1
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Verteramo ML, Ignjatović MM, Kumar R, Wernersson S, Ekberg V, Wallerstein J, Carlström G, Chadimová V, Leffler H, Zetterberg F, Logan DT, Ryde U, Akke M, Nilsson UJ. Interplay of halogen bonding and solvation in protein-ligand binding. iScience 2024; 27:109636. [PMID: 38633000 PMCID: PMC11021960 DOI: 10.1016/j.isci.2024.109636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/13/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Halogen bonding is increasingly utilized in efforts to achieve high affinity and selectivity of molecules designed to bind proteins, making it paramount to understand the relationship between structure, dynamics, and thermodynamic driving forces. We present a detailed analysis addressing this problem using a series of protein-ligand complexes involving single halogen substitutions - F, Cl, Br, and I - and nearly identical structures. Isothermal titration calorimetry reveals an increasingly favorable binding enthalpy from F to I that correlates with the halogen size and σ-hole electropositive character, but is partially counteracted by unfavorable entropy, which is constant from F to Cl and Br, but worse for I. Consequently, the binding free energy is roughly equal for Cl, Br, and I. QM and solvation-free-energy calculations reflect an intricate balance between halogen bonding, hydrogen bonds, and solvation. These advances have the potential to aid future drug design initiatives involving halogenated compounds.
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Affiliation(s)
| | | | - Rohit Kumar
- Department of Chemistry, Lund University, Lund, Sweden
| | | | | | | | | | | | - Hakon Leffler
- Microbiology, Immunology, and Glycobiology, Department of Experimental Medicine, Lund University, Lund, Sweden
| | | | | | - Ulf Ryde
- Department of Chemistry, Lund University, Lund, Sweden
| | - Mikael Akke
- Department of Chemistry, Lund University, Lund, Sweden
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2
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Mahanti M, Pal KB, Kumar R, Schulze M, Leffler H, Logan DT, Nilsson UJ. Ligand Sulfur Oxidation State Progressively Alters Galectin-3-Ligand Complex Conformations To Induce Affinity-Influencing Hydrogen Bonds. J Med Chem 2023; 66:14716-14723. [PMID: 37878264 PMCID: PMC10641817 DOI: 10.1021/acs.jmedchem.3c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Indexed: 10/26/2023]
Abstract
Galectins play biological roles in immune regulation and tumor progression. Ligands with high affinity for the shallow, hydrophilic galectin-3 ligand binding site rely primarily on a galactose core with appended aryltriazole moieties, making hydrophobic interactions and π-stacking. We designed and synthesized phenyl sulfone, sulfoxide, and sulfide-triazolyl thiogalactoside derivatives to create affinity-enhancing hydrogen bonds, hydrophobic and π-interactions. Crystal structures and thermodynamic analyses revealed that the sulfoxide and sulfone ligands form hydrogen bonds while retaining π-interactions, resulting in improved affinities and unique binding poses. The sulfoxide, bearing one hydrogen bond acceptor, leads to an affinity decrease compared to the sulfide, whereas the corresponding sulfone forms three hydrogen bonds, two directly with Asn and Arg side chains and one water-mediated to an Asp side chain, respectively, which alters the complex structure and increases affinity. These findings highlight that the sulfur oxidation state influences both the interaction thermodynamics and structure.
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Affiliation(s)
- Mukul Mahanti
- Department
of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Kumar Bhaskar Pal
- Department
of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Rohit Kumar
- Division
of Biochemistry & Structural Biology, Centre for Molecular Protein
Science, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Markus Schulze
- Department
of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Hakon Leffler
- Department
of Laboratory Medicine, Section MIG, Lund
University, BMC-C1228b Klinikgatan 28, 221 84 Lund, Sweden
| | - Derek T. Logan
- Division
of Biochemistry & Structural Biology, Centre for Molecular Protein
Science, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Ulf J. Nilsson
- Department
of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
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3
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Składanowska K, Bloch Y, Strand J, White KF, Hua J, Aldridge D, Welin M, Logan DT, Soete A, Merceron R, Murphy C, Provost M, Bazan JF, Hunter CA, Hill JA, Savvides SN. Structural basis of activation and antagonism of receptor signaling mediated by interleukin-27. Cell Rep 2022; 41:111490. [PMID: 36261006 PMCID: PMC9597551 DOI: 10.1016/j.celrep.2022.111490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/14/2022] [Accepted: 09/21/2022] [Indexed: 11/19/2022] Open
Abstract
Interleukin-27 (IL-27) uniquely assembles p28 and EBI3 subunits to a heterodimeric cytokine that signals via IL-27Rα and gp130. To provide the structural framework for receptor activation by IL-27 and its emerging therapeutic targeting, we report here crystal structures of mouse IL-27 in complex with IL-27Rα and of human IL-27 in complex with SRF388, a monoclonal antibody undergoing clinical trials with oncology indications. One face of the helical p28 subunit interacts with EBI3, while the opposite face nestles into the interdomain elbow of IL-27Rα to juxtapose IL-27Rα to EBI3. This orients IL-27Rα for paired signaling with gp130, which only uses its immunoglobulin domain to bind to IL-27. Such a signaling complex is distinct from those mediated by IL-12 and IL-23. The SRF388 binding epitope on IL-27 overlaps with the IL-27Rα interaction site explaining its potent antagonistic properties. Collectively, our findings will facilitate the mechanistic interrogation, engineering, and therapeutic targeting of IL-27.
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Affiliation(s)
- Katarzyna Składanowska
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | - Yehudi Bloch
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | - Jamie Strand
- Surface Oncology, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Kerry F White
- Surface Oncology, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Jing Hua
- Surface Oncology, 50 Hampshire Street, Cambridge, MA 02139, USA
| | - Daniel Aldridge
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martin Welin
- SARomics Biostructures AB, Medicon Village, Scheelevägen 2, 223 63 Lund, Sweden
| | - Derek T Logan
- SARomics Biostructures AB, Medicon Village, Scheelevägen 2, 223 63 Lund, Sweden
| | - Arne Soete
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Ghent, Belgium; Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Romain Merceron
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | - Casey Murphy
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | - Mathias Provost
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | - J Fernando Bazan
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium; ħ Bioconsulting, Stillwater, MN, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan A Hill
- Surface Oncology, 50 Hampshire Street, Cambridge, MA 02139, USA.
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium.
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4
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Wilson LFL, Dendooven T, Hardwick SW, Echevarría-Poza A, Tryfona T, Krogh KBRM, Chirgadze DY, Luisi BF, Logan DT, Mani K, Dupree P. The structure of EXTL3 helps to explain the different roles of bi-domain exostosins in heparan sulfate synthesis. Nat Commun 2022; 13:3314. [PMID: 35676258 PMCID: PMC9178029 DOI: 10.1038/s41467-022-31048-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/31/2022] [Indexed: 11/08/2022] Open
Abstract
Heparan sulfate is a highly modified O-linked glycan that performs diverse physiological roles in animal tissues. Though quickly modified, it is initially synthesised as a polysaccharide of alternating β-D-glucuronosyl and N-acetyl-α-D-glucosaminyl residues by exostosins. These enzymes generally possess two glycosyltransferase domains (GT47 and GT64)-each thought to add one type of monosaccharide unit to the backbone. Although previous structures of murine exostosin-like 2 (EXTL2) provide insight into the GT64 domain, the rest of the bi-domain architecture is yet to be characterised; hence, how the two domains co-operate is unknown. Here, we report the structure of human exostosin-like 3 (EXTL3) in apo and UDP-bound forms. We explain the ineffectiveness of EXTL3's GT47 domain to transfer β-D-glucuronosyl units, and we observe that, in general, the bi-domain architecture would preclude a processive mechanism of backbone extension. We therefore propose that heparan sulfate backbone polymerisation occurs by a simple dissociative mechanism.
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Affiliation(s)
- L F L Wilson
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
| | - T Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - S W Hardwick
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - A Echevarría-Poza
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - T Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - K B R M Krogh
- Department of Protein Biochemistry and Stability, Novozymes A/S, Krogshøjvej 36, 2880, Bagsværd, Denmark
| | - D Y Chirgadze
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - B F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - D T Logan
- Biochemistry and Structural Biology, Centre for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00, Lund, Sweden
| | - K Mani
- Department of Experimental Medical Science, Division of Neuroscience, Glycobiology Group, Lund University, SE-221 00, Lund, Sweden.
| | - P Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
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5
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Rozman Grinberg I, Martínez-Carranza M, Bimai O, Nouaïria G, Shahid S, Lundin D, Logan DT, Sjöberg BM, Stenmark P. A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases. Nat Commun 2022; 13:2700. [PMID: 35577776 PMCID: PMC9110341 DOI: 10.1038/s41467-022-30328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractRibonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of RNR genes and, often, its own, in most bacteria and some archaea. NrdR senses the concentration of nucleotides through its ATP-cone, an evolutionarily mobile domain that also regulates the enzymatic activity of many RNRs, while a Zn-ribbon domain mediates binding to NrdR boxes upstream of and overlapping the transcription start site of RNR genes. Here, we combine biochemical and cryo-EM studies of NrdR from Streptomyces coelicolor to show, at atomic resolution, how NrdR binds to DNA. The suggested mechanism involves an initial dodecamer loaded with two ATP molecules that cannot bind to DNA. When dATP concentrations increase, an octamer forms that is loaded with one molecule each of dATP and ATP per monomer. A tetramer derived from this octamer then binds to DNA and represses transcription of RNR. In many bacteria — including well-known pathogens such as Mycobacterium tuberculosis — NrdR simultaneously controls multiple RNRs and hence DNA synthesis, making it an excellent target for novel antibiotics development.
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6
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Zhang Y, Towers CG, Singh UK, Liu J, Håkansson M, Logan DT, Donini O, Kutateladze TG. Dusquetide modulates innate immune response through binding to p62. Structure 2022; 30:1055-1061.e7. [PMID: 35640615 PMCID: PMC9357125 DOI: 10.1016/j.str.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/10/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
SQSTM1/p62 is an autophagic receptor that plays a major role in mediating stress and innate immune responses. Preclinical studies identified p62 as a target of the prototype innate defense regulator (IDR); however, the molecular mechanism of this process remains unclear. Here, we describe the structural basis and biological consequences of the interaction of p62 with the next generation of IDRs, dusquetide. Both electrostatic and hydrophobic contacts drive the formation of the complex between dusquetide and the ZZ domain of p62. We show that dusquetide penetrates the cell membrane and associates with p62 in vivo. Dusquetide binding modulates the p62-RIP1 complex, increases p38 phosphorylation, and enhances CEBP/B expression without activating autophagy. Our findings provide molecular details underlying the IDR action that may help in the development of new strategies to pharmacologically target p62.
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7
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Maurer MF, Lewis KE, Kuijper JL, Ardourel D, Gudgeon CJ, Chandrasekaran S, Mudri SL, Kleist KN, Navas C, Wolfson MF, Rixon MW, Swanson R, Dillon SR, Levin SD, Kimbung YR, Akutsu M, Logan DT, Walse B, Swiderek KM, Peng SL. The engineered CD80 variant fusion therapeutic davoceticept combines checkpoint antagonism with conditional CD28 costimulation for anti-tumor immunity. Nat Commun 2022; 13:1790. [PMID: 35379805 PMCID: PMC8980021 DOI: 10.1038/s41467-022-29286-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/09/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractDespite the recent clinical success of T cell checkpoint inhibition targeting the CTLA-4 and PD-1 pathways, many patients either fail to achieve objective responses or they develop resistance to therapy. In some cases, poor responses to checkpoint blockade have been linked to suboptimal CD28 costimulation and the inability to generate and maintain a productive adaptive anti-tumor immune response. To address this, here we utilize directed evolution to engineer a CD80 IgV domain with increased PD-L1 affinity and fuse this to an immunoglobulin Fc domain, creating a therapeutic (ALPN-202, davoceticept) capable of providing CD28 costimulation in a PD-L1-dependent fashion while also antagonizing PD-1 - PD-L1 and CTLA-4–CD80/CD86 interactions. We demonstrate that by combining CD28 costimulation and dual checkpoint inhibition, ALPN-202 enhances T cell activation and anti-tumor efficacy in cell-based assays and mouse tumor models more potently than checkpoint blockade alone and thus has the potential to generate potent, clinically meaningful anti-tumor immunity in humans.
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8
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Goebel EJ, Kattamuri C, Gipson GR, Krishnan L, Chavez M, Czepnik M, Maguire MC, Grenha R, Håkansson M, Logan DT, Grinberg AV, Sako D, Castonguay R, Kumar R, Thompson TB. Structures of activin ligand traps using natural sets of type I and type II TGFβ receptors. iScience 2022; 25:103590. [PMID: 35005539 PMCID: PMC8718839 DOI: 10.1016/j.isci.2021.103590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/18/2021] [Accepted: 12/06/2021] [Indexed: 12/14/2022] Open
Abstract
The 30+ unique ligands of the TGFβ family signal by forming complexes using different combinations of type I and type II receptors. Therapeutically, the extracellular domain of a single receptor fused to an Fc molecule can effectively neutralize subsets of ligands. Increased ligand specificity can be accomplished by using the extracellular domains of both the type I and type II receptor to mimic the naturally occurring signaling complex. Here, we report the structure of one "type II-type I-Fc" fusion, ActRIIB-Alk4-Fc, in complex with two TGFβ family ligands, ActA, and GDF11, providing a snapshot of this therapeutic platform. The study reveals that extensive contacts are formed by both receptors, replicating the ternary signaling complex, despite the inherent low affinity of Alk4. Our study shows that low-affinity type I interactions support altered ligand specificity and can be visualized at the molecular level using this platform.
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Affiliation(s)
- Erich J. Goebel
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, 231 Albert Sabin Way ML 0524, Cincinnati, OH 45267, USA
| | - Chandramohan Kattamuri
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, 231 Albert Sabin Way ML 0524, Cincinnati, OH 45267, USA
| | - Gregory R. Gipson
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, 231 Albert Sabin Way ML 0524, Cincinnati, OH 45267, USA
| | | | | | - Magdalena Czepnik
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, 231 Albert Sabin Way ML 0524, Cincinnati, OH 45267, USA
| | | | - Rosa Grenha
- Acceleron Pharma, Inc., Cambridge, MA 02139, USA
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, Scheeletorget 1, 223 63, Lund, Sweden
| | - Derek T. Logan
- SARomics Biostructures AB, Medicon Village, Scheeletorget 1, 223 63, Lund, Sweden
| | | | - Dianne Sako
- Acceleron Pharma, Inc., Cambridge, MA 02139, USA
| | | | | | - Thomas B. Thompson
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, 231 Albert Sabin Way ML 0524, Cincinnati, OH 45267, USA
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9
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Caldararu O, Ekberg V, Logan DT, Oksanen E, Ryde U. Exploring ligand dynamics in protein crystal structures with ensemble refinement. Acta Crystallogr D Struct Biol 2021; 77:1099-1115. [PMID: 34342282 PMCID: PMC8329865 DOI: 10.1107/s2059798321006513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein-ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein-ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and Rfree values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Vilhelm Ekberg
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Derek T. Logan
- Biochemistry and Structural Biology, Centre for Molecular Protein Science, Department of Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source Consortium ESS ERIC, PO Box 176, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
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10
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Hasan M, Banerjee I, Rozman Grinberg I, Sjöberg BM, Logan DT. Solution Structure of the dATP-Inactivated Class I Ribonucleotide Reductase From Leeuwenhoekiella blandensis by SAXS and Cryo-Electron Microscopy. Front Mol Biosci 2021; 8:713608. [PMID: 34381817 PMCID: PMC8350387 DOI: 10.3389/fmolb.2021.713608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/21/2021] [Indexed: 01/14/2023] Open
Abstract
The essential enzyme ribonucleotide reductase (RNR) is highly regulated both at the level of overall activity and substrate specificity. Studies of class I, aerobic RNRs have shown that overall activity is downregulated by the binding of dATP to a small domain known as the ATP-cone often found at the N-terminus of RNR subunits, causing oligomerization that prevents formation of a necessary α2β2 complex between the catalytic (α2) and radical generating (β2) subunits. In some relatively rare organisms with RNRs of the subclass NrdAi, the ATP-cone is found at the N-terminus of the β subunit rather than more commonly the α subunit. Binding of dATP to the ATP-cone in β results in formation of an unusual β4 tetramer. However, the structural basis for how the formation of the active complex is hindered by such oligomerization has not been studied. Here we analyse the low-resolution three-dimensional structures of the separate subunits of an RNR from subclass NrdAi, as well as the α4β4 octamer that forms in the presence of dATP. The results reveal a type of oligomer not previously seen for any class of RNR and suggest a mechanism for how binding of dATP to the ATP-cone switches off catalysis by sterically preventing formation of the asymmetrical α2β2 complex.
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Affiliation(s)
- Mahmudul Hasan
- Biochemistry and Structural Biology, Dept. of Chemistry, Lund University, Lund, Sweden
| | - Ipsita Banerjee
- Biochemistry and Structural Biology, Dept. of Chemistry, Lund University, Lund, Sweden
| | | | - Britt-Marie Sjöberg
- Dept. of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Dept. of Chemistry, Lund University, Lund, Sweden
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11
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Wallerstein J, Ekberg V, Ignjatović MM, Kumar R, Caldararu O, Peterson K, Wernersson S, Brath U, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C. JACS Au 2021; 1:484-500. [PMID: 34467311 PMCID: PMC8395690 DOI: 10.1021/jacsau.0c00094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 06/13/2023]
Abstract
Molecular recognition is fundamental to biological signaling. A central question is how individual interactions between molecular moieties affect the thermodynamics of ligand binding to proteins and how these effects might propagate beyond the immediate neighborhood of the binding site. Here, we investigate this question by introducing minor changes in ligand structure and characterizing the effects of these on ligand affinity to the carbohydrate recognition domain of galectin-3, using a combination of isothermal titration calorimetry, X-ray crystallography, NMR relaxation, and computational approaches including molecular dynamics (MD) simulations and grid inhomogeneous solvation theory (GIST). We studied a congeneric series of ligands with a fluorophenyl-triazole moiety, where the fluorine substituent varies between the ortho, meta, and para positions (denoted O, M, and P). The M and P ligands have similar affinities, whereas the O ligand has 3-fold lower affinity, reflecting differences in binding enthalpy and entropy. The results reveal surprising differences in conformational and solvation entropy among the three complexes. NMR backbone order parameters show that the O-bound protein has reduced conformational entropy compared to the M and P complexes. By contrast, the bound ligand is more flexible in the O complex, as determined by 19F NMR relaxation, ensemble-refined X-ray diffraction data, and MD simulations. Furthermore, GIST calculations indicate that the O-bound complex has less unfavorable solvation entropy compared to the other two complexes. Thus, the results indicate compensatory effects from ligand conformational entropy and water entropy, on the one hand, and protein conformational entropy, on the other hand. Taken together, these different contributions amount to entropy-entropy compensation among the system components involved in ligand binding to a target protein.
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Affiliation(s)
- Johan Wallerstein
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Vilhelm Ekberg
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | | | - Rohit Kumar
- Biochemistry
and Structural Biology, Center for Molecular Protein Science, Department
of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Octav Caldararu
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | - Kristoffer Peterson
- Centre
for Analysis and Synthesis, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Sven Wernersson
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulrika Brath
- The
Swedish NMR Center, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Hakon Leffler
- Microbiology,
Immunology, and Glycobiology, Department of Experimental Medicine, Lund University, 221 00 Lund, Sweden
| | - Esko Oksanen
- European
Spallation Source ESS ERIC, 225 92 Lund, Sweden
| | - Derek T. Logan
- Biochemistry
and Structural Biology, Center for Molecular Protein Science, Department
of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulf J. Nilsson
- Centre
for Analysis and Synthesis, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulf Ryde
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | - Mikael Akke
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
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12
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Shilova A, Lebrette H, Aurelius O, Nan J, Welin M, Kovacic R, Ghosh S, Safari C, Friel RJ, Milas M, Matej Z, Högbom M, Brändén G, Kloos M, Shoeman RL, Doak B, Ursby T, Håkansson M, Logan DT, Mueller U. Current status and future opportunities for serial crystallography at MAX IV Laboratory. J Synchrotron Radiat 2020; 27:1095-1102. [PMID: 32876583 PMCID: PMC7467353 DOI: 10.1107/s1600577520008735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Over the last decade, serial crystallography, a method to collect complete diffraction datasets from a large number of microcrystals delivered and exposed to an X-ray beam in random orientations at room temperature, has been successfully implemented at X-ray free-electron lasers and synchrotron radiation facility beamlines. This development relies on a growing variety of sample presentation methods, including different fixed target supports, injection methods using gas-dynamic virtual-nozzle injectors and high-viscosity extrusion injectors, and acoustic levitation of droplets, each with unique requirements. In comparison with X-ray free-electron lasers, increased beam time availability makes synchrotron facilities very attractive to perform serial synchrotron X-ray crystallography (SSX) experiments. Within this work, the possibilities to perform SSX at BioMAX, the first macromolecular crystallography beamline at MAX IV Laboratory in Lund, Sweden, are described, together with case studies from the SSX user program: an implementation of a high-viscosity extrusion injector to perform room temperature serial crystallography at BioMAX using two solid supports - silicon nitride membranes (Silson, UK) and XtalTool (Jena Bioscience, Germany). Future perspectives for the dedicated serial crystallography beamline MicroMAX at MAX IV Laboratory, which will provide parallel and intense micrometre-sized X-ray beams, are discussed.
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Affiliation(s)
- Anastasya Shilova
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, Stockholm 10691, Sweden
| | - Oskar Aurelius
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Jie Nan
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Martin Welin
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Rebeka Kovacic
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Ross J. Friel
- School of Information Technology, Halmstad University, Halmstad 30118, Sweden
| | - Mirko Milas
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Zdenek Matej
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, Stockholm 10691, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Robert L. Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas Ursby
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
| | - Maria Håkansson
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Derek T. Logan
- SARomics Biostructures, Medicon Village, Scheeletorget 1, Lund 22363, Sweden
| | - Uwe Mueller
- MAX IV Laboratory, Lund University, Fotongatan 2, Lund 22484, Sweden
- Macromolecular Crystallography Group, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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13
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Lima GMA, Talibov VO, Jagudin E, Sele C, Nyblom M, Knecht W, Logan DT, Sjögren T, Mueller U. FragMAX: the fragment-screening platform at the MAX IV Laboratory. Acta Crystallogr D Struct Biol 2020; 76:771-777. [PMID: 32744259 PMCID: PMC7397489 DOI: 10.1107/s205979832000889x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/30/2020] [Indexed: 01/06/2023] Open
Abstract
Advances in synchrotron storage rings and beamline automation have pushed data-collection rates to thousands of data sets per week. With this increase in throughput, massive projects such as in-crystal fragment screening have become accessible to a larger number of research groups. The quality of support offered at large-scale facilities allows medicinal chemistry-focused or biochemistry-focused groups to supplement their research with structural biology. Preparing the experiment, analysing multiple data sets and prospecting for interesting complexes of protein and fragments require, for both newcomers and experienced users, efficient management of the project and extensive computational power for data processing and structure refinement. Here, FragMAX, a new complete platform for fragment screening at the BioMAX beamline of the MAX IV Laboratory, is described. The ways in which users are assisted in X-ray-based fragment screenings and in which the fourth-generation storage ring available at the facility is best exploited are also described.
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Affiliation(s)
| | | | - Elmir Jagudin
- BioMAX, MAX IV Laboratory, Fotongatan 2, 224 84 Lund, Sweden
| | - Céleste Sele
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | - Maria Nyblom
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | - Wolfgang Knecht
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | - Derek T. Logan
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, Box 124, 221 00 Lund, Sweden
- SARomics Biostructures AB, Medicon Village, Scheeletorget 1, 223 63 Lund, Sweden
| | - Tove Sjögren
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Uwe Mueller
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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14
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Caldararu O, Manzoni F, Oksanen E, Logan DT, Ryde U. Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Corrigendum. Acta Crystallogr D Struct Biol 2020; 76:85-86. [PMID: 31909746 PMCID: PMC8573741 DOI: 10.1107/s2059798319016383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/04/2019] [Indexed: 11/10/2022] Open
Abstract
Corrections are published for the article by Caldararu et al. [(2019), Acta Cryst. D75, 368–380].
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15
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Dahlqvist A, Mandal S, Peterson K, Håkansson M, Logan DT, Zetterberg FR, Leffler H, Nilsson UJ. 3-Substituted 1-Naphthamidomethyl-C-galactosyls Interact with Two Unique Sub-sites for High-Affinity and High-Selectivity Inhibition of Galectin-3. Molecules 2019; 24:molecules24244554. [PMID: 31842451 PMCID: PMC6943516 DOI: 10.3390/molecules24244554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 11/21/2022] Open
Abstract
The galectins are a family of galactose-binding proteins playing key roles in inflammatory processes and cancer. However, they are structurally very closely related, and discovery of highly selective inhibitors is challenging. In this work, we report the design of novel inhibitors binding to a subsite unique to galectin-3, which confers both high selectivity and affinity towards galectin-3. Olefin cross metathesis between allyl β-C-galactopyranosyl and 1-vinylnaphthalenes or acylation of aminomethyl β-C-galactopyranosyl with 1-naphthoic acid derivatives gave C-galactopyranosyls carrying 1-naphthamide structural elements that interacted favorably with a galectin-3 unique subsite according to molecular modeling and X-ray structural analysis of two inhibitor-galectin-3 complexes. Affinities were down to sub-µM and selectivities over galectin-1, 2, 4 N-terminal domain, 4 C-terminal domain, 7, 8 N-terminal domain, 9 N-terminal domain, and 9 C-terminal domain were high. These results show that high affinity and selectivity for a single galectin can be achieved by targeting unique subsites, which holds promise for further development of small and selective galectin inhibitors.
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Affiliation(s)
- Alexander Dahlqvist
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, POB124, SE-22100 Lund, Sweden; (A.D.); (S.M.); (K.P.)
| | - Santanu Mandal
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, POB124, SE-22100 Lund, Sweden; (A.D.); (S.M.); (K.P.)
| | - Kristoffer Peterson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, POB124, SE-22100 Lund, Sweden; (A.D.); (S.M.); (K.P.)
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 63 Lund, Sweden; (M.H.); (D.T.L.)
| | - Derek T. Logan
- SARomics Biostructures AB, Medicon Village, SE-223 63 Lund, Sweden; (M.H.); (D.T.L.)
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, POB124, SE-22100 Lund, Sweden
| | - Fredrik R. Zetterberg
- Galecto Biotech AB, Sahlgrenska Science Park, Medicinaregatan 8 A, SE-413 46 Gothenburg, Sweden;
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan 28, 221 84 Lund, Sweden;
| | - Ulf J. Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, POB124, SE-22100 Lund, Sweden; (A.D.); (S.M.); (K.P.)
- Correspondence:
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16
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Grāve K, Lambert W, Berggren G, Griese JJ, Bennett MD, Logan DT, Högbom M. Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access. J Biol Inorg Chem 2019; 24:849-861. [PMID: 31410573 PMCID: PMC6754363 DOI: 10.1007/s00775-019-01703-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022]
Abstract
Class Ib ribonucleotide reductases (RNR) utilize a di-nuclear manganese or iron cofactor for reduction of superoxide or molecular oxygen, respectively. This generates a stable tyrosyl radical (Y·) in the R2 subunit (NrdF), which is further used for ribonucleotide reduction in the R1 subunit of RNR. Here, we report high-resolution crystal structures of Bacillus anthracis NrdF in the metal-free form (1.51 Å) and in complex with manganese (MnII/MnII, 1.30 Å). We also report three structures of the protein in complex with iron, either prepared anaerobically (FeII/FeII form, 1.32 Å), or prepared aerobically in the photo-reduced FeII/FeII form (1.63 Å) and with the partially oxidized metallo-cofactor (1.46 Å). The structures reveal significant conformational dynamics, likely to be associated with the generation, stabilization, and transfer of the radical to the R1 subunit. Based on observed redox-dependent structural changes, we propose that the passage for the superoxide, linking the FMN cofactor of NrdI and the metal site in NrdF, is closed upon metal oxidation, blocking access to the metal and radical sites. In addition, we describe the structural mechanics likely to be involved in this process.
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Affiliation(s)
- Kristīne Grāve
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden
| | - Wietske Lambert
- PRA Health Sciences, Amerikaweg 18, 9407 TK, Assen, The Netherlands
| | - Gustav Berggren
- Department of Chemistry, Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 75120, Uppsala, Sweden
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden.,Department of Cell and Molecular Biology, Uppsala University. BMC, Box 596, 75124, Uppsala, Sweden
| | - Matthew D Bennett
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, 221 00, Lund, Sweden.
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden.
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17
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Kumar R, Ignjatović MM, Peterson K, Olsson M, Leffler H, Ryde U, Nilsson UJ, Logan DT. Structure and Energetics of Ligand-Fluorine Interactions with Galectin-3 Backbone and Side-Chain Amides: Insight into Solvation Effects and Multipolar Interactions. ChemMedChem 2019; 14:1528-1536. [PMID: 31246331 PMCID: PMC6772088 DOI: 10.1002/cmdc.201900293] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/18/2019] [Indexed: 12/22/2022]
Abstract
Multipolar fluorine–amide interactions with backbone and side‐chain amides have been described as important for protein–ligand interactions and have been used to improve the potency of synthetic inhibitors. In this study, fluorine interactions within a well‐defined binding pocket on galectin‐3 were investigated systematically using phenyltriazolyl‐thiogalactosides fluorinated singly or multiply at various positions on the phenyl ring. X‐ray structures of the C‐terminal domain of galectin‐3 in complex with eight of these ligands revealed potential orthogonal fluorine–amide interactions with backbone amides and one with a side‐chain amide. The two interactions involving main‐chain amides seem to have a strong influence on affinity as determined by fluorescence anisotropy. In contrast, the interaction with the side‐chain amide did not influence affinity. Quantum mechanics calculations were used to analyze the relative contributions of these interactions to the binding energies. No clear correlation could be found between the relative energies of the fluorine–main‐chain amide interactions and the overall binding energy. Instead, dispersion and desolvation effects play a larger role. The results confirm that the contribution of fluorine–amide interactions to protein–ligand interactions cannot simply be predicted, on geometrical considerations alone, but require careful consideration of the energetic components.
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Affiliation(s)
- Rohit Kumar
- Department of Chemistry, Division of Biochemistry & Structural Biology, Lund University, Box 124, 22100, Lund, Sweden
| | - Majda Misini Ignjatović
- Department of Chemistry, Division of Theoretical Chemistry, Lund University, Box 124, 22100, Lund, Sweden
| | - Kristoffer Peterson
- Department of Chemistry, Center for Analysis and Synthesis, Lund University, Box 124, 22100, Lund, Sweden
| | - Martin Olsson
- Department of Chemistry, Division of Theoretical Chemistry, Lund University, Box 124, 22100, Lund, Sweden
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University, BMC-C1228b, Klinikgatan 28, 22184, Lund, Sweden
| | - Ulf Ryde
- Department of Chemistry, Division of Theoretical Chemistry, Lund University, Box 124, 22100, Lund, Sweden
| | - Ulf J Nilsson
- Department of Chemistry, Center for Analysis and Synthesis, Lund University, Box 124, 22100, Lund, Sweden
| | - Derek T Logan
- Department of Chemistry, Division of Biochemistry & Structural Biology, Lund University, Box 124, 22100, Lund, Sweden
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18
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Bågenholm V, Wiemann M, Reddy SK, Bhattacharya A, Rosengren A, Logan DT, Stålbrand H. A surface-exposed GH26 β-mannanase from Bacteroides ovatus: Structure, role, and phylogenetic analysis of BoMan26B. J Biol Chem 2019; 294:9100-9117. [PMID: 31000630 PMCID: PMC6556568 DOI: 10.1074/jbc.ra118.007171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/17/2019] [Indexed: 12/27/2022] Open
Abstract
The galactomannan utilization locus (BoManPUL) of the human gut bacterium Bacteroides ovatus encodes BoMan26B, a cell-surface–exposed endomannanase whose functional and structural features have been unclear. Our study now places BoMan26B in context with related enzymes and reveals the structural basis for its specificity. BoMan26B prefers longer substrates and is less restricted by galactose side-groups than the mannanase BoMan26A of the same locus. Using galactomannan, BoMan26B generated a mixture of (galactosyl) manno-oligosaccharides shorter than mannohexaose. Three defined manno-oligosaccharides had affinity for the SusD-like surface–exposed glycan-binding protein, predicted to be implicated in saccharide transport. Co-incubation of BoMan26B and the periplasmic α-galactosidase BoGal36A increased the rate of galactose release by about 10-fold compared with the rate without BoMan26B. The results suggested that BoMan26B performs the initial attack on galactomannan, generating oligosaccharides that after transport to the periplasm are processed by BoGal36A. A crystal structure of BoMan26B with galactosyl-mannotetraose bound in subsites −5 to −2 revealed an open and long active-site cleft with Trp-112 in subsite −5 concluded to be involved in mannosyl interaction. Moreover, Lys-149 in the −4 subsite interacted with the galactosyl side-group of the ligand. A phylogenetic tree consisting of GH26 enzymes revealed four strictly conserved GH26 residues and disclosed that BoMan26A and BoMan26B reside on two distinct phylogenetic branches (A and B). The three other branches contain lichenases, xylanases, or enzymes with unknown activities. Lys-149 is conserved in a narrow part of branch B, and Trp-112 is conserved in a wider group within branch B.
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Affiliation(s)
- Viktoria Bågenholm
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
| | - Mathias Wiemann
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
| | - Sumitha K Reddy
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences Box 7015, 750 07, Uppsala, Sweden
| | - Abhishek Bhattacharya
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
| | - Anna Rosengren
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
| | - Derek T Logan
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
| | - Henrik Stålbrand
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
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19
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Korkmaz B, Lesner A, Wysocka M, Gieldon A, Håkansson M, Gauthier F, Logan DT, Jenne DE, Lauritzen C, Pedersen J. Structure-based design and in vivo anti-arthritic activity evaluation of a potent dipeptidyl cyclopropyl nitrile inhibitor of cathepsin C. Biochem Pharmacol 2019; 164:349-367. [PMID: 30978322 DOI: 10.1016/j.bcp.2019.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/07/2019] [Indexed: 12/30/2022]
Abstract
Cathepsin C (CatC) is a dipeptidyl-exopeptidase which activates neutrophil serine protease precursors (elastase, proteinase 3, cathepsin G and NSP4) by removing their N-terminal propeptide in bone marrow cells at the promyelocytic stage of neutrophil differentiation. The resulting active proteases are implicated in chronic inflammatory and autoimmune diseases. Hence, inhibition of CatC represents a therapeutic strategy to suppress excessive protease activities in various neutrophil mediated diseases. We designed and synthesized a series of dipeptidyl cyclopropyl nitrile compounds as putative CatC inhibitors. One compound, IcatCXPZ-01 ((S)-2-amino-N-((1R,2R)-1-cyano-2-(4'-(4-methylpiperazin-1-ylsulfonyl)biphenyl-4-yl)cyclopropyl)butanamide)) was identified as a potent inhibitor of both human and rodent CatC. In mice, pharmacokinetic studies revealed that IcatCXPZ-01 accumulated in the bone marrow reaching levels suitable for CatC inhibition. Subcutaneous administration of IcatCXPZ-01 in a monoclonal anti-collagen antibody induced mouse model of rheumatoid arthritis resulted in statistically significant anti-arthritic activity with persistent decrease in arthritis scores and paw thickness.
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Affiliation(s)
- Brice Korkmaz
- INSERM, UMR 1100, "Centre d'Etude des Pathologies Respiratoires", 37032 Tours, France; Université de Tours, 37032 Tours, France.
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
| | | | - Artur Gieldon
- Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
| | | | - Francis Gauthier
- INSERM, UMR 1100, "Centre d'Etude des Pathologies Respiratoires", 37032 Tours, France; Université de Tours, 37032 Tours, France
| | | | - Dieter E Jenne
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, German Center for Lung Research (DZL), 81377 Munich, Germany; Max Planck Institute of Neurobiology, 82152 Planegg-Martinsried, Germany
| | | | - John Pedersen
- Neuprozyme Therapeutics A/S, 2970 Hörsholm, Denmark.
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20
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Casaletto JB, Geddie ML, Abu-Yousif AO, Masson K, Fulgham A, Boudot A, Maiwald T, Kearns JD, Kohli N, Su S, Razlog M, Raue A, Kalra A, Håkansson M, Logan DT, Welin M, Chattopadhyay S, Harms BD, Nielsen UB, Schoeberl B, Lugovskoy AA, MacBeath G. MM-131, a bispecific anti-Met/EpCAM mAb, inhibits HGF-dependent and HGF-independent Met signaling through concurrent binding to EpCAM. Proc Natl Acad Sci U S A 2019; 116:7533-7542. [PMID: 30898885 PMCID: PMC6462049 DOI: 10.1073/pnas.1819085116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Activation of the Met receptor tyrosine kinase, either by its ligand, hepatocyte growth factor (HGF), or via ligand-independent mechanisms, such as MET amplification or receptor overexpression, has been implicated in driving tumor proliferation, metastasis, and resistance to therapy. Clinical development of Met-targeted antibodies has been challenging, however, as bivalent antibodies exhibit agonistic properties, whereas monovalent antibodies lack potency and the capacity to down-regulate Met. Through computational modeling, we found that the potency of a monovalent antibody targeting Met could be dramatically improved by introducing a second binding site that recognizes an unrelated, highly expressed antigen on the tumor cell surface. Guided by this prediction, we engineered MM-131, a bispecific antibody that is monovalent for both Met and epithelial cell adhesion molecule (EpCAM). MM-131 is a purely antagonistic antibody that blocks ligand-dependent and ligand-independent Met signaling by inhibiting HGF binding to Met and inducing receptor down-regulation. Together, these mechanisms lead to inhibition of proliferation in Met-driven cancer cells, inhibition of HGF-mediated cancer cell migration, and inhibition of tumor growth in HGF-dependent and -independent mouse xenograft models. Consistent with its design, MM-131 is more potent in EpCAM-high cells than in EpCAM-low cells, and its potency decreases when EpCAM levels are reduced by RNAi. Evaluation of Met, EpCAM, and HGF levels in human tumor samples reveals that EpCAM is expressed at high levels in a wide range of Met-positive tumor types, suggesting a broad opportunity for clinical development of MM-131.
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Affiliation(s)
| | - Melissa L Geddie
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Adnan O Abu-Yousif
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Kristina Masson
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Aaron Fulgham
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Antoine Boudot
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Tim Maiwald
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Jeffrey D Kearns
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Neeraj Kohli
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Stephen Su
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Maja Razlog
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Andreas Raue
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139;
| | - Ashish Kalra
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81 Lund, Sweden
| | - Derek T Logan
- SARomics Biostructures AB, Medicon Village, SE-223 81 Lund, Sweden
| | - Martin Welin
- SARomics Biostructures AB, Medicon Village, SE-223 81 Lund, Sweden
| | | | - Brian D Harms
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Ulrik B Nielsen
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Birgit Schoeberl
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Alexey A Lugovskoy
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139
| | - Gavin MacBeath
- Discovery Division, Merrimack Pharmaceuticals, Inc., Cambridge, MA 02139;
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21
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Caldararu O, Manzoni F, Oksanen E, Logan DT, Ryde U. Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Acta Crystallogr D Struct Biol 2019; 75:368-380. [PMID: 30988254 PMCID: PMC6465982 DOI: 10.1107/s205979831900175x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/30/2019] [Indexed: 11/20/2022]
Abstract
A method has been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. Applications to structures of the galectin-3C–lactose complex and lytic polysaccharide monooxygenase show that it can improve the geometry of hydrogen bonds, particularly those involving water molecules, as well as determine the protonation states of key residues. Neutron crystallography is a powerful method to determine the positions of H atoms in macromolecular structures. However, it is sometimes hard to judge what would constitute a chemically reasonable model, and the geometry of H atoms depends more on the surroundings (for example the formation of hydrogen bonds) than heavy atoms, so that the empirical geometry information for the H atoms used to supplement the experimental data is often less accurate. These problems may be reduced by using quantum-mechanical calculations. A method has therefore been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. A first validation of this method is provided by re-refining the structure of the galectin-3 carbohydrate-recognition domain in complex with lactose. The geometry is improved, in particular for water molecules, for which the method leads to better-resolved hydrogen-bonding interactions. The method has also been applied to the active copper site of lytic polysaccharide monooxygenase and shows that the protonation state of the amino-terminal histidine residue can be determined.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Francesco Manzoni
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
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22
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Kumar R, Peterson K, Misini Ignjatović M, Leffler H, Ryde U, Nilsson UJ, Logan DT. Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects. Org Biomol Chem 2019; 17:1081-1089. [PMID: 30632578 DOI: 10.1039/c8ob02888e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the β-d-galactopyranoside-binding protein galectin-3, synthetic inhibitors substituted at the 3-position of a thiodigalactoside core cause the formation of an aglycone binding pocket through the displacement of an arginine residue (Arg144) from its position in the apoprotein. To examine in detail the role of different molecular interactions in this pocket, we have synthesized a series of nine 3-(4-(2,3,5,6-tetrafluorophenyl)-1,2,3-triazol-1-yl)-thiogalactosides with different para substituents and measured their affinities to galectin-3 using a fluorescence polarization assay. High-resolution crystal structures (<1.3 Å) have been determined for five of the ligands in complex with the C-terminal domain of galectin-3. The binding affinities are rationalised with the help of the three-dimensional structures and quantum-mechanical calculations. Three effects seem to be involved: Firstly, the binding pocket is too small for the largest ligands with ethyl and methyl. Secondly, for the other ligands, the affinity seems to be determined mainly by desolvation effects, disfavouring the polar substituents, but this is partly counteracted by the cation-π interaction with Arg144, which stacks on top of the substituted tetrafluorophenyl group in all complexes. The results provide detailed insight into interactions of fluorinated phenyl moieties with arginine-containing protein binding sites and the complex interplay of different energetic components in defining the binding affinity.
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Affiliation(s)
- Rohit Kumar
- Biochemistry and Structural Biology, Centre for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden.
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23
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Andersen MCF, Boos I, Kinnaert C, Awan SI, Pedersen HL, Kračun SK, Lanz G, Rydahl MG, Kjærulff L, Håkansson M, Kimbung R, Logan DT, Gotfredsen CH, Willats WGT, Clausen MH. Synthesis of branched and linear 1,4-linked galactan oligosaccharides. Org Biomol Chem 2019; 16:1157-1162. [PMID: 29367995 DOI: 10.1039/c7ob03035e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the synthesis of linear and branched (1→4)-d-galactans. Four tetrasaccharides and one pentasaccharide were accessed by adopting a procedure of regioselective ring opening of a 4,6-O-naphthylidene protecting group followed by glycosylation using phenyl thioglycoside donors. The binding of the linear pentasaccharide with galectin-3 is also investigated by the determination of a co-crystal structure. The binding of the (1→4)-linked galactan to Gal-3 highlights the oligosaccharides of pectic galactan, which is abundant in the human diet, as putative Gal-3 ligands.
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Affiliation(s)
- Mathias C F Andersen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800, Kgs. Lyngby, Denmark.
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24
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Verteramo ML, Stenström O, Ignjatović MM, Caldararu O, Olsson MA, Manzoni F, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding. J Am Chem Soc 2019; 141:2012-2026. [PMID: 30618244 DOI: 10.1021/jacs.8b11099] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding the driving forces underlying molecular recognition is of fundamental importance in chemistry and biology. The challenge is to unravel the binding thermodynamics into separate contributions and to interpret these in molecular terms. Entropic contributions to the free energy of binding are particularly difficult to assess in this regard. Here we pinpoint the molecular determinants underlying differences in ligand affinity to the carbohydrate recognition domain of galectin-3, using a combination of isothermal titration calorimetry, X-ray crystallography, NMR relaxation, and molecular dynamics simulations followed by conformational entropy and grid inhomogeneous solvation theory (GIST) analyses. Using a pair of diastereomeric ligands that have essentially identical chemical potential in the unbound state, we reduced the problem of dissecting the thermodynamics to a comparison of the two protein-ligand complexes. While the free energies of binding are nearly equal for the R and S diastereomers, greater differences are observed for the enthalpy and entropy, which consequently exhibit compensatory behavior, ΔΔ H°(R - S) = -5 ± 1 kJ/mol and - TΔΔ S°(R - S) = 3 ± 1 kJ/mol. NMR relaxation experiments and molecular dynamics simulations indicate that the protein in complex with the S-stereoisomer has greater conformational entropy than in the R-complex. GIST calculations reveal additional, but smaller, contributions from solvation entropy, again in favor of the S-complex. Thus, conformational entropy apparently dominates over solvation entropy in dictating the difference in the overall entropy of binding. This case highlights an interplay between conformational entropy and solvation entropy, pointing to both opportunities and challenges in drug design.
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Affiliation(s)
- Maria Luisa Verteramo
- Centre for Analysis and Synthesis, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Olof Stenström
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | | | - Octav Caldararu
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Martin A Olsson
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Francesco Manzoni
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Hakon Leffler
- Microbiology, Immunology, and Glycobiology, Department of Laboratory Medicine , Lund University , 221 00 Lund , Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC , 225 92 Lund , Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Ulf Ryde
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
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25
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Caldararu O, Kumar R, Oksanen E, Logan DT, Ryde U. Are crystallographic B-factors suitable for calculating protein conformational entropy? Phys Chem Chem Phys 2019; 21:18149-18160. [DOI: 10.1039/c9cp02504a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is not possible to obtain reliable entropy estimates from crystallographic B-factors even with re-refined or room-temperature crystal structures.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| | - Rohit Kumar
- Department of Biophysical Chemistry
- Centre for Molecular Protein Science
- Lund University
- Chemical Centre
- SE-221 00 Lund
| | - Esko Oksanen
- Department of Biophysical Chemistry
- Centre for Molecular Protein Science
- Lund University
- Chemical Centre
- SE-221 00 Lund
| | - Derek T. Logan
- Department of Biophysical Chemistry
- Centre for Molecular Protein Science
- Lund University
- Chemical Centre
- SE-221 00 Lund
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
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26
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Yang F, Wang H, Logan DT, Mu X, Danielsson J, Oliveberg M. The Cost of Long Catalytic Loops in Folding and Stability of the ALS-Associated Protein SOD1. J Am Chem Soc 2018; 140:16570-16579. [PMID: 30359015 DOI: 10.1021/jacs.8b08141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A conspicuous feature of the amyotrophic lateral sclerosis (ALS)-associated protein SOD1 is that its maturation into a functional enzyme relies on local folding of two disordered loops into a catalytic subdomain. To drive the disorder-to-order transition, the protein employs a single Zn2+ ion. The question is then if the entropic penalty of maintaining such disordered loops in the immature apoSOD1 monomer is large enough to explain its unusually low stability, slow folding, and pathological aggregation in ALS. To find out, we determined the effects of systematically altering the SOD1-loop lengths by protein redesign. The results show that the loops destabilize the apoSOD1 monomer by ∼3 kcal/mol, rendering the protein marginally stable and accounting for its aggregation behavior. Yet the effect on the global folding kinetics remains much smaller with a transition-state destabilization of <1 kcal/mol. Notably, this 1/3 transition-state to folded-state stability ratio provides a clear-cut example of the enigmatic disagreement between the Leffler α value from loop-length alterations (typically 1/3) and the "standard" reaction coordinates based on solvent perturbations (typically >2/3). Reconciling the issue, we demonstrate that the disagreement disappears when accounting for the progressive loop shortening that occurs along the folding pathway. The approach assumes a consistent Flory loop entropy scaling factor of c = 1.48 for both equilibrium and kinetic data and has the added benefit of verifying the tertiary interactions of the folding nucleus as determined by phi-value analysis. Thus, SOD1 not only represents a case where evolution of key catalytic function has come with the drawback of a destabilized apo state but also stands out as a well-suited model system for exploring the physicochemical details of protein self-organization.
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Affiliation(s)
- Fan Yang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences , Stockholm University , S-106 91 Stockholm , Sweden
| | - Huabing Wang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences , Stockholm University , S-106 91 Stockholm , Sweden
| | - Derek T Logan
- Division of Biochemistry & Structural Biology, Department of Chemistry , Lund University , Box 124, 22100 Lund , Sweden
| | - Xin Mu
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences , Stockholm University , S-106 91 Stockholm , Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences , Stockholm University , S-106 91 Stockholm , Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences , Stockholm University , S-106 91 Stockholm , Sweden
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27
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Ruggieri F, van Langen LM, Logan DT, Walse B, Berglund P. Transaminase-Catalyzed Racemization with Potential for Dynamic Kinetic Resolutions. ChemCatChem 2018; 10:5012-5018. [PMID: 30546495 PMCID: PMC6282829 DOI: 10.1002/cctc.201801049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Indexed: 11/11/2022]
Abstract
Dynamic kinetic resolution (DKR) reactions in which a stereoselective enzyme and a racemization step are coupled in one pot would represent powerful tools for the production of enantiopure amines through enantioconvergence of racemates. The exploitation of DKR strategies is currently hampered by the lack of effective, enzyme-compatible and scalable racemization strategies for amines. In the present work, the proof of concept of a fully biocatalytic method for amine racemization is presented. Both enantiomers of the model compound 1-methyl-3-phenylpropylamine could be racemized in water and at room temperature using a couple of wild-type, non-proprietary, enantiocomplementary amine transaminases and a minimum amount of pyruvate/alanine as a co-substrate couple. The biocatalytic simultaneous parallel cascade reaction presented here poses itself as a customizable amine racemization system with potential for the chemical industry in competition with traditional transition-metal catalysis.
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Affiliation(s)
- Federica Ruggieri
- Department of Industrial Biotechnology KTH Royal Institute of TechnologyAlbaNova University CenterStockholmSE-106 91Sweden
- SARomics Biostructures AB Medicon VillageLundSE-223 81Sweden
| | | | - Derek T. Logan
- SARomics Biostructures AB Medicon VillageLundSE-223 81Sweden
| | - Björn Walse
- SARomics Biostructures AB Medicon VillageLundSE-223 81Sweden
| | - Per Berglund
- Department of Industrial Biotechnology KTH Royal Institute of TechnologyAlbaNova University CenterStockholmSE-106 91Sweden
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28
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Manzoni F, Wallerstein J, Schrader TE, Ostermann A, Coates L, Akke M, Blakeley MP, Oksanen E, Logan DT. Elucidation of Hydrogen Bonding Patterns in Ligand-Free, Lactose- and Glycerol-Bound Galectin-3C by Neutron Crystallography to Guide Drug Design. J Med Chem 2018; 61:4412-4420. [PMID: 29672051 DOI: 10.1021/acs.jmedchem.8b00081] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The medically important drug target galectin-3 binds galactose-containing moieties on glycoproteins through an intricate pattern of hydrogen bonds to a largely polar surface-exposed binding site. All successful inhibitors of galectin-3 to date have been based on mono- or disaccharide cores closely resembling natural ligands. A detailed understanding of the H-bonding networks in these natural ligands will provide an improved foundation for the design of novel inhibitors. Neutron crystallography is an ideal technique to reveal the geometry of hydrogen bonds because the positions of hydrogen atoms are directly detected rather than being inferred from the positions of heavier atoms as in X-ray crystallography. We present three neutron crystal structures of the C-terminal carbohydrate recognition domain of galectin-3: the ligand-free form and the complexes with the natural substrate lactose and with glycerol, which mimics important interactions made by lactose. The neutron crystal structures reveal unambiguously the exquisite fine-tuning of the hydrogen bonding pattern in the binding site to the natural disaccharide ligand. The ligand-free structure shows that most of these hydrogen bonds are preserved even when the polar groups of the ligand are replaced by water molecules. The protonation states of all histidine residues in the protein are also revealed and correlate well with NMR observations. The structures give a solid starting point for molecular dynamics simulations and computational estimates of ligand binding affinity that will inform future drug design.
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Affiliation(s)
- Francesco Manzoni
- Department of Biochemistry & Structural Biology , Lund University , S-221 00 Lund , Sweden
| | - Johan Wallerstein
- Department of Biophysical Chemistry , Lund University , S-221 00 Lund , Sweden
| | - Tobias E Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) , Forschungszentrum Jülich GmbH , Lichtenbergstrasse 1 , 85747 Garching , Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ) , Technische Universität München , Lichtenbergstrasse 1 , 85748 Garching , Germany
| | - Leighton Coates
- Neutron Scattering Division , Oak Ridge National Laboratory , 1 Bethel Valley Road , Oak Ridge , Tennessee 37831 , United States
| | - Mikael Akke
- Department of Biophysical Chemistry , Lund University , S-221 00 Lund , Sweden
| | - Matthew P Blakeley
- Institut Laue-Langevin , 71 avenue des Martyrs , 38000 Grenoble , France
| | - Esko Oksanen
- Department of Biochemistry & Structural Biology , Lund University , S-221 00 Lund , Sweden.,Instrument Division , European Spallation Source ERIC , Box 176, S-221 00 Lund , Sweden
| | - Derek T Logan
- Department of Biochemistry & Structural Biology , Lund University , S-221 00 Lund , Sweden
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29
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Awad W, Kjellström S, Svensson Birkedal G, Mani K, Logan DT. Structural and Biophysical Characterization of Human EXTL3: Domain Organization, Glycosylation, and Solution Structure. Biochemistry 2018; 57:1166-1177. [PMID: 29346724 DOI: 10.1021/acs.biochem.7b00557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heparan sulfate proteoglycans are proteins substituted with one or more heparan sulfate (HS) polysaccharides, found in abundance at cell surfaces. HS chains influence the activity of many biologically important molecules involved in cellular communication and signaling. The exostosin (EXT) proteins are glycosyltransferases in the Golgi apparatus that assemble HS chains on HSPGs. The EXTL3 enzyme mainly works as an initiator in HS biosynthesis. In this work, human lumenal N-glycosylated EXTL3 (EXTL3ΔN) was cloned, expressed in human embryonic kidney cells, and purified. Various biophysical and biochemical approaches were then employed to elucidate the N-glycosylation sites and the function of their attached N-glycans. Furthermore, the stability and conformation of the purified EXTL3ΔN protein in solution have been analyzed. Our data show that EXTL3ΔN has N-glycans at least at two positions, Asn290 and Asn592, which seem to be critical for proper protein folding and/or release. EXTL3ΔN is quite stable, as high temperature (∼59 °C) was required for denaturation. Deconvolution of the EXTL3ΔN far-UV CD spectrum revealed a substantial fraction of β sheets (25%) with a minor proportion of α-helices (14%) in the secondary structure. Solution small-angle X-ray scattering and dynamic light scattering revealed an extended structure suggestive of a dimeric arrangement and consisting of two distinct regions, narrow and broad, respectively. This is consistent with bioinformatics analyses suggesting a 3-domain structure with two glycosyltransferase domains and a coiled-coil domain.
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Affiliation(s)
- Wael Awad
- Biochemistry and Structural Biology, Centre for Molecular Protein Science, Deptartment of Chemistry, Lund University , SE-221 00 Lund, Sweden.,Department of Biophysics, Faculty of Science, Cairo University , 12316 Cairo, Egypt
| | - Sven Kjellström
- Biochemistry and Structural Biology, Centre for Molecular Protein Science, Deptartment of Chemistry, Lund University , SE-221 00 Lund, Sweden
| | - Gabriel Svensson Birkedal
- Department of Experimental Medical Science, Division of Neuroscience, Glycobiology Group, Lund University , SE-221 00 Lund, Sweden
| | - Katrin Mani
- Department of Experimental Medical Science, Division of Neuroscience, Glycobiology Group, Lund University , SE-221 00 Lund, Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Centre for Molecular Protein Science, Deptartment of Chemistry, Lund University , SE-221 00 Lund, Sweden
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30
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Rozman Grinberg I, Lundin D, Hasan M, Crona M, Jonna VR, Loderer C, Sahlin M, Markova N, Borovok I, Berggren G, Hofer A, Logan DT, Sjöberg BM. Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit. eLife 2018; 7:31529. [PMID: 29388911 PMCID: PMC5794259 DOI: 10.7554/elife.31529] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 12/23/2017] [Indexed: 12/27/2022] Open
Abstract
Ribonucleotide reductases (RNRs) are key enzymes in DNA metabolism, with allosteric mechanisms controlling substrate specificity and overall activity. In RNRs, the activity master-switch, the ATP-cone, has been found exclusively in the catalytic subunit. In two class I RNR subclasses whose catalytic subunit lacks the ATP-cone, we discovered ATP-cones in the radical-generating subunit. The ATP-cone in the Leeuwenhoekiella blandensis radical-generating subunit regulates activity via quaternary structure induced by binding of nucleotides. ATP induces enzymatically competent dimers, whereas dATP induces non-productive tetramers, resulting in different holoenzymes. The tetramer forms by interactions between ATP-cones, shown by a 2.45 Å crystal structure. We also present evidence for an MnIIIMnIV metal center. In summary, lack of an ATP-cone domain in the catalytic subunit was compensated by transfer of the domain to the radical-generating subunit. To our knowledge, this represents the first observation of transfer of an allosteric domain between components of the same enzyme complex. When a cell copies its DNA, it uses four different building blocks called deoxyribonucleotides (dNTPs). These consist of one of the four ‘bases’ (A, T, C and G), which pair up to link the two strands of DNA in the double helix, bound to a sugar and a phosphate group. If the cell contains too little or too much of one of these building blocks, an incorrect base may be inserted into the DNA. This results in a mutation, which in bacteria can cause death, and in animals may lead to cancer. The enzyme that fabricates and carefully controls the amount of each dNTP building block inside a cell is called ribonucleotide reductase. Once there are enough building blocks in a cell the enzyme is turned off. A part of the enzyme called the ATP-cone acts as an on/off switch to control this activity. The ribonucleotide reductase consists of a large component and a small component. Until now, studies of the ATP-cone have found it only in the large component of the enzyme. However, when looking through a public database of sequence data, Rozman Grinberg et al. noticed that ribonucleotide reductases in some bacteria have their ATP-cone joined to the small component. Does this ATP-cone also control the amounts of dNTP building blocks inside cells and, if so, how? Rozman Grinberg et al. studied one such ATP-cone in a ribonucleotide reductase from a bacterium (named Leeuwenhoekiella blandensis) found in the Mediterranean Sea. This revealed that when the amount of dNTP building blocks reaches a certain limit, the ATP-cone turns off the enzyme. Examining the three-dimensional structure of the enzyme using a technique called X-ray crystallography revealed that when turned off, the enzyme’s small components are glued together in pairs. This prevents them from working. Rozman Grinberg et al. also discovered that this enzyme contains a new type of metal center with two manganese ions suggesting that a new reaction mechanism may operate in this class of ribonucleotide reductase. These findings support a theory that biological on/off switches can evolve rapidly. In addition to its evolutionary and biomedical interest, understanding how the ATP-cone works might help to improve the enzymes used in industrial processes.
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Affiliation(s)
- Inna Rozman Grinberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Mahmudul Hasan
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | | | | | - Christoph Loderer
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Gustav Berggren
- Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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31
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Zetterberg FR, Peterson K, Johnsson RE, Brimert T, Håkansson M, Logan DT, Leffler H, Nilsson UJ. Monosaccharide Derivatives with Low-Nanomolar Lectin Affinity and High Selectivity Based on Combined Fluorine-Amide, Phenyl-Arginine, Sulfur-π, and Halogen Bond Interactions. ChemMedChem 2018; 13:133-137. [PMID: 29194992 DOI: 10.1002/cmdc.201700744] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Indexed: 12/20/2022]
Abstract
The design of small and high-affinity lectin inhibitors remains a major challenge because the natural ligand binding sites of lectin are often shallow and have polar character. Herein we report that derivatizing galactose with un-natural structural elements that form multiple non-natural lectin-ligand interactions (orthogonal multipolar fluorine-amide, phenyl-arginine, sulfur-π, and halogen bond) can provide inhibitors with extraordinary affinity (low nanomolar) for the model lectin, galectin-3, which is more than five orders of magnitude higher than the parent galactose; moreover, is selective over other galectins.
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Affiliation(s)
- Fredrik R Zetterberg
- Galecto Biotech AB, Sahlgrenska Science Park, Medicinaregatan 8A, 413 46, Gothenburg, Sweden
| | - Kristoffer Peterson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, 221 00, Lund, Sweden
| | | | - Thomas Brimert
- Red Glead Discovery AB, Medicon Village, 223 63, Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, 223 63, Lund, Sweden
| | - Derek T Logan
- SARomics Biostructures AB, Medicon Village, 223 63, Lund, Sweden.,Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, 221 00, Lund, Sweden
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan 28, 221 84, Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, 221 00, Lund, Sweden
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Peterson K, Kumar R, Stenström O, Verma P, Verma PR, Håkansson M, Kahl-Knutsson B, Zetterberg F, Leffler H, Akke M, Logan DT, Nilsson UJ. Systematic Tuning of Fluoro-galectin-3 Interactions Provides Thiodigalactoside Derivatives with Single-Digit nM Affinity and High Selectivity. J Med Chem 2018; 61:1164-1175. [PMID: 29284090 DOI: 10.1021/acs.jmedchem.7b01626] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Symmetrical and asymmetrical fluorinated phenyltriazolyl-thiodigalactoside derivatives have been synthesized and evaluated as inhibitors of galectin-1 and galectin-3. Systematic tuning of the phenyltriazolyl-thiodigalactosides' fluoro-interactions with galectin-3 led to the discovery of inhibitors with exceptional affinities (Kd down to 1-2 nM) in symmetrically substituted thiodigalactosides as well as unsurpassed combination of high affinity (Kd 7.5 nM) and selectivity (46-fold) over galectin-1 for asymmetrical thiodigalactosides by carrying one trifluorphenyltriazole and one coumaryl moiety. Studies of the inhibitor-galectin complexes with isothermal titration calorimetry and X-ray crystallography revealed the importance of fluoro-amide interaction for affinity and for selectivity. Finally, the high affinity of the discovered inhibitors required two competitive titration assay tools to be developed: a new high affinity fluorescent probe for competitive fluorescent polarization and a competitive ligand optimal for analyzing high affinity galectin-3 inhibitors with competitive isothermal titration calorimetry.
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Affiliation(s)
- Kristoffer Peterson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University , Box 124, SE-221 00 Lund, Sweden
| | - Rohit Kumar
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University , Box 124, SE-221 00 Lund, Sweden
| | - Olof Stenström
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University , Box 124, SE-221 00 Lund, Sweden
| | - Priya Verma
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University , Box 124, SE-221 00 Lund, Sweden
| | - Prashant R Verma
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University , Box 124, SE-221 00 Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures AB , Medicon Village, SE-223 63 Lund, Sweden
| | - Barbro Kahl-Knutsson
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b , Klinikgatan 28, 221 84 Lund, Sweden
| | - Fredrik Zetterberg
- Galecto Biotech AB , Sahlgrenska Science Park, Medicinaregatan 8 A, SE-413 46 Gothenburg, Sweden
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b , Klinikgatan 28, 221 84 Lund, Sweden
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University , Box 124, SE-221 00 Lund, Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University , Box 124, SE-221 00 Lund, Sweden.,SARomics Biostructures AB , Medicon Village, SE-223 63 Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University , Box 124, SE-221 00 Lund, Sweden
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Noresson AL, Aurelius O, Öberg CT, Engström O, Sundin AP, Håkansson M, Stenström O, Akke M, Logan DT, Leffler H, Nilsson UJ. Designing interactions by control of protein-ligand complex conformation: tuning arginine-arene interaction geometry for enhanced electrostatic protein-ligand interactions. Chem Sci 2017; 9:1014-1021. [PMID: 29675148 PMCID: PMC5883865 DOI: 10.1039/c7sc04749e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/01/2017] [Indexed: 01/13/2023] Open
Abstract
3-Benzamido-2-O-sulfo-galactosides can be designed to control protein conformation into forming entropically favourable galectin-3-arginine salt bridges with ligand sulfates.
We investigated galectin-3 binding to 3-benzamido-2-O-sulfo-galactoside and -thiodigalactoside ligands using a combination of site-specific mutagenesis, X-ray crystallography, computational approaches, and binding thermodynamics measurements. The results reveal a conformational variability in a surface-exposed arginine (R144) side chain in response to different aromatic C3-substituents of bound galactoside-based ligands. Fluorinated C3-benzamido substituents induced a shift in the side-chain conformation of R144 to allow for an entropically favored electrostatic interaction between its guanidine group and the 2-O-sulfate of the ligand. By contrast, binding of ligands with non-fluorinated substituents did not trigger a conformational change of R144. Hence, a sulfate–arginine electrostatic interaction can be tuned by the choice of ligand C3-benzamido structures to favor specific interaction modes and geometries. These results have important general implications for ligand design, as the proper choice of arginine–aromatic interacting partners opens up for ligand-controlled protein conformation that in turn may be systematically exploited in ligand design.
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Affiliation(s)
- A-L Noresson
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden .
| | - O Aurelius
- Section for Biochemistry and Structural Biology , Center for Molecular Protein Science , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden
| | - C T Öberg
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden .
| | - O Engström
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden .
| | - A P Sundin
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden .
| | - M Håkansson
- SARomics Biostructures AB , Medicon Village , SE-223 81 Lund , Sweden
| | - O Stenström
- Biophysical Chemistry , Center for Molecular Protein Science , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden
| | - M Akke
- Biophysical Chemistry , Center for Molecular Protein Science , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden
| | - D T Logan
- Section for Biochemistry and Structural Biology , Center for Molecular Protein Science , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden.,SARomics Biostructures AB , Medicon Village , SE-223 81 Lund , Sweden
| | - H Leffler
- Department of Laboratory Medicine , Section MIG , Lund University , Sölvegatan 23, SE-223 62 , Lund , Sweden
| | - U J Nilsson
- Centre for Analysis and Synthesis , Department of Chemistry , Lund University , Box 124 , SE-221 00 Lund , Sweden .
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Linares-Pastén JA, Falck P, Albasri K, Kjellström S, Adlercreutz P, Logan DT, Karlsson EN. Three-dimensional structures and functional studies of two GH43 arabinofuranosidases fromWeissellasp. strain 142 andLactobacillus brevis. FEBS J 2017; 284:2019-2036. [DOI: 10.1111/febs.14101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/13/2017] [Accepted: 05/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
| | - Peter Falck
- Biotechnology; Department of Chemistry; Lund University; Sweden
| | - Khalil Albasri
- Biotechnology; Department of Chemistry; Lund University; Sweden
| | - Sven Kjellström
- Biochemistry and Structural Biology; Department of Chemistry; Lund University; Sweden
| | | | - Derek T. Logan
- Biochemistry and Structural Biology; Department of Chemistry; Lund University; Sweden
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Kulkarni TS, Khan S, Villagomez R, Mahmood T, Lindahl S, Logan DT, Linares-Pastén JA, Nordberg Karlsson E. Cover Image, Volume 85, Issue 6. Proteins 2017. [DOI: 10.1002/prot.25312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tejas S. Kulkarni
- Biotechnology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
| | - Samiullah Khan
- Biotechnology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
- Department of Microbiology, Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad 45320 Pakistan
| | - Rodrigo Villagomez
- Centre for Analysis and Synthesis, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
| | - Tahir Mahmood
- Biotechnology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
| | - Sofia Lindahl
- Centre for Analysis and Synthesis, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
- Borregaard; Sarpsborg 1701 Norway
| | - Derek T. Logan
- Biochemistry and Structural Biology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
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Kulkarni TS, Khan S, Villagomez R, Mahmood T, Lindahl S, Logan DT, Linares-Pastén JA, Nordberg Karlsson E. Cover Image, Volume 85, Issue 5. Proteins 2017. [DOI: 10.1002/prot.25294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tejas S. Kulkarni
- Biotechnology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
| | - Samiullah Khan
- Biotechnology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
- Department of Microbiology, Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad 45320 Pakistan
| | - Rodrigo Villagomez
- Centre for Analysis and Synthesis, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
| | - Tahir Mahmood
- Biotechnology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
| | - Sofia Lindahl
- Centre for Analysis and Synthesis, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
- Borregaard; Sarpsborg 1701 Norway
| | - Derek T. Logan
- Biochemistry and Structural Biology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
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Kulkarni TS, Khan S, Villagomez R, Mahmood T, Lindahl S, Logan DT, Linares-Pastén JA, Nordberg Karlsson E. Crystal structure of β-glucosidase 1A fromThermotoga neapolitanaand comparison of active site mutants for hydrolysis of flavonoid glucosides. Proteins 2017; 85:872-884. [DOI: 10.1002/prot.25256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/14/2017] [Accepted: 01/18/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Tejas S. Kulkarni
- Biotechnology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
| | - Samiullah Khan
- Biotechnology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
- Department of Microbiology, Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad 45320 Pakistan
| | - Rodrigo Villagomez
- Centre for Analysis and Synthesis, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
| | - Tahir Mahmood
- Biotechnology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
| | - Sofia Lindahl
- Centre for Analysis and Synthesis, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
- Borregaard; Sarpsborg 1701 Norway
| | - Derek T. Logan
- Biochemistry and Structural Biology, Department of Chemistry; Lund University; Lund SE-221 00 Sweden
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Rämisch S, Pramhed A, Tillgren V, Aspberg A, Logan DT. Crystal structure of human chondroadherin: solving a difficult molecular-replacement problem usingde novomodels. Acta Crystallogr D Struct Biol 2017; 73:53-63. [DOI: 10.1107/s205979831601980x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/12/2016] [Indexed: 02/08/2023]
Abstract
Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen as well as with cell-surface heparin sulfate proteoglycans and α2β1integrins. The integrin-binding site is located in a region of hitherto unknown structure at the C-terminal end of CHAD. Peptides based on the C-terminal human CHAD (hCHAD) sequence have shown therapeutic potential for treating osteoporosis. This article describes a still-unconventional structure solution by phasing withde novomodels, the first of a β-rich protein. Structure determination of hCHAD using traditional, though nonsystematic, molecular replacement was unsuccessful in the hands of the authors, possibly owing to a combination of low sequence identity to other LRR proteins, four copies in the asymmetric unit and weak translational pseudosymmetry. However, it was possible to solve the structure by generating a large number ofde novomodels for the central LRR domain usingRosettaand multiple parallel molecular-replacement attempts usingAMPLE. The hCHAD structure reveals an ordered C-terminal domain belonging to the LRRCT fold, with the integrin-binding motif (WLEAK) being part of a regular α-helix, and suggests ways in which experimental therapeutic peptides can be improved. The crystal structure itself and docking simulations further support that hCHAD dimers form in a similar manner to other matrix LRR proteins.
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Affiliation(s)
- Huabing Wang
- Arrhenius
Laboratories of Natural Sciences, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Lisa Lang
- Arrhenius
Laboratories of Natural Sciences, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Derek T. Logan
- Division
of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Box
124, 221 00 Lund, Sweden
| | - Jens Danielsson
- Arrhenius
Laboratories of Natural Sciences, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Mikael Oliveberg
- Arrhenius
Laboratories of Natural Sciences, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
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Bågenholm V, Reddy SK, Bouraoui H, Morrill J, Kulcinskaja E, Bahr CM, Aurelius O, Rogers T, Xiao Y, Logan DT, Martens EC, Koropatkin NM, Stålbrand H. Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus of Bacteroides ovatus: ENZYME SYNERGY AND CRYSTAL STRUCTURE OF A β-MANNANASE. J Biol Chem 2016; 292:229-243. [PMID: 27872187 PMCID: PMC5217682 DOI: 10.1074/jbc.m116.746438] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 11/18/2016] [Indexed: 01/15/2023] Open
Abstract
A recently identified polysaccharide utilization locus (PUL) from Bacteroides ovatus ATCC 8483 is transcriptionally up-regulated during growth on galacto- and glucomannans. It encodes two glycoside hydrolase family 26 (GH26) β-mannanases, BoMan26A and BoMan26B, and a GH36 α-galactosidase, BoGal36A. The PUL also includes two glycan-binding proteins, confirmed by β-mannan affinity electrophoresis. When this PUL was deleted, B. ovatus was no longer able to grow on locust bean galactomannan. BoMan26A primarily formed mannobiose from mannan polysaccharides. BoMan26B had higher activity on galactomannan with a high degree of galactosyl substitution and was shown to be endo-acting generating a more diverse mixture of oligosaccharides, including mannobiose. Of the two β-mannanases, only BoMan26B hydrolyzed galactoglucomannan. A crystal structure of BoMan26A revealed a similar structure to the exo-mannobiohydrolase CjMan26C from Cellvibrio japonicus, with a conserved glycone region (−1 and −2 subsites), including a conserved loop closing the active site beyond subsite −2. Analysis of cellular location by immunolabeling and fluorescence microscopy suggests that BoMan26B is surface-exposed and associated with the outer membrane, although BoMan26A and BoGal36A are likely periplasmic. In light of the cellular location and the biochemical properties of the two characterized β-mannanases, we propose a scheme of sequential action by the glycoside hydrolases encoded by the β-mannan PUL and involved in the β-mannan utilization pathway in B. ovatus. The outer membrane-associated BoMan26B initially acts on the polysaccharide galactomannan, producing comparably large oligosaccharide fragments. Galactomanno-oligosaccharides are further processed in the periplasm, degalactosylated by BoGal36A, and subsequently hydrolyzed into mainly mannobiose by the β-mannanase BoMan26A.
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Affiliation(s)
- Viktoria Bågenholm
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Sumitha K Reddy
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Hanene Bouraoui
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Johan Morrill
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Evelina Kulcinskaja
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Constance M Bahr
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Oskar Aurelius
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Theresa Rogers
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Yao Xiao
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Derek T Logan
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
| | - Eric C Martens
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Nicole M Koropatkin
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Henrik Stålbrand
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00 Lund, Sweden and
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Manzoni F, Saraboji K, Sprenger J, Kumar R, Noresson AL, Nilsson UJ, Leffler H, Fisher SZ, Schrader TE, Ostermann A, Coates L, Blakeley MP, Oksanen E, Logan DT. Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C. Acta Crystallogr D Struct Biol 2016; 72:1194-1202. [PMID: 27841752 PMCID: PMC5108347 DOI: 10.1107/s2059798316015540] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/03/2016] [Indexed: 11/11/2022]
Abstract
Galectin-3 is an important protein in molecular signalling events involving carbohydrate recognition, and an understanding of the hydrogen-bonding patterns in the carbohydrate-binding site of its C-terminal domain (galectin-3C) is important for the development of new potent inhibitors. The authors are studying these patterns using neutron crystallography. Here, the production of perdeuterated human galectin-3C and successive improvement in crystal size by the development of a crystal-growth protocol involving feeding of the crystallization drops are described. The larger crystals resulted in improved data quality and reduced data-collection times. Furthermore, protocols for complete removal of the lactose that is necessary for the production of large crystals of apo galectin-3C suitable for neutron diffraction are described. Five data sets have been collected at three different neutron sources from galectin-3C crystals of various volumes. It was possible to merge two of these to generate an almost complete neutron data set for the galectin-3C-lactose complex. These data sets provide insights into the crystal volumes and data-collection times necessary for the same system at sources with different technologies and data-collection strategies, and these insights are applicable to other systems.
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Affiliation(s)
- Francesco Manzoni
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Kadhirvel Saraboji
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Janina Sprenger
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Rohit Kumar
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Ann Louise Noresson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University, S-221 00 Lund, Sweden
| | - S Zoë Fisher
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Tobias E Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Esko Oksanen
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
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Johansson R, Jonna VR, Kumar R, Nayeri N, Lundin D, Sjöberg BM, Hofer A, Logan DT. Structural Mechanism of Allosteric Activity Regulation in a Ribonucleotide Reductase with Double ATP Cones. Structure 2016; 24:1432-1434. [PMID: 27486915 DOI: 10.1016/j.str.2016.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Badarau A, Rouha H, Malafa S, Battles MB, Walker L, Nielson N, Dolezilkova I, Teubenbacher A, Banerjee S, Maierhofer B, Weber S, Stulik L, Logan DT, Welin M, Mirkina I, Pleban C, Zauner G, Gross K, Jägerhofer M, Magyarics Z, Nagy E. Context matters: The importance of dimerization-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralizing antibodies. MAbs 2016; 8:1347-1360. [PMID: 27467113 PMCID: PMC5058624 DOI: 10.1080/19420862.2016.1215791] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
LukGH (LukAB) is a potent leukocidin of Staphylococcus aureus that lyses human phagocytic cells and is thought to contribute to immune evasion. Unlike the other bi-component leukocidins of S. aureus, LukGH forms a heterodimer before binding to its receptor, CD11b expressed on professional phagocytic cells, and displays significant sequence variation. We employed a high diversity human IgG1 library presented on yeast cells to discover monoclonal antibodies (mAbs) neutralizing the cytolytic activity of LukGH. Recombinant LukG and LukH monomers or a LukGH dimer were used as capture antigens in the library selections. We found that mAbs identified with LukG or LukH as bait had no or very low toxin neutralization potency. In contrast, LukGH dimer-selected antibodies proved to be highly potent, and several mAbs were able to neutralize even the most divergent LukGH variants. Based on biolayer interferometry and mesoscale discovery, the high affinity antibody binding site on the LukGH complex was absent on the individual monomers, suggesting that it was generated upon formation of the LukG-LukH dimer. X-ray crystallography analysis of the complex between the LukGH dimer and the antigen-binding fragment of a very potent mAb (PDB code 5K59) indicated that the epitope is located in the predicted cell binding region (rim domain) of LukGH. The corresponding IgG inhibited the binding of LukGH dimer to target cells. Our data suggest that knowledge of the native conformation of target molecules is essential to generate high affinity and functional mAbs.
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Affiliation(s)
- Adriana Badarau
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Harald Rouha
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Stefan Malafa
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | | | | | | | | | - Srijib Banerjee
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | - Susanne Weber
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Lukas Stulik
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Derek T Logan
- c SARomics Biostructures AB , Medicon Village, Lund , Sweden
| | - Martin Welin
- c SARomics Biostructures AB , Medicon Village, Lund , Sweden
| | - Irina Mirkina
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Clara Pleban
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Gerhild Zauner
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Karin Gross
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | - Zoltán Magyarics
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Eszter Nagy
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
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Nilsson LM, Green LC, Muralidharan SV, Demir D, Welin M, Bhadury J, Logan DT, Walse B, Nilsson JA. Cancer Differentiating Agent Hexamethylene Bisacetamide Inhibits BET Bromodomain Proteins. Cancer Res 2016; 76:2376-83. [PMID: 26941288 DOI: 10.1158/0008-5472.can-15-2721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/18/2016] [Indexed: 11/16/2022]
Abstract
Agents that trigger cell differentiation are highly efficacious in treating certain cancers, but such approaches are not generally effective in most malignancies. Compounds such as DMSO and hexamethylene bisacetamide (HMBA) have been used to induce differentiation in experimental systems, but their mechanisms of action and potential range of uses on that basis have not been developed. Here, we show that HMBA, a compound first tested in the oncology clinic over 25 years ago, acts as a selective bromodomain inhibitor. Biochemical and structural studies revealed an affinity of HMBA for the second bromodomain of BET proteins. Accordingly, both HMBA and the prototype BET inhibitor JQ1 induced differentiation of mouse erythroleukemia cells. As expected of a BET inhibitor, HMBA displaced BET proteins from chromatin, caused massive transcriptional changes, and triggered cell-cycle arrest and apoptosis in Myc-induced B-cell lymphoma cells. Furthermore, HMBA exerted anticancer effects in vivo in mouse models of Myc-driven B-cell lymphoma. This study illuminates the function of an early anticancer agent and suggests an intersection with ongoing clinical trials of BET inhibitor, with several implications for predicting patient selection and response rates to this therapy and starting points for generating BD2-selective BET inhibitors. Cancer Res; 76(8); 2376-83. ©2016 AACR.
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Affiliation(s)
- Lisa M Nilsson
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | - Lydia C Green
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | - Somsundar Veppil Muralidharan
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | - Dağsu Demir
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | | | - Joydeep Bhadury
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden
| | | | | | - Jonas A Nilsson
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden.
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Fisher SZ, von Schantz L, Håkansson M, Logan DT, Ohlin M. Neutron crystallographic studies reveal hydrogen bond and water-mediated interactions between a carbohydrate-binding module and its bound carbohydrate ligand. Biochemistry 2015; 54:6435-8. [PMID: 26451738 DOI: 10.1021/acs.biochem.5b01058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Carbohydrate-binding modules (CBMs) are key components of many carbohydrate-modifying enzymes. CBMs affect the activity of these enzymes by modulating bonding and catalysis. To further characterize and study CBM-ligand binding interactions, neutron crystallographic studies of an engineered family 4-type CBM in complex with a branched xyloglucan ligand were conducted. The first neutron crystal structure of a CBM-ligand complex reported here shows numerous atomic details of hydrogen bonding and water-mediated interactions and reveals the charged state of key binding cleft amino acid side chains.
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Affiliation(s)
- S Zoë Fisher
- European Spallation Source , S-221 00 Lund, Sweden
| | - Laura von Schantz
- Department of Immunotechnology, Lund University , Medicon Village, S-223 81 Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures AB , Medicon Village, S-223 81 Lund, Sweden
| | - Derek T Logan
- SARomics Biostructures AB , Medicon Village, S-223 81 Lund, Sweden.,Department of Biochemistry and Structural Biology, Lund University , S-221 00 Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University , Medicon Village, S-223 81 Lund, Sweden
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Awad W, Adamczyk B, Örnros J, Karlsson NG, Mani K, Logan DT. Structural Aspects of N-Glycosylations and the C-terminal Region in Human Glypican-1. J Biol Chem 2015; 290:22991-3008. [PMID: 26203194 PMCID: PMC4645609 DOI: 10.1074/jbc.m115.660878] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/10/2015] [Indexed: 11/06/2022] Open
Abstract
Glypicans are multifunctional cell surface proteoglycans involved in several important cellular signaling pathways. Glypican-1 (Gpc1) is the predominant heparan sulfate proteoglycan in the developing and adult human brain. The two N-linked glycans and the C-terminal domain that attach the core protein to the cell membrane are not resolved in the Gpc1 crystal structure. Therefore, we have studied Gpc1 using crystallography, small angle x-ray scattering, and chromatographic approaches to elucidate the composition, structure, and function of the N-glycans and the C terminus and also the topology of Gpc1 with respect to the membrane. The C terminus is shown to be highly flexible in solution, but it orients the core protein transverse to the membrane, directing a surface evolutionarily conserved in Gpc1 orthologs toward the membrane, where it may interact with signaling molecules and/or membrane receptors on the cell surface, or even the enzymes involved in heparan sulfate substitution in the Golgi apparatus. Furthermore, the N-glycans are shown to extend the protein stability and lifetime by protection against proteolysis and aggregation.
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Affiliation(s)
- Wael Awad
- From the Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Box 124, SE-221 00 Lund
| | - Barbara Adamczyk
- the Department of Biochemistry and Cell Biology, University of Gothenburg, Box 440, SE-40530 Gothenburg, and
| | - Jessica Örnros
- the Department of Biochemistry and Cell Biology, University of Gothenburg, Box 440, SE-40530 Gothenburg, and
| | - Niclas G Karlsson
- the Department of Biochemistry and Cell Biology, University of Gothenburg, Box 440, SE-40530 Gothenburg, and
| | - Katrin Mani
- the Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden
| | - Derek T Logan
- From the Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Box 124, SE-221 00 Lund,
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Thunnissen M, Appio R, Unge J, Nan J, Equiraun M, Nardella A, Logan DT, Ward C, Ursby T. The macromolecular crystallography beamlines BioMAX and MicroMAX at the MAX IV laboratory. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315097193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Aurelius O, Johansson R, Bågenholm V, Lundin D, Tholander F, Balhuizen A, Beck T, Sahlin M, Emanuelsson C, Sjöberg BM, Mulliez E, Logan DT. What can we learn about nucleotide metabolism from a thermophilic anaerobic ribonucleotide reductase? Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315096497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Ohlin M, von Schantz L, Schrader TE, Ostermann A, Logan DT, Fisher SZ. Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase. Acta Crystallogr F Struct Biol Commun 2015; 71:1072-7. [PMID: 26249702 PMCID: PMC4528944 DOI: 10.1107/s2053230x15011383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/11/2015] [Indexed: 11/10/2022] Open
Abstract
Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that bind specific types of carbohydrates. Ultra high-resolution X-ray crystallographic studies of CBMs have helped to decipher the basis for specificity in carbohydrate-protein interactions. However, additional studies are needed to better understand which structural determinants confer which carbohydrate-binding properties. To address these issues, neutron crystallographic studies were initiated on one experimentally engineered CBM derived from a xylanase, X-2 L110F, a protein that is able to bind several different plant carbohydrates such as xylan, β-glucan and xyloglucan. This protein evolved from a CBM present in xylanase Xyn10A of Rhodothermus marinus. The protein was complexed with a branched xyloglucan heptasaccharide. Large single crystals of hydrogenous protein (∼1.6 mm(3)) were grown at room temperature and subjected to H/D exchange. Both neutron and X-ray diffraction data sets were collected to 1.6 Å resolution. Joint neutron and X-ray refinement using phenix.refine showed significant density for residues involved in carbohydrate binding and revealed the details of a hydrogen-bonded water network around the binding site. This is the first report of a neutron structure of a CBM and will add to the understanding of protein-carbohydrate binding interactions.
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Affiliation(s)
- Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village, Building 406, 223 81 Lund, Sweden
| | - Laura von Schantz
- Department of Immunotechnology, Lund University, Medicon Village, Building 406, 223 81 Lund, Sweden
| | - Tobias E. Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Derek T. Logan
- Department of Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - S. Zoë Fisher
- Scientific Activities Division, European Spallation Source, Tunavägen 24, 221 00 Lund, Sweden
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Aurelius O, Johansson R, Bågenholm V, Lundin D, Tholander F, Balhuizen A, Beck T, Sahlin M, Sjöberg BM, Mulliez E, Logan DT. The Crystal Structure of Thermotoga maritima Class III Ribonucleotide Reductase Lacks a Radical Cysteine Pre-Positioned in the Active Site. PLoS One 2015; 10:e0128199. [PMID: 26147435 PMCID: PMC4493059 DOI: 10.1371/journal.pone.0128199] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 04/24/2015] [Indexed: 12/05/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to deoxyribonucleotides, the building blocks for DNA synthesis, and are found in all but a few organisms. RNRs use radical chemistry to catalyze the reduction reaction. Despite RNR having evolved several mechanisms for generation of different kinds of essential radicals across a large evolutionary time frame, this initial radical is normally always channelled to a strictly conserved cysteine residue directly adjacent to the substrate for initiation of substrate reduction, and this cysteine has been found in the structures of all RNRs solved to date. We present the crystal structure of an anaerobic RNR from the extreme thermophile Thermotoga maritima (tmNrdD), alone and in several complexes, including with the allosteric effector dATP and its cognate substrate CTP. In the crystal structure of the enzyme as purified, tmNrdD lacks a cysteine for radical transfer to the substrate pre-positioned in the active site. Nevertheless activity assays using anaerobic cell extracts from T. maritima demonstrate that the class III RNR is enzymatically active. Other genetic and microbiological evidence is summarized indicating that the enzyme is important for T. maritima. Mutation of either of two cysteine residues in a disordered loop far from the active site results in inactive enzyme. We discuss the possible mechanisms for radical initiation of substrate reduction given the collected evidence from the crystal structure, our activity assays and other published work. Taken together, the results suggest either that initiation of substrate reduction may involve unprecedented conformational changes in the enzyme to bring one of these cysteine residues to the expected position, or that alternative routes for initiation of the RNR reduction reaction may exist. Finally, we present a phylogenetic analysis showing that the structure of tmNrdD is representative of a new RNR subclass IIIh, present in all Thermotoga species plus a wider group of bacteria from the distantly related phyla Firmicutes, Bacteroidetes and Proteobacteria.
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Affiliation(s)
- Oskar Aurelius
- Dept. of Biochemistry & Structural Biology, Lund University, Box 124, S-221 00 Lund, Sweden
| | - Renzo Johansson
- Dept. of Biochemistry & Structural Biology, Lund University, Box 124, S-221 00 Lund, Sweden
| | - Viktoria Bågenholm
- Dept. of Biochemistry & Structural Biology, Lund University, Box 124, S-221 00 Lund, Sweden
| | - Daniel Lundin
- Dept. of Biochemistry & Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Fredrik Tholander
- Dept. of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Alexander Balhuizen
- Dept. of Biochemistry & Structural Biology, Lund University, Box 124, S-221 00 Lund, Sweden
| | - Tobias Beck
- Dept. of Inorganic Chemistry, Georg-August Universität Göttingen, Göttingen, Germany
| | - Margareta Sahlin
- Dept. of Biochemistry & Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Britt-Marie Sjöberg
- Dept. of Biochemistry & Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Etienne Mulliez
- LCBM, Groupe de Biocatalyse, CEA-Grenoble, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 38054 Grenoble Cedex 09, France
| | - Derek T. Logan
- Dept. of Biochemistry & Structural Biology, Lund University, Box 124, S-221 00 Lund, Sweden
- * E-mail:
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