1
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Pichkur EB, Vorovitch MF, Ivanova AL, Protopopova EV, Loktev VB, Osolodkin DI, Ishmukhametov AA, Samygina VR. The structure of inactivated mature tick-borne encephalitis virus at 3.0 Å resolution. Emerg Microbes Infect 2024; 13:2313849. [PMID: 38465849 DOI: 10.1080/22221751.2024.2313849] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024]
Abstract
Tick-borne encephalitis virus (TBEV) causes a severe disease, tick-borne encephalitis (TBE), that has a substantial epidemiological importance for Northern Eurasia. Between 10,000 and 15,000 TBE cases are registered annually despite the availability of effective formaldehyde-inactivated full-virion vaccines due to insufficient vaccination coverage, as well as sporadic cases of vaccine breakthrough. The development of improved vaccines would benefit from the atomic resolution structure of the antigen. Here we report the refined single-particle cryo-electron microscopy (cryo-EM) structure of the inactivated mature TBEV vaccine strain Sofjin-Chumakov (Far-Eastern subtype) at a resolution of 3.0 Å. The increase of the resolution with respect to the previously published structures of TBEV strains Hypr and Kuutsalo-14 (European subtype) was reached due to improvement of the virus sample quality achieved by the optimized preparation methods. All the surface epitopes of TBEV were structurally conserved in the inactivated virions. ELISA studies with monoclonal antibodies supported the hypothesis of TBEV protein shell cross-linking upon inactivation with formaldehyde.
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Affiliation(s)
| | - Mikhail F Vorovitch
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Alla L Ivanova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
| | - Elena V Protopopova
- State Research Center of Virology and Biotechnology "Vector", Novosibirsk, Russian Federation
| | - Valery B Loktev
- State Research Center of Virology and Biotechnology "Vector", Novosibirsk, Russian Federation
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russian Federation
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2
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Miyasaka Y, Yokoyama K, Kozono T, Kitano Y, Miyazaki T, Sakaguchi M, Nishikawa A, Tonozuka T. Structural basis for the recognition of α-1,6-branched α-glucan by GH13_47 α-amylase from Rhodothermus marinus. Proteins 2024; 92:984-997. [PMID: 38641972 DOI: 10.1002/prot.26695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/22/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Glycoside hydrolase (GH) family 13 is among the main families of enzymes acting on starch; recently, subfamily 47 of GH13 (GH13_47) has been established. The crystal structure and function of a GH13_47 enzyme from Bacteroides ovatus has only been reported to date. This enzyme has α-amylase activity, while the GH13_47 enzymes comprise approximately 800-900 amino acid residues which are almost double those of typical α-amylases. It is important to know how different the GH13_47 enzymes are from other α-amylases. Rhodothermus marinus JCM9785, a thermophilic bacterium, possesses a gene for the GH13_47 enzyme, which is designated here as RmGH13_47A. Its structure has been predicted to be composed of seven domains: N1, N2, N3, A, B, C, and D. We constructed a plasmid encoding Gly266-Glu886, which contains the N3, A, B, and C domains and expressed the protein in Escherichia coli. The enzyme hydrolyzed starch and pullulan by a neopullulanase-type action. Additionally, the enzyme acted on maltotetraose, and saccharides with α-1,6-glucosidic linkages were observed in the products. Following the replacement of the catalytic residue Asp563 with Ala, the crystal structure of the variant D563A in complex with the enzymatic products from maltotetraose was determined; as a result, electron density for an α-1,6-branched pentasaccharide was observed in the catalytic pocket, and Ile762 and Asp763 interacted with the branched chain of the pentasaccharide. These findings suggest that RmGH13_47A is an α-amylase that prefers α-1,6-branched parts of starch to produce oligosaccharides.
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Affiliation(s)
- Yuki Miyasaka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Kohei Yokoyama
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takuma Kozono
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yoshikazu Kitano
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takatsugu Miyazaki
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Masayoshi Sakaguchi
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
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3
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Lee K, Barone M, Waterbury AL, Jiang H, Nam E, DuBois-Coyne SE, Whedon SD, Wang ZA, Caroli J, Neal K, Ibeabuchi B, Dhoondia Z, Kuroda MI, Liau BB, Beck S, Mattevi A, Cole PA. Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1. Nat Chem Biol 2024:10.1038/s41589-024-01671-9. [PMID: 38965385 DOI: 10.1038/s41589-024-01671-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 06/07/2024] [Indexed: 07/06/2024]
Abstract
Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation, but its functional significance in cells has been difficult to discern. Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine-specific demethylase 1 (LSD1). In the present study, we engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. K562 cells with the Y391K LSD1 CRISPR knockin show decreased expression of a set of genes associated with cellular adhesion and myeloid leukocyte activation. Chromatin profiling revealed that the cis-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme.
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Affiliation(s)
- Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Marco Barone
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy
| | - Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eunju Nam
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sarah E DuBois-Coyne
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jonatan Caroli
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy
| | - Katherine Neal
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Brian Ibeabuchi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zuzer Dhoondia
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Samuel Beck
- Department of Dermatology, Boston University School of Medicine & Boston Medical Center, Boston, MA, USA.
| | - Andrea Mattevi
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy.
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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4
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Nasseri SA, Lazarski AC, Lemmer IL, Zhang CY, Brencher E, Chen HM, Sim L, Panwar D, Betschart L, Worrall LJ, Brumer H, Strynadka NCJ, Withers SG. An alternative broad-specificity pathway for glycan breakdown in bacteria. Nature 2024; 631:199-206. [PMID: 38898276 DOI: 10.1038/s41586-024-07574-y] [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: 06/22/2023] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
The vast majority of glycosidases characterized to date follow one of the variations of the 'Koshland' mechanisms1 to hydrolyse glycosidic bonds through substitution reactions. Here we describe a large-scale screen of a human gut microbiome metagenomic library using an assay that selectively identifies non-Koshland glycosidase activities2. Using this, we identify a cluster of enzymes with extremely broad substrate specificities and thoroughly characterize these, mechanistically and structurally. These enzymes not only break glycosidic linkages of both α and β stereochemistry and multiple connectivities, but also cleave substrates that are not hydrolysed by standard glycosidases. These include thioglycosides, such as the glucosinolates from plants, and pseudoglycosidic bonds of pharmaceuticals such as acarbose. This is achieved through a distinct mechanism of hydrolysis that involves oxidation/reduction and elimination/hydration steps, each catalysed by enzyme modules that are in many cases interchangeable between organisms and substrate classes. Homologues of these enzymes occur in both Gram-positive and Gram-negative bacteria associated with the gut microbiome and other body parts, as well as other environments, such as soil and sea. Such alternative step-wise mechanisms appear to constitute largely unrecognized but abundant pathways for glycan degradation as part of the metabolism of carbohydrates in bacteria.
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Affiliation(s)
- Seyed Amirhossein Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aleksander C Lazarski
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Center for Blood Research, University of British Columbia, Vancouver, Canada
| | - Imke L Lemmer
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chloe Y Zhang
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eva Brencher
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hong-Ming Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lyann Sim
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Deepesh Panwar
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leo Betschart
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Center for Blood Research, University of British Columbia, Vancouver, Canada
| | - Harry Brumer
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Center for Blood Research, University of British Columbia, Vancouver, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
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5
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Skubák P. Deep-learning map segmentation for protein X-ray crystallographic structure determination. Acta Crystallogr D Struct Biol 2024; 80:528-534. [PMID: 38935341 PMCID: PMC11220839 DOI: 10.1107/s2059798324005217] [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: 04/09/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
When solving a structure of a protein from single-wavelength anomalous diffraction X-ray data, the initial phases obtained by phasing from an anomalously scattering substructure usually need to be improved by an iterated electron-density modification. In this manuscript, the use of convolutional neural networks (CNNs) for segmentation of the initial experimental phasing electron-density maps is proposed. The results reported demonstrate that a CNN with U-net architecture, trained on several thousands of electron-density maps generated mainly using X-ray data from the Protein Data Bank in a supervised learning, can improve current density-modification methods.
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Affiliation(s)
- Pavol Skubák
- Leiden University Medical Center2333 ZALeidenThe Netherlands
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6
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Prajapati A, Palva A, von Ossowski I, Krishnan V. The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis. Acta Crystallogr D Struct Biol 2024; 80:474-492. [PMID: 38935340 DOI: 10.1107/s2059798324005114] [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: 03/25/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Sortase-dependent pili are long surface appendages that mediate attachment, colonization and biofilm formation in certain genera and species of Gram-positive bacteria. Ligilactobacillus ruminis is an autochthonous gut commensal that relies on sortase-dependent LrpCBA pili for host adherence and persistence. X-ray crystal structure snapshots of the backbone pilin LrpA were captured in two atypical bent conformations leading to a zigzag morphology in the LrpCBA pilus structure. Small-angle X-ray scattering and structural analysis revealed that LrpA also adopts the typical linear conformation, resulting in an elongated pilus morphology. Various conformational analyses and biophysical experiments helped to demonstrate that a hinge region located at the end of the flexible N-terminal domain of LrpA facilitates a new closure-and-twist motion for assembling dynamic pili during the assembly process and host attachment. Further, the incongruent combination of flexible domain-driven conformational dynamics and rigid isopeptide bond-driven stability observed in the LrpCBA pilus might also extend to the sortase-dependent pili of other bacteria colonizing a host.
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Affiliation(s)
- Amar Prajapati
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR, Biotech Science Cluster, Faridabad 121 001, India
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR, Biotech Science Cluster, Faridabad 121 001, India
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7
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Paketurytė-Latvė V, Smirnov A, Manakova E, Baranauskiene L, Petrauskas V, Zubrienė A, Matulienė J, Dudutienė V, Čapkauskaitė E, Zakšauskas A, Leitans J, Gražulis S, Tars K, Matulis D. From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system. IUCRJ 2024; 11:556-569. [PMID: 38856178 PMCID: PMC11220870 DOI: 10.1107/s2052252524004627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/17/2024] [Indexed: 06/11/2024]
Abstract
Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein-ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure-thermodynamics correlations for the novel inhibitors of CA IX is discussed - an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein-Ligand Binding Database to understand general protein-ligand recognition principles that could be used in drug discovery.
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Affiliation(s)
- Vaida Paketurytė-Latvė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Elena Manakova
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Jurgita Matulienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Virginija Dudutienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Janis Leitans
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, 1067 Riga, Latvia
| | - Saulius Gražulis
- Sector of Crystallography and Chemical Informatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, 1067 Riga, Latvia
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
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8
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Clarke JD, Douangamath A, Mikolajek H, Bonnet-Di Placido M, Ren J, Fry EE, Stuart DI, Hammond JA, Owens RJ. The impact of exchanging the light and heavy chains on the structures of bovine ultralong antibodies. Acta Crystallogr F Struct Biol Commun 2024; 80:154-163. [PMID: 38958188 PMCID: PMC11229553 DOI: 10.1107/s2053230x2400606x] [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: 03/11/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
The third complementary-determining regions of the heavy-chain (CDR3H) variable regions (VH) of some cattle antibodies are highly extended, consisting of 48 or more residues. These `ultralong' CDR3Hs form β-ribbon stalks that protrude from the surface of the antibody with a disulfide cross-linked knob region at their apex that dominates antigen interactions over the other CDR loops. The structure of the Fab fragment of a naturally paired bovine ultralong antibody (D08), identified by single B-cell sequencing, has been determined to 1.6 Å resolution. By swapping the D08 native light chain with that of an unrelated antigen-unknown ultralong antibody, it is shown that interactions between the CDR3s of the variable domains potentially affect the fine positioning of the ultralong CDR3H; however, comparison with other crystallographic structures shows that crystalline packing is also a major contributor. It is concluded that, on balance, the exact positioning of ultralong CDR3H loops is most likely to be due to the constraints of crystal packing.
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Affiliation(s)
- John D. Clarke
- The Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
- Macromolecular CrystallographyDiamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUnited Kingdom
- ImmunogeneticsThe Pirbright InstituteAsh RoadPirbrightWokingGU24 0NFUnited Kingdom
| | - Alice Douangamath
- Macromolecular CrystallographyDiamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUnited Kingdom
| | - Halina Mikolajek
- Macromolecular CrystallographyDiamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUnited Kingdom
- CrystallographyThe Research Complex at HarwellHarwell Science and Innovation CampusDidcotOX11 0FAUnited Kingdom
| | | | - Jingshan Ren
- The Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
| | - Elizabeth E. Fry
- The Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
| | - Dave I. Stuart
- The Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
- Macromolecular CrystallographyDiamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUnited Kingdom
| | - John A. Hammond
- ImmunogeneticsThe Pirbright InstituteAsh RoadPirbrightWokingGU24 0NFUnited Kingdom
| | - Raymond J. Owens
- The Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, DidcotOX11 0QX, United Kingdom
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9
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Zyla DS, Della Marca R, Niemeyer G, Zipursky G, Stearns K, Leedale C, Sobolik EB, Callaway HM, Hariharan C, Peng W, Parekh D, Marcink TC, Diaz Avalos R, Horvat B, Mathieu C, Snijder J, Greninger AL, Hastie KM, Niewiesk S, Moscona A, Porotto M, Ollmann Saphire E. A neutralizing antibody prevents postfusion transition of measles virus fusion protein. Science 2024; 384:eadm8693. [PMID: 38935733 DOI: 10.1126/science.adm8693] [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: 11/10/2023] [Accepted: 04/28/2024] [Indexed: 06/29/2024]
Abstract
Measles virus (MeV) presents a public health threat that is escalating as vaccine coverage in the general population declines and as populations of immunocompromised individuals, who cannot be vaccinated, increase. There are no approved therapeutics for MeV. Neutralizing antibodies targeting viral fusion are one potential therapeutic approach but have not yet been structurally characterized or advanced to clinical use. We present cryo-electron microscopy (cryo-EM) structures of prefusion F alone [2.1-angstrom (Å) resolution], F complexed with a fusion-inhibitory peptide (2.3-Å resolution), F complexed with the neutralizing and protective monoclonal antibody (mAb) 77 (2.6-Å resolution), and an additional structure of postfusion F (2.7-Å resolution). In vitro assays and examination of additional EM classes show that mAb 77 binds prefusion F, arrests F in an intermediate state, and prevents transition to the postfusion conformation. These structures shed light on antibody-mediated neutralization that involves arrest of fusion proteins in an intermediate state.
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Affiliation(s)
- Dawid S Zyla
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Roberta Della Marca
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli," 81100 Caserta, Italy
| | - Gele Niemeyer
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Luebeck, D-23538 Luebeck, Germany
| | - Gillian Zipursky
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Kyle Stearns
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Cameron Leedale
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Elizabeth B Sobolik
- Department of Laboratory Medicine and Pathology Virology Division, University of Washington, Seattle, WA 98109, USA
| | - Heather M Callaway
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Chitra Hariharan
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Weiwei Peng
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, Netherlands
- Netherlands Proteomics Center, 3584 CH Utrecht, Netherlands
| | - Diptiben Parekh
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Tara C Marcink
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Ruben Diaz Avalos
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Branka Horvat
- Immunobiology of Viral Infections, International Center for Infectiology Research-CIRI, INSERM U1111, CNRS UMR5308, University Lyon 1, ENS de Lyon, 69007 Lyon, France
| | - Cyrille Mathieu
- Centre International de Recherche en Infectiologie équipe Neuro-Invasion, TROpism and VIRal Encephalitis (NITROVIRE), INSERM U1111-Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, 69007 Lyon, France
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, Netherlands
- Netherlands Proteomics Center, 3584 CH Utrecht, Netherlands
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology Virology Division, University of Washington, Seattle, WA 98109, USA
| | - Kathryn M Hastie
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Stefan Niewiesk
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Anne Moscona
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Matteo Porotto
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli," 81100 Caserta, Italy
| | - Erica Ollmann Saphire
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
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10
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Błaszczyk L, Ryczek M, Das B, Mateja-Pluta M, Bejger M, Śliwiak J, Nakatani K, Kiliszek A. Antisense RNA C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms a triplex-like structure and binds small synthetic ligand. Nucleic Acids Res 2024; 52:6707-6717. [PMID: 38738637 PMCID: PMC11194091 DOI: 10.1093/nar/gkae376] [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: 10/24/2023] [Revised: 04/05/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
The abnormal expansion of GGGGCC/GGCCCC hexanucleotide repeats (HR) in C9orf72 is associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Structural polymorphisms of HR result in the multifactorial pathomechanism of ALS/FTD. Consequently, many ongoing studies are focused at developing therapies targeting pathogenic HR RNA. One of them involves small molecules blocking sequestration of important proteins, preventing formation of toxic nuclear foci. However, rational design of potential therapeutics is hindered by limited number of structural studies of RNA-ligand complexes. We determined the crystal structure of antisense HR RNA in complex with ANP77 ligand (1.1 Å resolution) and in the free form (0.92 and 1.5 Å resolution). HR RNA folds into a triplex structure composed of four RNA chains. ANP77 interacted with two neighboring single-stranded cytosines to form pseudo-canonical base pairs by adopting sandwich-like conformation and adjusting the position of its naphthyridine units to the helical twist of the RNA. In the unliganded structure, the cytosines formed a peculiar triplex i-motif, assembled by trans C•C+ pair and a third cytosine located at the Hoogsteen edge of the C•C+ pair. These results extend our knowledge of the structural polymorphisms of HR and can be used for rational design of small molecules targeting disease-related RNAs.
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Affiliation(s)
- Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Marcin Ryczek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Bimolendu Das
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Martyna Mateja-Pluta
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
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11
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Kim M, Kang R, Jeon TJ, Ryu SE. Protein purification, crystallization, and structure determination of transcription factor YhaJ in complex with DNT metabolites. STAR Protoc 2024; 5:102999. [PMID: 38573865 PMCID: PMC11000171 DOI: 10.1016/j.xpro.2024.102999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024] Open
Abstract
The microbial transcription factor YhaJ responds to 2,4-dinitrotoluene (DNT) derivatives. Here, we describe steps for overexpression and purification of the protein, characterization for the binding of a DNT derivative methylhydroquinone, and crystallization by using a random seeding technique. We then detail procedures for structure determination by employing the crystal-twin resolving processes. This protocol can also be performed using other DNT derivatives. For complete details on the use and execution of this protocol, please refer to Kim et al.1.
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Affiliation(s)
- Myeongbin Kim
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04673, Republic of Korea.
| | - Ryun Kang
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04673, Republic of Korea
| | - Tae Jin Jeon
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04673, Republic of Korea; National Instrumentation Center for Environmental Management (NICEM), Seoul National University, Seoul 08826, Republic of Korea
| | - Seong Eon Ryu
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04673, Republic of Korea.
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12
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González-López A, Larsson DSD, Koripella RK, Cain BN, Chavez MG, Hergenrother PJ, Sanyal S, Selmer M. Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane. Sci Rep 2024; 14:14253. [PMID: 38902339 PMCID: PMC11190147 DOI: 10.1038/s41598-024-64868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024] Open
Abstract
The antibiotic fusidic acid (FA) is used to treat Staphylococcus aureus infections. It inhibits protein synthesis by binding to elongation factor G (EF-G) and preventing its release from the ribosome after translocation. While FA, due to permeability issues, is only effective against gram-positive bacteria, the available structures of FA-inhibited complexes are from gram-negative model organisms. To fill this knowledge gap, we solved cryo-EM structures of the S. aureus ribosome in complex with mRNA, tRNA, EF-G and FA to 2.5 Å resolution and the corresponding complex structures with the recently developed FA derivative FA-cyclopentane (FA-CP) to 2.0 Å resolution. With both FA variants, the majority of the ribosomal particles are observed in chimeric state and only a minor population in post-translocational state. As expected, FA binds in a pocket between domains I, II and III of EF-G and the sarcin-ricin loop of 23S rRNA. FA-CP binds in an identical position, but its cyclopentane moiety provides additional contacts to EF-G and 23S rRNA, suggesting that its improved resistance profile towards mutations in EF-G is due to higher-affinity binding. These high-resolution structures reveal new details about the S. aureus ribosome, including confirmation of many rRNA modifications, and provide an optimal starting point for future structure-based drug discovery on an important clinical drug target.
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Affiliation(s)
- Adrián González-López
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
| | - Daniel S D Larsson
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
| | - Ravi Kiran Koripella
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, USA
| | - Brett N Cain
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Martin Garcia Chavez
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
| | - Maria Selmer
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden.
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13
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Bagchi A, Stayrook SE, Xenaki KT, Starbird CA, Doulkeridou S, El Khoulati R, Roovers RC, Schmitz KR, van Bergen En Henegouwen PMP, Ferguson KM. Structural insights into the role and targeting of EGFRvIII. Structure 2024:S0969-2126(24)00195-3. [PMID: 38908376 DOI: 10.1016/j.str.2024.05.018] [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: 11/03/2023] [Revised: 04/06/2024] [Accepted: 05/28/2024] [Indexed: 06/24/2024]
Abstract
The epidermal growth factor receptor (EGFR) is a well-known oncogenic driver in lung and other cancers. In glioblastoma multiforme (GBM), the EGFR deletion variant III (EGFRvIII) is frequently found alongside EGFR amplification. Agents targeting the EGFR axis have shown limited clinical benefits in GBM and the role of EGFRvIII in GBM is poorly understood. To shed light on the role of EGFRvIII and its potential as a therapeutic target, we determined X-ray crystal structures of a monomeric EGFRvIII extracellular region (ECR). The EGFRvIII ECR resembles the unliganded conformation of EGFR, including the orientation of the C-terminal region of domain II. Domain II is mostly disordered, but the ECR structure is compact. We selected a nanobody with preferential binding to EGFRvIII relative to EGFR and structurally defined an epitope on domain IV that is occluded in the unliganded intact EGFR. These findings suggest new avenues for EGFRvIII targeting in GBM.
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Affiliation(s)
- Atrish Bagchi
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven E Stayrook
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Katerina T Xenaki
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Chrystal A Starbird
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Sofia Doulkeridou
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Rachid El Khoulati
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Rob C Roovers
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Karl R Schmitz
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Paul M P van Bergen En Henegouwen
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Kathryn M Ferguson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA.
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14
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Faure C, Min Ng Y, Belle C, Soler-Lopez M, Khettabi L, Saïdi M, Berthet N, Maresca M, Philouze C, Rachidi W, Réglier M, du Moulinet d'Hardemare A, Jamet H. Interactions of Phenylalanine Derivatives with Human Tyrosinase: Lessons from Experimental and Theoretical tudies. Chembiochem 2024; 25:e202400235. [PMID: 38642076 DOI: 10.1002/cbic.202400235] [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: 03/13/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/22/2024]
Abstract
The pigmentation of the skin, modulated by different actors in melanogenesis, is mainly due to the melanins (protective pigments). In humans, these pigments' precursors are synthetized by an enzyme known as tyrosinase (TyH). The regulation of the enzyme activity by specific modulators (inhibitors or activators) can offer a means to fight hypo- and hyper-pigmentations responsible for medical, psychological and societal handicaps. Herein, we report the investigation of phenylalanine derivatives as TyH modulators. Interacting with the binuclear copper active site of the enzyme, phenylalanine derivatives combine effects induced by combination with known resorcinol inhibitors and natural substrate/intermediate (amino acid part). Computational studies including docking, molecular dynamics and free energy calculations combined with biological activity assays on isolated TyH and in human melanoma MNT-1 cells, and X-ray crystallography analyses with the TyH analogue Tyrp1, provide conclusive evidence of the interactions of phenylalanine derivatives with human tyrosinase. In particular, our findings indicate that an analogue of L-DOPA, namely (S)-3-amino-tyrosine, stands out as an amino phenol derivative with inhibitory properties against TyH.
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Affiliation(s)
- Clarisse Faure
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Yi Min Ng
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Catherine Belle
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Montserrat Soler-Lopez
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Lyna Khettabi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Mélissa Saïdi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Nathalie Berthet
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Marc Maresca
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France)
| | - Christian Philouze
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Walid Rachidi
- IRIG-BGE U1038, INSERM, Univ. Grenoble Alpes, Biomics, 38054, Grenoble, France
| | - Marius Réglier
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France)
| | | | - Hélène Jamet
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
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15
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Simpson JB, Walker ME, Sekela JJ, Ivey SM, Jariwala PB, Storch CM, Kowalewski ME, Graboski AL, Lietzan AD, Walton WG, Davis KA, Cloer EW, Borlandelli V, Hsiao YC, Roberts LR, Perlman DH, Liang X, Overkleeft HS, Bhatt AP, Lu K, Redinbo MR. Gut microbial β-glucuronidases influence endobiotic homeostasis and are modulated by diverse therapeutics. Cell Host Microbe 2024; 32:925-944.e10. [PMID: 38754417 PMCID: PMC11176022 DOI: 10.1016/j.chom.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/18/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024]
Abstract
Hormones and neurotransmitters are essential to homeostasis, and their disruptions are connected to diseases ranging from cancer to anxiety. The differential reactivation of endobiotic glucuronides by gut microbial β-glucuronidase (GUS) enzymes may influence interindividual differences in the onset and treatment of disease. Using multi-omic, in vitro, and in vivo approaches, we show that germ-free mice have reduced levels of active endobiotics and that distinct gut microbial Loop 1 and FMN GUS enzymes drive hormone and neurotransmitter reactivation. We demonstrate that a range of FDA-approved drugs prevent this reactivation by intercepting the catalytic cycle of the enzymes in a conserved fashion. Finally, we find that inhibiting GUS in conventional mice reduces free serotonin and increases its inactive glucuronide in the serum and intestines. Our results illuminate the indispensability of gut microbial enzymes in sustaining endobiotic homeostasis and indicate that therapeutic disruptions of this metabolism promote interindividual response variabilities.
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Affiliation(s)
- Joshua B Simpson
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Morgan E Walker
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Joshua J Sekela
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Samantha M Ivey
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Parth B Jariwala
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Cameron M Storch
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Mark E Kowalewski
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Amanda L Graboski
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Adam D Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Kacey A Davis
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Erica W Cloer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Valentina Borlandelli
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lee R Roberts
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - David H Perlman
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Xue Liang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Hermen S Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Aadra P Bhatt
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
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16
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Legare S, Heide F, Gabir H, Rafiei F, Meier M, Padilla-Meier GP, Koch M, Stetefeld J. Identifying the molecular basis of Laminin N-terminal domain Ca 2+ binding using a hybrid approach. Biophys J 2024:S0006-3495(24)00388-6. [PMID: 38851889 DOI: 10.1016/j.bpj.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/13/2024] [Accepted: 06/06/2024] [Indexed: 06/10/2024] Open
Abstract
Ca2+ is a highly abundant ion involved in numerous biological processes, particularly in multicellular eukaryotic organisms where it exerts many of these functions through interactions with Ca2+ binding proteins. The laminin N-terminal (LN) domain is found in members of the laminin and netrin protein families where it plays a critical role in the function of these proteins. The LN domain of laminins and netrins is a Ca2+ binding domain and in many cases requires Ca2+ to perform its biological function. Here, we conduct a detailed examination of the molecular basis of the LN domain Ca2+ interaction combining structural, computational, bioinformatics, and biophysical techniques. By combining computational and bioinformatic techniques with x-ray crystallography we explore the molecular basis of the LN domain Ca2+ interaction and identify a conserved sequence present in Ca2+ binding LN domains. These findings enable a sequence-based prediction of LN domain Ca2+ binding ability. We use thermal shift assays and isothermal titration calorimetry to explore the biophysical properties of the LN domain Ca2+ interaction. We show that the netrin-1 LN domain exhibits a high affinity and specificity for Ca2+, which structurally stabilizes the LN domain. This study elucidates the molecular foundation of the LN domain Ca2+ binding interaction and provides a detailed functional characterization of this essential interaction, advancing our understanding of protein-Ca2+ dynamics within the context of the LN domain.
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Affiliation(s)
- Scott Legare
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Fabian Heide
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Haben Gabir
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Faride Rafiei
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Manuel Koch
- Center for Biochemistry II, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Institute for Dental Research and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
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17
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Sánchez-Ruiz MI, Santillana E, Linde D, Romero A, Martínez AT, Ruiz-Dueñas FJ. Structure-function characterization of two enzymes from novel subfamilies of manganese peroxidases secreted by the lignocellulose-degrading Agaricales fungi Agrocybe pediades and Cyathus striatus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:74. [PMID: 38824538 PMCID: PMC11144326 DOI: 10.1186/s13068-024-02517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 05/11/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Manganese peroxidases (MnPs) are, together with lignin peroxidases and versatile peroxidases, key elements of the enzymatic machineries secreted by white-rot fungi to degrade lignin, thus providing access to cellulose and hemicellulose in plant cell walls. A recent genomic analysis of 52 Agaricomycetes species revealed the existence of novel MnP subfamilies differing in the amino-acid residues that constitute the manganese oxidation site. Following this in silico analysis, a comprehensive structure-function study is needed to understand how these enzymes work and contribute to transform the lignin macromolecule. RESULTS Two MnPs belonging to the subfamilies recently classified as MnP-DGD and MnP-ESD-referred to as Ape-MnP1 and Cst-MnP1, respectively-were identified as the primary peroxidases secreted by the Agaricales species Agrocybe pediades and Cyathus striatus when growing on lignocellulosic substrates. Following heterologous expression and in vitro activation, their biochemical characterization confirmed that these enzymes are active MnPs. However, crystal structure and mutagenesis studies revealed manganese coordination spheres different from those expected after their initial classification. Specifically, a glutamine residue (Gln333) in the C-terminal tail of Ape-MnP1 was found to be involved in manganese binding, along with Asp35 and Asp177, while Cst-MnP1 counts only two amino acids (Glu36 and Asp176), instead of three, to function as a MnP. These findings led to the renaming of these subfamilies as MnP-DDQ and MnP-ED and to re-evaluate their evolutionary origin. Both enzymes were also able to directly oxidize lignin-derived phenolic compounds, as seen for other short MnPs. Importantly, size-exclusion chromatography analyses showed that both enzymes cause changes in polymeric lignin in the presence of manganese, suggesting their relevance in lignocellulose transformation. CONCLUSIONS Understanding the mechanisms used by basidiomycetes to degrade lignin is of particular relevance to comprehend carbon cycle in nature and to design biotechnological tools for the industrial use of plant biomass. Here, we provide the first structure-function characterization of two novel MnP subfamilies present in Agaricales mushrooms, elucidating the main residues involved in catalysis and demonstrating their ability to modify the lignin macromolecule.
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Affiliation(s)
- María Isabel Sánchez-Ruiz
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Elena Santillana
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Antonio Romero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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18
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Herre C, Ho A, Eisenbraun B, Vincent J, Nicholson T, Boutsioukis G, Meyer PA, Ottaviano M, Krause KL, Key J, Sliz P. Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection. Acta Crystallogr D Struct Biol 2024; 80:439-450. [PMID: 38832828 PMCID: PMC11154594 DOI: 10.1107/s2059798324004881] [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: 03/01/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024] Open
Abstract
The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs and configures over 530 specialized software applications for use in the on-premises and cloud-based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules rely on a collection of programmatically generated bash scripts that work together to isolate the runtime environment of one application from all other applications, thereby providing a transparent cross-platform solution without requiring specialized tools or elevated account privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict-free environment. The SBGrid platform, which combines Capsules with the SBGrid collection of structural biology applications, aligns with FAIR goals by enhancing the findability, accessibility, interoperability and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields.
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Affiliation(s)
- Carol Herre
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Alex Ho
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ben Eisenbraun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - James Vincent
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas Nicholson
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Peter A. Meyer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Michelle Ottaviano
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kurt L. Krause
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Jason Key
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Piotr Sliz
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts, USA
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19
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Bjelčić M, Aurelius O, Nan J, Neutze R, Ursby T. Room-temperature serial synchrotron crystallography structure of Spinacia oleracea RuBisCO. Acta Crystallogr F Struct Biol Commun 2024; 80:117-124. [PMID: 38809540 PMCID: PMC11189101 DOI: 10.1107/s2053230x24004643] [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: 03/19/2024] [Accepted: 05/18/2024] [Indexed: 05/30/2024] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the enzyme responsible for the first step of carbon dioxide (CO2) fixation in plants, which proceeds via the carboxylation of ribulose 1,5-biphosphate. Because of the enormous importance of this reaction in agriculture and the environment, there is considerable interest in the mechanism of fixation of CO2 by RuBisCO. Here, a serial synchrotron crystallography structure of spinach RuBisCO is reported at 2.3 Å resolution. This structure is consistent with earlier single-crystal X-ray structures of this enzyme and the results are a good starting point for a further push towards time-resolved serial synchrotron crystallography in order to better understand the mechanism of the reaction.
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Affiliation(s)
- Monika Bjelčić
- MAX IV Laboratory, Lund UniversityPO Box 118221 00LundSweden
| | - Oskar Aurelius
- MAX IV Laboratory, Lund UniversityPO Box 118221 00LundSweden
| | - Jie Nan
- MAX IV Laboratory, Lund UniversityPO Box 118221 00LundSweden
| | - Richard Neutze
- Department of Chemistry and Molecular BiologyUniversity of GothenburgMedicinaregatan 9C413 90GothenburgSweden
| | - Thomas Ursby
- MAX IV Laboratory, Lund UniversityPO Box 118221 00LundSweden
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20
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Mizgalska D, Rodríguez-Banqueri A, Veillard F, Książęk M, Goulas T, Guevara T, Eckhard U, Potempa J, Gomis-Rüth FX. Structural and functional insights into the C-terminal signal domain of the Bacteroidetes type-IX secretion system. Open Biol 2024; 14:230448. [PMID: 38862016 DOI: 10.1098/rsob.230448] [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: 12/12/2023] [Accepted: 02/20/2024] [Indexed: 06/13/2024] Open
Abstract
Gram-negative bacteria from the Bacteroidota phylum possess a type-IX secretion system (T9SS) for protein secretion, which requires cargoes to have a C-terminal domain (CTD). Structurally analysed CTDs are from Porphyromonas gingivalis proteins RgpB, HBP35, PorU and PorZ, which share a compact immunoglobulin-like antiparallel 3+4 β-sandwich (β1-β7). This architecture is essential as a P. gingivalis strain with a single-point mutant of RgpB disrupting the interaction of the CTD with its preceding domain prevented secretion of the protein. Next, we identified the C-terminus ('motif C-t.') and the loop connecting strands β3 and β4 ('motif Lβ3β4') as conserved. We generated two strains with insertion and replacement mutants of PorU, as well as three strains with ablation and point mutants of RgpB, which revealed both motifs to be relevant for T9SS function. Furthermore, we determined the crystal structure of the CTD of mirolase, a cargo of the Tannerella forsythia T9SS, which shares the same general topology as in Porphyromonas CTDs. However, motif Lβ3β4 was not conserved. Consistently, P. gingivalis could not properly secrete a chimaeric protein with the CTD of peptidylarginine deiminase replaced with this foreign CTD. Thus, the incompatibility of the CTDs between these species prevents potential interference between their T9SSs.
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Affiliation(s)
- Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Arturo Rodríguez-Banqueri
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Catalonia 08028, Spain
| | - Florian Veillard
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Mirosław Książęk
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Theodoros Goulas
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Thessaly, Karditsa 43100, Greece
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Catalonia 08028, Spain
| | - Ulrich Eckhard
- Synthetic Structural Biology Group, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Catalonia 08028, Spain
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY 40202, USA
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Catalonia 08028, Spain
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21
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Brookner DE, Hekstra DR. MatchMaps: non-isomorphous difference maps for X-ray crystallography. J Appl Crystallogr 2024; 57:885-895. [PMID: 38846758 PMCID: PMC11151677 DOI: 10.1107/s1600576724003510] [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: 01/08/2024] [Accepted: 04/19/2024] [Indexed: 06/09/2024] Open
Abstract
Conformational change mediates the biological functions of macromolecules. Crystallographic measurements can map these changes with extraordinary sensitivity as a function of mutations, ligands and time. A popular method for detecting structural differences between crystallographic data sets is the isomorphous difference map. These maps combine the phases of a chosen reference state with the observed changes in structure factor amplitudes to yield a map of changes in electron density. Such maps are much more sensitive to conformational change than structure refinement is, and are unbiased in the sense that observed differences do not depend on refinement of the perturbed state. However, even modest changes in unit-cell properties can render isomorphous difference maps useless. This is unnecessary. Described here is a generalized procedure for calculating observed difference maps that retains the high sensitivity to conformational change and avoids structure refinement of the perturbed state. This procedure is implemented in an open-source Python package, MatchMaps, that can be run in any software environment supporting PHENIX [Liebschner et al. (2019). Acta Cryst. D75, 861-877] and CCP4 [Agirre et al. (2023). Acta Cryst. D79, 449-461]. Worked examples show that MatchMaps 'rescues' observed difference electron-density maps for poorly isomorphous crystals, corrects artifacts in nominally isomorphous difference maps, and extends to detecting differences across copies within the asymmetric unit or across altogether different crystal forms.
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Affiliation(s)
- Dennis E. Brookner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Doeke R. Hekstra
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
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22
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Ma S, Damfo S, Bowler MW, Mykhaylyk V, Kozielski F. High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms. Acta Crystallogr D Struct Biol 2024; 80:451-463. [PMID: 38841886 PMCID: PMC11154595 DOI: 10.1107/s2059798324004480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024] Open
Abstract
Fragment-based drug design using X-ray crystallography is a powerful technique to enable the development of new lead compounds, or probe molecules, against biological targets. This study addresses the need to determine fragment binding orientations for low-occupancy fragments with incomplete electron density, an essential step before further development of the molecule. Halogen atoms play multiple roles in drug discovery due to their unique combination of electronegativity, steric effects and hydrophobic properties. Fragments incorporating halogen atoms serve as promising starting points in hit-to-lead development as they often establish halogen bonds with target proteins, potentially enhancing binding affinity and selectivity, as well as counteracting drug resistance. Here, the aim was to unambiguously identify the binding orientations of fragment hits for SARS-CoV-2 nonstructural protein 1 (nsp1) which contain a combination of sulfur and/or chlorine, bromine and iodine substituents. The binding orientations of carefully selected nsp1 analogue hits were focused on by employing their anomalous scattering combined with Pan-Dataset Density Analysis (PanDDA). Anomalous difference Fourier maps derived from the diffraction data collected at both standard and long-wavelength X-rays were compared. The discrepancies observed in the maps of iodine-containing fragments collected at different energies were attributed to site-specific radiation-damage stemming from the strong X-ray absorption of I atoms, which is likely to cause cleavage of the C-I bond. A reliable and effective data-collection strategy to unambiguously determine the binding orientations of low-occupancy fragments containing sulfur and/or halogen atoms while mitigating radiation damage is presented.
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Affiliation(s)
- Shumeng Ma
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Shymaa Damfo
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Mounawarah 30078, Saudi Arabia
| | | | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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23
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Alberti M, Poli G, Broggini L, Sainas S, Rizzi M, Boschi D, Ferraris DM, Martino E, Ricagno S, Tuccinardi T, Lolli ML, Miggiano R. An alternative conformation of the N-terminal loop of human dihydroorotate dehydrogenase drives binding to a potent antiproliferative agent. Acta Crystallogr D Struct Biol 2024; 80:386-396. [PMID: 38805244 DOI: 10.1107/s2059798324004066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024] Open
Abstract
Over the years, human dihydroorotate dehydrogenase (hDHODH), which is a key player in the de novo pyrimidine-biosynthesis pathway, has been targeted in the treatment of several conditions, including autoimmune disorders and acute myelogenous leukaemia, as well as in host-targeted antiviral therapy. A molecular exploration of its inhibitor-binding behaviours yielded promising candidates for innovative drug design. A detailed description of the enzymatic pharmacophore drove the decoration of well-established inhibitory scaffolds, thus gaining further in vitro and in vivo efficacy. In the present work, using X-ray crystallography, an atypical rearrangement was identified in the binding pose of a potent inhibitor characterized by a polar pyridine-based moiety (compound 18). The crystal structure shows that upon binding compound 18 the dynamics of a protein loop involved in a gating mechanism at the cofactor-binding site is modulated by the presence of three water molecules, thus fine-tuning the polarity/hydrophobicity of the binding pocket. These solvent molecules are engaged in the formation of a hydrogen-bond mesh in which one of them establishes a direct contact with the pyridine moiety of compound 18, thus paving the way for a reappraisal of the inhibition of hDHODH. Using an integrated approach, the thermodynamics of such a modulation is described by means of isothermal titration calorimetry coupled with molecular modelling. These structural insights will guide future drug design to obtain a finer Kd/logD7.4 balance and identify membrane-permeable molecules with a drug-like profile in terms of water solubility.
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Affiliation(s)
- Marta Alberti
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via G. Bovio 6, 28100 Novara, Italy
| | - Giulio Poli
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Luca Broggini
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan, 20097 San Donato Milanese, Italy
| | - Stefano Sainas
- Department of Sciences and Drug Technology, University of Torino, Via P. Giuria 9, 10125 Torino, Italy
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via G. Bovio 6, 28100 Novara, Italy
| | - Donatella Boschi
- Department of Sciences and Drug Technology, University of Torino, Via P. Giuria 9, 10125 Torino, Italy
| | - Davide M Ferraris
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via G. Bovio 6, 28100 Novara, Italy
| | - Elena Martino
- Department of Sciences and Drug Technology, University of Torino, Via P. Giuria 9, 10125 Torino, Italy
| | - Stefano Ricagno
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan, 20097 San Donato Milanese, Italy
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Marco L Lolli
- Department of Sciences and Drug Technology, University of Torino, Via P. Giuria 9, 10125 Torino, Italy
| | - Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via G. Bovio 6, 28100 Novara, Italy
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24
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Clement PC, Sapam T, Nair DT. A conserved polar residue plays a critical role in mismatch detection in A-family DNA polymerases. Int J Biol Macromol 2024; 269:131965. [PMID: 38697428 DOI: 10.1016/j.ijbiomac.2024.131965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024]
Abstract
In A-family DNA polymerases (dPols), a functional 3'-5' exonuclease activity is known to proofread newly synthesized DNA. The identification of a mismatch in substrate DNA leads to transfer of the primer strand from the polymerase active site to the exonuclease active site. To shed more light regarding the mechanism responsible for the detection of mismatches, we have utilized DNA polymerase 1 from Aquifex pyrophilus (ApPol1). The enzyme synthesized DNA with high fidelity and exhibited maximal exonuclease activity with DNA substrates bearing mismatches at the -2 and - 3 positions. The crystal structure of apo-ApPol1 was utilized to generate a computational model of the functional ternary complex of this enzyme. The analysis of the model showed that N332 forms interactions with minor groove atoms of the base pairs at the -2 and - 3 positions. The majority of known A-family dPols show the presence of Asn at a position equivalent to N332. The N332L mutation led to a decrease in the exonuclease activity for representative purine-pyrimidine, and pyrimidine-pyrimidine mismatches at -2 and - 3 positions, respectively. Overall, our findings suggest that conserved polar residues located towards the minor groove may facilitate the detection of position-specific mismatches to enhance the fidelity of DNA synthesis.
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Affiliation(s)
- Patterson C Clement
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121 001, Haryana (NCR Delhi), India
| | - Tuleshwori Sapam
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121 001, Haryana (NCR Delhi), India
| | - Deepak T Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121 001, Haryana (NCR Delhi), India.
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25
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Jeong C, Kim HJ. YabJ from Staphylococcus aureus entraps chlorides within its pocket. Biochem Biophys Res Commun 2024; 710:149892. [PMID: 38581951 DOI: 10.1016/j.bbrc.2024.149892] [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: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Chlorination is a potent disinfectant against various microorganisms, including bacteria and viruses, by inducing protein modifications and functional changes. Chlorine, in the form of sodium hypochlorite, stands out as the predominant sanitizer choice due to its cost-effectiveness and powerful antimicrobial properties. Upon exposure to chlorination, proteins undergo modifications, with amino acids experiencing alterations through the attachment of chloride or oxygen atoms. These modifications lead to shifts in protein function and the modulation of downstream signaling pathways, ultimately resulting in a bactericidal effect. However, certain survival proteins, such as chaperones or transcription factors, aid organisms in overcoming harsh chlorination conditions. The expression of YabJ, a highly conserved protein from Staphylococcus aureus, is regulated by a stress-activated sigma factor called sigma B (σB). This research revealed that S. aureus YabJ maintains its structural integrity even under intense chlorination conditions and harbors sodium hypochlorite molecules within its surface pocket. Notably, the pocket of S. aureus YabJ is primarily composed of amino acids less susceptible to chlorination-induced damage, rendering it resistant to such effects. This study elucidates how S. aureus YabJ evades the detrimental effects of chlorination and highlights its role in sequestering sodium hypochlorite within its structure. Consequently, this process enhances resilience and facilitates adaptation to challenging environmental conditions.
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Affiliation(s)
- Cheolwoo Jeong
- College of Pharmacy, Woosuk University, Wanju, 55338, Republic of Korea
| | - Hyo Jung Kim
- College of Pharmacy, Woosuk University, Wanju, 55338, Republic of Korea.
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26
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Rajapaksha N, Yao H, Cook A, Seibold S, Liu L, Battaile KP, Fontenot L, Donnarumma F, Lovell S, Rivera M. Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity. Front Mol Biosci 2024; 11:1390745. [PMID: 38841187 PMCID: PMC11150526 DOI: 10.3389/fmolb.2024.1390745] [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: 02/23/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
We report the biochemical, structural, and functional characterization of the protein coded by gene PA4880 in the P. aeruginosa PAO1 genome. The PA4880 gene had been annotated as coding a probable bacterioferritin. Our structural work shows that the product of gene PA4880 is a protein that adopts the Dps subunit fold, which oligomerizes into a 12-mer quaternary structure. Unlike Dps, however, the ferroxidase di-iron centers and iron coordinating ligands are buried within each subunit, in a manner identical to that observed in the ferroxidase center of P. aeruginosa bacterioferritin. Since these structural characteristics correspond to Dps-like proteins, we term the protein as P. aeruginosa Dps-like, or Pa DpsL. The ferroxidase centers in Pa DpsL catalyze the oxidation of Fe2+ utilizing O2 or H2O2 as oxidant, and the resultant Fe3+ is compartmentalized in the interior cavity. Interestingly, incubating Pa DpsL with plasmid DNA results in efficient nicking of the DNA and at higher concentrations of Pa DpsL the DNA is linearized and eventually degraded. The nickase and endonuclease activities suggest that Pa DpsL, in addition to participating in the defense of P. aeruginosa cells against iron-induced toxicity, may also participate in the innate immune mechanisms consisting of restriction endonucleases and cognate methyl transferases.
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Affiliation(s)
- Nimesha Rajapaksha
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Huili Yao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Aisha Cook
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Steve Seibold
- Protein Structure & X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, United States
| | - Lijun Liu
- Protein Structure & X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, United States
| | | | - Leo Fontenot
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Scott Lovell
- Protein Structure & X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, United States
| | - Mario Rivera
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
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27
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Kumar RP, Matos JO, Black BY, Ellenburg WH, Chen J, Patterson M, Gehtman JA, Theobald DL, Krauss IJ, Oprian DD. Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592530. [PMID: 38746203 PMCID: PMC11092760 DOI: 10.1101/2024.05.04.592530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
In a continuing effort to understand reaction mechanisms of terpene synthases catalyzing initial anti-Markovnikov cyclization reactions, we solved the X-ray crystal structure of (+)-caryolan-1-ol synthase (CS) from Streptomyces griseus , with and without an inactive analog of the FPP substrate, 2-fluorofarnesyl diphosphate (2FFPP), bound in the active site of the enzyme. The CS-2FFPP complex was solved to 2.65 Å resolution and showed the ligand in a linear, elongated orientation, incapable of undergoing the initial cyclization event to form a bond between carbons C1 and C11. Intriguingly, the apo CS structure (2.2 Å) also had electron density in the active site, in this case density that was well fit with a curled-up tetraethylene glycol molecule presumably recruited from the crystallization medium. The density was also well fit by a molecule of farnesene suggesting that the structure may mimic an intermediate along the reaction coordinate. The curled-up conformation of tetraethylene glycol was accompanied by dramatic rotamer shifts among active-site residues. Most notably, W56 was observed to undergo a 90° rotation between the 2FFPP complex and apo-enzyme structures, suggesting that it contributes to steric interactions that help curl the tetraethylene glycol molecule in the active site, and by extension perhaps also a derivative of the FPP substrate in the normal course of the cyclization reaction. In support of this proposal, the CS W56L variant lost the ability to cyclize the FPP substrate and produced only the linear terpene products farnesol and α- and β-farnesene.
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28
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Li Y, Hou Y, Sun Q, Zeng H, Meng F, Tian X, He Q, Shao F, Ding J. Cleavage-independent activation of ancient eukaryotic gasdermins and structural mechanisms. Science 2024; 384:adm9190. [PMID: 38662913 DOI: 10.1126/science.adm9190] [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: 11/13/2023] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
Gasdermins (GSDMs) are pore-forming proteins that execute pyroptosis for immune defense. GSDMs are two-domain proteins activated by proteolytic removal of the inhibitory domain. In this work, we report two types of cleavage-independent GSDM activation. First, TrichoGSDM, a pore-forming domain-only protein from the basal metazoan Trichoplax adhaerens, is a disulfides-linked autoinhibited dimer activated by reduction of the disulfides. The cryo-electron microscopy (cryo-EM) structure illustrates the assembly mechanism for the 44-mer TrichoGSDM pore. Second, RCD-1-1 and RCD-1-2, encoded by the polymorphic regulator of cell death-1 (rcd-1) gene in filamentous fungus Neurospora crassa, are also pore-forming domain-only GSDMs. RCD-1-1 and RCD-1-2, when encountering each other, form pores and cause pyroptosis, underlying allorecognition in Neurospora. The cryo-EM structure reveals a pore of 11 RCD-1-1/RCD-1-2 heterodimers and a heterodimerization-triggered pore assembly mechanism. This study shows mechanistic diversities in GSDM activation and indicates versatile functions of GSDMs.
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Affiliation(s)
- Yueyue Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yanjie Hou
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Sun
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Huan Zeng
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Fanyi Meng
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xiang Tian
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qun He
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Feng Shao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing 102206, China
- Changping Laboratory, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- New Cornerstone Science Laboratory, Shenzhen 518054, China
| | - Jingjin Ding
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
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29
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Shang J, Kojetin DJ. Unanticipated mechanisms of covalent inhibitor and synthetic ligand cobinding to PPARγ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594037. [PMID: 38798544 PMCID: PMC11118368 DOI: 10.1101/2024.05.15.594037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor transcription factor that regulates gene expression programs in response to ligand binding. Endogenous lipids and synthetic ligands, including covalent antagonist inhibitors such as GW9662 and T0070907, are thought to compete for the orthosteric pocket in the ligand-binding domain (LBD). However, we previously showed that synthetic PPARγ ligands can cooperatively cobind with and reposition a bound endogenous orthosteric ligand to an alternate site, synergistically regulating PPARγ structure and function (Shang et al., 2018). Here, we reveal the structural mechanism of cobinding between a synthetic covalent antagonist inhibitor with other synthetic ligands. Biochemical and NMR data show that covalent antagonist inhibitors weaken-but do not prevent-the binding of other synthetic ligands via an allosteric mechanism rather than direct ligand clashing. The covalent ligands shift the LBD ensemble toward a transcriptionally repressive conformation, which structurally clashes with and reduces the orthosteric binding affinity of non-covalent synthetic ligands. Crystal structures reveal different non-covalent synthetic ligand-specific cobinding mechanisms ranging from alternate site binding to unexpectedly adopting an orthosteric binding mode by altering the covalent ligand binding pose. Our findings not only highlight the significant flexibility of the PPARγ orthosteric pocket and its ability to accommodate multiple ligands simultaneously, but also demonstrate that GW9662 and T0070907 should not be used as reliable chemical tools to inhibit the binding of other ligands to PPARγ.
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Affiliation(s)
- Jinsai Shang
- Department of Integrative Structural and Computational Biology, Scripps Research and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, United States
- School of Basic Medical Sciences, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Douglas J. Kojetin
- Department of Integrative Structural and Computational Biology, Scripps Research and The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, United States
- Center for Applied AI in Protein Dynamics, Vanderbilt University, Nashville, Tennessee, United States
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30
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Chen Z, Zanotti G. Emerging Topics in Protein Crystallography. Int J Mol Sci 2024; 25:5311. [PMID: 38791349 PMCID: PMC11121128 DOI: 10.3390/ijms25105311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Protein crystallography is the discipline concerned with the determination of the three-dimensional structure of biological macromolecules in a crystalline state [...].
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Affiliation(s)
- Zhongzhou Chen
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 48B, 35131 Padova, Italy
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31
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Kim HM, Kim KJ, Lee K, Yoon MJ, Choih J, Hong TJ, Cho EJ, Jung HJ, Kim J, Park JS, Na HY, Heo YS, Park CG, Park H, Han S, Bae D. GNUV201, a novel human/mouse cross-reactive and low pH-selective anti-PD-1 monoclonal antibody for cancer immunotherapy. BMC Immunol 2024; 25:29. [PMID: 38730320 PMCID: PMC11088064 DOI: 10.1186/s12865-024-00609-z] [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: 10/18/2023] [Accepted: 02/13/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Several PD-1 antibodies approved as anti-cancer therapies work by blocking the interaction of PD-1 with its ligand PD-L1, thus restoring anti-cancer T cell activities. These PD-1 antibodies lack inter-species cross-reactivity, necessitating surrogate antibodies for preclinical studies, which may limit the predictability and translatability of the studies. RESULTS To overcome this limitation, we have developed an inter-species cross-reactive PD-1 antibody, GNUV201, by utilizing an enhanced diversity mouse platform (SHINE MOUSE™). GNUV201 equally binds to human PD-1 and mouse PD-1, equally inhibits the binding of human PD-1/PD-L1 and mouse PD-1/PD-L1, and effectively suppresses tumor growth in syngeneic mouse models. The epitope of GNUV201 mapped to the "FG loop" of hPD-1, distinct from those of Keytruda® ("C'D loop") and Opdivo® (N-term). Notably, the structural feature where the protruding epitope loop fits into GNUV201's binding pocket supports the enhanced binding affinity due to slower dissociation (8.7 times slower than Keytruda®). Furthermore, GNUV201 shows a stronger binding affinity at pH 6.0 (5.6 times strong than at pH 7.4), which mimics the hypoxic and acidic tumor microenvironment (TME). This phenomenon is not observed with marketed antibodies (Keytruda®, Opdivo®), implying that GNUV201 achieves more selective binding to and better occupancy on PD-1 in the TME. CONCLUSIONS In summary, GNUV201 exhibited enhanced affinity for PD-1 with slow dissociation and preferential binding in TME-mimicking low pH. Human/monkey/mouse inter-species cross-reactivity of GNUV201 could enable more predictable and translatable efficacy and toxicity preclinical studies. These results suggest that GNUV201 could be an ideal antibody candidate for anti-cancer drug development.
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MESH Headings
- Animals
- Humans
- Programmed Cell Death 1 Receptor/immunology
- Programmed Cell Death 1 Receptor/metabolism
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Mice
- Cross Reactions/immunology
- Immunotherapy/methods
- Hydrogen-Ion Concentration
- Neoplasms/immunology
- Neoplasms/therapy
- B7-H1 Antigen/immunology
- B7-H1 Antigen/metabolism
- B7-H1 Antigen/antagonists & inhibitors
- Cell Line, Tumor
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal/therapeutic use
- Immune Checkpoint Inhibitors/pharmacology
- Epitopes/immunology
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Monoclonal, Humanized/pharmacology
- Mice, Inbred C57BL
- Female
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Affiliation(s)
- Hae-Mi Kim
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
| | - Kyoung-Jin Kim
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
| | - Kwanghyun Lee
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
| | - Myeong Jin Yoon
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
| | - Jenny Choih
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
- Genuv US Subsidiary, CIC, 1 Broadway, Cambridge, MA, USA
| | - Tae-Joon Hong
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
| | - Eun Ji Cho
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
| | - Hak-Jun Jung
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
| | - Jayoung Kim
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
| | - Ji Soo Park
- Laboratory of Immunology, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 PLUS/FOUR Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hye Young Na
- Laboratory of Immunology, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Neurology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yong-Seok Heo
- Department of Chemistry, Konkuk University, 120 Neungdong-Ro, Gwangjin-Gu, Seoul, 05029, Republic of Korea
| | - Chae Gyu Park
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
- Laboratory of Immunology, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Heungrok Park
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
| | - Sungho Han
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea
- Genuv US Subsidiary, CIC, 1 Broadway, Cambridge, MA, USA
| | - Donggoo Bae
- Genuv Inc., B1 Shinyoung Building, 14 Gyeonghuigung-gil, Jongno-gu, Seoul, Republic of Korea.
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32
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Pulsford SB, Outram MA, Förster B, Rhodes T, Williams SJ, Badger MR, Price GD, Jackson CJ, Long BM. Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP. SCIENCE ADVANCES 2024; 10:eadk7283. [PMID: 38728392 PMCID: PMC11086599 DOI: 10.1126/sciadv.adk7283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024]
Abstract
Cyanobacterial CO2 concentrating mechanisms (CCMs) sequester a globally consequential proportion of carbon into the biosphere. Proteinaceous microcompartments, called carboxysomes, play a critical role in CCM function, housing two enzymes to enhance CO2 fixation: carbonic anhydrase (CA) and Rubisco. Despite its importance, our current understanding of the carboxysomal CAs found in α-cyanobacteria, CsoSCA, remains limited, particularly regarding the regulation of its activity. Here, we present a structural and biochemical study of CsoSCA from the cyanobacterium Cyanobium sp. PCC7001. Our results show that the Cyanobium CsoSCA is allosterically activated by the Rubisco substrate ribulose-1,5-bisphosphate and forms a hexameric trimer of dimers. Comprehensive phylogenetic and mutational analyses are consistent with this regulation appearing exclusively in cyanobacterial α-carboxysome CAs. These findings clarify the biologically relevant oligomeric state of α-carboxysomal CAs and advance our understanding of the regulation of photosynthesis in this globally dominant lineage.
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Affiliation(s)
- Sacha B. Pulsford
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Megan A. Outram
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Britta Förster
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Timothy Rhodes
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Simon J. Williams
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Murray R. Badger
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - G. Dean Price
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Colin J. Jackson
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Benedict M. Long
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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33
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Leong SL, Murdolo L, Maddumage JC, Koutsakos M, Kedzierska K, Purcell AW, Gras S, Grant EJ. Characterisation of novel influenza-derived HLA-B*18:01-restricted epitopes. Clin Transl Immunology 2024; 13:e1509. [PMID: 38737448 PMCID: PMC11087170 DOI: 10.1002/cti2.1509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Objectives Seasonal influenza viruses cause roughly 650 000 deaths annually despite available vaccines. CD8+ T cells typically recognise influenza-derived peptides from internal structural and non-structural influenza proteins and are an attractive avenue for future vaccine design as they could reduce the severity of disease following infection with diverse influenza strains. CD8+ T cells recognise peptides presented by the highly polymorphic Human Leukocyte Antigens class I molecules (HLA-I). Each HLA-I variant has distinct peptide binding preferences, representing a significant obstacle for designing vaccines that elicit CD8+ T cell responses across broad populations. Consequently, the rational design of a CD8+ T cell-mediated vaccine would require the identification of highly immunogenic peptides restricted to a range of different HLA molecules. Methods Here, we assessed the immunogenicity of six recently published novel influenza-derived peptides identified by mass-spectrometry and predicted to bind to the prevalent HLA-B*18:01 molecule. Results Using CD8+ T cell activation assays and protein biochemistry, we showed that 3/6 of the novel peptides were immunogenic in several HLA-B*18:01+ individuals and confirmed their HLA-B*18:01 restriction. We subsequently compared CD8+ T cell responses towards the previously identified highly immunogenic HLA-B*18:01-restricted NP219 peptide. Using X-ray crystallography, we solved the first crystal structures of HLA-B*18:01 presenting immunogenic influenza-derived peptides. Finally, we dissected the first TCR repertoires specific for HLA-B*18:01 restricted pathogen-derived peptides, identifying private and restricted repertoires against each of the four peptides. Conclusion Overall the characterisation of these novel immunogenic peptides provides additional HLA-B*18:01-restricted vaccine targets derived from the Matrix protein 1 and potentially the non-structural protein and the RNA polymerase catalytic subunit of influenza viruses.
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Affiliation(s)
- Samuel Liwei Leong
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
| | - Lawton Murdolo
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
| | - Janesha C Maddumage
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVICAustralia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVICAustralia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Stephanie Gras
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Emma J Grant
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
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34
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Rodríguez-Hernández D, Fenwick MK, Zigweid R, Sankaran B, Myler PJ, Sunnerhagen P, Kaushansky A, Staker BL, Grøtli M. Exploring Subsite Selectivity within Plasmodium vivax N-Myristoyltransferase Using Pyrazole-Derived Inhibitors. J Med Chem 2024; 67:7312-7329. [PMID: 38680035 PMCID: PMC11089503 DOI: 10.1021/acs.jmedchem.4c00168] [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: 01/19/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
N-myristoyltransferase (NMT) is a promising antimalarial drug target. Despite biochemical similarities between Plasmodium vivax and human NMTs, our recent research demonstrated that high selectivity is achievable. Herein, we report PvNMT-inhibiting compounds aimed at identifying novel mechanisms of selectivity. Various functional groups are appended to a pyrazole moiety in the inhibitor to target a pocket formed beneath the peptide binding cleft. The inhibitor core group polarity, lipophilicity, and size are also varied to probe the water structure near a channel. Selectivity index values range from 0.8 to 125.3. Cocrystal structures of two selective compounds, determined at 1.97 and 2.43 Å, show that extensions bind the targeted pocket but with different stabilities. A bulky naphthalene moiety introduced into the core binds next to instead of displacing protein-bound waters, causing a shift in the inhibitor position and expanding the binding site. Our structure-activity data provide a conceptual foundation for guiding future inhibitor optimizations.
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Affiliation(s)
- Diego Rodríguez-Hernández
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, S-405 30 Gothenburg, Sweden
- Department
of Structural and Functional Biology, Synthetic Biology Laboratory,
Institute of Biology, University of Campinas, Campinas, SP 13083-862, Brazil
| | - Michael K. Fenwick
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Rachael Zigweid
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Banumathi Sankaran
- Molecular
Biophysics and Integrated Bioimaging, Berkeley Center for Structural
Biology, Advanced Light Source, Berkeley
National Laboratory, Berkeley, California 94720, United States
| | - Peter J. Myler
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Per Sunnerhagen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Alexis Kaushansky
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Bart L. Staker
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Morten Grøtli
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, S-405 30 Gothenburg, Sweden
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35
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Fagnani E, Cocomazzi P, Pellegrino S, Tedeschi G, Scalvini FG, Cossu F, Da Vela S, Aliverti A, Mastrangelo E, Milani M. CHCHD4 binding affects the active site of apoptosis inducing factor (AIF): Structural determinants for allosteric regulation. Structure 2024; 32:594-602.e4. [PMID: 38460521 DOI: 10.1016/j.str.2024.02.008] [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: 10/03/2023] [Revised: 01/08/2024] [Accepted: 02/13/2024] [Indexed: 03/11/2024]
Abstract
Apoptosis-inducing factor (AIF), which is confined to mitochondria of normal healthy cells, is the first identified caspase-independent cell death effector. Moreover, AIF is required for the optimal functioning of the respiratory chain machinery. Recent findings have revealed that AIF fulfills its pro-survival function by interacting with CHCHD4, a soluble mitochondrial protein which promotes the entrance and the oxidative folding of different proteins in the inner membrane space. Here, we report the crystal structure of the ternary complex involving the N-terminal 27-mer peptide of CHCHD4, NAD+, and AIF harboring its FAD (flavin adenine dinucleotide) prosthetic group in oxidized form. Combining this information with biophysical and biochemical data on the CHCHD4/AIF complex, we provide a detailed structural description of the interaction between the two proteins, validated by both chemical cross-linking mass spectrometry analysis and site-directed mutagenesis.
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Affiliation(s)
- Elisa Fagnani
- Biophysics Institute, CNR-IBF, Via Corti 12, 20133 Milan, Italy; Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Paolo Cocomazzi
- Biophysics Institute, CNR-IBF, Via Corti 12, 20133 Milan, Italy; Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Sara Pellegrino
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Gabriella Tedeschi
- Department of Veterinary Medicine and Animal Science (DIVAS), Università degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy; Cimaina, Università degli Studi di Milano, Milan, Italy
| | - Francesca Grassi Scalvini
- Department of Veterinary Medicine and Animal Science (DIVAS), Università degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy
| | - Federica Cossu
- Biophysics Institute, CNR-IBF, Via Corti 12, 20133 Milan, Italy; Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Stefano Da Vela
- Hochschule Bremerhaven, Karlstadt 8, 27568 Bremerhaven, Germany
| | - Alessandro Aliverti
- Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
| | - Eloise Mastrangelo
- Biophysics Institute, CNR-IBF, Via Corti 12, 20133 Milan, Italy; Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
| | - Mario Milani
- Biophysics Institute, CNR-IBF, Via Corti 12, 20133 Milan, Italy; Department of Bioscience, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.
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36
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Bochtler M. X-rays, electrons, and neutrons as probes of atomic matter. Structure 2024; 32:630-643.e6. [PMID: 38412856 DOI: 10.1016/j.str.2024.01.015] [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: 11/29/2022] [Revised: 03/21/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Abstract
X-rays, electrons, and neutrons probe different properties of matter. X-rays feel electron density (ED). Electrons sense the electrostatic potential (ESP) of electrons and nuclei. Neutrons are sensitive to nuclear coherent scattering length (NCSL). While NCSL maps are widely understood to be different, ED and ESP maps are tacitly assumed to be similar. Here, I show that the belief in ED and ESP map equivalence is mistaken, but contains a grain of truth. Using density functional theory (DFT), the Bethe-Mott (BM) relation, and the Thomas-Fermi (TF) and Cromer-Mann (CM) atomic models, I show that ED and ESP maps are indeed more similar to each other than to NCSL maps. Nevertheless, peak and integrated map values depend differently on the atomic order number and on the contributions from electrons in the inner and outer CM shells. ED and ESP maps also differ in the sign and relative magnitude of excess charge effects.
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Affiliation(s)
- Matthias Bochtler
- IIMCB, Trojdena 4, 02-109 Warsaw, Poland; Polish Academy of Sciences, IBB, Pawinskiego 5a, 02-106 Warsaw, Poland.
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37
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Vilela-Alves G, Rebelo Manuel R, Pedrosa N, Cardoso Pereira IA, Romão MJ, Mota C. Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2024; 80:98-106. [PMID: 38699971 PMCID: PMC11134731 DOI: 10.1107/s2053230x24003911] [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: 02/26/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024] Open
Abstract
Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO2 to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine Sδ interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO2 reduction, together with an increased sensitivity to oxygen inactivation.
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Affiliation(s)
- Guilherme Vilela-Alves
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Neide Pedrosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Inês A. Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Maria João Romão
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Cristiano Mota
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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38
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Diaz N, Perez C, Escribano AM, Sanz G, Priego J, Lafuente C, Barberis M, Calle L, Espinosa JF, Priest BT, Zhang HY, Nosie AK, Haas JV, Cannady E, Borel A, Schultze AE, Sauder JM, Hendle J, Weichert K, Nicholls SJ, Michael LF. Discovery of potent small-molecule inhibitors of lipoprotein(a) formation. Nature 2024; 629:945-950. [PMID: 38720069 PMCID: PMC11111404 DOI: 10.1038/s41586-024-07387-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 04/04/2024] [Indexed: 05/24/2024]
Abstract
Lipoprotein(a) (Lp(a)), an independent, causal cardiovascular risk factor, is a lipoprotein particle that is formed by the interaction of a low-density lipoprotein (LDL) particle and apolipoprotein(a) (apo(a))1,2. Apo(a) first binds to lysine residues of apolipoprotein B-100 (apoB-100) on LDL through the Kringle IV (KIV) 7 and 8 domains, before a disulfide bond forms between apo(a) and apoB-100 to create Lp(a) (refs. 3-7). Here we show that the first step of Lp(a) formation can be inhibited through small-molecule interactions with apo(a) KIV7-8. We identify compounds that bind to apo(a) KIV7-8, and, through chemical optimization and further application of multivalency, we create compounds with subnanomolar potency that inhibit the formation of Lp(a). Oral doses of prototype compounds and a potent, multivalent disruptor, LY3473329 (muvalaplin), reduced the levels of Lp(a) in transgenic mice and in cynomolgus monkeys. Although multivalent molecules bind to the Kringle domains of rat plasminogen and reduce plasmin activity, species-selective differences in plasminogen sequences suggest that inhibitor molecules will reduce the levels of Lp(a), but not those of plasminogen, in humans. These data support the clinical development of LY3473329-which is already in phase 2 studies-as a potent and specific orally administered agent for reducing the levels of Lp(a).
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Affiliation(s)
- Nuria Diaz
- Lilly Research Laboratories, Alcobendas, Spain
| | | | | | - Gema Sanz
- Lilly Research Laboratories, Alcobendas, Spain
| | | | | | | | - Luis Calle
- Lilly Research Laboratories, Alcobendas, Spain
| | | | | | - Hong Y Zhang
- Lilly Research Laboratories, Indianapolis, IN, USA
| | | | | | | | | | | | | | - Jörg Hendle
- Lilly Research Laboratories, San Diego, CA, USA
| | | | - Stephen J Nicholls
- Victorian Heart Institute, Monash University, Clayton, Victoria, Australia
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39
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Shelley KL, Garman EF. Identifying and avoiding radiation damage in macromolecular crystallography. Acta Crystallogr D Struct Biol 2024; 80:314-327. [PMID: 38700059 PMCID: PMC11066884 DOI: 10.1107/s2059798324003243] [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: 02/29/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Radiation damage remains one of the major impediments to accurate structure solution in macromolecular crystallography. The artefacts of radiation damage can manifest as structural changes that result in incorrect biological interpretations being drawn from a model, they can reduce the resolution to which data can be collected and they can even prevent structure solution entirely. In this article, we discuss how to identify and mitigate against the effects of radiation damage at each stage in the macromolecular crystal structure-solution pipeline.
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Affiliation(s)
- Kathryn L. Shelley
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
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40
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Feracci M, Hernandez S, Garlatti L, Mondielli C, Vincentelli R, Canard B, Reguera J, Ferron F, Alvarez K. Biophysical and structural study of La Crosse virus endonuclease inhibition for the development of new antiviral options. IUCRJ 2024; 11:374-383. [PMID: 38656310 PMCID: PMC11067750 DOI: 10.1107/s205225252400304x] [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: 12/13/2023] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
The large Bunyavirales order includes several families of viruses with a segmented ambisense (-) RNA genome and a cytoplasmic life cycle that starts by synthesizing viral mRNA. The initiation of transcription, which is common to all members, relies on an endonuclease activity that is responsible for cap-snatching. In La Crosse virus, an orthobunyavirus, it has previously been shown that the cap-snatching endonuclease resides in the N-terminal domain of the L protein. Orthobunyaviruses are transmitted by arthropods and cause diseases in cattle. However, California encephalitis virus, La Crosse virus and Jamestown Canyon virus are North American species that can cause encephalitis in humans. No vaccines or antiviral drugs are available. In this study, three known Influenza virus endonuclease inhibitors (DPBA, L-742,001 and baloxavir) were repurposed on the La Crosse virus endonuclease. Their inhibition was evaluated by fluorescence resonance energy transfer and their mode of binding was then assessed by differential scanning fluorimetry and microscale thermophoresis. Finally, two crystallographic structures were obtained in complex with L-742,001 and baloxavir, providing access to the structural determinants of inhibition and offering key information for the further development of Bunyavirales endonuclease inhibitors.
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Affiliation(s)
- Mikael Feracci
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB)–UMR7257 CNRS–Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France
| | - Sergio Hernandez
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB)–UMR7257 CNRS–Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France
- Université Lille; INSERM, UMR-S 1172, Lille Neuroscience and Cognition Research Centre, 59000 Lille, France
| | - Laura Garlatti
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB)–UMR7257 CNRS–Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France
- OmegaChem, Lévis, 480 Rue Perreault, Québec G6W 7V6, Canada
| | - Clemence Mondielli
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB)–UMR7257 CNRS–Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France
- Evotec (France) SAS, Campus Curie, 195 Route d’Espagne, 31036 Toulouse, France
| | - Renaud Vincentelli
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB)–UMR7257 CNRS–Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France
| | - Bruno Canard
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB)–UMR7257 CNRS–Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Juan Reguera
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB)–UMR7257 CNRS–Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France
| | - François Ferron
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB)–UMR7257 CNRS–Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Karine Alvarez
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB)–UMR7257 CNRS–Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France
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41
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Neumann P, Heidemann JL, Wollenhaupt J, Dickmanns A, Agthe M, Weiss MS, Ficner R. A small step towards an important goal: fragment screen of the c-di-AMP-synthesizing enzyme CdaA. Acta Crystallogr D Struct Biol 2024; 80:350-361. [PMID: 38682668 PMCID: PMC11066881 DOI: 10.1107/s205979832400336x] [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: 02/22/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
CdaA is the most widespread diadenylate cyclase in many bacterial species, including several multidrug-resistant human pathogens. The enzymatic product of CdaA, cyclic di-AMP, is a secondary messenger that is essential for the viability of many bacteria. Its absence in humans makes CdaA a very promising and attractive target for the development of new antibiotics. Here, the structural results are presented of a crystallographic fragment screen against CdaA from Listeria monocytogenes, a saprophytic Gram-positive bacterium and an opportunistic food-borne pathogen that can cause listeriosis in humans and animals. Two of the eight fragment molecules reported here were localized in the highly conserved ATP-binding site. These fragments could serve as potential starting points for the development of antibiotics against several CdaA-dependent bacterial species.
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Affiliation(s)
- Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Jana L. Heidemann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Achim Dickmanns
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Michael Agthe
- Institut für Nanostruktur- und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
- Cluster of Excellence ‘Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells’ (MBExC), University of Göttingen, 37075 Göttingen, Germany
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42
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Żygowska J, Orlikowska M, Zhukov I, Bal W, Szymańska A. Copper interaction with cystatin C: effects on protein structure and oligomerization. FEBS J 2024; 291:1974-1991. [PMID: 38349797 DOI: 10.1111/febs.17092] [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: 06/18/2023] [Revised: 01/09/2024] [Accepted: 02/01/2024] [Indexed: 02/15/2024]
Abstract
Human cystatin C (hCC), a small secretory protein, has gained attention beyond its classical role as a cysteine protease inhibitor owing to its potential involvement in neurodegenerative disorders. This study investigates the interaction between copper(II) ions [Cu(II)] and hCC, specifically targeting histidine residues known to participate in metal binding. Through various analytical techniques, including mutagenesis, circular dichroism, fluorescence assays, gel filtration chromatography, and electron microscopy, we evaluated the impact of Cu(II) ions on the structure and oligomerization of hCC. The results show that Cu(II) does not influence the secondary and tertiary structure of the studied hCC variants but affects their stability. To explore the Cu(II)-binding site, nuclear magnetic resonance (NMR) and X-ray studies were conducted. NMR experiments revealed notable changes in signal intensities and linewidths within the region 86His-Asp-Gln-Pro-His90, suggesting its involvement in Cu(II) coordination. Both histidine residues from this fragment were found to serve as a primary anchor of Cu(II) in solution, depending on the structural context and the presence of other Cu(II)-binding agents. The presence of Cu(II) led to significant destabilization and altered thermal stability of the wild-type and H90A variant, confirming differentiation between His residues in Cu(II) binding. In conclusion, this study provides valuable insights into the interaction between Cu(II) and hCC, elucidating the impact of copper ions on protein stability and identifying potential Cu(II)-binding residues. Understanding these interactions enhances our knowledge of the role of copper in neurodegenerative disorders and may facilitate the development of therapeutic strategies targeting copper-mediated processes in protein aggregation and associated pathologies.
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Affiliation(s)
- Justyna Żygowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Poland
| | - Marta Orlikowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Poland
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Poland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Poland
| | - Aneta Szymańska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Poland
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43
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Graef J, Ehrt C, Reim T, Rarey M. Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. J Chem Inf Model 2024; 64:3332-3349. [PMID: 38470439 DOI: 10.1021/acs.jcim.3c01462] [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: 03/13/2024]
Abstract
Analyzing the similarity of protein interfaces in protein-protein interactions gives new insights into protein function and assists in discovering new drugs. Usually, tools that assess the similarity focus on the interactions between two protein interfaces, while sometimes we only have one predicted interface. Herein, we present PiMine, a database-driven protein interface similarity search. It compares interface residues of one or two interacting chains by calculating and searching tetrahedral geometric patterns of α-carbon atoms and calculating physicochemical and shape-based similarity. On a dedicated, tailor-made dataset, we show that PiMine outperforms commonly used comparison tools in terms of early enrichment when considering interfaces of sequentially and structurally unrelated proteins. In an application example, we demonstrate its usability for protein interaction partner prediction by comparing predicted interfaces to known protein-protein interfaces.
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Affiliation(s)
- Joel Graef
- Universität Hamburg, ZBH─Center for Bioinformatics , Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, ZBH─Center for Bioinformatics , Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
| | - Thorben Reim
- Universität Hamburg, ZBH─Center for Bioinformatics , Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH─Center for Bioinformatics , Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany
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44
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Hill JA, Nyathi Y, Horrell S, von Stetten D, Axford D, Owen RL, Beddard GS, Pearson AR, Ginn HM, Yorke BA. An ultraviolet-driven rescue pathway for oxidative stress to eye lens protein human gamma-D crystallin. Commun Chem 2024; 7:81. [PMID: 38600176 PMCID: PMC11006947 DOI: 10.1038/s42004-024-01163-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Human gamma-D crystallin (HGD) is a major constituent of the eye lens. Aggregation of HGD contributes to cataract formation, the leading cause of blindness worldwide. It is unique in its longevity, maintaining its folded and soluble state for 50-60 years. One outstanding question is the structural basis of this longevity despite oxidative aging and environmental stressors including ultraviolet radiation (UV). Here we present crystallographic structures evidencing a UV-induced crystallin redox switch mechanism. The room-temperature serial synchrotron crystallographic (SSX) structure of freshly prepared crystallin mutant (R36S) shows no post-translational modifications. After aging for nine months in the absence of light, a thiol-adduct (dithiothreitol) modifying surface cysteines is observed by low-dose SSX. This is shown to be UV-labile in an acutely light-exposed structure. This suggests a mechanism by which a major source of crystallin damage, UV, may also act as a rescuing factor in a finely balanced redox system.
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Affiliation(s)
- Jake A Hill
- School of Chemistry and Biosciences, University of Bradford, Richmond Road, Bradford, BD7 1DP, United Kingdom
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, United Kingdom
| | - Yvonne Nyathi
- Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, United Kingdom
| | - Sam Horrell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - David von Stetten
- European Molecular Biology Laboratory, Notkestraße 85, 22607, Hamburg, Germany
| | - Danny Axford
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Robin L Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Godfrey S Beddard
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, United Kingdom
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Arwen R Pearson
- HARBOR, Institute for Nanostructure and Solid State Physics, Hamburg, 22761, Germany
| | - Helen M Ginn
- HARBOR, Institute for Nanostructure and Solid State Physics, Hamburg, 22761, Germany.
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
| | - Briony A Yorke
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, United Kingdom.
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45
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Thisted T, Smith FD, Mukherjee A, Kleschenko Y, Feng F, Jiang ZG, Eitas T, Malhotra K, Biesova Z, Onumajuru A, Finley F, Cifuentes A, Zhang G, Martin GH, Takeuchi Y, Thiam K, Schreiber RD, van der Horst EH. VISTA checkpoint inhibition by pH-selective antibody SNS-101 with optimized safety and pharmacokinetic profiles enhances PD-1 response. Nat Commun 2024; 15:2917. [PMID: 38575562 PMCID: PMC10995192 DOI: 10.1038/s41467-024-47256-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
VISTA, an inhibitory myeloid-T-cell checkpoint, holds promise as a target for cancer immunotherapy. However, its effective targeting has been impeded by issues such as rapid clearance and cytokine release syndrome observed with previous VISTA antibodies. Here we demonstrate that SNS-101, a newly developed pH-selective VISTA antibody, addresses these challenges. Structural and biochemical analyses confirmed the pH-selectivity and unique epitope targeted by SNS-101. These properties confer favorable pharmacokinetic and safety profiles on SNS-101. In syngeneic tumor models utilizing human VISTA knock-in mice, SNS-101 shows in vivo efficacy when combined with a PD-1 inhibitor, modulates cytokine and chemokine signaling, and alters the tumor microenvironment. In summary, SNS-101, currently in Phase I clinical trials, emerges as a promising therapeutic biologic for a wide range of patients whose cancer is refractory to current immunotherapy regimens.
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Affiliation(s)
- Thomas Thisted
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - F Donelson Smith
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Arnab Mukherjee
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Yuliya Kleschenko
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Feng Feng
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Zhi-Gang Jiang
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Timothy Eitas
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Kanam Malhotra
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Zuzana Biesova
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Adejumoke Onumajuru
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Faith Finley
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Anokhi Cifuentes
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | - Guolin Zhang
- Sensei Biotherapeutics Inc., 1405 Research Blvd, Suite 125, Rockville, MD, 20850, USA
| | | | - Yoshiko Takeuchi
- Department of Pathology and Immunology, Washington Univ. School of Medicine, Mailstop 8118, 425 South Euclid Ave, St. Louis, MO, 63110, USA
| | - Kader Thiam
- genOway, Technopark Gerland, 69007, Lyon, France
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington Univ. School of Medicine, Mailstop 8118, 425 South Euclid Ave, St. Louis, MO, 63110, USA
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46
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Krawinski P, Smithers L, van Dalsen L, Boland C, Ostrovitsa N, Pérez J, Caffrey M. 7.10 MAG. A Novel Host Monoacylglyceride for In Meso (Lipid Cubic Phase) Crystallization of Membrane Proteins. CRYSTAL GROWTH & DESIGN 2024; 24:2985-3001. [PMID: 38585376 PMCID: PMC10995948 DOI: 10.1021/acs.cgd.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
A novel monoacylglycerol, 7.10 MAG, has been produced for use in the in meso (lipid cubic phase) crystallization of membrane proteins and complexes. 7.10 MAG differs from monoolein, the most extensively used lipid for in meso crystallization, in that it is shorter in chain length by one methylene and its cis olefinic bond is two carbons closer to the glycerol headgroup. These changes in structure alter the phase behavior of the hydrated lipid and the microstructure of the corresponding mesophases formed. Temperature-composition phase diagrams for 7.10 MAG have been constructed using small- and wide-angle X-ray scattering over a range of temperatures and hydration levels that span those used for crystallization. The phase diagrams include lamellar crystalline, fluid isotropic, lamellar liquid-crystalline, cubic-Ia3d, and cubic-Pn3m phases, as observed with monoolein. Conspicuous by its absence is the inverted hexagonal phase which is rationalized on the basis of 7.10 MAG's chemical constitution. The cubic phase prepared with the new lipid facilitates the growth of crystals that were used to generate high-resolution structures of intramembrane β-barrel and α-helical proteins. Compatibility of fully hydrated 7.10 MAG with cholesterol and phosphatidylcholine means that these two lipids can be used as additives to optimize crystallogenesis in screening trials with 7.10 MAG as the host lipid.
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Affiliation(s)
- Pawel Krawinski
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Luke Smithers
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Leendert van Dalsen
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Coilin Boland
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Nikita Ostrovitsa
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Javier Pérez
- SWING
Beamline, Synchrotron Soleil, Saint-Aubin 91190, France
| | - Martin Caffrey
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
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47
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Ran X, Parikh P, Abendroth J, Arakaki TL, Clifton MC, Edwards TE, Lorimer DD, Mayclin S, Staker BL, Myler P, McLaughlin KJ. Structural and functional characterization of FabG4 from Mycolicibacterium smegmatis. Acta Crystallogr F Struct Biol Commun 2024; 80:82-91. [PMID: 38656226 PMCID: PMC11058512 DOI: 10.1107/s2053230x2400356x] [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: 03/11/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024] Open
Abstract
The rise in antimicrobial resistance is a global health crisis and necessitates the development of novel strategies to treat infections. For example, in 2022 tuberculosis (TB) was the second leading infectious killer after COVID-19, with multi-drug-resistant strains of TB having an ∼40% fatality rate. Targeting essential biosynthetic pathways in pathogens has proven to be successful for the development of novel antimicrobial treatments. Fatty-acid synthesis (FAS) in bacteria proceeds via the type II pathway, which is substantially different from the type I pathway utilized in animals. This makes bacterial fatty-acid biosynthesis (Fab) enzymes appealing as drug targets. FabG is an essential FASII enzyme, and some bacteria, such as Mycobacterium tuberculosis, the causative agent of TB, harbor multiple homologs. FabG4 is a conserved, high-molecular-weight FabG (HMwFabG) that was first identified in M. tuberculosis and is distinct from the canonical low-molecular-weight FabG. Here, structural and functional analyses of Mycolicibacterium smegmatis FabG4, the third HMwFabG studied to date, are reported. Crystal structures of NAD+ and apo MsFabG4, along with kinetic analyses, show that MsFabG4 preferentially binds and uses NADH when reducing CoA substrates. As M. smegmatis is often used as a model organism for M. tuberculosis, these studies may aid the development of drugs to treat TB and add to the growing body of research that distinguish HMwFabGs from the archetypal low-molecular-weight FabG.
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Affiliation(s)
- Xinping Ran
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Prashit Parikh
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | | | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- UCB Pharma, Bedford, Massachusetts, USA
| | | | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Peter Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Krystle J. McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
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48
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Breeze CW, Nakano Y, Campbell EC, Frkic RL, Lupton DW, Jackson CJ. Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase. Acta Crystallogr D Struct Biol 2024; 80:289-298. [PMID: 38512071 PMCID: PMC10994177 DOI: 10.1107/s2059798324002316] [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: 12/16/2023] [Accepted: 03/10/2024] [Indexed: 03/22/2024] Open
Abstract
Lanthanide ions have ideal chemical properties for catalysis, such as hard Lewis acidity, fast ligand-exchange kinetics, high coordination-number preferences and low geometric requirements for coordination. As a result, many small-molecule lanthanide catalysts have been described in the literature. Yet, despite the ability of enzymes to catalyse highly stereoselective reactions under gentle conditions, very few lanthanoenzymes have been investigated. In this work, the mononuclear binding of europium(III) and gadolinium(III) to the active site of a mutant of the model enzyme phosphotriesterase are described using X-ray crystallography at 1.78 and 1.61 Å resolution, respectively. It is also shown that despite coordinating a single non-natural metal cation, the PTE-R18 mutant is still able to maintain esterase activity.
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Affiliation(s)
- Callum W. Breeze
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Yuji Nakano
- School of Chemistry, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Eleanor C. Campbell
- Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, VIC 3168, Australia
| | - Rebecca L. Frkic
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - David W. Lupton
- School of Chemistry, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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49
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Ahmad N, Sharma P, Sharma S, Singh TP. Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 Å resolution. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:147-157. [PMID: 38456905 DOI: 10.1007/s00249-024-01703-1] [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: 11/24/2023] [Revised: 01/16/2024] [Accepted: 02/10/2024] [Indexed: 03/09/2024]
Abstract
Phosphopantetheine adenylyltransferase (EC. 2.7.7.3, PPAT) catalyzes the penultimate step of the multistep reaction in the coenzyme A (CoA) biosynthesis pathway. In this step, an adenylyl group from adenosine triphosphate (ATP) is transferred to 4'-phosphopantetheine (PNS) yielding 3'-dephospho-coenzyme A (dpCoA) and pyrophosphate (PPi). PPAT from strain C3 of Klebsiella pneumoniae (KpPPAT) was cloned, expressed and purified. It was crystallized using 0.1 M HEPES buffer and PEG10000 at pH 7.5. The crystals belonged to tetragonal space group P41212 with cell dimensions of a = b = 72.82 Å and c = 200.37 Å. The structure was determined using the molecular replacement method and refined to values of 0.208 and 0.255 for Rcryst and Rfree factors, respectively. The structure determination showed the presence of three crystallographically independent molecules A, B and C in the asymmetric unit. The molecules A and B are observed in the form of a dimer in the asymmetric unit while molecule C belongs to the second dimer whose partner is related by crystallographic twofold symmetry. The polypeptide chain of KpPPAT folds into a β/α structure. The conformations of the side chains of several residues in the substrate binding site in KpPPAT are significantly different from those reported in other PPATs. As a result, the modes of binding of substrates, phosphopantetheine (PNS) and adenosine triphosphate (ATP) differ considerably. The binding studies using fluorescence spectroscopy indicated a KD value of 3.45 × 10-4 M for ATP which is significantly lower than the corresponding values reported for PPAT from other species.
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Affiliation(s)
- Nabeel Ahmad
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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50
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Dötsch L, Davies C, Hennes E, Schönfeld J, Kumar A, Guita CDC, Ehrler JH, Hiesinger K, Thavam S, Janning P, Sievers S, Knapp S, Proschak E, Ziegler S, Waldmann H. Discovery of the sEH Inhibitor Epoxykynin as a Potent Kynurenine Pathway Modulator. J Med Chem 2024; 67:4691-4706. [PMID: 38470246 PMCID: PMC10983002 DOI: 10.1021/acs.jmedchem.3c02245] [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: 11/29/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024]
Abstract
Disease-related phenotypic assays enable unbiased discovery of novel bioactive small molecules and may provide novel insights into physiological systems and unprecedented molecular modes of action (MMOA). Herein, we report the identification and characterization of epoxykynin, a potent inhibitor of the soluble epoxide hydrolase (sEH). Epoxykynin was discovered by means of a cellular assay monitoring modulation of kynurenine (Kyn) levels in BxPC-3 cells upon stimulation with the cytokine interferon-γ (IFN-γ) and subsequent target identification employing affinity-based chemical proteomics. Increased Kyn levels are associated with immune suppression in the tumor microenvironment and, thus, the Kyn pathway and its key player indoleamine 2,3-dioxygenase 1 (IDO1) are appealing targets in immuno-oncology. However, targeting IDO1 directly has led to limited success in clinical investigations, demonstrating that alternative approaches to reduce Kyn levels are in high demand. We uncover a cross-talk between sEH and the Kyn pathway that may provide new opportunities to revert cancer-induced immune tolerance.
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Affiliation(s)
- Lara Dötsch
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Department
of Chemical Biology, Technical University
of Dortmund, Otto-Hahn-Strasse
6, Dortmund 44227, Germany
| | - Caitlin Davies
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Elisabeth Hennes
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Julia Schönfeld
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Adarsh Kumar
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
- Structural
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, Frankfurt 60438, Germany
| | - Celine Da Cruz
Lopes Guita
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Johanna H.M. Ehrler
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Kerstin Hiesinger
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Sasikala Thavam
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Petra Janning
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sonja Sievers
- Compound
Management and Screening Center (COMAS), Otto-Hahn-Strasse 15, Dortmund 44227, Germany
| | - Stefan Knapp
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
- Structural
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, Frankfurt 60438, Germany
| | - Ewgenij Proschak
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Slava Ziegler
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Herbert Waldmann
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Department
of Chemical Biology, Technical University
of Dortmund, Otto-Hahn-Strasse
6, Dortmund 44227, Germany
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