151
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Holgado A, Braun H, Van Nuffel E, Detry S, Schuijs MJ, Deswarte K, Vergote K, Haegman M, Baudelet G, Haustraete J, Hammad H, Lambrecht BN, Savvides SN, Afonina IS, Beyaert R. IL-33trap is a novel IL-33-neutralizing biologic that inhibits allergic airway inflammation. J Allergy Clin Immunol 2019; 144:204-215. [PMID: 30876911 PMCID: PMC7610802 DOI: 10.1016/j.jaci.2019.02.028] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND The emergence of IL-33 as a key molecular player in the development and propagation of widespread inflammatory diseases, including asthma and atopic dermatitis, has established the need for effective IL-33-neutralizing biologics. OBJECTIVE Here we describe the development and validation of a new antagonist of IL-33, termed IL-33trap, which combines the extracellular domains of the IL-33 receptor (ST2) and its coreceptor, IL-1 receptor accessory protein, into a single fusion protein. METHODS We produced and purified recombinant IL-33trap from human cells and analyzed its IL-33-binding affinity and IL-33 antagonistic activity in cultured cells and mice. IL-33trap activity was also benchmarked with a recombinant soluble ST2 corresponding to the naturally occurring IL-33 decoy receptor. Finally, we studied the effect of IL-33trap in the Alternaria alternata mouse model of allergic airway inflammation. RESULTS In vitro IL-33trap binds IL-33 and inhibits IL-33 activity to a much stronger degree than soluble ST2. Furthermore, IL-33trap inhibits eosinophil infiltration, splenomegaly, and production of signature cytokines in splenic lymphocytes and lung tissue on IL-33 injection. Finally, administration of IL-33trap at the time of allergen challenge inhibits inflammatory responses in a preclinical mouse model of acute allergic airway inflammation. CONCLUSIONS IL-33trap is a novel IL-33 antagonist that outperforms the natural IL-33 decoy receptor and shows anti-inflammatory activities in a preclinical mouse model of acute allergic airway inflammation when administered at the time of allergen challenge.
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Affiliation(s)
- Aurora Holgado
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Harald Braun
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Elien Van Nuffel
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Sammy Detry
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Martijn J Schuijs
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Kim Deswarte
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Karl Vergote
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Mira Haegman
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Griet Baudelet
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jurgen Haustraete
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Protein Service Facility, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Hamida Hammad
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Bart N Lambrecht
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Savvas N Savvides
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Inna S Afonina
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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152
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Greule A, Izoré T, Iftime D, Tailhades J, Schoppet M, Zhao Y, Peschke M, Ahmed I, Kulik A, Adamek M, Goode RJA, Schittenhelm RB, Kaczmarski JA, Jackson CJ, Ziemert N, Krenske EH, De Voss JJ, Stegmann E, Cryle MJ. Kistamicin biosynthesis reveals the biosynthetic requirements for production of highly crosslinked glycopeptide antibiotics. Nat Commun 2019; 10:2613. [PMID: 31197182 PMCID: PMC6565677 DOI: 10.1038/s41467-019-10384-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 05/07/2019] [Indexed: 01/25/2023] Open
Abstract
Kistamicin is a divergent member of the glycopeptide antibiotics, a structurally complex class of important, clinically relevant antibiotics often used as the last resort against resistant bacteria. The extensively crosslinked structure of these antibiotics that is essential for their activity makes their chemical synthesis highly challenging and limits their production to bacterial fermentation. Kistamicin contains three crosslinks, including an unusual 15-membered A-O-B ring, despite the presence of only two Cytochrome P450 Oxy enzymes thought to catalyse formation of such crosslinks within the biosynthetic gene cluster. In this study, we characterise the kistamicin cyclisation pathway, showing that the two Oxy enzymes are responsible for these crosslinks within kistamicin and that they function through interactions with the X-domain, unique to glycopeptide antibiotic biosynthesis. We also show that the kistamicin OxyC enzyme is a promiscuous biocatalyst, able to install multiple crosslinks into peptides containing phenolic amino acids.
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Affiliation(s)
- Anja Greule
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Thierry Izoré
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Dumitrita Iftime
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Iftekhar Ahmed
- Department of Chemistry, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Robert J A Goode
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Monash Biomedical Proteomics Facility, Monash University, Clayton, VIC, 3800, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Monash Biomedical Proteomics Facility, Monash University, Clayton, VIC, 3800, Australia
| | - Joe A Kaczmarski
- Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Elizabeth H Krenske
- Department of Chemistry, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - James J De Voss
- Department of Chemistry, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076, Tübingen, Germany.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia.
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153
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Sjekloća L, Ferré-D'Amaré AR. Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence. Cell Chem Biol 2019; 26:1159-1168.e4. [PMID: 31178406 DOI: 10.1016/j.chembiol.2019.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/08/2019] [Accepted: 04/29/2019] [Indexed: 12/21/2022]
Abstract
Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes and its fluorescence turn-on, we determined its co-crystal structure with the homodimeric RNA Corn, which contains two G quadruplexes. We found that two ThT molecules bind in the dimer interface, constrained by a G quartet from each protomer into a maximally fluorescent planar conformation. The unliganded Corn homodimer crystal structure reveals a collapsed fluorophore-binding site. In solution, Corn must fluctuate between this and an open, binding-competent conformation. A co-crystal structure with another benzothiazole derivate, thiazole orange (TO), also shows binding at the Corn homodimer interface. As the bound ThT and TO make no interactions with the RNA backbone, their Corn co-crystal structures likely explain their fluorescence activation upon sequence-independent DNA and RNA G-quadruplex binding.
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Affiliation(s)
- Ljiljana Sjekloća
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA.
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154
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Bose S, Purkait D, Joseph D, Nayak V, Subramanian R. Structural and functional characterization of CMP-N-acetylneuraminate synthetase from Vibrio cholerae. Acta Crystallogr D Struct Biol 2019; 75:564-577. [PMID: 31205019 PMCID: PMC6580227 DOI: 10.1107/s2059798319006831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 05/13/2019] [Indexed: 11/10/2022] Open
Abstract
Several pathogenic bacteria utilize sialic acid, including host-derived N-acetylneuraminic acid (Neu5Ac), in at least two ways: they use it as a nutrient source and as a host-evasion strategy by coating themselves with Neu5Ac. Given the significant role of sialic acid in pathogenesis and host-gut colonization by various pathogenic bacteria, including Neisseria meningitidis, Haemophilus influenzae, Pasteurella multocida and Vibrio cholerae, several enzymes of the sialic acid catabolic, biosynthetic and incorporation pathways are considered to be potential drug targets. In this work, findings on the structural and functional characterization of CMP-N-acetylneuraminate synthetase (CMAS), a key enzyme in the incorporation pathway, from Vibrio cholerae are reported. CMAS catalyzes the synthesis of CMP-sialic acid by utilizing CTP and sialic acid. Crystal structures of the apo and the CDP-bound forms of the enzyme were determined, which allowed the identification of the metal cofactor Mg2+ in the active site interacting with CDP and the invariant Asp215 residue. While open and closed structural forms of the enzyme from eukaryotic and other bacterial species have already been characterized, a partially closed structure of V. cholerae CMAS (VcCMAS) observed upon CDP binding, representing an intermediate state, is reported here. The kinetic data suggest that VcCMAS is capable of activating the two most common sialic acid derivatives, Neu5Ac and Neu5Gc. Amino-acid sequence and structural comparison of the active site of VcCMAS with those of eukaryotic and other bacterial counterparts reveal a diverse hydrophobic pocket that interacts with the C5 substituents of sialic acid. Analyses of the thermodynamic signatures obtained from the binding of the nucleotide (CTP) and the product (CMP-sialic acid) to VcCMAS provide fundamental information on the energetics of the binding process.
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Affiliation(s)
- Sucharita Bose
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore 560 065, India
| | - Debayan Purkait
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore 560 065, India
| | - Deepthi Joseph
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore 560 065, India
| | - Vinod Nayak
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore 560 065, India
| | - Ramaswamy Subramanian
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore 560 065, India
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155
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Kairys V, Baranauskiene L, Kazlauskiene M, Matulis D, Kazlauskas E. Binding affinity in drug design: experimental and computational techniques. Expert Opin Drug Discov 2019; 14:755-768. [DOI: 10.1080/17460441.2019.1623202] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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156
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Wang J, Varin T, Vieth M, Elkins JM. Crystal structure of human RIOK2 bound to a specific inhibitor. Open Biol 2019; 9:190037. [PMID: 30991936 PMCID: PMC6501643 DOI: 10.1098/rsob.190037] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/20/2019] [Indexed: 11/21/2022] Open
Abstract
The RIO kinases (RIOKs) are a universal family of atypical kinases that are essential for assembly of the pre-40S ribosome complex. Here, we present the crystal structure of human RIO kinase 2 (RIOK2) bound to a specific inhibitor. This first crystal structure of an inhibitor-bound RIO kinase reveals the binding mode of the inhibitor and explains the structure-activity relationship of the inhibitor series. The inhibitor binds in the ATP-binding site and forms extensive hydrophobic interactions with residues at the entrance to the ATP-binding site. Analysis of the conservation of active site residues reveals the reasons for the specificity of the inhibitor for RIOK2 over RIOK1 and RIOK3, and it provides a template for inhibitor design against the human RIOK family.
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Affiliation(s)
- Jing Wang
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Thibault Varin
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Michal Vieth
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Biotechnology Center, 10290 Campus Point Drive, San Diego, CA 92121, USA
| | - Jonathan M. Elkins
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello 550, Barão Geraldo, Campinas/SP 13083-886, Brazil
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157
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Tejera B, López RE, Hidalgo P, Cárdenas R, Ballesteros G, Rivillas L, French L, Amero C, Pastor N, Santiago Á, Groitl P, Dobner T, Gonzalez RA. The human adenovirus type 5 E1B 55kDa protein interacts with RNA promoting timely DNA replication and viral late mRNA metabolism. PLoS One 2019; 14:e0214882. [PMID: 30943256 PMCID: PMC6447194 DOI: 10.1371/journal.pone.0214882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/21/2019] [Indexed: 12/25/2022] Open
Abstract
The E1B 55kDa produced by human adenovirus type 5 is a multifunctional protein that participates in the regulation of several steps during the viral replication cycle. Previous studies suggest this protein plays an important role in postranscriptional regulation of viral and cellular gene expression, as it is required for the selective accumulation of maximal levels of viral late mRNA in the cytoplasm of the infected cell; however the molecular mechanisms that are altered or regulated by this protein have not been elucidated. A ribonucleoprotein motif that could implicate the direct interaction of the protein with RNA was initially predicted and tested in vitro, but the interaction with RNA could not be detected in infected cells, suggesting the interaction may be weak or transient. Here it was determined that the E1B 55kDa interacts with RNA in the context of the viral infection in non-transformed human cells, and its contribution to the adenovirus replication cycle was evaluated. Using recombinant adenoviruses with amino acid substitutions or a deletion in the ribonucleoprotein motif the interaction of E1B 55kDa with RNA was found to correlate with timely and efficient viral DNA replication and viral late mRNA accumulation and splicing.
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Affiliation(s)
- Berto Tejera
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Raúl E. López
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Paloma Hidalgo
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Reinier Cárdenas
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Grisel Ballesteros
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Lina Rivillas
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Leidys French
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Carlos Amero
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Ángel Santiago
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Peter Groitl
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Thomas Dobner
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ramón A. Gonzalez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
- * E-mail:
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158
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Padavannil A, Sarkar P, Kim SJ, Cagatay T, Jiou J, Brautigam CA, Tomchick DR, Sali A, D'Arcy S, Chook YM. Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone. eLife 2019; 8:e43630. [PMID: 30855230 PMCID: PMC6453568 DOI: 10.7554/elife.43630] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/09/2019] [Indexed: 01/29/2023] Open
Abstract
We report the crystal structure of nuclear import receptor Importin-9 bound to its cargo, the histones H2A-H2B. Importin-9 wraps around the core, globular region of H2A-H2B to form an extensive interface. The nature of this interface coupled with quantitative analysis of deletion mutants of H2A-H2B suggests that the NLS-like sequences in the H2A-H2B tails play a minor role in import. Importin-9•H2A-H2B is reminiscent of interactions between histones and histone chaperones in that it precludes H2A-H2B interactions with DNA and H3-H4 as seen in the nucleosome. Like many histone chaperones, which prevent inappropriate non-nucleosomal interactions, Importin-9 also sequesters H2A-H2B from DNA. Importin-9 appears to act as a storage chaperone for H2A-H2B while escorting it to the nucleus. Surprisingly, RanGTP does not dissociate Importin-9•H2A-H2B but assembles into a RanGTP•Importin-9•H2A-H2B complex. The presence of Ran in the complex, however, modulates Imp9-H2A-H2B interactions to facilitate its dissociation by DNA and assembly into a nucleosome.
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Affiliation(s)
- Abhilash Padavannil
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Prithwijit Sarkar
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Seung Joong Kim
- Department of PhysicsKorea Advanced Institute of Science and Technology (KAIST)DaejeonKorea
| | - Tolga Cagatay
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Jenny Jiou
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Chad A Brautigam
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Diana R Tomchick
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative BiosciencesUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Pharmaceutical Chemistry, California Institute for Quantitative BiosciencesUniversity of California, San FranciscoSan FranciscoUnited states
| | - Sheena D'Arcy
- Department of Chemistry and BiochemistryUniversity of Texas at DallasRichardsonUnited States
| | - Yuh Min Chook
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
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159
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Structural Insight into DNA-Dependent Activation of Human Metalloprotease Spartan. Cell Rep 2019; 26:3336-3346.e4. [DOI: 10.1016/j.celrep.2019.02.082] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/04/2018] [Accepted: 02/21/2019] [Indexed: 11/18/2022] Open
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160
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Talavera A, Tamman H, Ainelo A, Konijnenberg A, Hadži S, Sobott F, Garcia-Pino A, Hõrak R, Loris R. A dual role in regulation and toxicity for the disordered N-terminus of the toxin GraT. Nat Commun 2019; 10:972. [PMID: 30814507 PMCID: PMC6393540 DOI: 10.1038/s41467-019-08865-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 01/31/2019] [Indexed: 11/09/2022] Open
Abstract
Bacterial toxin-antitoxin (TA) modules are tightly regulated to maintain growth in favorable conditions or growth arrest during stress. A typical regulatory strategy involves the antitoxin binding and repressing its own promoter while the toxin often acts as a co-repressor. Here we show that Pseudomonas putida graTA-encoded antitoxin GraA and toxin GraT differ from other TA proteins in the sense that not the antitoxin but the toxin possesses a flexible region. GraA auto-represses the graTA promoter: two GraA dimers bind cooperatively at opposite sides of the operator sequence. Contrary to other TA modules, GraT is a de-repressor of the graTA promoter as its N-terminal disordered segment prevents the binding of the GraT2A2 complex to the operator. Removal of this region restores operator binding and abrogates Gr aT toxicity. GraTA represents a TA module where a flexible region in the toxin rather than in the antitoxin controls operon expression and toxin activity. The Pseudomonas putida toxin GraT and antitoxin GraA form a type II toxin-antoxin module. Here the authors present the crystal structures of the GraA dimer, GraTA and GraA-DNA complexes and show that GraT contains a functionally important N-terminal intrinsic disordered region that prevents the binding of the GraTA complex to the operator.
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Affiliation(s)
- Ariel Talavera
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium. .,Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium.
| | - Hedvig Tamman
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Andres Ainelo
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Albert Konijnenberg
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium.,Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium.,Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium
| | - San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium.,Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Abel Garcia-Pino
- Biologie Structurale et Biophysique, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, B-6041, Gosselies, Belgium
| | - Rita Hõrak
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium. .,Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium.
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161
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Duff MR, Desai N, Craig MA, Agarwal PK, Howell EE. Crowders Steal Dihydrofolate Reductase Ligands through Quinary Interactions. Biochemistry 2019; 58:1198-1213. [PMID: 30724552 DOI: 10.1021/acs.biochem.8b01110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) reduces dihydrofolate (DHF) to tetrahydrofolate using NADPH as a cofactor. Due to its role in one carbon metabolism, chromosomal DHFR is the target of the antibacterial drug, trimethoprim. Resistance to trimethoprim has resulted in a type II DHFR that is not structurally related to the chromosomal enzyme target. Because of its metabolic significance, understanding DHFR kinetics and ligand binding behavior in more cell-like conditions, where the total macromolecule concentration can be as great as 300 mg/mL, is important. The progress-curve kinetics and ligand binding properties of the drug target (chromosomal E. coli DHFR) and the drug resistant (R67 DHFR) enzymes were studied in the presence of macromolecular cosolutes. There were varied effects on NADPH oxidation and binding to the two DHFRs, with some cosolutes increasing affinity and others weakening binding. However, DHF binding and reduction in both DHFRs decreased in the presence of all cosolutes. The decreased binding of ligands is mostly attributed to weak associations with the macromolecules, as opposed to crowder effects on the DHFRs. Computer simulations found weak, transient interactions for both ligands with several proteins. The net charge of protein cosolutes correlated with effects on NADP+ binding, with near neutral and positively charged proteins having more detrimental effects on binding. For DHF binding, effects correlated more with the size of binding pockets on the protein crowders. These nonspecific interactions between DHFR ligands and proteins predict that the in vivo efficiency of DHFRs may be much lower than expected from their in vitro rates.
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Affiliation(s)
- Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Nidhi Desai
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Michael A Craig
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
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162
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Yoshizawa T, Ali R, Jiou J, Fung HYJ, Burke KA, Kim SJ, Lin Y, Peeples WB, Saltzberg D, Soniat M, Baumhardt JM, Oldenbourg R, Sali A, Fawzi NL, Rosen MK, Chook YM. Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites. Cell 2019; 173:693-705.e22. [PMID: 29677513 DOI: 10.1016/j.cell.2018.03.003] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 11/29/2017] [Accepted: 02/28/2018] [Indexed: 01/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) is believed to underlie formation of biomolecular condensates, cellular compartments that concentrate macromolecules without surrounding membranes. Physical mechanisms that control condensate formation/dissolution are poorly understood. The RNA-binding protein fused in sarcoma (FUS) undergoes LLPS in vitro and associates with condensates in cells. We show that the importin karyopherin-β2/transportin-1 inhibits LLPS of FUS. This activity depends on tight binding of karyopherin-β2 to the C-terminal proline-tyrosine nuclear localization signal (PY-NLS) of FUS. Nuclear magnetic resonance (NMR) analyses reveal weak interactions of karyopherin-β2 with sequence elements and structural domains distributed throughout the entirety of FUS. Biochemical analyses demonstrate that most of these same regions also contribute to LLPS of FUS. The data lead to a model where high-affinity binding of karyopherin-β2 to the FUS PY-NLS tethers the proteins together, allowing multiple, distributed weak intermolecular contacts to disrupt FUS self-association, blocking LLPS. Karyopherin-β2 may act analogously to control condensates in diverse cellular contexts.
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Affiliation(s)
- Takuya Yoshizawa
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rustam Ali
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jenny Jiou
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ho Yee Joyce Fung
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kathleen A Burke
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Seung Joong Kim
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuan Lin
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute (HHMI) Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - William B Peeples
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute (HHMI) Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Daniel Saltzberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Soniat
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jordan M Baumhardt
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rudolf Oldenbourg
- Marine Biological Laboratories, 7 MBL Street, Woods Hole, MA 02543, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute (HHMI) Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute (HHMI) Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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163
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Zinc regulates ERp44-dependent protein quality control in the early secretory pathway. Nat Commun 2019; 10:603. [PMID: 30723194 PMCID: PMC6363758 DOI: 10.1038/s41467-019-08429-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/09/2019] [Indexed: 01/14/2023] Open
Abstract
Zinc ions (Zn2+) are imported into the early secretory pathway by Golgi-resident transporters, but their handling and functions are not fully understood. Here, we show that Zn2+ binds with high affinity to the pH-sensitive chaperone ERp44, modulating its localization and ability to retrieve clients like Ero1α and ERAP1 to the endoplasmic reticulum (ER). Silencing the Zn2+ transporters that uptake Zn2+ into the Golgi led to ERp44 dysfunction and increased secretion of Ero1α and ERAP1. High-resolution crystal structures of Zn2+-bound ERp44 reveal that Zn2+ binds to a conserved histidine-cluster. The consequent large displacements of the regulatory C-terminal tail expose the substrate-binding surface and RDEL motif, ensuring client capture and retrieval. ERp44 also forms Zn2+-bridged homodimers, which dissociate upon client binding. Histidine mutations in the Zn2+-binding sites compromise ERp44 activity and localization. Our findings reveal a role of Zn2+ as a key regulator of protein quality control at the ER-Golgi interface. Zinc ions (Zn2+) are imported by Golgi-resident transporters but the function of zinc in the early secretory pathway has remained unknown. Here the authors find that Zn2+ regulates protein quality control in the early secretory pathway by demonstrating that the pH-sensitive chaperone ERp44 binds Zn2+ and solving the Zn2+-bound ERp44 structure.
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164
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Moldenhauer D, Fuenzalida Werner JP, Strassert CA, Gröhn F. Light-Responsive Size of Self-Assembled Spiropyran-Lysozyme Nanoparticles with Enzymatic Function. Biomacromolecules 2019; 20:979-991. [PMID: 30570257 DOI: 10.1021/acs.biomac.8b01605] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel light-responsive nanoassemblies with switchable size and enzymatic activity are built from a protein and a water-soluble spiropyran. Assemblies are created by electrostatic self-assembly in aqueous solution such that the photochromic property of the spiropyran enables light responsiveness. Upon visible light exposure, the aggregate size increases from 200 to 400 nm. The enzyme retains its activity upon aggregation into the assembly, while it decreases through visible light irradiation. Fundamentally, we show how the two different spiropyran isomers, the open-ring merocyanine form and the closed-ring spiropyran form, bind differently to the protein, which triggers the assembly size and use of thermodynamic data to understand the binding process and the size response. Thus, as a proof of concept, a self-assembly driven light-tunable enzyme activity in conjunction with a triggerable assembly size is demonstrated for a model system. The concept bears future potential for various possible biological applications ranging from genetic control over vaccine applications to the detection of certain proteins.
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Affiliation(s)
- Daniel Moldenhauer
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
| | - Juan Pablo Fuenzalida Werner
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
| | - Cristian A Strassert
- Institute of Physics and Center for Nanotechnology , Westfälische Wilhelms-Universität Münster , Heisenbergstraße 11 , D-48149 Münster , Germany
| | - Franziska Gröhn
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
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165
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Agajanian MJ, Walker MP, Axtman AD, Ruela-de-Sousa RR, Serafin DS, Rabinowitz AD, Graham DM, Ryan MB, Tamir T, Nakamichi Y, Gammons MV, Bennett JM, Couñago RM, Drewry DH, Elkins JM, Gileadi C, Gileadi O, Godoi PH, Kapadia N, Müller S, Santiago AS, Sorrell FJ, Wells CI, Fedorov O, Willson TM, Zuercher WJ, Major MB. WNT Activates the AAK1 Kinase to Promote Clathrin-Mediated Endocytosis of LRP6 and Establish a Negative Feedback Loop. Cell Rep 2019; 26:79-93.e8. [PMID: 30605688 PMCID: PMC6315376 DOI: 10.1016/j.celrep.2018.12.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/27/2018] [Accepted: 12/03/2018] [Indexed: 11/28/2022] Open
Abstract
β-Catenin-dependent WNT signal transduction governs development, tissue homeostasis, and a vast array of human diseases. Signal propagation through a WNT-Frizzled/LRP receptor complex requires proteins necessary for clathrin-mediated endocytosis (CME). Paradoxically, CME also negatively regulates WNT signaling through internalization and degradation of the receptor complex. Here, using a gain-of-function screen of the human kinome, we report that the AP2 associated kinase 1 (AAK1), a known CME enhancer, inhibits WNT signaling. Reciprocally, AAK1 genetic silencing or its pharmacological inhibition using a potent and selective inhibitor activates WNT signaling. Mechanistically, we show that AAK1 promotes clearance of LRP6 from the plasma membrane to suppress the WNT pathway. Time-course experiments support a transcription-uncoupled, WNT-driven negative feedback loop; prolonged WNT treatment drives AAK1-dependent phosphorylation of AP2M1, clathrin-coated pit maturation, and endocytosis of LRP6. We propose that, following WNT receptor activation, increased AAK1 function and CME limits WNT signaling longevity.
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Affiliation(s)
- Megan J Agajanian
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew P Walker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Roberta R Ruela-de-Sousa
- Structural Genomics Consortium, Universidade Estadual de Campinas - UNICAMP, Campinas, SP 13083-970, Brazil
| | - D Stephen Serafin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alex D Rabinowitz
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David M Graham
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meagan B Ryan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tigist Tamir
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yuko Nakamichi
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Institute for Oral Science, Matsumoto Dental University, Nagano 399-0704, Japan
| | - Melissa V Gammons
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0SL, UK
| | - James M Bennett
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Rafael M Couñago
- Structural Genomics Consortium, Universidade Estadual de Campinas - UNICAMP, Campinas, SP 13083-970, Brazil
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan M Elkins
- Structural Genomics Consortium, Universidade Estadual de Campinas - UNICAMP, Campinas, SP 13083-970, Brazil; Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Carina Gileadi
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Opher Gileadi
- Structural Genomics Consortium, Universidade Estadual de Campinas - UNICAMP, Campinas, SP 13083-970, Brazil; Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Paulo H Godoi
- Structural Genomics Consortium, Universidade Estadual de Campinas - UNICAMP, Campinas, SP 13083-970, Brazil
| | - Nirav Kapadia
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main 60438, Germany
| | - André S Santiago
- Structural Genomics Consortium, Universidade Estadual de Campinas - UNICAMP, Campinas, SP 13083-970, Brazil
| | - Fiona J Sorrell
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oleg Fedorov
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Timothy M Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William J Zuercher
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael B Major
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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166
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Jones CP, Piszczek G, Ferré-D'Amaré AR. Isothermal Titration Calorimetry Measurements of Riboswitch-Ligand Interactions. Methods Mol Biol 2019; 1964:75-87. [PMID: 30929236 DOI: 10.1007/978-1-4939-9179-2_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
One of the many ways by which bacteria control gene expression is through cis-acting regulatory mRNA elements called riboswitches. By specifically binding to small molecules or metabolites and pairing the binding event to an RNA structure change, riboswitches link a metabolic input to a transcriptional or translational output. For over a decade, isothermal titration calorimetry (ITC) has been used to investigate how riboswitches interact with small molecules. We present methods for assaying RNA-ligand interactions using ITC and analyzing resulting data to estimate thermodynamic parameters associated with binding.
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Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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167
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Shang J, Brust R, Mosure SA, Bass J, Munoz-Tello P, Lin H, Hughes TS, Tang M, Ge Q, Kamenekca TM, Kojetin DJ. Cooperative cobinding of synthetic and natural ligands to the nuclear receptor PPARγ. eLife 2018; 7:43320. [PMID: 30575522 PMCID: PMC6317912 DOI: 10.7554/elife.43320] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 12/18/2018] [Indexed: 12/16/2022] Open
Abstract
Crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) have revealed overlapping binding modes for synthetic and natural/endogenous ligands, indicating competition for the orthosteric pocket. Here we show that cobinding of a synthetic ligand to the orthosteric pocket can push natural and endogenous PPARγ ligands (fatty acids) out of the orthosteric pocket towards an alternate ligand-binding site near the functionally important omega (Ω)-loop. X-ray crystallography, NMR spectroscopy, all-atom molecular dynamics simulations, and mutagenesis coupled to quantitative biochemical functional and cellular assays reveal that synthetic ligand and fatty acid cobinding can form a 'ligand link' to the Ω-loop and synergistically affect the structure and function of PPARγ. These findings contribute to a growing body of evidence indicating ligand binding to nuclear receptors can be more complex than the classical one-for-one orthosteric exchange of a natural or endogenous ligand with a synthetic ligand.
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Affiliation(s)
- Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States
| | - Richard Brust
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States
| | - Sarah A Mosure
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Summer Undergraduate Research Fellows (SURF) program, The Scripps Research Institute, Jupiter, United States.,Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, United States
| | - Jared Bass
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States
| | - Paola Munoz-Tello
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States
| | - Hua Lin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Travis S Hughes
- Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, United States.,Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, United States
| | - Miru Tang
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, United States
| | - Qingfeng Ge
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, United States
| | - Theodore M Kamenekca
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
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168
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Intrinsic disorder in the regulatory N-terminal domain of diacylglycerol acyltransferase 1 from Brassica napus. Sci Rep 2018; 8:16665. [PMID: 30420764 PMCID: PMC6232145 DOI: 10.1038/s41598-018-34339-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022] Open
Abstract
Proteins with multifunctional regulatory domains often demonstrate structural plasticity or protein disorder, allowing the binding of multiple regulatory factors and post-translational modifications. While the importance of protein disorder is clear, it also poses a challenge for in vitro characterization. Here, we report protein intrinsic disorder in a plant molecular system, which despite its prevalence is less studied. We present a detailed biophysical characterization of the entire cytoplasmic N-terminal domain of Brassica napus diacylglycerol acyltransferase, (DGAT1), which includes an inhibitory module and allosteric binding sites. Our results demonstrate that the monomeric N-terminal domain can be stabilized for biophysical characterization and is largely intrinsically disordered in solution. This domain interacts with allosteric modulators of DGAT1, CoA and oleoyl-CoA, at micromolar concentrations. While solution scattering studies indicate conformational heterogeneity in the N-terminal domain of DGAT1, there is a small gain of secondary structure induced by ligand binding.
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169
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Cockburn JJB, Hesketh SJ, Mulhair P, Thomsen M, O'Connell MJ, Way M. Insights into Kinesin-1 Activation from the Crystal Structure of KLC2 Bound to JIP3. Structure 2018; 26:1486-1498.e6. [PMID: 30197037 PMCID: PMC6224480 DOI: 10.1016/j.str.2018.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/03/2018] [Accepted: 07/25/2018] [Indexed: 12/11/2022]
Abstract
Kinesin-1 transports numerous cellular cargoes along microtubules. The kinesin-1 light chain (KLC) mediates cargo binding and regulates kinesin-1 motility. To investigate the molecular basis for kinesin-1 recruitment and activation by cargoes, we solved the crystal structure of the KLC2 tetratricopeptide repeat (TPR) domain bound to the cargo JIP3. This, combined with biophysical and molecular evolutionary analyses, reveals a kinesin-1 cargo binding site, located on KLC TPR1, which is conserved in homologs from sponges to humans. In the complex, JIP3 crosslinks two KLC2 TPR domains via their TPR1s. We show that TPR1 forms a dimer interface that mimics JIP3 binding in all crystal structures of the unbound KLC TPR domain. We propose that cargo-induced dimerization of the KLC TPR domains via TPR1 is a general mechanism for activating kinesin-1. We relate this to activation by tryptophan-acidic cargoes, explaining how different cargoes activate kinesin-1 through related molecular mechanisms.
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Affiliation(s)
- Joseph J B Cockburn
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Sophie J Hesketh
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Peter Mulhair
- Computational and Molecular Evolutionary Biology Research Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Maren Thomsen
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Research Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Michael Way
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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170
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Bajaj R, Bollen M, Peti W, Page R. KNL1 Binding to PP1 and Microtubules Is Mutually Exclusive. Structure 2018; 26:1327-1336.e4. [PMID: 30100357 PMCID: PMC6601351 DOI: 10.1016/j.str.2018.06.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/19/2018] [Accepted: 06/29/2018] [Indexed: 01/07/2023]
Abstract
The kinetochore scaffold 1 (KNL1) protein coordinates the spindle assembly checkpoint (SAC), a signaling pathway that delays chromosome segregation until all sister chromatids are properly attached to spindle microtubules. Recently, microtubules and protein phosphatase 1 (PP1), which both bind the N-terminal domain of KNL1, have emerged as regulators of the SAC; however, how these proteins interact to contribute to SAC signaling is unknown. Here, we use X-ray crystallography, nuclear magnetic resonance spectroscopy, and biochemical assays to show how KNL1 binds both PP1 and microtubules. Unexpectedly, we discovered that PP1 and microtubules bind KNL1 via overlapping binding sites. Further, we showed that Aurora B kinase phosphorylation results in distinct patterns of KNL1 complex disruption. Finally, combining this data with co-sedimentation assays unequivocally demonstrated that microtubules and PP1 binding to KNL1 is mutually exclusive, with preferential formation of the KNL1:PP1 holoenzyme in the presence of PP1.
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Affiliation(s)
- Rakhi Bajaj
- Department of Chemistry and Biochemistry, University of Arizona, AZ 85721, USA
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, Department of Cellular and Molecular Medicine, KU Leuven, Belgium
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, AZ 85721, USA
| | - Rebecca Page
- Department of Chemistry and Biochemistry, University of Arizona, AZ 85721, USA;,Corresponding (lead contact) author: Rebecca Page, Department of Chemistry and Biochemistry, University of Arizona, AZ 85721, USA., 520.626.0389,
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171
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Deka RK, Liu WZ, Tso SC, Norgard MV, Brautigam CA. Biophysical insights into a highly selective l-arginine-binding lipoprotein of a pathogenic treponeme. Protein Sci 2018; 27:2037-2050. [PMID: 30242931 DOI: 10.1002/pro.3510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 11/11/2022]
Abstract
Biophysical and biochemical studies on the lipoproteins and other periplasmic proteins from the spirochetal species Treponema pallidum have yielded numerous insights into the functioning of the organism's peculiar membrane organization, its nutritional requirements, and intermediary metabolism. However, not all T. pallidum proteins have proven to be amenable to biophysical studies. One such recalcitrant protein is Tp0309, a putative polar-amino-acid-binding protein of an ABC transporter system. To gain further information on its possible function, a homolog of the protein from the related species T. vincentii was used as a surrogate. This protein, Tv2483, was crystallized, resulting in the determination of its crystal structure at a resolution of 1.75 Å. The protein has a typical fold for a ligand-binding protein, and a single molecule of l-arginine was bound between its two lobes. Differential scanning fluorimetry and isothermal titration calorimetry experiments confirmed that l-arginine bound to the protein with unusually high selectivity. However, further comparison to Tp0309 showed differences in key amino-acid-binding residues may impart an alternate specificity for the T. pallidum protein.
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Affiliation(s)
- Ranjit K Deka
- Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390
| | - Wei Z Liu
- Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390
| | - Shih-Chia Tso
- Departments of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, 75390
| | - Michael V Norgard
- Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390
| | - Chad A Brautigam
- Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390.,Departments of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, 75390
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172
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Nguyen TH, Rustenburg AS, Krimmer SG, Zhang H, Clark JD, Novick PA, Branson K, Pande VS, Chodera JD, Minh DDL. Bayesian analysis of isothermal titration calorimetry for binding thermodynamics. PLoS One 2018; 13:e0203224. [PMID: 30212471 PMCID: PMC6136728 DOI: 10.1371/journal.pone.0203224] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/16/2018] [Indexed: 12/04/2022] Open
Abstract
Isothermal titration calorimetry (ITC) is the only technique able to determine both the enthalpy and entropy of noncovalent association in a single experiment. The standard data analysis method based on nonlinear regression, however, provides unrealistically small uncertainty estimates due to its neglect of dominant sources of error. Here, we present a Bayesian framework for sampling from the posterior distribution of all thermodynamic parameters and other quantities of interest from one or more ITC experiments, allowing uncertainties and correlations to be quantitatively assessed. For a series of ITC measurements on metal:chelator and protein:ligand systems, the Bayesian approach yields uncertainties which represent the variability from experiment to experiment more accurately than the standard data analysis. In some datasets, the median enthalpy of binding is shifted by as much as 1.5 kcal/mol. A Python implementation suitable for analysis of data generated by MicroCal instruments (and adaptable to other calorimeters) is freely available online.
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Affiliation(s)
- Trung Hai Nguyen
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Ariën S. Rustenburg
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY, United States of America
| | - Stefan G. Krimmer
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, Marburg, Germany
| | - Hexi Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, United States of America
| | - John D. Clark
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Paul A. Novick
- Department of Chemistry, Stanford University, Stanford, CA, United States of America
| | - Kim Branson
- Department of Chemistry, Stanford University, Stanford, CA, United States of America
| | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, CA, United States of America
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- * E-mail: (JDC); (DDLM)
| | - David D. L. Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, United States of America
- * E-mail: (JDC); (DDLM)
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173
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Baranauskiene L, Kuo TC, Chen WY, Matulis D. Isothermal titration calorimetry for characterization of recombinant proteins. Curr Opin Biotechnol 2018; 55:9-15. [PMID: 30031160 DOI: 10.1016/j.copbio.2018.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/22/2018] [Accepted: 06/27/2018] [Indexed: 12/11/2022]
Abstract
Isothermal titration calorimetry is widely used to measure the affinities and enthalpies of interaction between proteins and/or small molecules. The quantitative nature of the technique is especially useful in the characterization of recombinant proteins while determining the fraction of protein capable of binding a specific ligand and thus the protein purity. The revealed thermodynamic information sheds light on the binding mechanism, important for the targeted drug design of the biologics. Here we show examples how, together with the thermal shift assay, combination of both techniques enables characterization of protein stability and ligand binding. Furthermore, the binding-linked reactions that strongly affect the observed thermodynamic parameters and must be dissected to obtain the intrinsic parameters that are necessary for the structure-based rational drug design are being demonstrated using inhibitors of Hsp90, an anticancer target protein.
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Affiliation(s)
- Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Tai-Chih Kuo
- Department of Biochemistry, Taipei Medical University, Taipei, Taiwan
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li, Taoyuan City, Taiwan.
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
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174
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Tellinghuisen J. Critique of methods for estimating heats in isothermal titration calorimetry. Anal Biochem 2018; 563:79-86. [PMID: 30149027 DOI: 10.1016/j.ab.2018.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 11/30/2022]
Abstract
Isothermal titration calorimetry data recorded on a MicroCal/Malvern VP-ITC instrument for water-water blanks and for dilution of aqueous solutions of BaCl2 and Ba(NO3)2 are analyzed using Origin software, the freeware NITPIC program, and in-house algorithms, to compare precisions for estimating the heat per injection q. The data cover temperatures 6-47 °C, injection volumes 4-40 μL, and average heats 0-200 μcal. For water-water blanks, where baseline noise limits precision, NITPIC and the in-house algorithm achieve precisions of 0.05 μcal, which is better than Origin by a factor of 4. The precision differences decrease with increasing |q|, becoming insignificant for |q| > 200 μcal. In its default mode, NITPIC underestimates |q| for peaks with incomplete return to baseline, but the shortfall can be largely corrected by overriding the default injection time parameter. The variance estimates from 26 dilution experiments are used to assess the data variance function. The results determine the conditions under which weighted least squares should be used to estimate thermodynamic parameters from ITC data.
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Affiliation(s)
- Joel Tellinghuisen
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
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175
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French-Pacheco L, Cuevas-Velazquez CL, Rivillas-Acevedo L, Covarrubias AA, Amero C. Metal-binding polymorphism in late embryogenesis abundant protein AtLEA4-5, an intrinsically disordered protein. PeerJ 2018; 6:e4930. [PMID: 29892507 PMCID: PMC5994335 DOI: 10.7717/peerj.4930] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/18/2018] [Indexed: 12/22/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins accumulate in plants during adverse conditions and their main attributed function is to confer tolerance to stress. One of the deleterious effects of the adverse environment is the accumulation of metal ions to levels that generate reactive oxygen species, compromising the survival of cells. AtLEA4-5, a member of group 4 of LEAs in Arabidopsis, is an intrinsically disordered protein. It has been shown that their N-terminal region is able to undergo transitions to partially folded states and prevent the inactivation of enzymes. We have characterized metal ion binding to AtLEA4-5 by circular dichroism, electronic absorbance spectroscopy (UV–vis), electron paramagnetic resonance, dynamic light scattering, and isothermal titration calorimetry. The data shows that AtLEA4-5 contains a single binding site for Ni(II), while Zn(II) and Cu(II) have multiple binding sites and promote oligomerization. The Cu(II) interacts preferentially with histidine residues mostly located in the C-terminal region with moderate affinity and different coordination modes. These results and the lack of a stable secondary structure formation indicate that an ensemble of conformations remains accessible to the metal for binding, suggesting the formation of a fuzzy complex. Our results support the multifunctionality of LEA proteins and suggest that the C-terminal region of AtLEA4-5 could be responsible for antioxidant activity, scavenging metal ions under stress conditions while the N-terminal could function as a chaperone.
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Affiliation(s)
- Leidys French-Pacheco
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Cesar L Cuevas-Velazquez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Lina Rivillas-Acevedo
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carlos Amero
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
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176
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Zhu J, Zhou C, Caflisch A. Structure-based discovery of selective BRPF1 bromodomain inhibitors. Eur J Med Chem 2018; 155:337-352. [PMID: 29902720 DOI: 10.1016/j.ejmech.2018.05.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/05/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022]
Abstract
Bromodomain and plant homeodomain (PHD) finger containing protein 1 (BRPF1) is a member of subfamily IV of the human bromodomains. Experimental evidence suggests that BRPF1 is involved in leukemia. In a previous high-throughput docking campaign we identified several chemotypes targeting the BRPF1 bromodomain. Here, pharmacophore searches using the binding modes of two of these chemotypes resulted in two new series of ligands of the BRPF1 bromodomain. The 2,3-dioxo-quinoxaline 21 exhibits a 2-μM affinity for the BRPF1 bromodomain in two different competition binding assays, and more than 100-fold selectivity for BRPF1 against other members of subfamily IV and representatives of other subfamilies. Cellular activity is confirmed by a viability assay in a leukemia cell line. Isothermal titration calorimetry measurements reveal enthalpy-driven binding for compounds 21, 26 (KD = 3 μM), and the 2,4-dimethyl-oxazole derivative 42 (KD = 10 μM). Multiple molecular dynamics simulations and a dozen co-crystal structures at high resolution provide useful information for further optimization of affinity for the BRPF1 bromodomain.
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Affiliation(s)
- Jian Zhu
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Chunxian Zhou
- Department of Pathology, Shanghai University of Traditional Chinese Medicine, Cailun Road 1200, Pudong District, Shanghai, China
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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177
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Duvvuri H, Wheeler LC, Harms MJ. pytc: Open-Source Python Software for Global Analyses of Isothermal Titration Calorimetry Data. Biochemistry 2018; 57:2578-2583. [PMID: 29620867 PMCID: PMC5995568 DOI: 10.1021/acs.biochem.7b01264] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Here we describe pytc, an open-source Python package for global fits of thermodynamic models to multiple isothermal titration calorimetry experiments. Key features include simplicity, the ability to implement new thermodynamic models, a robust maximum likelihood fitter, a fast Bayesian Markov-Chain Monte Carlo sampler, rigorous implementation, extensive documentation, and full cross-platform compatibility. pytc fitting can be done using an application program interface or via a graphical user interface. It is available for download at https://github.com/harmslab/pytc .
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Affiliation(s)
- Hiranmayi Duvvuri
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Lucas C. Wheeler
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Michael J. Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
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178
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Macek P, Cliff MJ, Embrey KJ, Holdgate GA, Nissink JWM, Panova S, Waltho JP, Davies RA. Myc phosphorylation in its basic helix-loop-helix region destabilizes transient α-helical structures, disrupting Max and DNA binding. J Biol Chem 2018; 293:9301-9310. [PMID: 29695509 DOI: 10.1074/jbc.ra118.002709] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/16/2018] [Indexed: 01/01/2023] Open
Abstract
Myelocytomatosis proto-oncogene transcription factor (Myc) is an intrinsically disordered protein with critical roles in cellular homeostasis and neoplastic transformation. It is tightly regulated in the cell, with Myc phosphorylation playing a major role. In addition to the well-described tandem phosphorylation of Thr-52 and Ser-62 in the Myc transactivation domain linked to its degradation, P21 (RAC1)-activated kinase 2 (PAK2)-mediated phosphorylation of serine and threonine residues in the C-terminal basic helix-loop-helix leucine zipper (bHLH-LZ) region regulates Myc transcriptional activity. Here we report that PAK2 preferentially phosphorylates Myc twice, at Thr-358 and Ser-373, with only a minor fraction being modified at the previously identified Thr-400 site. For transcriptional activity, Myc binds E-box DNA elements, requiring its heterodimerization with Myc-associated factor X (Max) via the bHLH-LZ regions. Using isothermal calorimetry (ITC), we found that Myc phosphorylation destabilizes this ternary protein-DNA complex by decreasing Myc's affinity for Max by 2 orders of magnitude, suggesting a major effect of phosphorylation on this complex. Phosphomimetic substitutions revealed that Ser-373 dominates the effect on Myc-Max heterodimerization. Moreover, a T400D substitution disrupted Myc's affinity for Max. ITC, NMR, and CD analyses of several Myc variants suggested that the effect of phosphorylation on the Myc-Max interaction is caused by secondary structure disruption during heterodimerization rather than by a change in the structurally disordered state of Myc or by phosphorylation-induced electrostatic repulsion in the heterodimer. Our findings provide critical insights into the effects of PAK2-catalyzed phosphorylation of Myc on its interactions with Max and DNA.
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Affiliation(s)
- Pavel Macek
- From AstraZeneca, IMED Discovery Sciences, Alderley Park SK10 4TG, United Kingdom,
| | - Matthew J Cliff
- the Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Kevin J Embrey
- AstraZeneca, IMED Discovery Sciences, Cambridge CB4 0WG, United Kingdom
| | | | | | - Stanislava Panova
- the Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Jonathan P Waltho
- the Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rick A Davies
- From AstraZeneca, IMED Discovery Sciences, Alderley Park SK10 4TG, United Kingdom,
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179
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Dada O, Gutowski S, Brautigam CA, Chen Z, Sternweis PC. Direct regulation of p190RhoGEF by activated Rho and Rac GTPases. J Struct Biol 2018; 202:13-24. [PMID: 29196061 PMCID: PMC5835413 DOI: 10.1016/j.jsb.2017.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/21/2017] [Accepted: 11/27/2017] [Indexed: 12/16/2022]
Abstract
Rho family GTPases regulate a wide range of cellular processes. This includes cellular dynamics where three subfamilies, Rho, Rac, and Cdc42, are known to regulate cell shape and migration though coordinate action. Activation of Rho proteins largely depends on Rho Guanine nucleotide Exchange Factors (RhoGEFs) through a catalytic Dbl homology (DH) domain linked to a pleckstrin homology (PH) domain that subserves various functions. The PH domains from Lbc RhoGEFs, which specifically activate RhoA, have been shown to bind to activated RhoA. Here, p190RhoGEF is shown to also bind Rac1·GTP. Crystal structures reveal that activated Rac1 and RhoA use their effector-binding surfaces to associate with the same hydrophobic surface on the PH domain. Both activated RhoA and Rac1 can stimulate exchange of nucleotide on RhoA by localization of p190RhoGEF to its substrate, RhoA·GDP, in vitro. The binding of activated RhoA provides a mechanism for positive feedback regulation as previously proposed for the family of Lbc RhoGEFs. In contrast, the novel interaction between activated Rac1 and p190RhoGEF reveals a potential mechanism for cross-talk regulation where Rac can directly effect stimulation of RhoA. The greater capacity of Rac1 to stimulate p190RhoGEF among the Lbc RhoGEFs suggests functional specialization.
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Affiliation(s)
- Olugbenga Dada
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
| | - Stephen Gutowski
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
| | - Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA; Department of Microbiology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
| | - Zhe Chen
- Department of Biophysics, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
| | - Paul C Sternweis
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
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180
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Structural basis of mammalian glycan targeting by Vibrio cholerae cytolysin and biofilm proteins. PLoS Pathog 2018; 14:e1006841. [PMID: 29432487 PMCID: PMC5825169 DOI: 10.1371/journal.ppat.1006841] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 02/23/2018] [Accepted: 12/21/2017] [Indexed: 11/19/2022] Open
Abstract
Vibrio cholerae is an aquatic gram-negative microbe responsible for cholera, a pandemic disease causing life-threatening diarrheal outbreaks in populations with limited access to health care. Like most pathogenic bacteria, V. cholerae secretes virulence factors to assist colonization of human hosts, several of which bind carbohydrate receptors found on cell-surfaces. Understanding how pathogenic virulence proteins specifically target host cells is important for the development of treatment strategies to fight bacterial infections. Vibrio cholerae cytolysin (VCC) is a secreted pore-forming toxin with a carboxy-terminal β-prism domain that targets complex N-glycans found on mammalian cell-surface proteins. To investigate glycan selectivity, we studied the VCC β-prism domain and two additional β-prism domains found within the V. cholerae biofilm matrix protein RbmC. We show that the two RbmC β-prism domains target a similar repertoire of complex N-glycan receptors as VCC and find through binding and modeling studies that a branched pentasaccharide core (GlcNAc2-Man3) represents the likely footprint interacting with these domains. To understand the structural basis of V. cholerae β-prism selectivity, we solved high-resolution crystal structures of fragments of the pentasaccharide core bound to one RbmC β-prism domain and conducted mutagenesis experiments on the VCC toxin. Our results highlight a common strategy for cell-targeting utilized by both toxin and biofilm matrix proteins in Vibrio cholerae and provide a structural framework for understanding the specificity for individual receptors. Our results suggest that a common strategy for disrupting carbohydrate interactions could affect multiple virulence factors produced by V. cholerae, as well as similar β-prism domains found in other vibrio pathogens.
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181
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Yalçin E, Matković M, Jukić M, Obrovac LG, Piantanida I, Seferoğlu Z. Novel fluorene/fluorenone DNA and RNA binders as efficient non-toxic ds-RNA selective fluorescent probes. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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182
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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] [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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183
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Pflüger T, Hernández CF, Lewe P, Frank F, Mertens H, Svergun D, Baumstark MW, Lunin VY, Jetten MSM, Andrade SLA. Signaling ammonium across membranes through an ammonium sensor histidine kinase. Nat Commun 2018; 9:164. [PMID: 29323112 PMCID: PMC5764959 DOI: 10.1038/s41467-017-02637-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/15/2017] [Indexed: 01/07/2023] Open
Abstract
Sensing and uptake of external ammonium is essential for anaerobic ammonium-oxidizing (anammox) bacteria, and is typically the domain of the ubiquitous Amt/Rh ammonium transporters. Here, we report on the structure and function of an ammonium sensor/transducer from the anammox bacterium "Candidatus Kuenenia stuttgartiensis" that combines a membrane-integral ammonium transporter domain with a fused histidine kinase. It contains a high-affinity ammonium binding site not present in assimilatory Amt proteins. The levels of phosphorylated histidine in the kinase are coupled to the presence of ammonium, as conformational changes during signal recognition by the Amt module are transduced internally to modulate the kinase activity. The structural analysis of this ammonium sensor by X-ray crystallography and small-angle X-ray-scattering reveals a flexible, bipartite system that recruits a large uptake transporter as a sensory module and modulates its functionality to achieve a mechanistic coupling to a kinase domain in order to trigger downstream signaling events.
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Affiliation(s)
- Tobias Pflüger
- Institute for Biochemistry, University of Freiburg, Albertstr. 21, Freiburg, 79104, Germany
| | - Camila F Hernández
- Institute for Biochemistry, University of Freiburg, Albertstr. 21, Freiburg, 79104, Germany
| | - Philipp Lewe
- Institute for Biochemistry, University of Freiburg, Albertstr. 21, Freiburg, 79104, Germany
| | - Fabian Frank
- Institute for Biochemistry, University of Freiburg, Albertstr. 21, Freiburg, 79104, Germany
| | - Haydyn Mertens
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestr. 85, Hamburg, D-22603, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestr. 85, Hamburg, D-22603, Germany
| | - Manfred W Baumstark
- Center for Medicine, Institute for Exercise and Occupational Medicine, Medical Center, University of Freiburg, Hugstetterstr. 55, Freiburg, 79106, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany
| | - Vladimir Y Lunin
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Vitkevicha str. 1, Pushchino, 142290, Russia
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Institute for Water and Wetland Research, Heyendaalseweg 135, Nijmegen, NL-6525 AJ, The Netherlands
| | - Susana L A Andrade
- Institute for Biochemistry, University of Freiburg, Albertstr. 21, Freiburg, 79104, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, Freiburg, 79104, Germany.
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184
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Šmidlehner T, Piantanida I, Pescitelli G. Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids - tutorial. Beilstein J Org Chem 2018; 14:84-105. [PMID: 29441133 PMCID: PMC5789433 DOI: 10.3762/bjoc.14.5] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/13/2017] [Indexed: 01/19/2023] Open
Abstract
The structural characterization of non-covalent complexes between nucleic acids and small molecules (ligands) is of a paramount significance to bioorganic research. Highly informative methods about nucleic acid/ligand complexes such as single crystal X-ray diffraction or NMR spectroscopy cannot be performed under biologically compatible conditions and are extensively time consuming. Therefore, in search for faster methods which can be applied to conditions that are at least similar to the naturally occurring ones, a set of polarization spectroscopy methods has shown highly promising results. Electronic circular dichroism (ECD) is the most commonly used method for the characterization of the helical structure of DNA and RNA and their complexes with ligands. Less common but complementary to ECD, is flow-oriented linear dichroism (LD). Other methods such as vibrational CD (VCD) and emission-based methods (FDCD, CPL), can also be used for suitable samples. Despite the popularity of polarization spectroscopy in biophysics, aside several highly focused reviews on the application of these methods to DNA/RNA research, there is no systematic tutorial covering all mentioned methods as a tool for the characterization of adducts between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably.
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Affiliation(s)
- Tamara Šmidlehner
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute; P. O. Box 180, 10002 Zagreb, Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute; P. O. Box 180, 10002 Zagreb, Croatia
| | - Gennaro Pescitelli
- Department of Chemistry, University of Pisa, via Moruzzi 13, Pisa, Italy
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185
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Abstract
NMR spectroscopy and other solution methods are increasingly being used to obtain novel insights into the mechanisms by which MAPK regulatory proteins bind and direct the activity of MAPKs. Here, we describe how interactions between the MAPK p38α and its regulatory proteins are studied using NMR spectroscopy, isothermal titration calorimetry, and small angle X-ray scattering (SAXS).
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Affiliation(s)
- Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, 02912, USA. .,Department of Chemistry, Brown University, Providence, RI, 02912, USA.
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
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186
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Tellinghuisen J. Can you trust the parametric standard errors in nonlinear least squares? Yes, with provisos. Biochim Biophys Acta Gen Subj 2017; 1862:886-894. [PMID: 29289616 DOI: 10.1016/j.bbagen.2017.12.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 12/14/2017] [Accepted: 12/27/2017] [Indexed: 11/18/2022]
Abstract
BACKGROUND Questions about the reliability of parametric standard errors (SEs) from nonlinear least squares (LS) algorithms have led to a general mistrust of these precision estimators that is often unwarranted. METHODS The importance of non-Gaussian parameter distributions is illustrated by converting linear models to nonlinear by substituting eA, ln A, and 1/A for a linear parameter a. Monte Carlo (MC) simulations characterize parameter distributions in more complex cases, including when data have varying uncertainty and should be weighted, but weights are neglected. This situation leads to loss of precision and erroneous parametric SEs, as is illustrated for the Lineweaver-Burk analysis of enzyme kinetics data and the analysis of isothermal titration calorimetry data. RESULTS Non-Gaussian parameter distributions are generally asymmetric and biased. However, when the parametric SE is <10% of the magnitude of the parameter, both the bias and the asymmetry can usually be ignored. Sometimes nonlinear estimators can be redefined to give more normal distributions and better convergence properties. CONCLUSION Variable data uncertainty, or heteroscedasticity, can sometimes be handled by data transforms but more generally requires weighted LS, which in turn require knowledge of the data variance. GENERAL SIGNIFICANCE Parametric SEs are rigorously correct in linear LS under the usual assumptions, and are a trustworthy approximation in nonlinear LS provided they are sufficiently small - a condition favored by the abundant, precise data routinely collected in many modern instrumental methods.
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Affiliation(s)
- Joel Tellinghuisen
- Department of Chemistry, Vanderbilt University Nashville, TN 37235, USA.
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187
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Wheeler LC, Harms MJ. Human S100A5 binds Ca 2+ and Cu 2+ independently. BMC BIOPHYSICS 2017; 10:8. [PMID: 29201357 PMCID: PMC5700546 DOI: 10.1186/s13628-017-0040-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/08/2017] [Indexed: 12/21/2022]
Abstract
Background S100A5 is a calcium binding protein found in a small subset of amniote tissues. Little is known about the biological roles of S100A5, but it may be involved in inflammation and olfactory signaling. Previous work indicated that S100A5 displays antagonism between binding of Ca2+ and Cu2+ ions-one of the most commonly cited features of the protein. We set out to characterize the interplay between Ca2+ and Cu2+ binding by S100A5 using isothermal titration calorimetry (ITC), circular dichroism spectroscopy (CD), and analytical ultracentrifugation (AUC). Results We found that human S100A5 is capable of binding both Cu2+ and Ca2+ ions simultaneously. The wildtype protein was extremely aggregation-prone in the presence of Cu2+ and Ca2+. A Cys-free version of S100A5, however, was not prone to precipitation or oligomerization. Mutation of the cysteines does not disrupt the binding of either Ca2+ or Cu2+ to S100A5. In the Cys-free background, we measured Ca2+ and Cu2+ binding in the presence and absence of the other metal using ITC. Saturating concentrations of Ca2+ or Cu2+ do not disrupt the binding of one another. Ca2+ and Cu2+ binding induce structural changes in S100A5, which are measurable using CD spectroscopy. We show via sedimentation velocity AUC that the wildtype protein is prone to the formation of soluble oligomers, which are not present in Cys-free samples. Conclusions S100A5 can bind Ca2+ and Cu2+ ions simultaneously and independently. This observation is in direct contrast to previously-reported antagonism between binding of Cu2+ and Ca2+ ions. The previous result is likely due to metal-dependent aggregation. Little is known about the biology of S100A5, so an accurate understanding of the biochemistry is necessary to make informed biological hypotheses. Our observations suggest the possibility of independent biological functions for Cu2+ and Ca2+ binding by S100A5.
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Affiliation(s)
- Lucas C Wheeler
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, 97403 OR USA.,Insitute of Molecular Biology, University of Oregon, Eugene, 97403 OR USA
| | - Michael J Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, 97403 OR USA.,Insitute of Molecular Biology, University of Oregon, Eugene, 97403 OR USA
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188
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Bae SJ, Ni L, Osinski A, Tomchick DR, Brautigam CA, Luo X. SAV1 promotes Hippo kinase activation through antagonizing the PP2A phosphatase STRIPAK. eLife 2017; 6:30278. [PMID: 29063833 PMCID: PMC5663475 DOI: 10.7554/elife.30278] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 10/22/2017] [Indexed: 11/15/2022] Open
Abstract
The Hippo pathway controls tissue growth and homeostasis through a central MST-LATS kinase cascade. The scaffold protein SAV1 promotes the activation of this kinase cascade, but the molecular mechanisms remain unknown. Here, we discover SAV1-mediated inhibition of the PP2A complex STRIPAKSLMAP as a key mechanism of MST1/2 activation. SLMAP binding to autophosphorylated MST2 linker recruits STRIPAK and promotes PP2A-mediated dephosphorylation of MST2 at the activation loop. Our structural and biochemical studies reveal that SAV1 and MST2 heterodimerize through their SARAH domains. Two SAV1–MST2 heterodimers further dimerize through SAV1 WW domains to form a heterotetramer, in which MST2 undergoes trans-autophosphorylation. SAV1 directly binds to STRIPAK and inhibits its phosphatase activity, protecting MST2 activation-loop phosphorylation. Genetic ablation of SLMAP in human cells leads to spontaneous activation of the Hippo pathway and alleviates the need for SAV1 in Hippo signaling. Thus, SAV1 promotes Hippo activation through counteracting the STRIPAKSLMAP PP2A phosphatase complex.
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Affiliation(s)
- Sung Jun Bae
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Lisheng Ni
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Adam Osinski
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xuelian Luo
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
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189
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Hayoz S, Tiwari PB, Piszczek G, Üren A, Brelidze TI. Investigating cyclic nucleotide and cyclic dinucleotide binding to HCN channels by surface plasmon resonance. PLoS One 2017; 12:e0185359. [PMID: 28950029 PMCID: PMC5614581 DOI: 10.1371/journal.pone.0185359] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/11/2017] [Indexed: 11/19/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels control cardiac and neuronal rhythmicity. HCN channels contain cyclic nucleotide-binding domain (CNBD) in their C-terminal region linked to the pore-forming transmembrane segment with a C-linker. The C-linker couples the conformational changes caused by the direct binding of cyclic nucleotides to the HCN pore opening. Recently, cyclic dinucleotides were shown to antagonize the effect of cyclic nucleotides in HCN4 but not in HCN2 channels. Based on the structural analysis and mutational studies it has been proposed that cyclic dinucleotides affect HCN4 channels by binding to the C-linker pocket (CLP). Here, we first show that surface plasmon resonance (SPR) can be used to accurately measure cyclic nucleotide binding affinity to the C-linker/CNBD of HCN2 and HCN4 channels. We then used SPR to investigate cyclic dinucleotide binding in HCN channels. To our surprise, we detected no binding of cyclic dinucleotides to the isolated monomeric C-linker/CNBDs of HCN4 channels with SPR. The binding of cyclic dinucleotides was further examined with isothermal calorimetry (ITC), which indicated no binding of cyclic dinucleotides to both monomeric and tetrameric C-linker/CNBDs of HCN4 channels. Taken together, our results suggest that interaction of the C-linker/CNBD with other parts of the channel is necessary for cyclic-dinucleotide binding in HCN4 channels.
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Affiliation(s)
- Sebastien Hayoz
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Purushottam B. Tiwari
- Department of Oncology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Grzegorz Piszczek
- Biophysics Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Aykut Üren
- Department of Oncology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Tinatin I. Brelidze
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC, United States of America
- * E-mail:
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190
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Gabel SA, Duff MR, Pedersen LC, DeRose EF, Krahn JM, Howell EE, London RE. A Structural Basis for Biguanide Activity. Biochemistry 2017; 56:4786-4798. [PMID: 28766937 PMCID: PMC5740485 DOI: 10.1021/acs.biochem.7b00619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metformin is the most commonly prescribed treatment for type II diabetes and related disorders; however, molecular insights into its mode(s) of action have been limited by an absence of structural data. Structural considerations along with a growing body of literature demonstrating its effects on one-carbon metabolism suggest the possibility of folate mimicry and anti-folate activity. Motivated by the growing recognition that anti-diabetic biguanides may act directly upon the gut microbiome, we have determined structures of the complexes formed between the anti-diabetic biguanides (phenformin, buformin, and metformin) and Escherichia coli dihydrofolate reductase (ecDHFR) based on nuclear magnetic resonance, crystallographic, and molecular modeling studies. Interligand Overhauser effects indicate that metformin can form ternary complexes with p-aminobenzoyl-l-glutamate (pABG) as well as other ligands that occupy the region of the folate-binding site that interacts with pABG; however, DHFR inhibition is not cooperative. The biguanides competitively inhibit the activity of ecDHFR, with the phenformin inhibition constant being 100-fold lower than that of metformin. This inhibition may be significant at concentrations present in the gut of treated individuals, and inhibition of DHFR in intestinal mucosal cells may also occur if accumulation levels are sufficient. Perturbation of folate homeostasis can alter the pyridine nucleotide redox ratios that are important regulators of cellular metabolism.
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Affiliation(s)
- Scott A. Gabel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | - Michael R. Duff
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Lars C. Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | - Eugene F. DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | | | - Elizabeth E. Howell
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Robert E. London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
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191
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Arnott ZLP, Nozaki S, Monteiro DCF, Morgan HE, Pearson AR, Niki H, Webb ME. The Mechanism of Regulation of Pantothenate Biosynthesis by the PanD-PanZ·AcCoA Complex Reveals an Additional Mode of Action for the Antimetabolite N-Pentyl Pantothenamide (N5-Pan). Biochemistry 2017; 56:4931-4939. [PMID: 28832133 PMCID: PMC5724930 DOI: 10.1021/acs.biochem.7b00509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
antimetabolite pentyl pantothenamide has broad spectrum antibiotic
activity but exhibits enhanced activity against Escherichia
coli. The PanDZ complex has been proposed to regulate the
pantothenate biosynthetic pathway in E. coli by limiting
the supply of β-alanine in response to coenzyme A concentration.
We show that formation of such a complex between activated aspartate
decarboxylase (PanD) and PanZ leads to sequestration of the pyruvoyl
cofactor as a ketone hydrate and demonstrate that both PanZ overexpression-linked
β-alanine auxotrophy and pentyl pantothenamide toxicity are
due to formation of this complex. This both demonstrates that the
PanDZ complex regulates pantothenate biosynthesis in a cellular context
and validates the complex as a target for antibiotic development.
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Affiliation(s)
- Zoe L P Arnott
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds , Leeds LS2 9JT, U.K.,Hamburg Center for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, University of Hamburg , Luruper Chaussee 149, Hamburg 22761, Germany
| | - Shingo Nozaki
- Microbial Genetics Laboratory, Genetics Strains Research Center, National Institute of Genetics , 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Diana C F Monteiro
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds , Leeds LS2 9JT, U.K.,Hamburg Center for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, University of Hamburg , Luruper Chaussee 149, Hamburg 22761, Germany
| | - Holly E Morgan
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds , Leeds LS2 9JT, U.K
| | - Arwen R Pearson
- Hamburg Center for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, University of Hamburg , Luruper Chaussee 149, Hamburg 22761, Germany
| | - Hironori Niki
- Microbial Genetics Laboratory, Genetics Strains Research Center, National Institute of Genetics , 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, Graduate University for Advanced Studies (Sokendai) , 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Michael E Webb
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds , Leeds LS2 9JT, U.K
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192
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Chaturvedi SK, Ma J, Zhao H, Schuck P. Use of fluorescence-detected sedimentation velocity to study high-affinity protein interactions. Nat Protoc 2017; 12:1777-1791. [PMID: 28771239 PMCID: PMC7466938 DOI: 10.1038/nprot.2017.064] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Sedimentation velocity (SV) analytical ultracentrifugation (AUC) is a classic technique for the real-time observation of free macromolecular migration in solution driven by centrifugal force. This enables the analysis of macromolecular mass, shape, size distribution, and interactions. Although traditionally limited to determination of the sedimentation coefficient and binding affinity of proteins in the micromolar range, the implementation of modern detection and data analysis techniques has resulted in marked improvements in detection sensitivity and size resolution during the past decades. Fluorescence optical detection now permits the detection of recombinant proteins with fluorescence excitation at 488 or 561 nm at low picomolar concentrations, allowing for the study of high-affinity protein self-association and hetero-association. Compared with other popular techniques for measuring high-affinity protein-protein interactions, such as biosensing or calorimetry, the high size resolution of complexes at picomolar concentrations obtained with SV offers a distinct advantage in sensitivity and flexibility of the application. Here, we present a basic protocol for carrying out fluorescence-detected SV experiments and the determination of the size distribution and affinity of protein-antibody complexes with picomolar KD values. Using an EGFP-nanobody interaction as a model, this protocol describes sample preparation, ultracentrifugation, data acquisition, and data analysis. A variation of the protocol applying traditional absorbance or an interference optical system can be used for protein-protein interactions in the micromolar KD value range. Sedimentation experiments typically take ∼3 h of preparation and 6-12 h of run time, followed by data analysis (typically taking 1-3 h).
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Affiliation(s)
- Sumit K. Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jia Ma
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
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193
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Krimmer SG, Cramer J, Schiebel J, Heine A, Klebe G. How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1′ Pocket of Thermolysin. J Am Chem Soc 2017; 139:10419-10431. [DOI: 10.1021/jacs.7b05028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Stefan G. Krimmer
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Jonathan Cramer
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Johannes Schiebel
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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194
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Cramer J, Krimmer SG, Heine A, Klebe G. Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors. J Med Chem 2017; 60:5791-5799. [DOI: 10.1021/acs.jmedchem.7b00490] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jonathan Cramer
- Institute of Pharmaceutical
Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Stefan G. Krimmer
- Institute of Pharmaceutical
Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Institute of Pharmaceutical
Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical
Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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195
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A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease. Nat Commun 2017; 8:14959. [PMID: 28466855 PMCID: PMC5418593 DOI: 10.1038/ncomms14959] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/16/2017] [Indexed: 11/09/2022] Open
Abstract
Human EXOG (hEXOG) is a 5′-exonuclease that is crucial for mitochondrial DNA repair; the enzyme belongs to a nonspecific nuclease family that includes the apoptotic endonuclease EndoG. Here we report biochemical and structural studies of hEXOG, including structures in its apo form and in a complex with DNA at 1.81 and 1.85 Å resolution, respectively. A Wing domain, absent in other ββα-Me members, suppresses endonuclease activity, but confers on hEXOG a strong 5′-dsDNA exonuclease activity that precisely excises a dinucleotide using an intrinsic ‘tape-measure'. The symmetrical apo hEXOG homodimer becomes asymmetrical upon binding to DNA, providing a structural basis for how substrate DNA bound to one active site allosterically regulates the activity of the other. These properties of hEXOG suggest a pathway for mitochondrial BER that provides an optimal substrate for subsequent gap-filling synthesis by DNA polymerase γ. Human EXOG is crucial for mitochondrial DNA repair. Here the authors present the crystal structures of hEXOG in apo form and as DNA complex and suggest a `tape-measure' activity to generate optimal substrates for mitochondrial base excision repair.
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196
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Ihms EC, Kleckner IR, Gollnick P, Foster MP. Mechanistic Models Fit to Variable Temperature Calorimetric Data Provide Insights into Cooperativity. Biophys J 2017; 112:1328-1338. [PMID: 28402876 DOI: 10.1016/j.bpj.2017.02.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/12/2017] [Accepted: 02/16/2017] [Indexed: 12/22/2022] Open
Abstract
Allostery pervades macromolecular function and drives cooperative binding of ligands to macromolecules. To decipher the mechanisms of cooperative ligand binding it is necessary to define at a microscopic level the structural and thermodynamic consequences of binding of each ligand to its allosterically coupled site(s). However, dynamic sampling of alternative conformations (microstates) in allosteric molecules complicates interpretation of both structural and thermodynamic data. Isothermal titration calorimetry has the potential to directly quantify the thermodynamics of allosteric interactions, but usually falls short of enabling mechanistic insight. This is because 1) its measurements reflect the sum of overlapping caloric processes involving binding-linked population shifts within and between microstates, and 2) data are generally fit with phenomenological binding polynomials that are underdetermined. Nevertheless, temperature-dependent binding data have the potential to resolve overlapping thermodynamic processes, while mechanistically constrained models enable hypothesis testing and identification of informative parameters. We globally fit temperature-dependent isothermal titration calorimetry data for binding of 11 tryptophan ligands to the homo-undecameric trp RNA-binding Attenuation Protein from Bacillus stearothermophilus using nearest-neighbor statistical thermodynamic models. This approach allowed us to distinguish alternative nearest-neighbor interaction models, and quantifies the thermodynamic contribution of neighboring ligands to individual binding sites. We also perform conventional Hill equation modeling and illustrate how comparatively limited it is in quantitative or mechanistic value. This work illustrates the potential of mechanistically constrained global fitting of binding data to yield the microscopic thermodynamic parameters essential for deciphering mechanisms of cooperativity in a wide range of ligand-regulated homo-oligomeric assemblies.
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Affiliation(s)
- Elihu C Ihms
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Ian R Kleckner
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio.
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197
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Structural basis of pH-dependent client binding by ERp44, a key regulator of protein secretion at the ER-Golgi interface. Proc Natl Acad Sci U S A 2017; 114:E3224-E3232. [PMID: 28373561 DOI: 10.1073/pnas.1621426114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ERp44 retrieves some endoplasmic reticulum (ER)-resident enzymes and immature oligomers of secretory proteins from the Golgi. Association of ERp44 with its clients is regulated by pH-dependent mechanisms, but the molecular details are not fully understood. Here we report high-resolution crystal structures of human ERp44 at neutral and weakly acidic pH. These structures reveal key regions in the C-terminal tail (C tail) missing in the original crystal structure, including a regulatory histidine-rich region and a subsequent extended loop. The former region forms a short α-helix (α16), generating a histidine-clustered site (His cluster). At low pH, the three Trx-like domains of ERp44 ("a," "b," and "b'") undergo significant rearrangements, likely induced by protonation of His157 located at the interface between the a and b domains. The α16-helix is partially unwound and the extended loop is disordered in weakly acidic conditions, probably due to electrostatic repulsion between the protonated histidines in the His cluster. Molecular dynamics simulations indicated that helix unwinding enhances the flexibility of the C tail, disrupting its normal hydrogen-bonding pattern. The observed pH-dependent conformational changes significantly enlarge the positively charged regions around the client-binding site of ERp44 at low pH. Mutational analyses showed that ERp44 forms mixed disulfides with specific cysteines residing on negatively charged loop regions of Ero1α. We propose that the protonation states of the essential histidines regulate the ERp44-client interaction by altering the C-tail dynamics and surface electrostatic potential of ERp44.
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198
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Lee YTC, Chang CY, Chen SY, Pan YR, Ho MR, Hsu STD. Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome. Sci Rep 2017; 7:45174. [PMID: 28338014 PMCID: PMC5364529 DOI: 10.1038/srep45174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/20/2017] [Indexed: 02/07/2023] Open
Abstract
Human ubiquitin C-terminal hydrolyase UCH-L5 is a topologically knotted deubiquitinase that is activated upon binding to the proteasome subunit Rpn13. The length of its intrinsically disordered cross-over loop is essential for substrate recognition. Here, we showed that the catalytic domain of UCH-L5 exhibits higher equilibrium folding stability with an unfolding rate on the scale of 10−8 s−1, over four orders of magnitudes slower than its paralogs, namely UCH-L1 and -L3, which have shorter cross-over loops. NMR relaxation dynamics analysis confirmed the intrinsic disorder of the cross-over loop. Hydrogen deuterium exchange analysis further revealed a positive correlation between the length of the cross-over loop and the degree of local fluctuations, despite UCH-L5 being thermodynamically and kinetically more stable than the shorter UCHs. Considering the role of UCH-L5 in removing K48-linked ubiquitin to prevent proteasomal degradation of ubiquitinated substrates, our findings offered mechanistic insights into the evolution of UCH-L5. Compared to its paralogs, it is entropically stabilized to withstand mechanical unfolding by the proteasome while maintaining structural plasticity. It can therefore accommodate a broad range of substrate geometries at the cost of unfavourable entropic loss.
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Affiliation(s)
- Yun-Tzai Cloud Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
| | - Chia-Yun Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
| | - Szu-Yu Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun-Ru Pan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
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199
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Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain. Sci Rep 2017; 7:44115. [PMID: 28327560 PMCID: PMC5361163 DOI: 10.1038/srep44115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 02/06/2017] [Indexed: 01/02/2023] Open
Abstract
Biomass waste products from green algae have recently been given new life, as these polysaccharides have potential applications in industry, agriculture, and medicine. One such polysaccharide group called ulvans displays many different, potentially useful properties that arise from their structural versatility. Hence, performing structural analyses on ulvan is crucial for future applications. However, chemical reaction–based analysis methods cannot fully characterize ulvan and tend to alter its structure. Thus, better methods require well-characterized ulvan-degrading enzymes. Therefore, we analysed a previously sequenced ulvan lyase (GenebankTM reference number JN104480) and characterized its domains. We suggest that the enzyme consists of a shorter than previously described catalytic domain, a newly identified substrate binding domain, and a C-terminal type 9 secretion system signal peptide. By separately expressing the two domains in E. coli, we confirmed that the binding domain is ulvan specific, having higher affinity for ulvan than most lectins for their ligands (affinity constant: 105 M−1). To our knowledge, this is the first description of an ulvan-binding domain. Overall, identifying this new binding domain is one step towards engineering ulvan enzymes that can be used to characterize ulvan, e.g. through enzymatic/mass spectrometric fingerprinting analyses, and help unlock its full potential.
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200
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Soufari H, Mackereth CD. Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family. RNA (NEW YORK, N.Y.) 2017; 23:308-316. [PMID: 28003515 PMCID: PMC5311487 DOI: 10.1261/rna.059733.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/19/2016] [Indexed: 05/16/2023]
Abstract
Precise regulation of mRNA processing, translation, localization, and stability relies on specific interactions with RNA-binding proteins whose biological function and target preference are dictated by their preferred RNA motifs. The RBPMS family of RNA-binding proteins is defined by a conserved RNA recognition motif (RRM) domain found in metazoan RBPMS/Hermes and RBPMS2, Drosophila couch potato, and MEC-8 from Caenorhabditis elegans In order to determine the parameters of RNA sequence recognition by the RBPMS family, we have first used the N-terminal domain from MEC-8 in binding assays and have demonstrated a preference for two GCAC motifs optimally separated by >6 nucleotides (nt). We have also determined the crystal structure of the dimeric N-terminal RRM domain from MEC-8 in the unbound form, and in complex with an oligonucleotide harboring two copies of the optimal GCAC motif. The atomic details reveal the molecular network that provides specificity to all four bases in the motif, including multiple hydrogen bonds to the initial guanine. Further studies with human RBPMS, as well as Drosophila couch potato, confirm a general preference for this double GCAC motif by other members of the protein family and the presence of this motif in known targets.
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Affiliation(s)
- Heddy Soufari
- University of Bordeaux, Institut Européen de Chimie et Biologie, F-33607 Pessac, France
- Inserm U1212, CNRS UMR 5320, ARNA Laboratory, F-33076 Bordeaux, France
| | - Cameron D Mackereth
- University of Bordeaux, Institut Européen de Chimie et Biologie, F-33607 Pessac, France
- Inserm U1212, CNRS UMR 5320, ARNA Laboratory, F-33076 Bordeaux, France
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