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Fields JK, Gyllenbäck EJ, Bogacz M, Obi J, Birkedal GS, Sjöström K, Maravillas K, Grönberg C, Rattik S, Kihn K, Flowers M, Smith AK, Hansen N, Fioretos T, Huyhn C, Liberg D, Deredge D, Sundberg EJ. Antibodies targeting the shared cytokine receptor IL-1 receptor accessory protein invoke distinct mechanisms to block all cytokine signaling. Cell Rep 2024:114099. [PMID: 38636519 DOI: 10.1016/j.celrep.2024.114099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/24/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Interleukin-1 (IL-1)-family cytokines are potent modulators of inflammation, coordinating a vast array of immunological responses across innate and adaptive immune systems. Dysregulated IL-1-family cytokine signaling, however, is involved in a multitude of adverse health effects, such as chronic inflammatory conditions, autoimmune diseases, and cancer. Within the IL-1 family of cytokines, six-IL-1α, IL-1β, IL-33, IL-36α, IL-36β, and IL-36γ-require the IL-1 receptor accessory protein (IL-1RAcP) as their shared co-receptor. Common features of cytokine signaling include redundancy of signaling pathways, sharing of cytokines and receptors, pleiotropy of the cytokines themselves, and multifaceted immune responses. Accordingly, targeting multiple cytokines simultaneously is an emerging therapeutic strategy and can provide advantages over targeting a single cytokine pathway. Here, we show that two monoclonal antibodies, CAN10 and 3G5, which target IL-1RAcP for broad blockade of all associated cytokines, do so through distinct mechanisms and provide therapeutic opportunities for the treatment of inflammatory diseases.
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Affiliation(s)
- James K Fields
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | | | - Marek Bogacz
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Juliet Obi
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | | | | | - Kino Maravillas
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | | - Kyle Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Maria Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ally K Smith
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Nils Hansen
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Chau Huyhn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
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2
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Klontz E, Obi JO, Wang Y, Glendening G, Carr J, Tsibouris C, Buddula S, Nallar S, Soares AS, Beckett D, Redzic JS, Eisenmesser E, Palm C, Schmidt K, Scudder AH, Obiorah T, Essuman K, Milbrandt J, Diantonio A, Ray K, Snyder MLD, Deredge D, Snyder GA. The structure of NAD + consuming protein Acinetobacter baumannii TIR domain shows unique kinetics and conformations. J Biol Chem 2023; 299:105290. [PMID: 37758001 PMCID: PMC10641520 DOI: 10.1016/j.jbc.2023.105290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Toll-like and interleukin-1/18 receptor/resistance (TIR) domain-containing proteins function as important signaling and immune regulatory molecules. TIR domain-containing proteins identified in eukaryotic and prokaryotic species also exhibit NAD+ hydrolase activity in select bacteria, plants, and mammalian cells. We report the crystal structure of the Acinetobacter baumannii TIR domain protein (AbTir-TIR) with confirmed NAD+ hydrolysis and map the conformational effects of its interaction with NAD+ using hydrogen-deuterium exchange-mass spectrometry. NAD+ results in mild decreases in deuterium uptake at the dimeric interface. In addition, AbTir-TIR exhibits EX1 kinetics indicative of large cooperative conformational changes, which are slowed down upon substrate binding. Additionally, we have developed label-free imaging using the minimally invasive spectroscopic method 2-photon excitation with fluorescence lifetime imaging, which shows differences in bacteria expressing native and mutant NAD+ hydrolase-inactivated AbTir-TIRE208A protein. Our observations are consistent with substrate-induced conformational changes reported in other TIR model systems with NAD+ hydrolase activity. These studies provide further insight into bacterial TIR protein mechanisms and their varying roles in biology.
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Affiliation(s)
- Erik Klontz
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Juliet O Obi
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Yajing Wang
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA; Department of Physiology, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Gabrielle Glendening
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Jahid Carr
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Constantine Tsibouris
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Sahthi Buddula
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Shreeram Nallar
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA; Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Alexei S Soares
- Brookhaven National Laboratory, National Synchrotron Light Source II, Structural Biology Program, Upton, New York, USA
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado, USA
| | - Elan Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado, USA
| | - Cheyenne Palm
- Department of Biological Sciences, Towson University, Towson, Maryland, USA
| | - Katrina Schmidt
- Department of Biological Sciences, Towson University, Towson, Maryland, USA
| | - Alexis H Scudder
- Department of Biological Sciences, Towson University, Towson, Maryland, USA
| | - Trinity Obiorah
- Department of Biological Sciences, Towson University, Towson, Maryland, USA
| | - Kow Essuman
- Department of Developmental Biology, Washington University School of Medicine, St Louis, Missouri, USA; Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jeffrey Milbrandt
- Department of Developmental Biology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Aaron Diantonio
- Department of Developmental Biology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA; Department of Biochemistry and Molecular Biology at the University of Maryland, School of Medicine, Baltimore, Maryland, USA
| | | | - Daniel Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Greg A Snyder
- Division of Vaccine Research, Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, Maryland, USA; Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA.
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3
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Smith CN, Kihn K, Williamson ZA, Chow KM, Hersh LB, Korotkov KV, Deredge D, Blackburn JS. Development and characterization of nanobodies that specifically target the oncogenic Phosphatase of Regenerating Liver-3 (PRL-3) and impact its interaction with a known binding partner, CNNM3. PLoS One 2023; 18:e0285964. [PMID: 37220097 DOI: 10.1371/journal.pone.0285964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Phosphatase of Regenerating Liver-3 (PRL-3) is associated with cancer progression and metastasis. The mechanisms that drive PRL-3's oncogenic functions are not well understood, partly due to a lack of research tools available to study this protein. We have begun to address these issues by developing alpaca-derived single domain antibodies, or nanobodies, targeting PRL-3 with a KD of 30-300 nM and no activity towards highly homologous family members PRL-1 and PRL-2. We found that longer and charged N-terminal tags on PRL-3, such as GFP and FLAG, changed PRL-3 localization compared to untagged protein, indicating that the nanobodies may provide new insights into PRL-3 trafficking and function. The nanobodies perform equally, if not better, than commercially available antibodies in immunofluorescence and immunoprecipitation. Finally, hydrogen-deuterium exchange mass spectrometry (HDX-MS) showed that the nanobodies bind partially within the PRL-3 active site and can interfere with PRL-3 phosphatase activity. Co-immunoprecipitation with a known PRL-3 active site binding partner, the CBS domain of metal transporter CNNM3, showed that the nanobodies reduced the amount of PRL-3:CBS inter-action. The potential of blocking this interaction is highly relevant in cancer, as multiple research groups have shown that PRL-3 binding to CNNM proteins is sufficient to promote metastatic growth in mouse models. The anti-PRL-3 nanobodies represent an important expansion of the research tools available to study PRL-3 function and can be used to define the role of PRL-3 in cancer progression.
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Affiliation(s)
- Caroline N Smith
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
- University of Kentucky Markey Cancer Center, Lexington, Kentucky, United States of America
| | - Kyle Kihn
- University of Maryland School of Pharmacy, Baltimore, Maryland, United States of America
| | - Zachary A Williamson
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - K Martin Chow
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Louis B Hersh
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Konstantin V Korotkov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Daniel Deredge
- University of Maryland School of Pharmacy, Baltimore, Maryland, United States of America
| | - Jessica S Blackburn
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
- University of Kentucky Markey Cancer Center, Lexington, Kentucky, United States of America
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4
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Kaur U, Kihn KC, Ke H, Kuo W, Gierasch LM, Hebert DN, Wintrode PL, Deredge D, Gershenson A. The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control. bioRxiv 2023:2023.04.24.537978. [PMID: 37163105 PMCID: PMC10168285 DOI: 10.1101/2023.04.24.537978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many multi-domain proteins including the serpin family of serine protease inhibitors contain non-sequential domains composed of regions that are far apart in sequence. Because proteins are translated vectorially from N- to C-terminus, such domains pose a particular challenge: how to balance the conformational lability necessary to form productive interactions between early and late translated regions while avoiding aggregation. This balance is mediated by the protein sequence properties and the interactions of the folding protein with the cellular quality control machinery. For serpins, particularly α 1 -antitrypsin (AAT), mutations often lead to polymer accumulation in cells and consequent disease suggesting that the lability/aggregation balance is especially precarious. Therefore, we investigated the properties of progressively longer AAT N-terminal fragments in solution and in cells. The N-terminal subdomain, residues 1-190 (AAT190), is monomeric in solution and efficiently degraded in cells. More β -rich fragments, 1-290 and 1-323, form small oligomers in solution, but are still efficiently degraded, and even the polymerization promoting Siiyama (S53F) mutation did not significantly affect fragment degradation. In vitro, the AAT190 region is among the last regions incorporated into the final structure. Hydrogen-deuterium exchange mass spectrometry and enhanced sampling molecular dynamics simulations show that AAT190 has a broad, dynamic conformational ensemble that helps protect one particularly aggregation prone β -strand from solvent. These AAT190 dynamics result in transient exposure of sequences that are buried in folded, full-length AAT, which may provide important recognition sites for the cellular quality control machinery and facilitate degradation and, under favorable conditions, reduce the likelihood of polymerization.
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Affiliation(s)
- Upneet Kaur
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Kyle C. Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Haiping Ke
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Weiwei Kuo
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Daniel N. Hebert
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Anne Gershenson
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
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5
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Trastoy B, Du JJ, Cifuente JO, Rudolph L, García-Alija M, Klontz EH, Deredge D, Sultana N, Huynh CG, Flowers MW, Li C, Sastre DE, Wang LX, Corzana F, Mallagaray A, Sundberg EJ, Guerin ME. Mechanism of antibody-specific deglycosylation and immune evasion by Streptococcal IgG-specific endoglycosidases. Nat Commun 2023; 14:1705. [PMID: 36973249 PMCID: PMC10042849 DOI: 10.1038/s41467-023-37215-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
Bacterial pathogens have evolved intricate mechanisms to evade the human immune system, including the production of immunomodulatory enzymes. Streptococcus pyogenes serotypes secrete two multi-modular endo-β-N-acetylglucosaminidases, EndoS and EndoS2, that specifically deglycosylate the conserved N-glycan at Asn297 on IgG Fc, disabling antibody-mediated effector functions. Amongst thousands of known carbohydrate-active enzymes, EndoS and EndoS2 represent just a handful of enzymes that are specific to the protein portion of the glycoprotein substrate, not just the glycan component. Here, we present the cryoEM structure of EndoS in complex with the IgG1 Fc fragment. In combination with small-angle X-ray scattering, alanine scanning mutagenesis, hydrolytic activity measurements, enzyme kinetics, nuclear magnetic resonance and molecular dynamics analyses, we establish the mechanisms of recognition and specific deglycosylation of IgG antibodies by EndoS and EndoS2. Our results provide a rational basis from which to engineer novel enzymes with antibody and glycan selectivity for clinical and biotechnological applications.
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Affiliation(s)
- Beatriz Trastoy
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Javier O Cifuente
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Lorena Rudolph
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Mikel García-Alija
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Erik H Klontz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Nazneen Sultana
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chau G Huynh
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Maria W Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Diego E Sastre
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Francisco Corzana
- Departamento Química and Centro de Investigación en Síntesis Quı́mica, Universidad de La Rioja, 26006, Rioja, Spain
| | - Alvaro Mallagaray
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, Ratzeburger Allee 160, 23562, Lübeck, Germany.
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
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6
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Kihn KC, Montes N, Hom K, Yu W, Xue F, MacKerell AD, Wilks A, Deredge D. HDX-MS guided ensemble reweighting approach reveals cryptic drug binding sites in the cytoplasmic heme binding protein, PhuS. Biophys J 2023; 122:330a. [PMID: 36783669 DOI: 10.1016/j.bpj.2022.11.1845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Kyle C Kihn
- School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| | - Nicholas Montes
- School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| | - Kellie Hom
- School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| | - Wenbo Yu
- School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| | - Fengtian Xue
- School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, MD, USA
| | - Angela Wilks
- School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| | - Daniel Deredge
- School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
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7
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Du JJ, Sastre D, Trastoy B, Roberts B, Deredge D, Klontz EH, Flowers MW, Sultana N, Guerin ME, Sundberg EJ. Mass Spectrometry-Based Methods to Determine the Substrate Specificities and Kinetics of N-Linked Glycan Hydrolysis by Endo-β-N-Acetylglucosaminidases. Methods Mol Biol 2023; 2674:147-167. [PMID: 37258966 PMCID: PMC10988651 DOI: 10.1007/978-1-0716-3243-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Glycosylation is a common posttranslational modification of proteins and refers to the covalent addition of glycans, chains of polysaccharides, onto proteins producing glycoproteins. The glycans influence the structure, function, and stability of proteins. They also play an integral role in the immune system, and aberrantly glycosylated proteins have wide ranging effects, including leading to diseases such as autoimmune conditions and cancer. Carbohydrate-active enzymes (CAZymes) are produced in bacteria, fungi, and humans and are enzymes which modify glycans via the addition or subtraction of individual or multiple saccharides from glycans. One of the hurdles in studying these enzymes is determining the types of substrates each enzyme is specific for and the kinetics of enzymatic activity. In this chapter, we discuss methods which are currently used to study the substrate specificity and kinetics of CAZymes and introduce a novel mass spectrometry-based technique which enables the specificity and kinetics of CAZymes to be determined accurately and efficiently.
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Affiliation(s)
- Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
| | - Diego Sastre
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Beatriz Trastoy
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
| | - Blaine Roberts
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Erik H Klontz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maria W Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Nazneen Sultana
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
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8
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Chun H, Kurasawa JH, Olivares P, Marakasova ES, Shestopal SA, Hassink GU, Karnaukhova E, Migliorini M, Obi JO, Smith AK, Wintrode PL, Durai P, Park K, Deredge D, Strickland DK, Sarafanov AG. Characterization of interaction between blood coagulation factor VIII and LRP1 suggests dynamic binding by alternating complex contacts. J Thromb Haemost 2022; 20:2255-2269. [PMID: 35810466 PMCID: PMC9804390 DOI: 10.1111/jth.15817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/15/2022] [Accepted: 07/01/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Deficiency in blood coagulation factor VIII (FVIII) results in life-threating bleeding (hemophilia A) treated by infusions of FVIII concentrates. To improve disease treatment, FVIII has been modified to increase its plasma half-life, which requires understanding mechanisms of FVIII catabolism. An important catabolic actor is hepatic low density lipoprotein receptor-related protein 1 (LRP1), which also regulates many other clinically significant processes. Previous studies showed complexity of FVIII site for binding LRP1. OBJECTIVES To characterize binding sites between FVIII and LRP1 and suggest a model of the interaction. METHODS A series of recombinant ligand-binding complement-type repeat (CR) fragments of LRP1 including mutated variants was generated in a baculovirus system and tested for FVIII interaction using surface plasmon resonance, tissue culture model, hydrogen-deuterium exchange mass spectrometry, and in silico. RESULTS Multiple CR doublets within LRP1 clusters II and IV were identified as alternative FVIII-binding sites. These interactions follow the canonical binding mode providing major binding energy, and additional weak interactions are contributed by adjacent CR domains. A representative CR doublet was shown to have multiple contact sites on FVIII. CONCLUSIONS FVIII and LRP1 interact via formation of multiple complex contacts involving both canonical and non-canonical binding combinations. We propose that FVIII-LRP1 interaction occurs via switching such alternative binding combinations in a dynamic mode, and that this mechanism is relevant to other ligand interactions of the low-density lipoprotein receptor family members including LRP1.
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Affiliation(s)
- Haarin Chun
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
| | - James H. Kurasawa
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
- Present address:
Biologics Engineering, R&D, AstraZeneca, GaithersburgMarylandUSA
| | - Philip Olivares
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
| | - Ekaterina S. Marakasova
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
- Present address:
(1) Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver SpringMarylandUSA
- Present address:
George Mason University, School of Systems Biology, FairfaxVirginiaUSA
| | - Svetlana A. Shestopal
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
| | - Gabriela U. Hassink
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
- Present address:
GSK‐Rockville Center for Vaccines Research, RockvilleMarylandUSA
| | - Elena Karnaukhova
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
| | - Mary Migliorini
- Center for Vascular and Inflammatory DiseasesDepartments of Surgery and PhysiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Juliet O. Obi
- Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreMarylandUSA
| | - Ally K. Smith
- Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreMarylandUSA
| | - Patrick L. Wintrode
- Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreMarylandUSA
| | - Prasannavenkatesh Durai
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungRepublic of Korea
| | - Keunwan Park
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungRepublic of Korea
| | - Daniel Deredge
- Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreMarylandUSA
| | - Dudley K. Strickland
- Center for Vascular and Inflammatory DiseasesDepartments of Surgery and PhysiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Andrey G. Sarafanov
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
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9
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Smith CN, Kihn K, Williamson ZA, Chow KM, Hersh LB, Korotkov K, Deredge D, Blackburn JS. Abstract 672: Development and validation of nanobodies specific to the oncogenic phosphatase protein tyrosine phosphatase 4A3 (PTP4A3 or PRL-3). Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Protein Tyrosine Phosphatase 4A3 (PTP4A3 or PRL-3) is an oncogenic dual-specificity phosphatase that drives tumor metastasis, promotes cancer cell survival, and is correlated with poor patient prognosis in a variety of solid tumors and leukemias. The mechanisms that drive PRL-3’s oncogenic functions are not well understood, in part due to a lack of research tools available to study this protein. The development of such tools has proven difficult, as the PRL family is ~80% homologous and the PRL catalytic binding pocket is shallow and hydrophobic. Currently available small molecules do not exhibit binding specificity for PRL-3 over PRL family members, and the only research antibody specific for PRL-3 can only recognize denatured protein. To address the lack of tools available to study PRL-3, we have developed alpaca-derived single domain antibodies, or nanobodies, targeting PRL-3. Nanobodies have emerged as a valuable research tool and show promise as cancer therapeutics as they are ~15kD and lack light chains, allowing them to reach cavities within active sites that conventional antibodies cannot normally reach. Nanobodies also maintain high specificity and affinity for their antigens. We identified seven unique nanobodies that bind to PRL-3 with no activity towards PRL-1 and PRL-2, making our nanobodies one of the first tools to selectively target PRL-3 in its native state. We used biolayer interferometry and found the nanobody binding affinity for PRL-3 to be within a KD of 30 - 300 nM, similar to that of antibodies currently on the market. We identified PRL-3:nanobody interactions with hydrogen-deuterium exchange mass spectrometry (HDX-MS) and showed binding outside the active site. These data were confirmed by analyzing the effects of nanobodies on PRL-3 phosphatase activity and substrate binding. Our anti-PRL-3 nanobodies specifically pulled down PRL-3 over PRL-1/-2 in immunoprecipitation experiments. Finally, we used these nanobodies to analyze PRL-3 localization in fixed immunofluorescence experiments in human cancer cells. We found that a C-terminal tag on PRL-3, such as FLAG or GFP, enhanced PRL-3 localization to the membrane, compared to untagged protein, which may have confounded previous PRL-3 functional studies. We are currently utilizing these nanobodies in two ways to understand PRL-3’s role in cancer. First, we will use the nanobody to stabilize PRL-3 for X-ray crystallography to develop higher resolution structures that could contribute to substrate identification and drug design. Secondly, we will examine PRL-3 function and trafficking during various cancer processes, such as proliferation, invasion, and stress, to determine how PRL-3 localization contributes to cancer progression.
Citation Format: Caroline Noel Smith, Kyle Kihn, Zachary A. Williamson, K. Martin Chow, Louis B. Hersh, Konstantin Korotkov, Daniel Deredge, Jessica S. Blackburn. Development and validation of nanobodies specific to the oncogenic phosphatase protein tyrosine phosphatase 4A3 (PTP4A3 or PRL-3) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 672.
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Affiliation(s)
| | - Kyle Kihn
- 2University of Maryland Baltimore, Baltimore, MD
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10
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Obi J, Fields J, McQueen L, Deredge D. Insights into the Binding of the Dengue Virus Nonstructural 5 (NS5) Protein to Stem Loop A (SLA). FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r6224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Juliet Obi
- Pharmaceutical SciencesUniversity of MarylandBaltimoreMD
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11
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Kihn KC, Wilson T, Smith AK, Bradshaw RT, Yu W, Wintrode PL, MacKerell AD, Forrest LR, Wilks A, Deredge D. HDX-MS guided ensemble reweighting approach to characterize the native state ensemble of the cytoplasmic heme binding protein, phus. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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12
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Fields JK, Kihn K, Birkedal GS, Klontz EH, Sjöström K, Günther S, Beadenkopf R, Forsberg G, Liberg D, Snyder GA, Deredge D, Sundberg EJ. Molecular Basis of Selective Cytokine Signaling Inhibition by Antibodies Targeting a Shared Receptor. Front Immunol 2022; 12:779100. [PMID: 35003094 PMCID: PMC8740070 DOI: 10.3389/fimmu.2021.779100] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022] Open
Abstract
Interleukin-1 (IL-1) family cytokines are potent mediators of inflammation, acting to coordinate local and systemic immune responses to a wide range of stimuli. Aberrant signaling by IL-1 family cytokine members, however, is linked to myriad inflammatory syndromes, autoimmune conditions and cancers. As such, blocking the inflammatory signals inherent to IL-1 family signaling is an established and expanding therapeutic strategy. While several FDA-approved IL-1 inhibitors exist, including an Fc fusion protein, a neutralizing antibody, and an antagonist cytokine, none specifically targets the co-receptor IL-1 receptor accessory protein (IL-1RAcP). Most IL-1 family cytokines form productive signaling complexes by binding first to their cognate receptors – IL-1RI for IL-1α and IL-1β; ST2 for IL-33; and IL-36R for IL-36α, IL-36β and IL-36γ – after which they recruit the shared secondary receptor IL-1RAcP to form a ternary cytokine/receptor/co-receptor complex. Recently, IL-1RAcP was identified as a biomarker for both AML and CML. IL-1RAcP has also been implicated in tumor progression in solid tumors and an anti-IL1RAP antibody (nadunolimab, CAN04) is in phase II clinical studies in pancreatic cancer and non-small cell lung cancer (NCT03267316). As IL-1RAcP is common to all of the abovementioned IL-1 family cytokines, targeting this co-receptor raises the possibility of selective signaling inhibition for different IL-1 family cytokines. Indeed, previous studies of IL-1β and IL-33 signaling complexes have revealed that these cytokines employ distinct mechanisms of IL-1RAcP recruitment even though their overall cytokine/receptor/co-receptor complexes are structurally similar. Here, using functional, biophysical, and structural analyses, we show that antibodies specific for IL-1RAcP can differentially block signaling by IL-1 family cytokines depending on the distinct IL-1RAcP epitopes that they engage. Our results indicate that targeting a shared cytokine receptor is a viable therapeutic strategy for selective cytokine signaling inhibition.
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Affiliation(s)
- James K Fields
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States.,Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, United States.,Program in Molecular Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Kyle Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | | | - Erik H Klontz
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States.,Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, United States.,Program in Molecular Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | - Sebastian Günther
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Robert Beadenkopf
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | | | - Greg A Snyder
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States.,Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - Eric J Sundberg
- Department of Biochemistry, Emory School of Medicine, Atlanta, GA, United States
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13
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Sha Z, Montano MM, Rochon K, Mears JA, Deredge D, Wintrode P, Szweda L, Mikita N, Lee I. A structure and function relationship study to identify the impact of the R721G mutation in the human mitochondrial lon protease. Arch Biochem Biophys 2021; 710:108983. [PMID: 34228963 DOI: 10.1016/j.abb.2021.108983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Lon is an ATP-dependent protease belonging to the "ATPase associated with diverse cellular activities" (AAA+) protein family. In humans, Lon is translated as a precursor and imported into the mitochondria matrix through deletion of the first 114 amino acid residues. In mice, embryonic knockout of lon is lethal. In humans, some dysfunctional lon mutations are tolerated but they cause a developmental disorder known as the CODAS syndrome. To gain a better understanding on the enzymology of human mitochondrial Lon, this study compares the structure-function relationship of the WT versus one of the CODAS mutants R721G to identify the mechanistic features in Lon catalysis that are affected. To this end, steady-state kinetics were used to quantify the difference in ATPase and ATP-dependent peptidase activities between WT and R721G. The Km values for the intrinsic as well as protein-stimulated ATPase were increased whereas the kcat value for ATP-dependent peptidase activity was decreased in the R721G mutant. The mutant protease also displayed substrate inhibition kinetics. In vitro studies revealed that R721G did not degrade the endogenous mitochondrial Lon substrate pyruvate dehydrogenase kinase isoform 4 (PDK4) effectively like WT hLon. Furthermore, the pyruvate dehydrogenase complex (PDH) protected PDK4 from hLon degradation. Using hydrogen deuterium exchange/mass spectrometry and negative stain electron microscopy, structural perturbations associated with the R721G mutation were identified. To validate the in vitro findings under a physiologically relevant condition, the intrinsic stability as well as proteolytic activity of WT versus R721G mutant towards PDK 4 were compared in cell lysates prepared from immortalized B lymphocytes expressing the respective protease. The lifetime of PDK4 is longer in the mutant cells, but the lifetime of Lon protein is longer in the WT cells, which corroborate the in vitro structure-functional relationship findings.
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Affiliation(s)
- Zhou Sha
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Monica M Montano
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kristy Rochon
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jason A Mears
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA; Center for Mitochondrial Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Patrick Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Luke Szweda
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Natalie Mikita
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA; Department of Chemistry, Missouri Western State University, St. Joseph, MO, 64507, USA.
| | - Irene Lee
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA.
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14
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Smith CN, Chow KM, Hersh LB, Deredge D, Blackburn JS. Abstract 2305: Development and validation of nanobodies specific to the oncogenic phosphatase protein tyrosine phosphatase 4A3 (PTP4A3 or PRL-3). Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Protein Tyrosine Phosphatase 4A3 (PTP4A3 or PRL-3) is an oncogenic dual specificity phosphatase that drives tumor metastasis, promotes cancer cell survival, and has been linked to poor patient prognosis in a variety of tumor types. The mechanisms by which PRL-3 promotes tumor progression are not well understood, which is in part due to lack of tools to study this protein. There is an intense need for research-grade antibodies in the PRL field. However, the development of such tools has proven difficult, as the PRL family is ~80% homologous and the PRL catalytic binding pocket is both shallow and hydrophobic. The most specific research antibody against PRL-3 only interacts with denatured protein, which limits its use experimentally. There is currently a humanized monoclonal antibody, PRL-3-zumab, that has good specificity for PRL-3 in cell culture and in vivo, and is in Phase 2 clinical trial for treating gastric and hepatocellular carcinomas; unfortunately, PRL-3-zumab is not currently available for the research community to use. To address this, we have designed, purified, and tested alpaca-derived PRL-3 single domain antibodies, or nanobodies. Nanobodies have emerged as a useful research tool and show promise as a cancer therapeutic. Nanobodies are only ~15kD, and lack light chains which allows them to fit into cavities in target proteins that conventional antibodies cannot normally reach. Other advantages of nanobodies include their stability under stringent conditions, lack of immunogenicity, and a high specificity and affinity for their antigens. We have identified 7 unique nanobodies that bind to PRL-3 in ELISA with no activity towards PRL-1 and PRL-2. Nanobodies were found to have variable binding affinity for PRL-3 using biolayer interferometry. Anti-PRL-3 nanobodies immunoprecipitated PRL-3 from HEK293T cell lysates both when overexpressed and using endogenous protein levels, with most nanobodies showing no cross-reactivity with PRL-1 and PRL-2. Each nanobody was also utilized to define PRL-3 localization in human colon cancer cells in immunofluorescence cell staining, which showed PRL-3 localized to the plasma membrane and the nucleus. Following validation of nanobody specificity for PRL-3, we began determining the binding site for each nanobody to PRL-3 as well as determining how nuclear PRL-3 contributes to cancer progression. These anti-PRL-3 nanobodies are the first tool that allow for the study of PRL-3 in multiple cell-based assays without the issue of cross-reactivity with other PRLs, a tool that has yet to exist in the PRL field. They can now be utilized to study the structure, function, and localization of PRL-3 in both normal and cancer cells to determine and define the oncogenic role that PRL-3 plays in multiple types of cancer. Finally, nanobodies against PRL-3 will also serve as a useful first step in the development of biologics to target PRL-3 in clinic.
Citation Format: Caroline N. Smith, K. Martin Chow, Louis B. Hersh, Daniel Deredge, Jessica S. Blackburn. Development and validation of nanobodies specific to the oncogenic phosphatase protein tyrosine phosphatase 4A3 (PTP4A3 or PRL-3) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2305.
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Affiliation(s)
| | | | | | - Daniel Deredge
- 2University of Maryland School of Pharmacy, Baltimore, MD
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15
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Klontz EH, Li C, Kihn K, Fields JK, Beckett D, Snyder GA, Wintrode PL, Deredge D, Wang LX, Sundberg EJ. Structure and dynamics of an α-fucosidase reveal a mechanism for highly efficient IgG transfucosylation. Nat Commun 2020; 11:6204. [PMID: 33277506 PMCID: PMC7718225 DOI: 10.1038/s41467-020-20044-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/15/2020] [Indexed: 11/26/2022] Open
Abstract
Fucosylation is important for the function of many proteins with biotechnical and medical applications. Alpha-fucosidases comprise a large enzyme family that recognizes fucosylated substrates with diverse α-linkages on these proteins. Lactobacillus casei produces an α-fucosidase, called AlfC, with specificity towards α(1,6)-fucose, the only linkage found in human N-glycan core fucosylation. AlfC and certain point mutants thereof have been used to add and remove fucose from monoclonal antibody N-glycans, with significant impacts on their effector functions. Despite the potential uses for AlfC, little is known about its mechanism. Here, we present crystal structures of AlfC, combined with mutational and kinetic analyses, hydrogen–deuterium exchange mass spectrometry, molecular dynamic simulations, and transfucosylation experiments to define the molecular mechanisms of the activities of AlfC and its transfucosidase mutants. Our results indicate that AlfC creates an aromatic subsite adjacent to the active site that specifically accommodates GlcNAc in α(1,6)-linkages, suggest that enzymatic activity is controlled by distinct open and closed conformations of an active-site loop, with certain mutations shifting the equilibrium towards open conformations to promote transfucosylation over hydrolysis, and provide a potentially generalizable framework for the rational creation of AlfC transfucosidase mutants. AlfC transfucosidase is used to modulate fucosylation of glycans decorating monoclonal antibodies. Herein, structural and biophysical characterization reveals the enzymatic mechanism of AlfC and a blueprint for the design of AlfC mutants with novel specificities and functions.
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Affiliation(s)
- Erik H Klontz
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Program in Molecular Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Kyle Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, College Park, MD, 21201, USA
| | - James K Fields
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Program in Molecular Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Greg A Snyder
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, College Park, MD, 21201, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, College Park, MD, 21201, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Eric J Sundberg
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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16
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Orlandi C, Deredge D, Ray K, Gohain N, Tolbert W, DeVico AL, Wintrode P, Pazgier M, Lewis GK. Antigen-Induced Allosteric Changes in a Human IgG1 Fc Increase Low-Affinity Fcγ Receptor Binding. Structure 2020; 28:516-527.e5. [PMID: 32209433 DOI: 10.1016/j.str.2020.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 02/07/2020] [Accepted: 03/05/2020] [Indexed: 11/15/2022]
Abstract
Antibody structure couples adaptive and innate immunity via Fab (antigen binding) and Fc (effector) domains that are connected by unique hinge regions. Because antibodies harbor two or more Fab domains, they are capable of crosslinking multi-determinant antigens, which is required for Fc-dependent functions through associative interactions with effector ligands, including C1q and cell surface Fc receptors. The modular nature of antibodies, with distal ligand binding sites for antigen and Fc-ligands, is reminiscent of allosteric proteins, suggesting that allosteric interactions might contribute to Fc-mediated effector functions. This hypothesis has been pursued for over 40 years and remains unresolved. Here, we provide evidence that allosteric interactions between Fab and Fc triggered by antigen binding modulate binding of Fc to low-affinity Fc receptors (FcγR) for a human IgG1. This work opens the path to further dissection of the relative roles of allosteric and associative interactions in Fc-mediated effector functions.
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Affiliation(s)
- Chiara Orlandi
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Krishanu Ray
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Neelakshi Gohain
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - William Tolbert
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Anthony L DeVico
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Patrick Wintrode
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Marzena Pazgier
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - George K Lewis
- Division of Vaccine Research, The Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA.
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17
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Deredge D, Wintrode PL, Tulapurkar ME, Nagarsekar A, Zhang Y, Weber DJ, Shapiro P, Hasday JD. A temperature-dependent conformational shift in p38α MAPK substrate-binding region associated with changes in substrate phosphorylation profile. J Biol Chem 2019; 294:12624-12637. [PMID: 31213525 DOI: 10.1074/jbc.ra119.007525] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 05/13/2019] [Indexed: 01/09/2023] Open
Abstract
Febrile-range hyperthermia worsens and hypothermia mitigates lung injury, and temperature dependence of lung injury is blunted by inhibitors of p38 mitogen-activated protein kinase (MAPK). Of the two predominant p38 isoforms, p38α is proinflammatory and p38β is cytoprotective. Here, we analyzed the temperature dependence of p38 MAPK activation, substrate interaction, and tertiary structure. Incubating HeLa cells at 39.5 °C stimulated modest p38 activation, but did not alter tumor necrosis factor-α (TNFα)-induced p38 activation. In in vitro kinase assays containing activated p38α and MAPK-activated kinase-2 (MK2), MK2 phosphorylation was 14.5-fold greater at 39.5 °C than at 33 °C. By comparison, we observed only 3.1- and 1.9-fold differences for activating transcription factor-2 (ATF2) and signal transducer and activator of transcription-1α (STAT1α) and a 7.7-fold difference for p38β phosphorylation of MK2. The temperature dependence of p38α:substrate binding affinity, as measured by surface plasmon resonance, paralleled substrate phosphorylation. Hydrogen-deuterium exchange MS (HDX-MS) of p38α performed at 33, 37, and 39.5 °C indicated temperature-dependent conformational changes in an α helix near the common docking and glutamate:aspartate substrate-binding domains at the known binding site for MK2. In contrast, HDX-MS analysis of p38β did not detect significant temperature-dependent conformational changes in this region. We observed no conformational changes in the catalytic domain of either isoform and no corresponding temperature dependence in the C-terminal p38α-interacting region of MK2. Because MK2 participates in the pathogenesis of lung injury, the observed changes in the structure and function of proinflammatory p38α may contribute to the temperature dependence of acute lung injury.
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Affiliation(s)
- Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
| | - Mohan E Tulapurkar
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Ashish Nagarsekar
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Yinghua Zhang
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - David J Weber
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
| | - Jeffrey D Hasday
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201 .,Medicine and Research Services, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland 21201
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18
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Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Filliben JJ, Huang RYC, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. Interlaboratory Comparison of Hydrogen-Deuterium Exchange Mass Spectrometry Measurements of the Fab Fragment of NISTmAb. Anal Chem 2019; 91:7336-7345. [PMID: 31045344 DOI: 10.1021/acs.analchem.9b01100] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an established, powerful tool for investigating protein-ligand interactions, protein folding, and protein dynamics. However, HDX-MS is still an emergent tool for quality control of biopharmaceuticals and for establishing dynamic similarity between a biosimilar and an innovator therapeutic. Because industry will conduct quality control and similarity measurements over a product lifetime and in multiple locations, an understanding of HDX-MS reproducibility is critical. To determine the reproducibility of continuous-labeling, bottom-up HDX-MS measurements, the present interlaboratory comparison project evaluated deuterium uptake data from the Fab fragment of NISTmAb reference material (PDB: 5K8A ) from 15 laboratories. Laboratories reported ∼89 800 centroid measurements for 430 proteolytic peptide sequences of the Fab fragment (∼78 900 centroids), giving ∼100% coverage, and ∼10 900 centroid measurements for 77 peptide sequences of the Fc fragment. Nearly half of peptide sequences are unique to the reporting laboratory, and only two sequences are reported by all laboratories. The majority of the laboratories (87%) exhibited centroid mass laboratory repeatability precisions of ⟨ sLab⟩ ≤ (0.15 ± 0.01) Da (1σx̅). All laboratories achieved ⟨sLab⟩ ≤ 0.4 Da. For immersions of protein at THDX = (3.6 to 25) °C and for D2O exchange times of tHDX = (30 s to 4 h) the reproducibility of back-exchange corrected, deuterium uptake measurements for the 15 laboratories is σreproducibility15 Laboratories( tHDX) = (9.0 ± 0.9) % (1σ). A nine laboratory cohort that immersed samples at THDX = 25 °C exhibited reproducibility of σreproducibility25C cohort( tHDX) = (6.5 ± 0.6) % for back-exchange corrected, deuterium uptake measurements.
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Affiliation(s)
- Jeffrey W Hudgens
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Elyssia S Gallagher
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Ioannis Karageorgos
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Kyle W Anderson
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - James J Filliben
- Statistical Engineering Division , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - George M Bou-Assaf
- Analytical Development , Biogen Inc. , 225 Binney Street , Cambridge , Massachusetts 02142 , United States
| | - Alfonso Espada
- Centro de Investigación Lilly S.A. , 28108 Alcobendas , Spain
| | - Michael J Chalmers
- Lilly Research Laboratories , Eli Lilly and Company , Indianapolis , Indiana 46285 , United States
| | | | - Hui-Min Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Benjamin T Walters
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jennifer Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - John Venable
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States.,Joint Center for Structural Genomics , La Jolla , California 92037 , United States
| | - Inhee Park
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Xiaojun Lu
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Ratnesh Pandey
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Arun Chandramohan
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Ganesh Srinivasan Anand
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Sasidhar N Nirudodhi
- Vaccine R&D , Pfizer Inc. , 401 N Middletown Rd , Pearl River, New York 10965 , United States
| | - Justin B Sperry
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Jason C Rouse
- Analytical R&D , Pfizer Inc. , 1 Burtt Road , Andover , Massachusetts 01810 , United States
| | - James A Carroll
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Kasper D Rand
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Ulrike Leurs
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - David D Weis
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Mohammed A Al-Naqshabandi
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States.,Department of General Science , Soran University , Kawa Street , Soran , Kurdistan Region, Iraq
| | - Tyler S Hageman
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Daniel Deredge
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Malvina Papanastasiou
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - John D Lambris
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - Sheng Li
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Sarah Urata
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
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19
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Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Huang RYC, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Centroid Data Measured between 3.6 °C and 25.4 °C for the Fab Fragment of NISTmAb. J Res Natl Inst Stand Technol 2019; 124:1-7. [PMID: 34877153 PMCID: PMC7339623 DOI: 10.6028/jres.124.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/10/2019] [Indexed: 06/13/2023]
Abstract
The spreadsheet file reported herein provides centroid data, descriptive of
deuterium uptake, for the FabFragment of NISTmAb (PDB: 5K8A) reference material, as
measured by the bottom-up hydrogen-deuterium exchange mass spectrometry (HDX-MS)
method. The protein sample was incubated in deuterium-rich solutions under uniform
pH and salt concentrations between 3.6 oC and 25.4 oC for seven intervals ranging
over (0 to 14,400) s plus a ∞pseudo s control. The deuterium content of peptic
peptide fragments were measured by mass spectrometry. These data were reported by
fifteen laboratories, which conducted the measurements using orbitrap and Q-TOF mass
spectrometers. The cohort reported ≈ 78,900 centroids for 430 proteolytic peptide
sequences of the heavy and light chains of NISTmAb, providing nearly 100 % coverage.
In addition, some groups reported ≈ 10,900 centroid measurements for 77 peptide
sequences of the Fc fragment. The instrumentation and physical and chemical
conditions under which these data were acquired are documented.
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Affiliation(s)
- Jeffrey W Hudgens
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Elyssia S Gallagher
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Ioannis Karageorgos
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Kyle W Anderson
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Richard Y-C Huang
- Bristol-Myers Squibb Company, Pharmaceutical Candidate Optimization, Research and Development, Princeton, NJ 08540, USA
| | - Guodong Chen
- Bristol-Myers Squibb Company, Pharmaceutical Candidate Optimization, Research and Development, Princeton, NJ 08540, USA
| | - George M Bou-Assaf
- Biogen Inc., Analytical Development, 225 Binney Street, Cambridge, MA 02142, USA
| | - Alfonso Espada
- Centro de Investigación Lilly S.A., 28108-Alcobendas, Spain
| | - Michael J Chalmers
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | - Hui-Min Zhang
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin T Walters
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jennifer Zhang
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - John Venable
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
- Joint Center for Structural Genomics, La Jolla, CA 92037, USA
| | - Inhee Park
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Xiaojun Lu
- MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Ratnesh Pandey
- MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Arun Chandramohan
- National University of Singapore, Department of Biological Sciences, 14, Science Drive 4, Singapore 117543
| | - Ganesh Srinivasan Anand
- National University of Singapore, Department of Biological Sciences, 14, Science Drive 4, Singapore 117543
| | | | - Justin B Sperry
- Pfizer Inc., Analytical R&D, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Jason C Rouse
- Pfizer Inc., Analytical R&D, 1 Burtt Road, Andover, MA 01810, USA
| | - James A Carroll
- Pfizer Inc., Analytical R&D, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Kasper D Rand
- University of Copenhagen, Department of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Ulrike Leurs
- University of Copenhagen, Department of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - David D Weis
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
| | - Mohammed A Al-Naqshabandi
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
- Soran University, Department of General Science, Kawa Street, Soran, Kurdistan Region, Iraq
| | - Tyler S Hageman
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
| | - Daniel Deredge
- University of Maryland, Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Patrick L Wintrode
- University of Maryland, Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Malvina Papanastasiou
- University of Pennsylvania, Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104-6100, USA
| | - John D Lambris
- University of Pennsylvania, Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104-6100, USA
| | - Sheng Li
- University of Southern California, Department of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sarah Urata
- University of Southern California, Department of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
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20
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Klontz EH, Trastoy B, Deredge D, Fields JK, Li C, Orwenyo J, Marina A, Beadenkopf R, Günther S, Flores J, Wintrode PL, Wang LX, Guerin ME, Sundberg EJ. Molecular Basis of Broad Spectrum N-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2. ACS Cent Sci 2019; 5:524-538. [PMID: 30937380 PMCID: PMC6439443 DOI: 10.1021/acscentsci.8b00917] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 06/02/2023]
Abstract
Immunoglobulin G (IgG) glycosylation critically modulates antibody effector functions. Streptococcus pyogenes secretes a unique endo-β-N-acetylglucosaminidase, EndoS2, which deglycosylates the conserved N-linked glycan at Asn297 on IgG Fc to eliminate its effector functions and evade the immune system. EndoS2 and specific point mutants have been used to chemoenzymatically synthesize antibodies with customizable glycosylation for gain of functions. EndoS2 is useful in these schemes because it accommodates a broad range of N-glycans, including high-mannose, complex, and hybrid types; however, its mechanism of substrate recognition is poorly understood. We present crystal structures of EndoS2 alone and bound to complex and high-mannose glycans; the broad N-glycan specificity is governed by critical loops that shape the binding site of EndoS2. Furthermore, hydrolytic experiments, domain-swap chimeras, and hydrogen-deuterium exchange mass spectrometry reveal the importance of the carbohydrate-binding module in the mechanism of IgG recognition by EndoS2, providing insights into engineering enzymes to catalyze customizable glycosylation reactions.
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Affiliation(s)
- Erik H. Klontz
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Beatriz Trastoy
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Daniel Deredge
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - James K. Fields
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Chao Li
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Jared Orwenyo
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Alberto Marina
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Robert Beadenkopf
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Sebastian Günther
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Photon
Science, Deutsches Elektronen-Synchrotron, Hamburg 22607, Germany
| | - Jair Flores
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Patrick L. Wintrode
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Lai-Xi Wang
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Marcelo E. Guerin
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48013 Bilbao, Spain
| | - Eric J. Sundberg
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Department
of Medicine, University of Maryland School
of Medicine, Baltimore, Maryland 21201, United States
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21
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Pritts JD, Oluyadi AA, Deredge D, Wintrode PL, Michel SL. Determination of the Mechanism of RNA Regulation by CPSF30 Utilizing Both Biophysical and Structural Approaches. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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22
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Bonsor DA, Zhao Q, Schmidinger B, Weiss E, Wang J, Deredge D, Beadenkopf R, Dow B, Fischer W, Beckett D, Wintrode PL, Haas R, Sundberg EJ. The Helicobacter pylori adhesin protein HopQ exploits the dimer interface of human CEACAMs to facilitate translocation of the oncoprotein CagA. EMBO J 2018; 37:embj.201798664. [PMID: 29724755 DOI: 10.15252/embj.201798664] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/27/2018] [Accepted: 04/05/2018] [Indexed: 01/06/2023] Open
Abstract
Helicobacter pylori infects half of the world's population, and strains that encode the cag type IV secretion system for injection of the oncoprotein CagA into host gastric epithelial cells are associated with elevated levels of cancer. CagA translocation into host cells is dependent on interactions between the H. pylori adhesin protein HopQ and human CEACAMs. Here, we present high-resolution structures of several HopQ-CEACAM complexes and CEACAMs in their monomeric and dimeric forms establishing that HopQ uses a coupled folding and binding mechanism to engage the canonical CEACAM dimerization interface for CEACAM recognition. By combining mutagenesis with biophysical and functional analyses, we show that the modes of CEACAM recognition by HopQ and CEACAMs themselves are starkly different. Our data describe precise molecular mechanisms by which microbes exploit host CEACAMs for infection and enable future development of novel oncoprotein translocation inhibitors and H. pylori-specific antimicrobial agents.
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Affiliation(s)
- Daniel A Bonsor
- Institute of Human Virology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Qing Zhao
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Barbara Schmidinger
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Evelyn Weiss
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jingheng Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Robert Beadenkopf
- Institute of Human Virology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Blaine Dow
- Institute of Human Virology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Wolfgang Fischer
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Rainer Haas
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site LMU, Munich, Germany
| | - Eric J Sundberg
- Institute of Human Virology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD, USA .,Department of Medicine, University of Maryland School of Medicine, University of Maryland, Baltimore, MD, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD, USA
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23
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Guenther S, Bowers AL, Deredge D, Bonsor DA, Beadenkopf R, Wintrode PL, Sundberg EJ. The Crystal Structure of the IL-33 Signaling Complex Reveals the Molecular Basis for Receptor Sharing in the IL-1 Family. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.133.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Cytokines of the IL-1 family are potent stimulators of the immune system. As seen in other cytokine families, cytokine redundancy due to receptor sharing is characteristic for the IL-1 family. Today five primary receptors have been described that each bind a subset of the 11 known cytokines within this family. Once an agonistic cytokine-receptor pair has formed, it can engage one of the two co-receptors and initiate signaling through MyD88. While IL-18Rβ is the unique co-receptor for the IL-18/IL-18Rα pair, IL-1RAcP is shared between the other four primary receptors, IL-1RI, IL-1RII, ST2 and IL-36R. Crystal structures of IL-1β bound to IL-1RI or IL-1RII in complex with IL-1RAcP previously revealed the general architecture of signaling complexes in the IL-1 family. IL-33 is the latest cytokine to be discovered in the IL-1 family. Since its first description in 2005 it has been recognized as a central driver of type 2 immunity. Here we present the crystal structure of IL-33 in complex with its receptors ST2 and IL-1RAcP. The structure reveals a remarkable conservation of the ternary architecture of signaling complexes in the IL-1 family. We observe common principles of co-receptor binding, also seen in the other two ternary structures containing IL-1RAcP. However, hydrogen/deuterium mass exchange spectroscopy and extensive alanine-scanning analysis combined with direct binding analysis of the IL-1β and IL-33 signaling complexes demonstrate that the binding energy is distributed quite differently within the two. Co-receptor binding of ST2/IL-33 is much less dependent on the cytokine than on the receptor, while for IL-1β/IL-1RI the cytokine plays a much more important role.
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24
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Postel S, Deredge D, Bonsor DA, Yu X, Diederichs K, Helmsing S, Vromen A, Friedler A, Hust M, Egelman EH, Beckett D, Wintrode PL, Sundberg EJ. Bacterial flagellar capping proteins adopt diverse oligomeric states. eLife 2016; 5. [PMID: 27664419 PMCID: PMC5072837 DOI: 10.7554/elife.18857] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/23/2016] [Indexed: 11/13/2022] Open
Abstract
Flagella are crucial for bacterial motility and pathogenesis. The flagellar capping protein (FliD) regulates filament assembly by chaperoning and sorting flagellin (FliC) proteins after they traverse the hollow filament and exit the growing flagellum tip. In the absence of FliD, flagella are not formed, resulting in impaired motility and infectivity. Here, we report the 2.2 Å resolution X-ray crystal structure of FliD from Pseudomonas aeruginosa, the first high-resolution structure of any FliD protein from any bacterium. Using this evidence in combination with a multitude of biophysical and functional analyses, we find that Pseudomonas FliD exhibits unexpected structural similarity to other flagellar proteins at the domain level, adopts a unique hexameric oligomeric state, and depends on flexible determinants for oligomerization. Considering that the flagellin filaments on which FliD oligomers are affixed vary in protofilament number between bacteria, our results suggest that FliD oligomer stoichiometries vary across bacteria to complement their filament assemblies. DOI:http://dx.doi.org/10.7554/eLife.18857.001 Many bacteria, including several that cause diseases in people, have long whip-like appendages called flagella that extend well beyond their cell walls. Flagella can rotate and propel the bacteria through liquids, such as water or blood, and they are constructed primarily from thousands of copies of a single protein called flagellin. When flagella are built, the flagellin proteins are placed in their proper positions by another protein called FliD, several copies of which form a cap on the end of flagella. Without FliD, bacteria cannot properly assemble flagella and, thus, can no longer swim; this also hinders their ability to cause disease. Determining the three-dimensional structure of a protein, down to the level of its individual atoms, can provide unique insights into how the protein operates. However, no one had resolved the structure of a FliD protein from any bacterium to this level of detail before. Now, Postel et al. report the high-resolution structure of a large fragment of FliD from the bacterium Pseudomonas aeruginosa. The structure reveals that parts of this FliD protein are shaped like parts of other proteins from which flagella are constructed, including the flagellin protein that FliD places into position. Some parts of the FliD protein are also very flexible and these parts of the protein are responsible for holding numerous FliD proteins together as a cap. Finally, Postel et al. saw that six copies of FliD bind to one another to form a protein complex on the end of flagella. This last finding was particularly unexpected since it was thought that all FliD proteins formed five-membered cap complexes, an assumption that was based largely on studies of FliD from another bacterium called Salmonella. The current structure covers about half of the FliD protein, and so the next challenge is to determine the structure of the full-length protein. An improved understanding of the structure of FliD may, in future, help researchers to design drugs that stop bacteria from building flagella and, therefore, from swimming and causing disease. DOI:http://dx.doi.org/10.7554/eLife.18857.002
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Affiliation(s)
- Sandra Postel
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, United States
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, United States
| | - Daniel A Bonsor
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, United States
| | - Xiong Yu
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, United States
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Saskia Helmsing
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Aviv Vromen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael Hust
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, United States
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland College Park, Baltimore, United States
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, United States
| | - Eric J Sundberg
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, United States.,Department of Medicine, University of Maryland School of Medicine, Baltimore, United States.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States
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25
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Tsutsui Y, Deredge D, Wintrode PL, Hays FA. Imatinib binding to human c-Src is coupled to inter-domain allostery and suggests a novel kinase inhibition strategy. Sci Rep 2016; 6:30832. [PMID: 27480221 PMCID: PMC4969603 DOI: 10.1038/srep30832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/11/2016] [Indexed: 12/31/2022] Open
Abstract
Imatinib (Gleevec), a non-receptor tyrosine kinase inhibitor (nRTKI), is one of the most successful anti-neoplastic drugs in clinical use. However, imatinib-resistant mutations are increasingly prevalent in patient tissues and driving development of novel imatinib analogs. We present a detailed study of the conformational dynamics, in the presence and absence of bound imatinib, for full-length human c-Src using hydrogen-deuterium exchange and mass spectrometry. Our results demonstrate that imatinib binding to the kinase domain effects dynamics of proline-rich or phosphorylated peptide ligand binding sites in distal c-Src SH3 and SH2 domains. These dynamic changes in functional regulatory sites, distal to the imatinib binding pocket, show similarities to structural transitions involved in kinase activation. These data also identify imatinib-sensitive, and imatinib-resistant, mutation sites. Thus, the current study identifies novel c-Src allosteric sites associated with imatinib binding and kinase activation and provide a framework for follow-on development of TKI binding modulators.
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Affiliation(s)
- Yuko Tsutsui
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Franklin A Hays
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA.,Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
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26
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Deredge D, Li J, Johnson KA, Wintrode PL. Hydrogen/Deuterium Exchange Kinetics Demonstrate Long Range Allosteric Effects of Thumb Site 2 Inhibitors of Hepatitis C Viral RNA-dependent RNA Polymerase. J Biol Chem 2016; 291:10078-88. [PMID: 27006396 DOI: 10.1074/jbc.m115.708370] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Indexed: 01/08/2023] Open
Abstract
New nonnucleoside analogs are being developed as part of a multi-drug regimen to treat hepatitis C viral infections. Particularly promising are inhibitors that bind to the surface of the thumb domain of the viral RNA-dependent RNA polymerase (NS5B). Numerous crystal structures have been solved showing small molecule non-nucleoside inhibitors bound to the hepatitis C viral polymerase, but these structures alone do not define the mechanism of inhibition. Our prior kinetic analysis showed that nonnucleoside inhibitors binding to thumb site-2 (NNI2) do not block initiation or elongation of RNA synthesis; rather, they block the transition from the initiation to elongation, which is thought to proceed with significant structural rearrangement of the enzyme-RNA complex. Here we have mapped the effect of three NNI2 inhibitors on the conformational dynamics of the enzyme using hydrogen/deuterium exchange kinetics. All three inhibitors rigidify an extensive allosteric network extending >40 Å from the binding site, thus providing a structural rationale for the observed disruption of the transition from distributive initiation to processive elongation. The two more potent inhibitors also suppress slow cooperative unfolding in the fingers extension-thumb interface and primer grip, which may contribute their stronger inhibition. These results establish that NNI2 inhibitors act through long range allosteric effects, reveal important conformational changes underlying normal polymerase function, and point the way to the design of more effective allosteric inhibitors that exploit this new information.
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Affiliation(s)
- Daniel Deredge
- From the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201 and
| | - Jiawen Li
- Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Kenneth A Johnson
- Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Patrick L Wintrode
- From the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201 and
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Li J, Deredge D, Wintrode PL, Johnson KA. Thumb Site 2 Inhibitors of Hepatitis C Viral RNA-Dependent RNA Polymerase Allosterically Block the Transition from Initiation to Elongation. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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White MR, Khan MM, Deredge D, Ross CR, Quintyn R, Zucconi BE, Wysocki VH, Wintrode PL, Wilson GM, Garcin ED. A dimer interface mutation in glyceraldehyde 3-phosphate dehydrogenase regulates its binding to AU-rich RNA. J Biol Chem 2015; 290:4129. [PMID: 25681510 DOI: 10.1074/jbc.a114.618165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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29
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Jois B, Deredge D, Johnson K, Wintrode P. Thumb II Site Inhibitor Allosterically Suppresses the Dynamics of HCV NS5B RNA‐Dependent RNA Polymerase. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.lb81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bhavna Jois
- Department of Chemistry and BiochemistryUniversity of Maryland Baltimore CountyBaltimoreMarylandUnited States
| | - Daniel Deredge
- Department of Pharmaceutical Sciences University of Maryland School of PharmacyBaltimoreMarylandUnited States
| | - Kenneth Johnson
- Institute of Cellular and Molecular Biology University of Texas at AustinAustinTexasUnited States
| | - Patrick Wintrode
- Department of Pharmaceutical Sciences University of Maryland School of PharmacyBaltimoreMarylandUnited States
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White M, Khan M, Deredge D, Ross C, Quintyn R, Zucconi B, Wysocki V, Wintrode P, Wilson G, Garcin E. Dynamics of Glyceraldehyde-3-Phosphate Dehydrogenase Interfacial Regions Affect Binding to AU-Rich RNA. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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31
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White MR, Khan MM, Deredge D, Ross CR, Quintyn R, Zucconi BE, Wysocki VH, Wintrode PL, Wilson GM, Garcin ED. A dimer interface mutation in glyceraldehyde-3-phosphate dehydrogenase regulates its binding to AU-rich RNA. J Biol Chem 2014; 290:1770-85. [PMID: 25451934 DOI: 10.1074/jbc.m114.618165] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an enzyme best known for its role in glycolysis. However, extra-glycolytic functions of GAPDH have been described, including regulation of protein expression via RNA binding. GAPDH binds to numerous adenine-uridine rich elements (AREs) from various mRNA 3'-untranslated regions in vitro and in vivo despite its lack of a canonical RNA binding motif. How GAPDH binds to these AREs is still unknown. Here we discovered that GAPDH binds with high affinity to the core ARE from tumor necrosis factor-α mRNA via a two-step binding mechanism. We demonstrate that a mutation at the GAPDH dimer interface impairs formation of the second RNA-GAPDH complex and leads to changes in the RNA structure. We investigated the effect of this interfacial mutation on GAPDH oligomerization by crystallography, small-angle x-ray scattering, nano-electrospray ionization native mass spectrometry, and hydrogen-deuterium exchange mass spectrometry. We show that the mutation does not significantly affect GAPDH tetramerization as previously proposed. Instead, the mutation promotes short-range and long-range dynamic changes in regions located at the dimer and tetramer interface and in the NAD(+) binding site. These dynamic changes are localized along the P axis of the GAPDH tetramer, suggesting that this region is important for RNA binding. Based on our results, we propose a model for sequential GAPDH binding to RNA via residues located at the dimer and tetramer interfaces.
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Affiliation(s)
- Michael R White
- From the Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Mohd M Khan
- From the Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
| | - Christina R Ross
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, and
| | - Royston Quintyn
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210
| | - Beth E Zucconi
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, and
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, and
| | - Elsa D Garcin
- From the Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250,
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Snyder G, Deredge D, Waldhuber A, Fresquez T, Smith P, Duerr S, Cirl C, Jiang J, Jennings W, Luchetti T, Snyder N, Sundberg E, Wintrode P, Miethke T, Xiao T. Development of microbial-derived inhibitory peptides using structural studies of microbial TIR proteins TcpB, TcpC and host adapters TIRAP and MyD88. (INM9P.449). The Journal of Immunology 2014. [DOI: 10.4049/jimmunol.192.supp.189.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Microbial pathogens have evolved mechanisms to regulate and evade innate immunity. One such mechanism involves the subversion of Toll-like receptor (TLR) signaling by bacterial TIR Interacting Proteins (TIPs). TIPs are thought to function by disruption of host Toll/IL-1 receptor (TIR) signaling proteins. For example, the TIP proteins TcpB from Brucella and TcpC from E. coli inhibit TLR signaling through direct interaction with host adapter proteins TIRAP and MyD88. We have previously reported the crystal structure of MyD88 and characterized TcpC peptides capable to inhibit TLR4 and MyD88 signaling. We now report the X-ray crystal structure of the Brucella TIR protein TcpB and characterize its interactions with TIRAP using hydrogen/ deuterium (H/D) exchange mass spectrometry, co-immunoprecipitation and NF-ΚB reporter assays. The crystal structure of TcpB reveals the BB loop microtubule-binding site as well as a symmetrical dimer involving the DD and EE loops. The dimer interface is further characterized through H/D exchange mass spectrometry, which identifies a set of candidate potential TcpB blocking peptides. A comparison between the microbial TcpB, TIRAP and MyD88 crystal structures reveal differences in the region that encompasses the BB loop. These findings lend insight into the molecular mechanisms of microbial mimicry of host signaling adapter proteins and provide a framework for identification and development of novel microbial-derived therapeutics.
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Affiliation(s)
- Greg Snyder
- 1Institute of Human Virology, Department of Medicine, School of Medicine., University of Maryland, Baltimore, MD
- 2Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Daniel Deredge
- 3Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Anna Waldhuber
- 4Institute of Medical Microbiology and Hygiene, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
| | - Theresa Fresquez
- 2Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Patrick Smith
- 2Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Suri Duerr
- 4Institute of Medical Microbiology and Hygiene, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
| | - Christine Cirl
- 4Institute of Medical Microbiology and Hygiene, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
| | - Jiansheng Jiang
- 2Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - William Jennings
- 2Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Timothy Luchetti
- 2Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Nathaniel Snyder
- 2Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Eric Sundberg
- 1Institute of Human Virology, Department of Medicine, School of Medicine., University of Maryland, Baltimore, MD
| | - Patrick Wintrode
- 3Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Thomas Miethke
- 4Institute of Medical Microbiology and Hygiene, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
| | - Tsan Xiao
- 2Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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Mistry P, Laird M, Schwarz R, Greene S, Dyson T, Jabre S, Snyder G, Deredge D, Chauhan J, Wintrode P, Xiao T, Sundberg E, Fletcher S, Toshchakov V, MacKerell A, Vogel S. Inhibition of TLR2 signaling by small molecule inhibitors targeting a novel putative pocket within the TLR2 TIR domain (INM9P.448). The Journal of Immunology 2014. [DOI: 10.4049/jimmunol.192.supp.189.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Overexuberant TLR2 signaling has been implicated in numerous diseases. Visual analysis of the TLR2 TIR domain crystal structure suggested the presence of a “pocket” adjacent to the highly conserved and functionally important proline and glycine residues of the BB loop. Given the importance of the BB loop in mediating TLR signal transduction, we hypothesized that Computer-Aided Drug Design (CADD) could be used to identify a small molecule inhibitor(s) that would fit within this “pocket” and blunt TLR2 signaling. Using CADD, ~150 small compounds were identified based on their predicted ability to bind in this pocket. Based on inhibition of IL-8 mRNA induced by TLR2 agonists, compound “C29” was found to inhibit TLR2/1 and TLR2/6 signaling in human HEK-TLR2 and THP-1 cells, but only TLR2/1 signaling in murine macrophages. C29 blocks heat-killed and live bacterial TLR2 agonist-induced proinflammatory cytokine mRNA. C29 prevents the early activation of TLR2-mediated signaling, including NF-κB and MAPKs, as well as MyD88 recruitment to TLR2 in THP-1 cells. C29 is cleavable and the byproduct, o-vanillin, reproduces comparable TLR2 inhibitory activity. O-vanillin covalently interacts with recombinant human TLR2 TIR domain dose-dependently. Mutagenesis of “pocket” residues revealed an indispensable role for TLR2/1, but not TLR2/6, signaling, suggesting divergent roles. Collectively, these results provide proof-of-principle for using CADD to identify inhibitors of TLR2 signaling.
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Affiliation(s)
- Pragnesh Mistry
- 1Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD
| | - Michelle Laird
- 1Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD
| | - Ryan Schwarz
- 1Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD
| | - Shannon Greene
- 2Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, MD
| | - Tristan Dyson
- 1Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD
| | - Sandra Jabre
- 1Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD
| | - Greg Snyder
- 1Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD
| | - Daniel Deredge
- 2Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, MD
| | - Jamal Chauhan
- 2Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, MD
| | - Patrick Wintrode
- 2Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, MD
| | - Tsan Xiao
- 3Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Eric Sundberg
- 1Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD
| | - Steven Fletcher
- 2Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, MD
| | - Vladimir Toshchakov
- 1Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD
| | | | - Stefanie Vogel
- 1Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD
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Snyder GA, Deredge D, Waldhuber A, Fresquez T, Wilkins DZ, Smith PT, Durr S, Cirl C, Jiang J, Jennings W, Luchetti T, Snyder N, Sundberg EJ, Wintrode P, Miethke T, Xiao TS. Crystal structures of the Toll/Interleukin-1 receptor (TIR) domains from the Brucella protein TcpB and host adaptor TIRAP reveal mechanisms of molecular mimicry. J Biol Chem 2013; 289:669-79. [PMID: 24275656 DOI: 10.1074/jbc.m113.523407] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Toll/IL-1 receptor (TIR) domains are crucial innate immune signaling modules. Microbial TIR domain-containing proteins inhibit Toll-like receptor (TLR) signaling through molecular mimicry. The TIR domain-containing protein TcpB from Brucella inhibits TLR signaling through interaction with host adaptor proteins TIRAP/Mal and MyD88. To characterize the microbial mimicry of host proteins, we have determined the X-ray crystal structures of the TIR domains from the Brucella protein TcpB and the host adaptor protein TIRAP. We have further characterized homotypic interactions of TcpB using hydrogen/deuterium exchange mass spectrometry and heterotypic TcpB and TIRAP interaction by co-immunoprecipitation and NF-κB reporter assays. The crystal structure of the TcpB TIR domain reveals the microtubule-binding site encompassing the BB loop as well as a symmetrical dimer mediated by the DD and EE loops. This dimerization interface is validated by peptide mapping through hydrogen/deuterium exchange mass spectrometry. The human TIRAP TIR domain crystal structure reveals a unique N-terminal TIR domain fold containing a disulfide bond formed by Cys(89) and Cys(134). A comparison between the TcpB and TIRAP crystal structures reveals substantial conformational differences in the region that encompasses the BB loop. These findings underscore the similarities and differences in the molecular features found in the microbial and host TIR domains, which suggests mechanisms of bacterial mimicry of host signaling adaptor proteins, such as TIRAP.
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Affiliation(s)
- Greg A Snyder
- From the Laboratory of Immunology, NIAID, National Institutes of Health, Bethesda, Maryland 20892
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Deredge D, Venencia C, Howard K, Barkley MD, Wintrode PL. Conformational Flexibility Mediates Resistance of HIV-1 Reverse Transcriptase to Nonucleoside Inhibitors. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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