 6XHis are rare. Here, we obtained a 2.5 Å resolution crystal structure of a single chain Fv antibody (scFv) bearing a C-terminal sortase motif, 6XHis and TwinStrep tags (LPETGHHHHHHWSHPQFEK[G3S]3WSHPQFEK). The structure, obtained in the presence of cobalt, reveals a unique tetramerization motif (TetrHis) stabilized by 8 Co2+ ions. The TetrHis motif contains four 6 residues-long β-strands, and each metal center coordinates 3 to 5 residues, including all 6XHis histidines. By combining dynamic light scattering, small angle x-ray scattering and molecular dynamics simulations, We investigated the influence of Co2+ on the conformational dynamics of scFv 2A2, observing an open/close equilibrium of the monomer and the formation of cobalt-stabilized tetramers. By using a similar scFv design, we demonstrate the transferability of the tetramerization property. This novel metal-dependent tetramerization motif might be used as a fiducial marker for cryoelectron microscopy of scFv complexes, or even provide a starting point for designing metal-loaded biomaterials.
Collapse
Affiliation(s)
- Robert D Healey
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Louise Couillaud
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - François Hoh
- Centre de Biologie Structurale, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Assia Mouhand
- Centre de Biologie Structurale, University of Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Pierre Couvineau
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Cédric Leyrat
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France.
| |
Collapse
|
39
|
Koren G, Meir S, Holschuh L, Mertens HDT, Ehm T, Yahalom N, Golombek A, Schwartz T, Svergun DI, Saleh OA, Dzubiella J, Beck R. Intramolecular structural heterogeneity altered by long-range contacts in an intrinsically disordered protein. Proc Natl Acad Sci U S A 2023; 120:e2220180120. [PMID: 37459524 PMCID: PMC10372579 DOI: 10.1073/pnas.2220180120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 06/02/2023] [Indexed: 07/20/2023] Open
Abstract
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of intrinsically disordered proteins (IDPs) and protein regions that fluctuate between ensembles of numerous conformations. Therefore, to understand their biological function, it is critical to depict how the structural ensemble statistics correlate to the IDPs' amino acid sequence. Here, using small-angle X-ray scattering and time-resolved Förster resonance energy transfer (trFRET), we study the intramolecular structural heterogeneity of the neurofilament low intrinsically disordered tail domain (NFLt). Using theoretical results of polymer physics, we find that the Flory scaling exponent of NFLt subsegments correlates linearly with their net charge, ranging from statistics of ideal to self-avoiding chains. Surprisingly, measuring the same segments in the context of the whole NFLt protein, we find that regardless of the peptide sequence, the segments' structural statistics are more expanded than when measured independently. Our findings show that while polymer physics can, to some level, relate the IDP's sequence to its ensemble conformations, long-range contacts between distant amino acids play a crucial role in determining intramolecular structures. This emphasizes the necessity of advanced polymer theories to fully describe IDPs ensembles with the hope that it will allow us to model their biological function.
Collapse
Affiliation(s)
- Gil Koren
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
| | - Sagi Meir
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
| | - Lennard Holschuh
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
| | | | - Tamara Ehm
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, MünchenD-80539, Germany
| | - Nadav Yahalom
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Adina Golombek
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Tal Schwartz
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg22607, Germany
| | - Omar A. Saleh
- BMSE Program, University of California, Santa Barbara, CA93110
- Materials Department, University of California, Santa Barbara, CA93110
| | - Joachim Dzubiella
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
| | - Roy Beck
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
| |
Collapse
|
40
|
Makraki E, Miliara S, Pagkalos M, Kokkinidis M, Mylonas E, Fadouloglou VE. Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA. Front Mol Biosci 2023; 10:1219668. [PMID: 37555016 PMCID: PMC10406553 DOI: 10.3389/fmolb.2023.1219668] [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: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023] Open
Abstract
The non-coding 6S RNA is a master regulator of the cell cycle in bacteria which binds to the RNA polymerase-σ70 holoenzyme during the stationary phase to inhibit transcription from the primary σ factor. Inhibition is reversed upon outgrowth from the stationary phase by synthesis of small product RNA transcripts (pRNAs). 6S and its complex with a pRNA were structurally characterized using Small Angle X-ray Scattering. The 3D models of 6S and 6S:pRNA complex presented here, demonstrate that the fairly linear and extended structure of 6S undergoes a major conformational change upon binding to pRNA. In particular, 6S:pRNA complex formation is associated with a compaction of the overall 6S size and an expansion of its central domain. Our structural models are consistent with the hypothesis that the resultant particle has a shape and size incompatible with binding to RNA polymerase-σ70. Overall, by use of an optimized in vivo methodological approach, especially useful for structural studies, our study considerably improves our understanding of the structural basis of 6S regulation by offering a mechanistic glimpse of the 6S transcriptional control.
Collapse
Affiliation(s)
- Eleni Makraki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Sophia Miliara
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Michalis Pagkalos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Vasiliki E. Fadouloglou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Komotini, Greece
| |
Collapse
|
41
|
Goretzki B, Wiedemann C, McCray BA, Schäfer SL, Jansen J, Tebbe F, Mitrovic SA, Nöth J, Cabezudo AC, Donohue JK, Jeffries CM, Steinchen W, Stengel F, Sumner CJ, Hummer G, Hellmich UA. Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity. Nat Commun 2023; 14:4165. [PMID: 37443299 PMCID: PMC10344929 DOI: 10.1038/s41467-023-39808-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Intrinsically disordered regions (IDRs) are essential for membrane receptor regulation but often remain unresolved in structural studies. TRPV4, a member of the TRP vanilloid channel family involved in thermo- and osmosensation, has a large N-terminal IDR of approximately 150 amino acids. With an integrated structural biology approach, we analyze the structural ensemble of the TRPV4 IDR and the network of antagonistic regulatory elements it encodes. These modulate channel activity in a hierarchical lipid-dependent manner through transient long-range interactions. A highly conserved autoinhibitory patch acts as a master regulator by competing with PIP2 binding to attenuate channel activity. Molecular dynamics simulations show that loss of the interaction between the PIP2-binding site and the membrane reduces the force exerted by the IDR on the structured core of TRPV4. This work demonstrates that IDR structural dynamics are coupled to TRPV4 activity and highlights the importance of IDRs for TRP channel function and regulation.
Collapse
Affiliation(s)
- Benedikt Goretzki
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Jena, Germany
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main, Germany
| | - Christoph Wiedemann
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Jena, Germany
| | - Brett A McCray
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stefan L Schäfer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Jasmin Jansen
- Department of Biology, University of Konstanz, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Frederike Tebbe
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Jena, Germany
| | - Sarah-Ana Mitrovic
- Department of Chemistry, Section Biochemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Julia Nöth
- Department of Chemistry, Section Biochemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Ainara Claveras Cabezudo
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Frankfurt am Main, Germany
| | - Jack K Donohue
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cy M Jeffries
- European Molecular Biology Laboratory, EMBL Hamburg Unit, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ute A Hellmich
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Jena, Germany.
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
| |
Collapse
|
42
|
Devlin T, Fleming PJ, Loza N, Fleming KG. Generation of unfolded outer membrane protein ensembles defined by hydrodynamic properties. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:415-425. [PMID: 36899114 DOI: 10.1007/s00249-023-01639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
Outer membrane proteins (OMPs) must exist as an unfolded ensemble while interacting with a chaperone network in the periplasm of Gram-negative bacteria. Here, we developed a method to model unfolded OMP (uOMP) conformational ensembles using the experimental properties of two well-studied OMPs. The overall sizes and shapes of the unfolded ensembles in the absence of a denaturant were experimentally defined by measuring the sedimentation coefficient as a function of urea concentration. We used these data to model a full range of unfolded conformations by parameterizing a targeted coarse-grained simulation protocol. The ensemble members were further refined by short molecular dynamics simulations to reflect proper torsion angles. The final conformational ensembles have polymer properties different from unfolded soluble and intrinsically disordered proteins and reveal inherent differences in the unfolded states that necessitate further investigation. Building these uOMP ensembles advances the understanding of OMP biogenesis and provides essential information for interpreting structures of uOMP-chaperone complexes.
Collapse
Affiliation(s)
- Taylor Devlin
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Patrick J Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Nicole Loza
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Karen G Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
| |
Collapse
|
43
|
Wang J, Koduru T, Harish B, McCallum SA, Larsen KP, Patel KS, Peters EV, Gillilan RE, Puglisi EV, Puglisi JD, Makhatadze G, Royer CA. Pressure pushes tRNA Lys3 into excited conformational states. Proc Natl Acad Sci U S A 2023; 120:e2215556120. [PMID: 37339210 PMCID: PMC10293818 DOI: 10.1073/pnas.2215556120] [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: 09/11/2022] [Accepted: 05/16/2023] [Indexed: 06/22/2023] Open
Abstract
Conformational dynamics play essential roles in RNA function. However, detailed structural characterization of excited states of RNA remains challenging. Here, we apply high hydrostatic pressure (HP) to populate excited conformational states of tRNALys3, and structurally characterize them using a combination of HP 2D-NMR, HP-SAXS (HP-small-angle X-ray scattering), and computational modeling. HP-NMR revealed that pressure disrupts the interactions of the imino protons of the uridine and guanosine U-A and G-C base pairs of tRNALys3. HP-SAXS profiles showed a change in shape, but no change in overall extension of the transfer RNA (tRNA) at HP. Configurations extracted from computational ensemble modeling of HP-SAXS profiles were consistent with the NMR results, exhibiting significant disruptions to the acceptor stem, the anticodon stem, and the D-stem regions at HP. We propose that initiation of reverse transcription of HIV RNA could make use of one or more of these excited states.
Collapse
Affiliation(s)
- Jinqiu Wang
- Graduate Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Tejaswi Koduru
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY12180
| | | | - Scott A. McCallum
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Kevin P. Larsen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Karishma S. Patel
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Edgar V. Peters
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY12180
| | | | - Elisabetta V. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Joseph D. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY12180
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY12180
| |
Collapse
|
44
|
Watkins M, Wang H, Burnim A, Ando N. Conformational switching and flexibility in cobalamin-dependent methionine synthase studied by small-angle X-ray scattering and cryoelectron microscopy. Proc Natl Acad Sci U S A 2023; 120:e2302531120. [PMID: 37339208 PMCID: PMC10293825 DOI: 10.1073/pnas.2302531120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Cobalamin-dependent methionine synthase (MetH) catalyzes the synthesis of methionine from homocysteine and 5-methyltetrahydrofolate (CH3-H4folate) using the unique chemistry of its cofactor. In doing so, MetH links the cycling of S-adenosylmethionine with the folate cycle in one-carbon metabolism. Extensive biochemical and structural studies on Escherichia coli MetH have shown that this flexible, multidomain enzyme adopts two major conformations to prevent a futile cycle of methionine production and consumption. However, as MetH is highly dynamic as well as both a photosensitive and oxygen-sensitive metalloenzyme, it poses special challenges for structural studies, and existing structures have necessarily come from a "divide and conquer" approach. In this study, we investigate E. coli MetH and a thermophilic homolog from Thermus filiformis using small-angle X-ray scattering (SAXS), single-particle cryoelectron microscopy (cryo-EM), and extensive analysis of the AlphaFold2 database to present a structural description of the full-length MetH in its entirety. Using SAXS, we describe a common resting-state conformation shared by both active and inactive oxidation states of MetH and the roles of CH3-H4folate and flavodoxin in initiating turnover and reactivation. By combining SAXS with a 3.6-Å cryo-EM structure of the T. filiformis MetH, we show that the resting-state conformation consists of a stable arrangement of the catalytic domains that is linked to a highly mobile reactivation domain. Finally, by combining AlphaFold2-guided sequence analysis and our experimental findings, we propose a general model for functional switching in MetH.
Collapse
Affiliation(s)
- Maxwell B. Watkins
- Department of Chemistry, Princeton University, Princeton, NJ08544
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Haoyue Wang
- Field of Biophysics, Cornell University, Ithaca, NY14853
| | - Audrey Burnim
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ08544
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- Field of Biophysics, Cornell University, Ithaca, NY14853
| |
Collapse
|
45
|
Tarrés-Solé A, Battistini F, Gerhold JM, Piétrement O, Martínez-García B, Ruiz-López E, Lyonnais S, Bernadó P, Roca J, Orozco M, Le Cam E, Sedman J, Solà M. Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism. Nucleic Acids Res 2023; 51:5864-5882. [PMID: 37207342 PMCID: PMC10287934 DOI: 10.1093/nar/gkad397] [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: 07/19/2022] [Revised: 04/01/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
The compaction of mitochondrial DNA (mtDNA) is regulated by architectural HMG-box proteins whose limited cross-species similarity suggests diverse underlying mechanisms. Viability of Candida albicans, a human antibiotic-resistant mucosal pathogen, is compromised by altering mtDNA regulators. Among them, there is the mtDNA maintenance factor Gcf1p, which differs in sequence and structure from its human and Saccharomyces cerevisiae counterparts, TFAM and Abf2p. Our crystallographic, biophysical, biochemical and computational analysis showed that Gcf1p forms dynamic protein/DNA multimers by a combined action of an N-terminal unstructured tail and a long helix. Furthermore, an HMG-box domain canonically binds the minor groove and dramatically bends the DNA while, unprecedentedly, a second HMG-box binds the major groove without imposing distortions. This architectural protein thus uses its multiple domains to bridge co-aligned DNA segments without altering the DNA topology, revealing a new mechanism of mtDNA condensation.
Collapse
Affiliation(s)
- Aleix Tarrés-Solé
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Department of Biochemistry, University of Barcelona, Barcelona 08028, Spain
| | - Joachim M Gerhold
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Olivier Piétrement
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy Campus, 114 rue Edouard Vaillant 94805VillejuifCedex, France
| | | | - Elena Ruiz-López
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Sébastien Lyonnais
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Inserm, CNRS and Université de Montpellier, France, Sébastien Lyonnais, UAR 3725 CNRS, Université de Montpellier, 34000 Montpellier, France
| | - Joaquim Roca
- Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Department of Biochemistry, University of Barcelona, Barcelona 08028, Spain
| | - Eric Le Cam
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy Campus, 114 rue Edouard Vaillant 94805VillejuifCedex, France
| | - Juhan Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Maria Solà
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| |
Collapse
|
46
|
Chamberlain SR, Moore S, Grant TD. Fitting high-resolution electron density maps from atomic models to solution scattering data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543451. [PMID: 37398274 PMCID: PMC10312546 DOI: 10.1101/2023.06.02.543451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Solution scattering techniques, such as small and wide-angle X-ray scattering (SWAXS), provide valuable insights into the structure and dynamics of biological macromolecules in solution. In this study, we present an approach to accurately predict solution X-ray scattering profiles at wide angles from atomic models by generating high-resolution electron density maps. Our method accounts for the excluded volume of bulk solvent by calculating unique adjusted atomic volumes directly from the atomic coordinates. This approach eliminates the need for a free fitting parameter commonly used in existing algorithms, resulting in improved accuracy of the calculated SWAXS profile. An implicit model of the hydration shell is generated which uses the form factor of water. Two parameters, namely the bulk solvent density and the mean hydration shell contrast, are adjusted to best fit the data. Results using eight publicly available SWAXS profiles show high quality fits to the data. In each case, the optimized parameter values show small adjustments demonstrating that the default values are close to the true solution. Disabling parameter optimization results in a significant improvement of the calculated scattering profiles compared to the leading software. The algorithm is computationally efficient, showing more than tenfold reduction in execution time compared to the leading software. The algorithm is encoded in a command line script called denss.pdb2mrc.py and is available open source as part of the DENSS v1.7.0 software package (https://github.com/tdgrant1/denss). In addition to improving the ability to compare atomic models to experimental SWAXS data, these developments pave the way for increasing the accuracy of modeling algorithms utilizing SWAXS data while decreasing the risk of overfitting.
Collapse
Affiliation(s)
- Sarah R. Chamberlain
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| | - Stephen Moore
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| | - Thomas D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| |
Collapse
|
47
|
Del Giudice A, Gurrieri L, Galantini L, Fanti S, Trost P, Sparla F, Fermani S. Conformational Disorder Analysis of the Conditionally Disordered Protein CP12 from Arabidopsis thaliana in Its Different Redox States. Int J Mol Sci 2023; 24:ijms24119308. [PMID: 37298260 DOI: 10.3390/ijms24119308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
CP12 is a redox-dependent conditionally disordered protein universally distributed in oxygenic photosynthetic organisms. It is primarily known as a light-dependent redox switch regulating the reductive step of the metabolic phase of photosynthesis. In the present study, a small angle X-ray scattering (SAXS) analysis of recombinant Arabidopsis CP12 (AtCP12) in a reduced and oxidized form confirmed the highly disordered nature of this regulatory protein. However, it clearly pointed out a decrease in the average size and a lower level of conformational disorder upon oxidation. We compared the experimental data with the theoretical profiles of pools of conformers generated with different assumptions and show that the reduced form is fully disordered, whereas the oxidized form is better described by conformers comprising both the circular motif around the C-terminal disulfide bond detected in previous structural analysis and the N-terminal disulfide bond. Despite the fact that disulfide bridges are usually thought to confer rigidity to protein structures, in the oxidized AtCP12, their presence coexists with a disordered nature. Our results rule out the existence of significant amounts of structured and compact conformations of free AtCP12 in a solution, even in its oxidized form, thereby highlighting the importance of recruiting partner proteins to complete its structured final folding.
Collapse
Affiliation(s)
| | - Libero Gurrieri
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Luciano Galantini
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy
| | - Silvia Fanti
- Department of Chemistry "G. Ciamician", University of Bologna, 40126 Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Francesca Sparla
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Simona Fermani
- Department of Chemistry "G. Ciamician", University of Bologna, 40126 Bologna, Italy
- Interdepartmental Centre for Industrial Research Health Sciences & Technologies, University of Bologna, 40064 Bologna, Italy
| |
Collapse
|
48
|
Jones RD, Jones AM. Model of ligand-triggered information transmission in G-protein coupled receptor complexes. Front Endocrinol (Lausanne) 2023; 14:1111594. [PMID: 37361529 PMCID: PMC10286511 DOI: 10.3389/fendo.2023.1111594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/21/2023] [Indexed: 06/28/2023] Open
Abstract
We present a model for the effects of ligands on information transmission in G-Protein Coupled Receptor (GPCR) complexes. The model is built ab initio entirely on principles of statistical mechanics and tenets of information transmission theory and was validated in part using agonist-induced effector activity and signaling bias for the angiotensin- and adrenergic-mediated signaling pathways, with in vitro observations of phosphorylation sites on the C tail of the GPCR complex, and single-cell information-transmission experiments. The model extends traditional kinetic models that form the basis for many existing models of GPCR signaling. It is based on maximizing the rates of entropy production and information transmission through the GPCR complex. The model predicts that (1) phosphatase-catalyzed reactions, as opposed to kinase-catalyzed reactions, on the C-tail and internal loops of the GPCR are responsible for controlling the signaling activity, (2) signaling favors the statistical balance of the number of switches in the ON state and the number in the OFF state, and (3) biased-signaling response depends discontinuously on ligand concentration.
Collapse
Affiliation(s)
- Roger D. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- European Centre for Living Technology, Ca’ Foscari University of Venice, Venice, Italy
- Systems Engineering and Research Center, Stevens Institute of Technology, Hoboken, NJ, United States
| | - Alan M. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
49
|
Svilenov HL, Delhommel F, Siebenmorgen T, Rührnößl F, Popowicz GM, Reiter A, Sattler M, Brockmeyer C, Buchner J. Extrinsic stabilization of antiviral ACE2-Fc fusion proteins targeting SARS-CoV-2. Commun Biol 2023; 6:386. [PMID: 37031320 PMCID: PMC10082628 DOI: 10.1038/s42003-023-04762-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
The angiotensin-converting enzyme 2 (ACE2) is a viral receptor used by sarbecoviruses to infect cells. Fusion proteins comprising extracellular ACE2 domains and the Fc part of immunoglobulins exhibit high virus neutralization efficiency, but the structure and stability of these molecules are poorly understood. We show that although the hinge between the ACE2 and the IgG4-Fc is highly flexible, the conformational dynamics of the two ACE2 domains is restricted by their association. Interestingly, the conformational stability of the ACE2 moiety is much lower than that of the Fc part. We found that chemical compounds binding to ACE2, such as DX600 and MLN4760, can be used to strongly increase the thermal stability of the ACE2 by different mechanisms. Together, our findings reveal a general concept for stabilizing the labile receptor segments of therapeutic antiviral fusion proteins by chemical compounds.
Collapse
Affiliation(s)
- Hristo L Svilenov
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany.
- Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | - Till Siebenmorgen
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | - Florian Rührnößl
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | | | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | | | - Johannes Buchner
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany.
| |
Collapse
|
50
|
Barclay A, Kragelund BB, Arleth L, Pedersen MC. Modeling of flexible membrane-bound biomolecular complexes for solution small-angle scattering. J Colloid Interface Sci 2023; 635:611-621. [PMID: 36634513 DOI: 10.1016/j.jcis.2022.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/18/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Recent advances in protein expression protocols, sample handling, and experimental set up of small-angle scattering experiments have allowed users of the technique to structurally investigate biomolecules of growing complexity and structural disorder. Notable examples include intrinsically disordered proteins, multi-domain proteins and membrane proteins in suitable carrier systems. Here, we outline a modeling scheme for calculating the scattering profiles from such complex samples. This kind of modeling is necessary for structural information to be refined from the corresponding data. The scheme bases itself on a hybrid of classical form factor based modeling and the well-known spherical harmonics-based formulation of small-angle scattering amplitudes. Our framework can account for flexible domains alongside other structurally elaborate components of the molecular system in question. We demonstrate the utility of this modeling scheme through a recent example of a structural model of the growth hormone receptor membrane protein in a phospholipid bilayer nanodisc which is refined against experimental SAXS data. Additionally we investigate how the scattering profiles from the complex would appear under different scattering contrasts. For each contrast situation we discuss what structural information is contained and the related consequences for modeling of the data.
Collapse
Affiliation(s)
- Abigail Barclay
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark.
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| |
Collapse
|