1
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Ertekin A, Morgan BR, Ryder SP, Massi F. Structure and Dynamics of the CCCH-Type Tandem Zinc Finger Domain of POS-1 and Implications for RNA Binding Specificity. Biochemistry 2024; 63:2632-2647. [PMID: 39321355 DOI: 10.1021/acs.biochem.4c00259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
CCCH-type tandem zinc finger (TZF) motifs are found in many RNA-binding proteins involved in regulating mRNA stability, translation, and splicing. In Caenorhabditis elegans, several RNA-binding proteins that regulate embryonic development and cell fate determination contain CCCH TZF domains, including POS-1. Previous biochemical studies have shown that despite high levels of sequence conservation, POS-1 recognizes a broader set of RNA sequences compared to the human homologue tristetraprolin. However, the molecular basis of these differences remains unknown. In this study, we refined the consensus RNA sequence and determined the differing binding specificities of the two zinc fingers of POS-1. We also determined the solution structure and characterized the internal dynamics of the TZF domain of POS-1. From the structure, we identified unique features that define the RNA binding specificity of POS-1. We also observed that the TZF domain of POS-1 is in equilibrium between interconverting conformations. Transitions between these conformations require internal motions involving many residues with correlated dynamics in each ZF. We propose that the correlated dynamics are necessary to allow allosteric communication between the nucleotide-binding pockets observed in the N-terminal ZF. Our study shows that both the structure and conformational plasticity of POS-1 are important in ensuring recognition of its RNA binding targets.
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Affiliation(s)
- Asli Ertekin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Brittany R Morgan
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Sean P Ryder
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Francesca Massi
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
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2
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Madheswaran M, Ventserova N, D’Abrosca G, Salzano G, Celauro L, Cazzaniga FA, Isernia C, Malgieri G, Moda F, Russo L, Legname G, Fattorusso R. Unfolding Mechanism and Fibril Formation Propensity of Human Prion Protein in the Presence of Molecular Crowding Agents. Int J Mol Sci 2024; 25:9916. [PMID: 39337404 PMCID: PMC11432716 DOI: 10.3390/ijms25189916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Revised: 09/10/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
The pathological process of prion diseases implicates that the normal physiological cellular prion protein (PrPC) converts into misfolded abnormal scrapie prion (PrPSc) through post-translational modifications that increase β-sheet conformation. We recently demonstrated that HuPrP(90-231) thermal unfolding is partially irreversible and characterized by an intermediate state (β-PrPI), which has been revealed to be involved in the initial stages of PrPC fibrillation, with a seeding activity comparable to that of human infectious prions. In this study, we report the thermal unfolding characterization, in cell-mimicking conditions, of the truncated (HuPrP(90-231)) and full-length (HuPrP(23-231)) human prion protein by means of CD and NMR spectroscopy, revealing that HuPrP(90-231) thermal unfolding is characterized by two successive transitions, as in buffer solution. The amyloidogenic propensity of HuPrP(90-231) under crowded conditions has also been investigated. Our findings show that although the prion intermediate, structurally very similar to β-PrPI, forms at a lower temperature compared to when it is dissolved in buffer solution, in cell-mimicking conditions, the formation of prion fibrils requires a longer incubation time, outlining how molecular crowding influences both the equilibrium states of PrP and its kinetic pathways of folding and aggregation.
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Affiliation(s)
- Manoj Madheswaran
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABiF), Università degli Studi della Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Nataliia Ventserova
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABiF), Università degli Studi della Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Gianluca D’Abrosca
- Department of Clinical and Experimental Medicine, Università degli Studi di Foggia, 71122 Foggia, Italy
| | - Giulia Salzano
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy
| | - Luigi Celauro
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy
| | - Federico Angelo Cazzaniga
- Division of Neurology 5–Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABiF), Università degli Studi della Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABiF), Università degli Studi della Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Fabio Moda
- SSD Laboratory Medicine, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABiF), Università degli Studi della Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Giuseppe Legname
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABiF), Università degli Studi della Campania Luigi Vanvitelli, 81100 Caserta, Italy
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3
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Senanayaka D, Zeng D, Alishiri S, Martin WJ, Moore KI, Patel R, Luka Z, Hirschi A, Reiter NJ. Autoregulatory mechanism of enzyme activity by the nuclear localization signal of lysine-specific demethylase 1. J Biol Chem 2024; 300:107607. [PMID: 39084460 PMCID: PMC11388019 DOI: 10.1016/j.jbc.2024.107607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
The N-terminal region of the human lysine-specific demethylase 1 (LSD1) has no predicted structural elements, contains a nuclear localization signal (NLS), undergoes multiple posttranslational modifications (PTMs), and acts as a protein-protein interaction hub. This intrinsically disordered region (IDR) extends from core LSD1 structure, resides atop the catalytic active site, and is known to be dispensable for catalysis. Here, we show differential nucleosome binding between the full-length and an N terminus deleted LSD1 and identify that a conserved NLS and PTM containing element of the N terminus contains an alpha helical structure, and that this conserved element impacts demethylation. Enzyme assays reveal that LSD1's own electropositive NLS amino acids 107 to 120 inhibit demethylation activity on a model histone 3 lysine 4 dimethyl (H3K4me2) peptide (Kiapp ∼ 3.3 μM) and histone 3 lysine 4 dimethyl nucleosome substrates (IC50 ∼ 30.4 μM), likely mimicking the histone H3 tail. Further, when the identical, inhibitory NLS region contains phosphomimetic modifications, inhibition is partially relieved. Based upon these results and biophysical data, a regulatory mechanism for the LSD1-catalyzed demethylation reaction is proposed whereby NLS-mediated autoinhibition can occur through electrostatic interactions, and be partially relieved through phosphorylation that occurs proximal to the NLS. Taken together, the results highlight a dynamic and synergistic role for PTMs, intrinsically disordered regions, and structured regions near LSD1 active site and introduces the notion that phosphorylated mediated NLS regions can function to fine-tune chromatin modifying enzyme activity.
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Affiliation(s)
- Dulmi Senanayaka
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Danyun Zeng
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Sahar Alishiri
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - William J Martin
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Khadijah I Moore
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Roshni Patel
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Zigmund Luka
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Alexander Hirschi
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Nicholas J Reiter
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA.
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4
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Diana D, Pirone L, Russo L, D'Abrosca G, Madheswaran M, Benfante R, Di Lascio S, Caldinelli L, Fornasari D, Acconcia C, Corvino A, Ventserova N, Pollegioni L, Isernia C, Di Gaetano S, Malgieri G, Pedone EM, Fattorusso R. Structural characterization of PHOX2B and its DNA interaction shed light on the molecular basis of the +7Ala variant pathogenicity in CCHS. Chem Sci 2024; 15:8858-8872. [PMID: 38873078 PMCID: PMC11168103 DOI: 10.1039/d3sc06427a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/12/2024] [Indexed: 06/15/2024] Open
Abstract
An expansion of poly-alanine up to +13 residues in the C-terminus of the transcription factor PHOX2B underlies the onset of congenital central hypoventilation syndrome (CCHS). Recent studies demonstrated that the alanine tract expansion influences PHOX2B folding and activity. Therefore, structural information on PHOX2B is an important target for obtaining clues to elucidate the insurgence of the alanine expansion-related syndrome and also for defining a viable therapy. Here we report by NMR spectroscopy the structural characterization of the homeodomain (HD) of PHOX2B and HD + C-terminus PHOX2B protein, free and in the presence of the target DNA. The obtained structural data are then exploited to obtain a structural model of the PHOX2B-DNA interaction. In addition, the variant +7Ala, responsible for one of the most frequent forms of the syndrome, was analysed, showing different conformational proprieties in solution and a strong propensity to aggregation. Our data suggest that the elongated poly-alanine tract would be related to disease onset through a loss-of-function mechanism. Overall, this study paves the way for the future rational design of therapeutic drugs, suggesting as a possible therapeutic route the use of specific anti-aggregating molecules capable of preventing variant aggregation and possibly restoring the DNA-binding activity of PHOX2B.
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Affiliation(s)
- Donatella Diana
- CNR - Institute of Biostructures and Bioimaging Via Pietro Castellino 111 80131 Naples Italy
| | - Luciano Pirone
- CNR - Institute of Biostructures and Bioimaging Via Pietro Castellino 111 80131 Naples Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Gianluca D'Abrosca
- Department of Clinical and Experimental Medicine - University of Foggia Viale Luigi Pinto 71122 Foggia Italy
| | - Manoj Madheswaran
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Roberta Benfante
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano Milan Italy
- CNR - Institute of Neuroscience Vedano Al Lambro (MB) Italy
- NeuroMi - Milan Center for Neuroscience, University of Milano Bicocca Milan Italy
| | - Simona Di Lascio
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano Milan Italy
| | - Laura Caldinelli
- Department of Biotechnology and Life Sciences, University of Insubria Via J.H. Dunant 3 21100 Varese Italy
| | - Diego Fornasari
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano Milan Italy
| | - Clementina Acconcia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Andrea Corvino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Nataliia Ventserova
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria Via J.H. Dunant 3 21100 Varese Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Sonia Di Gaetano
- CNR - Institute of Biostructures and Bioimaging Via Pietro Castellino 111 80131 Naples Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Emilia M Pedone
- CNR - Institute of Biostructures and Bioimaging Via Pietro Castellino 111 80131 Naples Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
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5
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High-Resolution Conformational Analysis of RGDechi-Derived Peptides Based on a Combination of NMR Spectroscopy and MD Simulations. Int J Mol Sci 2022; 23:ijms231911039. [PMID: 36232339 PMCID: PMC9569650 DOI: 10.3390/ijms231911039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
The crucial role of integrin in pathological processes such as tumor progression and metastasis formation has inspired intense efforts to design novel pharmaceutical agents modulating integrin functions in order to provide new tools for potential therapies. In the past decade, we have investigated the biological proprieties of the chimeric peptide RGDechi, containing a cyclic RGD motif linked to an echistatin C-terminal fragment, able to specifically recognize αvβ3 without cross reacting with αvβ5 and αIIbβ3 integrin. Additionally, we have demonstrated using two RGDechi-derived peptides, called RGDechi1-14 and ψRGDechi, that chemical modifications introduced in the C-terminal part of the peptide alter or abolish the binding to the αvβ3 integrin. Here, to shed light on the structural and dynamical determinants involved in the integrin recognition mechanism, we investigate the effects of the chemical modifications by exploring the conformational space sampled by RGDechi1-14 and ψRGDechi using an integrated natural-abundance NMR/MD approach. Our data demonstrate that the flexibility of the RGD-containing cycle is driven by the echistatin C-terminal region of the RGDechi peptide through a coupling mechanism between the N- and C-terminal regions.
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6
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Russo L, Salzano G, Corvino A, Bistaffa E, Moda F, Celauro L, D'Abrosca G, Isernia C, Milardi D, Giachin G, Malgieri G, Legname G, Fattorusso R. Structural and dynamical determinants of a β-sheet-enriched intermediate involved in amyloid fibrillar assembly of human prion protein. Chem Sci 2022; 13:10406-10427. [PMID: 36277622 PMCID: PMC9473526 DOI: 10.1039/d2sc00345g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/04/2022] [Indexed: 12/02/2022] Open
Abstract
The conformational conversion of the cellular prion protein (PrPC) into a misfolded, aggregated and infectious scrapie isoform is associated with prion disease pathology and neurodegeneration. Despite the significant number of experimental and theoretical studies the molecular mechanism regulating this structural transition is still poorly understood. Here, via Nuclear Magnetic Resonance (NMR) methodologies we investigate at the atomic level the mechanism of the human HuPrP(90–231) thermal unfolding and characterize the conformational equilibrium between its native structure and a β-enriched intermediate state, named β-PrPI. By comparing the folding mechanisms of metal-free and Cu2+-bound HuPrP(23–231) and HuPrP(90–231) we show that the coupling between the N- and C-terminal domains, through transient electrostatic interactions, is the key molecular process in tuning long-range correlated μs–ms dynamics that in turn modulate the folding process. Moreover, via thioflavin T (ThT)-fluorescence fibrillization assays we show that β-PrPI is involved in the initial stages of PrP fibrillation, overall providing a clear molecular description of the initial phases of prion misfolding. Finally, we show by using Real-Time Quaking-Induced Conversion (RT-QuIC) that the β-PrPI acts as a seed for the formation of amyloid aggregates with a seeding activity comparable to that of human infectious prions. The N-ter domain in HuPrP regulates the folding mechanism by tuning the long-range μs–ms dynamics. Removal of the N-ter domain triggers the formation of a stable β-enriched intermediate state inducing amyloid aggregates with HuPrPSc seeding activity.![]()
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Affiliation(s)
- Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Giulia Salzano
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Andrea Corvino
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Edoardo Bistaffa
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Division of Neurology 5 and Neuropathology, Milano, Italy
| | - Fabio Moda
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Division of Neurology 5 and Neuropathology, Milano, Italy
| | - Luigi Celauro
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Danilo Milardi
- Institute of Crystallography, National Research Council, Catania, Italy
| | - Gabriele Giachin
- Department of Chemical Sciences (DiSC), University of Padua, Padova, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- ELETTRA Laboratory, Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
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7
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Park SH, Siddiqi H, Castro DV, De Angelis AA, Oom AL, Stoneham CA, Lewinski MK, Clark AE, Croker BA, Carlin AF, Guatelli J, Opella SJ. Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. PLoS Pathog 2021; 17:e1009519. [PMID: 34003853 PMCID: PMC8184013 DOI: 10.1371/journal.ppat.1009519] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/07/2021] [Accepted: 04/29/2021] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 is the novel coronavirus that is the causative agent of COVID-19, a sometimes-lethal respiratory infection responsible for a world-wide pandemic. The envelope (E) protein, one of four structural proteins encoded in the viral genome, is a 75-residue integral membrane protein whose transmembrane domain exhibits ion channel activity and whose cytoplasmic domain participates in protein-protein interactions. These activities contribute to several aspects of the viral replication-cycle, including virion assembly, budding, release, and pathogenesis. Here, we describe the structure and dynamics of full-length SARS-CoV-2 E protein in hexadecylphosphocholine micelles by NMR spectroscopy. We also characterized its interactions with four putative ion channel inhibitors. The chemical shift index and dipolar wave plots establish that E protein consists of a long transmembrane helix (residues 8–43) and a short cytoplasmic helix (residues 53–60) connected by a complex linker that exhibits some internal mobility. The conformations of the N-terminal transmembrane domain and the C-terminal cytoplasmic domain are unaffected by truncation from the intact protein. The chemical shift perturbations of E protein spectra induced by the addition of the inhibitors demonstrate that the N-terminal region (residues 6–18) is the principal binding site. The binding affinity of the inhibitors to E protein in micelles correlates with their antiviral potency in Vero E6 cells: HMA ≈ EIPA > DMA >> Amiloride, suggesting that bulky hydrophobic groups in the 5’ position of the amiloride pyrazine ring play essential roles in binding to E protein and in antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. These studies provide the foundation for complete structure determination of E protein and for structure-based drug discovery targeting this protein. The novel coronavirus SARS-CoV-2, the causative agent of the world-wide pandemic of COVID-19, has become one of the greatest threats to human health. While rapid progress has been made in the development of vaccines, drug discovery has lagged, partly due to the lack of atomic-resolution structures of the free and drug-bound forms of the viral proteins. The SARS-CoV-2 envelope (E) protein, with its multiple activities that contribute to viral replication, is widely regarded as a potential target for COVID-19 treatment. As structural information is essential for drug discovery, we established an efficient sample preparation system for biochemical and structural studies of intact full-length SARS-CoV-2 E protein and characterized its structure and dynamics. We also characterized the interactions of amilorides with specific E protein residues and correlated this with their antiviral activity during viral replication. The binding affinity of the amilorides to E protein correlated with their antiviral potency, suggesting that E protein is indeed the likely target of their antiviral activity. We found that residue asparagine15 plays an important role in maintaining the conformation of the amiloride binding site, providing molecular guidance for the design of inhibitors targeting E protein.
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Affiliation(s)
- Sang Ho Park
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Haley Siddiqi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Daniela V. Castro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Anna A. De Angelis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Aaron L. Oom
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Charlotte A. Stoneham
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Mary K. Lewinski
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Alex E. Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Ben A. Croker
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - John Guatelli
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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8
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Kang M, Doddapaneni K, Sarni S, Heppner Z, Wysocki V, Wu Z. Solution structure of the nucleotide hydrolase BlsM: Implication of its substrate specificity. Protein Sci 2021; 29:1760-1773. [PMID: 31876335 DOI: 10.1002/pro.3812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/17/2019] [Accepted: 12/21/2019] [Indexed: 11/06/2022]
Abstract
Biosynthesis of the peptidyl nucleoside antifungal agent blasticidin S in Streptomyces griseochromogenes requires the hydrolytic function of a nucleotide hydrolase, BlsM, to excise the free cytosine from the 5'-monophosphate cytosine nucleotide. In addition to its hydrolytic activity, interestingly, BlsM has also been shown to possess a novel cytidine deaminase activity, converting cytidine, and deoxycytidine to uridine and deoxyuridine. To gain insight into the substrate specificity of BlsM and the mechanism by which it performs these dual function, the solution structure of BlsM was determined by multi-dimensional nuclear magnetic resonance approaches. BlsM displays a nucleoside deoxyribosyltransferase-like dimeric topology, with each monomer consisting of a five-stranded β-sheet that is sandwiched by five α-helixes. Compared with the purine nucleotide hydrolase RCL, each monomer of BlsM has a smaller active site pocket, enclosed by a group of conserved hydrophobic residues from both monomers. The smaller size of active site is consistent with its substrate specificity for a pyrimidine, whereas a much more open active site, as in RCL might be required to accommodate a larger purine ring. In addition, BlsM confers its substrate specificity for a ribosyl-nucleotide through a key residue, Phe19. When mutated to a tyrosine, F19Y reverses its substrate preference. While significantly impaired in its hydrolytic capability, F19Y exhibited a pronounced deaminase activity on CMP, presumably due to an altered substrate orientation as a result of a steric clash between the 2'-hydroxyl of CMP and the ζ-OH group of F19Y. Finally, Glu105 appears to be critical for the dual function of BlsM.
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Affiliation(s)
- Minhee Kang
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Kiran Doddapaneni
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Samantha Sarni
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Zach Heppner
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Vicki Wysocki
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Zhengrong Wu
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
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9
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Tarasov SA, Gorbunov EA, Don ES, Emelyanova AG, Kovalchuk AL, Yanamala N, Schleker ASS, Klein-Seetharaman J, Groenestein R, Tafani JP, van der Meide P, Epstein OI. Insights into the Mechanism of Action of Highly Diluted Biologics. THE JOURNAL OF IMMUNOLOGY 2020; 205:1345-1354. [PMID: 32727888 DOI: 10.4049/jimmunol.2000098] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/04/2020] [Indexed: 12/12/2022]
Abstract
The therapeutic use of Abs in cancer, autoimmunity, transplantation, and other fields is among the major biopharmaceutical advances of the 20th century. Broader use of Ab-based drugs is constrained because of their high production costs and frequent side effects. One promising approach to overcome these limitations is the use of highly diluted Abs, which are produced by gradual reduction of an Ab concentration to an extremely low level. This technology was used to create a group of drugs for the treatment of various diseases, depending on the specificity of the used Abs. Highly diluted Abs to IFN-γ (hd-anti-IFN-γ) have been demonstrated to be efficacious against influenza and other respiratory infections in a variety of preclinical and clinical studies. In the current study, we provide evidence for a possible mechanism of action of hd-anti-IFN-γ. Using high-resolution solution nuclear magnetic resonance spectroscopy, we show that the drug induced conformational changes in the IFN-γ molecule. Chemical shift changes occurred in the amino acids located primarily at the dimer interface and at the C-terminal region of IFN-γ. These molecular changes could be crucial for the function of the protein, as evidenced by an observed hd-anti-IFN-γ-induced increase in the specific binding of IFN-γ to its receptor in U937 cells, enhanced induced production of IFN-γ in human PBMC culture, and increased survival of influenza A-infected mice.
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Affiliation(s)
- Sergey A Tarasov
- OOO "NPF "Materia Medica Holding," 127473 Moscow, Russian Federation.,The Institute of General Pathology and Pathophysiology, 125315 Moscow, Russian Federation
| | | | - Elena S Don
- OOO "NPF "Materia Medica Holding," 127473 Moscow, Russian Federation.,The Institute of General Pathology and Pathophysiology, 125315 Moscow, Russian Federation
| | - Alexandra G Emelyanova
- OOO "NPF "Materia Medica Holding," 127473 Moscow, Russian Federation.,The Institute of General Pathology and Pathophysiology, 125315 Moscow, Russian Federation
| | | | - Naveena Yanamala
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - A Sylvia S Schleker
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - Judith Klein-Seetharaman
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | | | | | | | - Oleg I Epstein
- OOO "NPF "Materia Medica Holding," 127473 Moscow, Russian Federation.,The Institute of General Pathology and Pathophysiology, 125315 Moscow, Russian Federation
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10
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Danielsson J, Noel JK, Simien JM, Duggan BM, Oliveberg M, Onuchic JN, Jennings PA, Haglund E. The Pierced Lasso Topology Leptin has a Bolt on Dynamic Domain Composed by the Disordered Loops I and III. J Mol Biol 2020; 432:3050-3063. [PMID: 32081588 DOI: 10.1016/j.jmb.2020.01.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/18/2020] [Accepted: 01/24/2020] [Indexed: 02/08/2023]
Abstract
Leptin is an important signaling hormone, mostly known for its role in energy expenditure and satiety. Furthermore, leptin plays a major role in other proteinopathies, such as cancer, marked hyperphagia, impaired immune function, and inflammation. In spite of its biological relevance in human health, there are no NMR resonance assignments of the human protein available, obscuring high-resolution characterization of the soluble protein and/or its conformational dynamics, suggested as being important for receptor interaction and biological activity. Here, we report the nearly complete backbone resonance assignments of human leptin. Chemical shift-based secondary structure prediction confirms that in solution leptin forms a four-helix bundle including a pierced lasso topology. The conformational dynamics, determined on several timescales, show that leptin is monomeric, has a rigid four-helix scaffold, and a dynamic domain, including a transiently formed helix. The dynamic domain is anchored to the helical scaffold by a secondary hydrophobic core, pinning down the long loops of leptin to the protein body, inducing motional restriction without a well-defined secondary or tertiary hydrogen bond stabilized structure. This dynamic region is well suited for and may be involved in functional allosteric dynamics upon receptor binding.
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Affiliation(s)
- Jens Danielsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | | | | | - Brendan Michael Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, USA
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, USA; Department of Physics and Astronomy, Department of Chemistry, And Department of Biosciences, Rice University, Houston, USA
| | - Patricia Ann Jennings
- Department of Chemistry and Biochemistry, The University of California at San Diego, La Jolla, USA
| | - Ellinor Haglund
- The Department of Chemistry, University of Hawaii, Manoa, Honolulu, USA.
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11
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Kumar A, Estrada DF. Specificity of the Redox Complex between Cytochrome P450 24A1 and Adrenodoxin Relies on Carbon-25 Hydroxylation of Vitamin-D Substrate. Drug Metab Dispos 2019; 47:974-982. [PMID: 31289106 DOI: 10.1124/dmd.119.087759] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/01/2019] [Indexed: 11/22/2022] Open
Abstract
Metabolic deactivation of 1,25(OH)2D3 is initiated by modification of the vitamin-D side chain, as carried out by the mitochondrial cytochrome P450 24A1 (CYP24A1). In addition to its role in vitamin-D metabolism, CYP24A1 is involved in catabolism of vitamin-D analogs, thereby reducing their efficacy. CYP24A1 function relies on electron transfer from the soluble ferredoxin protein adrenodoxin (Adx). Recent structural evidence suggests that regioselectivity of the CYP24A1 reaction may correlate with distinct modes of Adx recognition. Here we used nuclear magnetic resonance (NMR) spectroscopy to monitor the structure of 15N-labeled full-length Adx from rat while forming the complex with rat CYP24A1 in the ligand-free state or bound to either 1,25(OH)2D3 or the vitamin-D supplement 1α(OH)D3. Although both vitamin-D ligands were found to induce a reduction in overall NMR peak broadening, thereby suggesting ligand-induced disruption of the complex, a crosslinking analysis suggested that ligand does not have a significant effect on the relative association affinities of the redox complexes. However, a key finding is that, whereas the presence of primary CYP24A1 substrate was found to induce NMR peak broadening focused on the putative recognition site α-helix 3 of rat adrenodoxin, the interaction in the presence of 1α(OH)D3, which is lacking the carbon-25 hydroxyl, results in disruption of the NMR peak broadening pattern, thus indicating a ligand-induced nonspecific protein interaction. These findings provide a structural basis for the poor substrate turnover of side-chain-modified vitamin-D analogs, while also confirming that specificity of the CYP24A1-ligand interaction influences specificity of CYP24A1-Adx recognition. SIGNIFICANCE STATEMENT: Mitochondrial cytochrome P450 enzymes, such as CYP24A1 responsible for catabolizing vitamin-D and its analogs, rely on a protein-protein interaction with a ferredoxin in order to receive delivery of the electrons required for catalysis. In this study, we demonstrate that this protein interaction is influenced by the enzyme-ligand interaction that precedes it. Specifically, vitamin-D missing carbon-25 hydroxylation binds the enzyme active site with high affinity but results in a loss of P450-ferredoxin binding specificity.
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Affiliation(s)
- Amit Kumar
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Science, University at Buffalo, Buffalo New York
| | - D Fernando Estrada
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Science, University at Buffalo, Buffalo New York
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12
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Molecular modeling of the effects of glycosylation on the structure and dynamics of human interferon-gamma. J Mol Model 2019; 25:127. [DOI: 10.1007/s00894-019-4013-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/29/2019] [Indexed: 02/07/2023]
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13
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Farina B, Del Gatto A, Comegna D, Di Gaetano S, Capasso D, Isernia C, Saviano M, Fattorusso R, Zaccaro L, Russo L. Conformational studies of RGDechi peptide by natural-abundance NMR spectroscopy. J Pept Sci 2019; 25:e3166. [PMID: 30884005 DOI: 10.1002/psc.3166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 12/24/2022]
Abstract
Integrins are heterodimeric cell-surface proteins that play important roles during developmental and pathological processes. Diverse human pathologies involve integrin adhesion including thrombotic diseases, inflammation, tumour progression, fibrosis, and infectious diseases. Although in the past decade, novel integrin-inhibitor drugs have been developed for integrin-based medical applications, the structural determinants modulating integrin-ligands recognition mechanisms are still poorly understood, reducing the number of integrin subtype exclusive antagonists. In this scenario, we have very recently showed, by means of chemical and biological assays, that a chimeric peptide (named RGDechi), containing a cyclic RGD motif linked to an echistatin C-terminal fragment, is able to interact with the components of integrin family with variable affinities, the highest for αv β3. Here, in order to understand the mechanistic details driving the molecular recognition mechanism of αv β3 by RGDechi, we have performed a detailed structural and dynamics characterization of the free peptide by natural abundance nuclear magnetic resonance (NMR) spectroscopy. Our data indicate that RGDechi presents in solution an heterogeneous conformational ensemble characterized by a more constrained and rigid pentacyclic ring and a largely unstructured acyclic region. Moreover, we propose that the molecular recognition of αv β3 integrin by RGDechi occurs by a combination of conformational selection and induced fit mechanisms. Finally, our study indicates that a detailed NMR characterization, by means of natural abundance 15 N and 13 C, of a mostly unstructured bioactive peptide may provide the molecular basis to get essential structural insights into the binding mechanism to the biological partner.
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Affiliation(s)
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Naples, Italy
| | - Daniela Comegna
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Naples, Italy
| | - Domenica Capasso
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | | | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Naples, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Caserta, Italy
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14
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Ramesh K, Lama D, Tan KW, Nguyen VS, Chew FT, Verma CS, Mok YK. Homologous Lympho-Epithelial Kazal-type Inhibitor Domains Delay Blood Coagulation by Inhibiting Factor X and XI with Differential Specificity. Structure 2018; 26:1178-1186.e3. [PMID: 30017565 DOI: 10.1016/j.str.2018.05.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/30/2018] [Accepted: 05/29/2018] [Indexed: 10/28/2022]
Abstract
Despite being initially identified in the blood filtrate, LEKTI is a 15-domain Kazal-type inhibitor mostly known in the regulation of skin desquamation. In the current study, screening of serine proteases in blood coagulation cascade showed that LEKTI domain 4 has inhibitory activity toward only FXIa, whereas LEKTI domain 6 inhibits both FXIa and FXaB (bovine FXa). Nuclear magnetic resonance structural and dynamic experiments plus molecular dynamics simulation revealed that LEKTI domain 4 has enhanced backbone flexibility at the reactive-site loop. A model of the LEKTI-protease complex revealed that FXaB has a narrower S4 pocket compared with FXIa and hence prefers only small side-chain residues at the P4 position, such as Ala in LEKTI domain 6. Mutational studies combined with a molecular complex model suggest that both a more flexible reactive-site loop and a bulky residue at the P4 position make LEKTI domain 4 a weaker but highly selective inhibitor of FXIa.
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Affiliation(s)
- Karthik Ramesh
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Dilraj Lama
- Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Kang Wei Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Van Sang Nguyen
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Chandra S Verma
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore.
| | - Yu Keung Mok
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore.
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15
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Kato J, Dey S, Soto JE, Butan C, Wilkinson MC, De Guzman RN, Galan JE. A protein secreted by the Salmonella type III secretion system controls needle filament assembly. eLife 2018; 7:e35886. [PMID: 30015613 PMCID: PMC6066329 DOI: 10.7554/elife.35886] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/16/2018] [Indexed: 12/14/2022] Open
Abstract
Type III protein secretion systems (T3SS) are encoded by several pathogenic or symbiotic bacteria. The central component of this nanomachine is the needle complex. Here we show in a Salmonella Typhimurium T3SS that assembly of the needle filament of this structure requires OrgC, a protein encoded within the T3SS gene cluster. Absence of OrgC results in significantly reduced number of needle substructures but does not affect needle length. We show that OrgC is secreted by the T3SS and that exogenous addition of OrgC can complement a ∆orgC mutation. We also show that OrgC interacts with the needle filament subunit PrgI and accelerates its polymerization into filaments in vitro. The structure of OrgC shows a novel fold with a shared topology with a domain from flagellar capping proteins. These findings identify a novel component of T3SS and provide new insight into the assembly of the type III secretion machine.
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Affiliation(s)
- Junya Kato
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
| | - Supratim Dey
- Department of Molecular BiosciencesUniversity of KansasLawrenceUnited States
| | - Jose E Soto
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
| | - Carmen Butan
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
| | - Mason C Wilkinson
- Department of Molecular BiosciencesUniversity of KansasLawrenceUnited States
| | - Roberto N De Guzman
- Department of Molecular BiosciencesUniversity of KansasLawrenceUnited States
| | - Jorge E Galan
- Department of Microbial PathogenesisYale University School of MedicineNew HavenUnited States
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16
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Roganowicz MD, Komurlu S, Mukherjee S, Plewka J, Alam SL, Skorupka KA, Wan Y, Dawidowski D, Cafiso DS, Ganser-Pornillos BK, Campbell EM, Pornillos O. TRIM5α SPRY/coiled-coil interactions optimize avid retroviral capsid recognition. PLoS Pathog 2017; 13:e1006686. [PMID: 29040325 PMCID: PMC5667893 DOI: 10.1371/journal.ppat.1006686] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 11/02/2017] [Accepted: 10/10/2017] [Indexed: 12/30/2022] Open
Abstract
Restriction factors are important components of intrinsic cellular defense mechanisms against viral pathogens. TRIM5α is a restriction factor that intercepts the incoming capsid cores of retroviruses such as HIV and provides an effective species-specific barrier to retroviral infection. The TRIM5α SPRY domain directly binds the capsid with only very weak, millimolar-level affinity, and productive capsid recognition therefore requires both TRIM5α dimerization and assembly of the dimers into a multivalent hexagonal lattice to promote avid binding. Here, we explore the important unresolved question of whether the SPRY domains are flexibly linked to the TRIM lattice or more precisely positioned to maximize avidity. Biochemical and biophysical experiments indicate that the linker segment connecting the SPRY domain to the coiled-coil domain adopts an α-helical fold, and that this helical portion mediates interactions between the two domains. Targeted mutations were generated to disrupt the putative packing interface without affecting dimerization or higher-order assembly, and we identified mutant proteins that were nevertheless deficient in capsid binding in vitro and restriction activity in cells. Our studies therefore support a model wherein substantial avidity gains during assembly-mediated capsid recognition by TRIM5α come in part from tailored spacing of tethered recognition domains.
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Affiliation(s)
- Marcin D. Roganowicz
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Sevnur Komurlu
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Santanu Mukherjee
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Jacek Plewka
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Steven L. Alam
- Department of Biochemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Katarzyna A. Skorupka
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Yueping Wan
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Damian Dawidowski
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - David S. Cafiso
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Barbie K. Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Edward M. Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
- * E-mail:
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17
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D'Abrosca G, Russo L, Palmieri M, Baglivo I, Netti F, de Paola I, Zaccaro L, Farina B, Iacovino R, Pedone PV, Isernia C, Fattorusso R, Malgieri G. The (unusual) aspartic acid in the metal coordination sphere of the prokaryotic zinc finger domain. J Inorg Biochem 2016; 161:91-8. [PMID: 27238756 DOI: 10.1016/j.jinorgbio.2016.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 11/29/2022]
Abstract
The possibility of choices of protein ligands and coordination geometries leads to diverse Zn(II) binding sites in zinc-proteins, allowing a range of important biological roles. The prokaryotic Cys2His2 zinc finger domain (originally found in the Ros protein from Agrobacterium tumefaciens) tetrahedrally coordinates zinc through two cysteine and two histidine residues and it does not adopt a correct fold in the absence of the metal ion. Ros is the first structurally characterized member of a family of bacterial proteins that presents several amino acid changes in the positions occupied in Ros by the zinc coordinating residues. In particular, the second position is very often occupied by an aspartic acid although the coordination of structural zinc by an aspartate in eukaryotic zinc fingers is very unusual. Here, by appropriately mutating the protein Ros, we characterize the aspartate role within the coordination sphere of this family of proteins demonstrating how the presence of this residue only slightly perturbs the functional structure of the prokaryotic zinc finger domain while it greatly influences its thermodynamic properties.
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Affiliation(s)
- Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Fortuna Netti
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ivan de Paola
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Laura Zaccaro
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Biancamaria Farina
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Rosa Iacovino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy.
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18
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Naiyer A, Hassan MI, Islam A, Sundd M, Ahmad F. Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques. J Biomol Struct Dyn 2015; 33:2267-84. [PMID: 25586676 DOI: 10.1080/07391102.2014.999354] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Almost all proteins fold via a number of partially structured intermediates such as molten globule (MG) and pre-molten globule states. Understanding the structure of these intermediates at atomic level is often a challenge, as these states are observed under extreme conditions of pH, temperature, and chemical denaturants. Furthermore, several other processes such as chemical modification, site-directed mutagenesis (or point mutation), and cleavage of covalent bond of natural proteins often lead to MG like partially unfolded conformation. However, the dynamic nature of proteins in these states makes them unsuitable for most structure determination at atomic level. Intermediate states studied so far have been characterized mostly by circular dichroism, fluorescence, viscosity, dynamic light scattering measurements, dye binding, infrared techniques, molecular dynamics simulations, etc. There is a limited amount of structural data available on these intermediate states by nuclear magnetic resonance (NMR) and hence there is a need to characterize these states at the molecular level. In this review, we present characterization of equilibrium intermediates by biophysical techniques with special reference to NMR.
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Affiliation(s)
- Abdullah Naiyer
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi - 110025 , India
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19
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Künze G, Theisgen S, Huster D. Backbone ¹H, ¹⁵N, and ¹³C and side chain ¹³Cβ NMR chemical shift assignment of murine interleukin-10. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:375-8. [PMID: 23982919 DOI: 10.1007/s12104-013-9521-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/16/2013] [Indexed: 05/22/2023]
Abstract
Almost complete assignment of backbone (1)H, (13)C, (15)N and side chain (13)Cβ resonances for the immune-regulatory cytokine IL-10 is reported. The protein was overexpressed in Escherichia coli and was refolded from inclusion bodies. The point mutation C149Y was introduced to suppress incorrect disulfide bond formation and to improve protein refolding.
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Affiliation(s)
- Georg Künze
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstraße 16/18, 04107, Leipzig, Germany,
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20
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Huang T, Schor SL, Hinck AP. Biological activity differences between TGF-β1 and TGF-β3 correlate with differences in the rigidity and arrangement of their component monomers. Biochemistry 2014; 53:5737-49. [PMID: 25153513 PMCID: PMC4165442 DOI: 10.1021/bi500647d] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
TGF-β1, -β2, and -β3 are small, secreted signaling proteins. They share 71-80% sequence identity and signal through the same receptors, yet the isoform-specific null mice have distinctive phenotypes and are inviable. The replacement of the coding sequence of TGF-β1 with TGF-β3 and TGF-β3 with TGF-β1 led to only partial rescue of the mutant phenotypes, suggesting that intrinsic differences between them contribute to the requirement of each in vivo. Here, we investigated whether the previously reported differences in the flexibility of the interfacial helix and arrangement of monomers was responsible for the differences in activity by generating two chimeric proteins in which residues 54-75 in the homodimer interface were swapped. Structural analysis of these using NMR and functional analysis using a dermal fibroblast migration assay showed that swapping the interfacial region swapped both the conformational preferences and activity. Conformational and activity differences were also observed between TGF-β3 and a variant with four helix-stabilizing residues from TGF-β1, suggesting that the observed changes were due to increased helical stability and the altered conformation, as proposed. Surface plasmon resonance analysis showed that TGF-β1, TGF-β3, and variants bound the type II signaling receptor, TβRII, nearly identically, but had small differences in the dissociation rate constant for recruitment of the type I signaling receptor, TβRI. However, the latter did not correlate with conformational preference or activity. Hence, the difference in activity arises from differences in their conformations, not their manner of receptor binding, suggesting that a matrix protein that differentially binds them might determine their distinct activities.
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Affiliation(s)
- Tao Huang
- Department of Biochemistry, University of Texas Health Science Center at San Antonio , San Antonio, Texas 78229-3900, United States
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21
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Vilar M, Sung TC, Chen Z, García-Carpio I, Fernandez EM, Xu J, Riek R, Lee KF. Heterodimerization of p45-p75 modulates p75 signaling: structural basis and mechanism of action. PLoS Biol 2014; 12:e1001918. [PMID: 25093680 PMCID: PMC4122344 DOI: 10.1371/journal.pbio.1001918] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/25/2014] [Indexed: 12/26/2022] Open
Abstract
The formation of a p45-p75 heterodimer overrides p75’s inhibition of nerve regeneration by stopping p75 homodimers from forming and creating a complex with the Nogo receptor. The p75 neurotrophin receptor, a member of the tumor necrosis factor receptor superfamily, is required as a co-receptor for the Nogo receptor (NgR) to mediate the activity of myelin-associated inhibitors such as Nogo, MAG, and OMgp. p45/NRH2/PLAIDD is a p75 homologue and contains a death domain (DD). Here we report that p45 markedly interferes with the function of p75 as a co-receptor for NgR. P45 forms heterodimers with p75 and thereby blocks RhoA activation and inhibition of neurite outgrowth induced by myelin-associated inhibitors. p45 binds p75 through both its transmembrane (TM) domain and DD. To understand the underlying mechanisms, we have determined the three-dimensional NMR solution structure of the intracellular domain of p45 and characterized its interaction with p75. We have identified the residues involved in such interaction by NMR and co-immunoprecipitation. The DD of p45 binds the DD of p75 by electrostatic interactions. In addition, previous reports suggested that Cys257 in the p75 TM domain is required for signaling. We found that the interaction of the cysteine 58 of p45 with the cysteine 257 of p75 within the TM domain is necessary for p45–p75 heterodimerization. These results suggest a mechanism involving both the TM domain and the DD of p45 to regulate p75-mediated signaling. Injuries to the brain and spinal cord often result in paralysis due to the fact that the injured nerves cannot regrow to reach their normal targets and carry out their functions. At the injury sites, there are proteins released from the damaged myelin that bind the Nogo receptor (NgR) on the nerve and inhibit its regeneration. The NgR needs to form a complex with the p75 neurotrophin receptor in order to mediate this inhibitory signal. Here we found that p45, a homologue of p75, can also bind to p75 and block its inhibitory activity when overexpressed. To perform its function, p75 needs to dimerize through both its transmembrane and intracellular domains, facilitating the recruitment of several proteins. Our structural and functional studies show that p45 binds specifically to conserved regions in the p75 transmembrane and the intracellular domain and that this blocks p75 dimerization along with its downstream signaling. Thus, this study demonstrates that altering the oligomerization of p75 is a good strategy to override p75's inhibitory effects on nerve regeneration, and it opens the door for the design of specific p75 inhibitors for therapeutic applications.
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Affiliation(s)
- Marçal Vilar
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute, La Jolla, California, United States of America
- Neurodegeneration Unit, Chronic Disease Program, Spanish Institute of Health Carlos III, Madrid, Spain
- * E-mail: (K.-F.L.); (R.R.); (M.V.)
| | - Tsung-Chang Sung
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute, La Jolla, California, United States of America
| | - Zhijiang Chen
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute, La Jolla, California, United States of America
| | - Irmina García-Carpio
- Neurodegeneration Unit, Chronic Disease Program, Spanish Institute of Health Carlos III, Madrid, Spain
| | - Eva M. Fernandez
- Neurodegeneration Unit, Chronic Disease Program, Spanish Institute of Health Carlos III, Madrid, Spain
| | - Jiqing Xu
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute, La Jolla, California, United States of America
| | - Roland Riek
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute, La Jolla, California, United States of America
- Laboratory for Physical Chemistry, ETH Zürich, Zürich, Switzerland
- * E-mail: (K.-F.L.); (R.R.); (M.V.)
| | - Kuo-Fen Lee
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute, La Jolla, California, United States of America
- * E-mail: (K.-F.L.); (R.R.); (M.V.)
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22
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Wang W, Naiyer N, Mitra M, Li J, Williams MC, Rouzina I, Gorelick RJ, Wu Z, Musier-Forsyth K. Distinct nucleic acid interaction properties of HIV-1 nucleocapsid protein precursor NCp15 explain reduced viral infectivity. Nucleic Acids Res 2014; 42:7145-59. [PMID: 24813443 PMCID: PMC4066767 DOI: 10.1093/nar/gku335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
During human immunodeficiency virus type 1 (HIV-1) maturation, three different forms of nucleocapsid (NC) protein—NCp15 (p9 + p6), NCp9 (p7 + SP2) and NCp7—appear successively. A mutant virus expressing NCp15 shows greatly reduced infectivity. Mature NCp7 is a chaperone protein that facilitates remodeling of nucleic acids (NAs) during reverse transcription. To understand the strict requirement for NCp15 processing, we compared the chaperone function of the three forms of NC. NCp15 anneals tRNA to the primer-binding site at a similar rate as NCp7, whereas NCp9 is the most efficient annealing protein. Assays to measure NA destabilization show a similar trend. Dynamic light scattering studies reveal that NCp15 forms much smaller aggregates relative to those formed by NCp7 and NCp9. Nuclear magnetic resonance studies suggest that the acidic p6 domain of HIV-1 NCp15 folds back and interacts with the basic zinc fingers. Neutralizing the acidic residues in p6 improves the annealing and aggregation activity of NCp15 to the level of NCp9 and increases the protein–NA aggregate size. Slower NCp15 dissociation kinetics is observed by single-molecule DNA stretching, consistent with the formation of electrostatic inter-protein contacts, which likely contribute to the distinct aggregate morphology, irregular HIV-1 core formation and non-infectious virus.
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Affiliation(s)
- Wei Wang
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Nada Naiyer
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mithun Mitra
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jialin Li
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Zhengrong Wu
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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23
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Lee YZ, Lee YT, Lin YJ, Chen YJ, Sue SC. A streamlined method for preparing split intein for NMR study. Protein Expr Purif 2014; 99:106-12. [PMID: 24751877 DOI: 10.1016/j.pep.2014.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/19/2014] [Accepted: 04/10/2014] [Indexed: 11/16/2022]
Abstract
A protein ligase, intein, mediates a protein-splicing reaction. It can be split into two complementary fragments and reconstituted as a whole intein scaffold to perform protein trans-splicing. To understand the association of intein fragments and the splicing mechanism, it is necessary to produce a large quantity of split intein for structural study. Conventionally, two fragments are prepared separately and assembled in solution, but severe aggregation of intein fragments occurs, and precise control of the relative concentration of each fragment is difficult. Here, we present a streamlined method to incorporate a circular permutation concept into the production of split intein. By circular permutation of the native split Nostoc punctiforme DnaE intein (NpuInt), a new backbone opening is relocated to the native split site at residue 102. As the protein splicing activity is preserved, the expressed NpuInt can immediately self-cleave into a two-piece split NpuInt. Because of a tight association between the two complementary fragments, split NpuInt can be purified in one step. The idea is simple and applicable to other split inteins. Employing the new preparation, we use NMR spectra to assign the backbone and side chain resonances for the native split NpuInt.
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Affiliation(s)
- Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yun-Tzai Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Jan Lin
- Graduate Institute of Natural Products and Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Ju Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan.
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan; Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.
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24
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Contursi P, Farina B, Pirone L, Fusco S, Russo L, Bartolucci S, Fattorusso R, Pedone E. Structural and functional studies of Stf76 from the Sulfolobus islandicus plasmid-virus pSSVx: a novel peculiar member of the winged helix-turn-helix transcription factor family. Nucleic Acids Res 2014; 42:5993-6011. [PMID: 24682827 PMCID: PMC4027180 DOI: 10.1093/nar/gku215] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The hybrid plasmid–virus pSSVx from Sulfolobus islandicus presents an open reading frame encoding a 76 amino acid protein, namely Stf76, that does not show significant sequence homology with any protein with known 3D structure. The recombinant protein recognizes specifically two DNA-binding sites located in its own promoter, thus suggesting an auto-regulated role of its expression. Circular dichroism, spectrofluorimetric, light scattering and isothermal titration calorimetry experiments indicated a 2:1 molar ratio (protein:DNA) upon binding to the DNA target containing a single site. Furthermore, the solution structure of Stf76, determined by nuclear magnetic resonance (NMR) using chemical shift Rosetta software, has shown that the protein assumes a winged helix–turn–helix fold. NMR chemical shift perturbation analysis has been performed for the identification of the residues responsible for DNA interaction. In addition, a model of the Stf76–DNA complex has been built using as template a structurally related homolog.
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Affiliation(s)
- Patrizia Contursi
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Biancamaria Farina
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | | | - Salvatore Fusco
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta 81100, Italy
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta 81100, Italy
| | - Emilia Pedone
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy Istituto di Biostrutture e Bioimmagini, C.N.R., Napoli 80134, Italy
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25
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Tuttle LM, Dyson HJ, Wright PE. Side chain conformational averaging in human dihydrofolate reductase. Biochemistry 2014; 53:1134-45. [PMID: 24498949 PMCID: PMC3985697 DOI: 10.1021/bi4015314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The three-dimensional structures
of the dihydrofolate reductase
enzymes from Escherichia coli (ecDHFR or ecE) and Homo sapiens (hDHFR or hE) are very similar, despite a rather
low level of sequence identity. Whereas the active site loops of ecDHFR
undergo major conformational rearrangements during progression through
the reaction cycle, hDHFR remains fixed in a closed loop conformation
in all of its catalytic intermediates. To elucidate the structural
and dynamic differences between the human and E. coli enzymes, we conducted a comprehensive analysis of side chain flexibility
and dynamics in complexes of hDHFR that represent intermediates in
the major catalytic cycle. Nuclear magnetic resonance relaxation dispersion
experiments show that, in marked contrast to the functionally important
motions that feature prominently in the catalytic intermediates of
ecDHFR, millisecond time scale fluctuations cannot be detected for
hDHFR side chains. Ligand flux in hDHFR is thought to be mediated
by conformational changes between a hinge-open state when the substrate/product-binding
pocket is vacant and a hinge-closed state when this pocket is occupied.
Comparison of X-ray structures of hinge-open and hinge-closed states
shows that helix αF changes position by sliding between the
two states. Analysis of χ1 rotamer populations derived
from measurements of 3JCγCO and 3JCγN couplings
indicates that many of the side chains that contact helix αF
exhibit rotamer averaging that may facilitate the conformational change.
The χ1 rotamer adopted by the Phe31 side chain depends
upon whether the active site contains the substrate or product. In
the holoenzyme (the binary complex of hDHFR with reduced nicotinamide
adenine dinucleotide phosphate), a combination of hinge opening and
a change in the Phe31 χ1 rotamer opens the active
site to facilitate entry of the substrate. Overall, the data suggest
that, unlike ecDHFR, hDHFR requires minimal backbone conformational
rearrangement as it proceeds through its enzymatic cycle, but that
ligand flux is brokered by more subtle conformational changes that
depend on the side chain motions of critical residues.
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Affiliation(s)
- Lisa M Tuttle
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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26
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Palmieri M, Russo L, Malgieri G, Esposito S, Baglivo I, Rivellino A, Farina B, de Paola I, Zaccaro L, Milardi D, Isernia C, Pedone PV, Fattorusso R. Deciphering the zinc coordination properties of the prokaryotic zinc finger domain: The solution structure characterization of Ros87 H42A functional mutant. J Inorg Biochem 2014; 131:30-6. [DOI: 10.1016/j.jinorgbio.2013.10.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/17/2013] [Accepted: 10/19/2013] [Indexed: 11/26/2022]
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27
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Wang DR, Hsiao JC, Wong CH, Li GC, Lin SC, Yu SSF, Chen W, Chang W, Tzou DLM. Vaccinia viral protein A27 is anchored to the viral membrane via a cooperative interaction with viral membrane protein A17. J Biol Chem 2014; 289:6639-6655. [PMID: 24451374 DOI: 10.1074/jbc.m114.547372] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The vaccinia viral protein A27 in mature viruses specifically interacts with heparan sulfate for cell surface attachment. In addition, A27 associates with the viral membrane protein A17 to anchor to the viral membrane; however, the specific interaction between A27 and A17 remains largely unclear. To uncover the active binding sites and the underlying binding mechanism, we expressed and purified the N-terminal (18-50 residues) and C-terminal (162-203 residues) fragments of A17, which are denoted A17-N and A17-C. Through surface plasmon resonance, the binding affinity of A27/A17-N (KA = 3.40 × 10(8) m(-1)) was determined to be approximately 3 orders of magnitude stronger than that of A27/A17-C (KA = 3.40 × 10(5) m(-1)), indicating that A27 prefers to interact with A17-N rather than A17-C. Despite the disordered nature of A17-N, the A27-A17 interaction is mediated by a specific and cooperative binding mechanism that includes two active binding sites, namely (32)SFMPK(36) (denoted as F1 binding) and (20)LDKDLFTEEQ(29) (F2). Further analysis showed that F1 has stronger binding affinity and is more resistant to acidic conditions than is F2. Furthermore, A27 mutant proteins that retained partial activity to interact with the F1 and F2 sites of the A17 protein were packaged into mature virus particles at a reduced level, demonstrating that the F1/F2 interaction plays a critical role in vivo. Using these results in combination with site-directed mutagenesis data, we established a computer model to explain the specific A27-A17 binding mechanism.
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Affiliation(s)
- Da-Rong Wang
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529
| | - Jye-Chian Hsiao
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529
| | - Chien-Hsuan Wong
- Department of Applied Chemistry, National Chia-Yi University, Chia-Yi, 60004, Taiwan, Republic of China
| | - Guo-Chian Li
- Department of Applied Chemistry, National Chia-Yi University, Chia-Yi, 60004, Taiwan, Republic of China
| | - Su-Ching Lin
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529
| | - Steve S-F Yu
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529
| | - Wenlung Chen
- Department of Applied Chemistry, National Chia-Yi University, Chia-Yi, 60004, Taiwan, Republic of China
| | - Wen Chang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529
| | - Der-Lii M Tzou
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529.
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28
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Inhibition of human neutrophil activity by an RNA aptamer bound to interleukin-8. Biomaterials 2013; 35:578-89. [PMID: 24129312 DOI: 10.1016/j.biomaterials.2013.09.107] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/26/2013] [Indexed: 02/04/2023]
Abstract
Interleukin-8 (IL-8) is a proinflammatory CXC chemokine that has been associated with the promotion of neutrophil chemotaxis, degranulation, and the pathogenesis of several neutrophil-infiltrating chronic inflammatory diseases. In the current study, we generated and characterized a 2'-fluoro-pyrimidine modified RNA aptamer (8A-35) against human IL-8. The 8A-35 aptamer binds to IL-8 with high specificity and affinity, yielding an estimated K(D) of 1.72 pM. NMR data revealed that the residues of Lys8, Leu10, Val63, Val66, Lys69 and Ala74 of IL-8 interact with aptamer. Moreover, the 8A-35 aptamer has a potent IL-8-neutralizing activity that can modulate multiple biological activities of IL-8 in human neutrophils, including migration, intracellular signaling, and intracellular Ca(2+) mobilization. Our results suggest that the 8A-35 aptamer has great potential to be a lead structure in the development of effective therapeutic agents against inflammatory diseases.
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29
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Saesen E, Sarrazin S, Laguri C, Sadir R, Maurin D, Thomas A, Imberty A, Lortat-Jacob H. Insights into the mechanism by which interferon-γ basic amino acid clusters mediate protein binding to heparan sulfate. J Am Chem Soc 2013; 135:9384-90. [PMID: 23734709 DOI: 10.1021/ja4000867] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The extensive functional repertoire of heparin and heparan sulfate, which relies on their ability to interact with a large number of proteins, has recently emerged. To understand the forces that drive such interactions the binding of heparin to interferon-γ (IFNγ), used as a model system, was investigated. NMR-based titration experiments demonstrated the involvement of two adjacent cationic domains (D1: KTGKRKR and D2: RGRR), both of which are present within the carboxy-terminal sequence of the cytokine. Kinetic analysis showed that these two domains contribute differently to the interaction: D1 is required to form a complex and constitutes the actual binding site, whereas D2, although unable to associate with heparin by itself, increased the association rate of the binding. These data are consistent with the view that D2, through nonspecific electrostatic forces, places the two molecules in favorable orientations for productive binding within the encounter complex. This mechanism was supported by electrostatic potential analysis and thermodynamic investigations. They showed that D1 association to heparin is driven by both favorable enthalpic and entropic contributions, as expected for a binding sequence, but that D2 gives rise to entropic penalty, which opposes binding in a thermodynamic sense. The binding mechanism described herein, by which the D2 domain kinetically drives the interaction, has important functional consequences and gives a structural framework to better understand how specific are the interactions between proteins and heparin.
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Affiliation(s)
- Els Saesen
- Institut de Biologie Structurale, CNRS, CEA, University Grenoble Alpes, UMR 5075, 41 rue Horowitz, 38027, Grenoble cedex 01, France
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30
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Mahler B, Chen Y, Ford J, Thiel C, Wistow G, Wu Z. Structure and dynamics of the fish eye lens protein, γM7-crystallin. Biochemistry 2013; 52:3579-87. [PMID: 23597261 DOI: 10.1021/bi400151c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vertebrate eye lens contains high concentrations of crystallins. The dense lenses of fish are particularly abundant in a class called γM-crystallin whose members are characterized by an unusually high methionine content and partial loss of the four tryptophan residues conserved in all γ-crystallins from mammals which are proposed to contribute to protection from UV-damage. Here, we present the structure and dynamics of γM7-crystallin from zebrafish (Danio rerio). The solution structure shares the typical two-domain, four-Greek-key motif arrangement of other γ-crystallins, with the major difference noted in the final loop of the N-terminal domain, spanning residues 65-72. This is likely due to the absence of the conserved tryptophans. Many of the methionine residues are exposed on the surface but are mostly well-ordered and frequently have contacts with aromatic side chains. This may contribute to the specialized surface properties of these proteins that exist under high molecular crowding in the fish lens. NMR relaxation data show increased backbone conformational motions in the loop regions of γM7 compared to those of mouse γS-crystallin and show that fast internal motion of the interdomain linker in γ-crystallins correlates with linker length. Unfolding studies monitored by tryptophan fluorescence confirm results from mutant mouse γS-crystallin and show that unfolding of a βγ-crystallin domain likely starts from unfolding of the variable loop containing the more fluorescently quenched tryptophan residue, resulting in a native-like unfolding intermediate.
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Affiliation(s)
- Bryon Mahler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yingwei Chen
- Section on Molecular Structure and Function, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jason Ford
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Caleb Thiel
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Graeme Wistow
- Section on Molecular Structure and Function, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zhengrong Wu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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31
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Yun JH, Ko S, Lee CK, Cheong HK, Cheong C, Yoon JB, Lee W. Solution structure and Rpn1 interaction of the UBL domain of human RNA polymerase II C-terminal domain phosphatase. PLoS One 2013; 8:e62981. [PMID: 23667555 PMCID: PMC3646893 DOI: 10.1371/journal.pone.0062981] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 04/01/2013] [Indexed: 12/26/2022] Open
Abstract
The ubiquitin-like modifier (UBL) domain of ubiquitin-like domain proteins (UDPs) interacts specifically with subunits of the 26 S proteasome. A novel UDP, ubiquitin-like domain-containing C-terminal domain phosphatase (UBLCP1), has been identified as an interacting partner of the 26 S proteasome. We determined the high-resolution solution structure of the UBL domain of human UBLCP1 by nuclear magnetic resonance spectroscopy. The UBL domain of hUBLCP1 has a unique β-strand (β3) and β3-α2 loop, instead of the canonical β4 observed in other UBL domains. The molecular topology and secondary structures are different from those of known UBL domains including that of fly UBLCP1. Data from backbone dynamics shows that the β3-α2 loop is relatively rigid although it might have intrinsic dynamic profile. The positively charged residues of the β3-α2 loop are involved in interacting with the C-terminal leucine-rich repeat-like domain of Rpn1.
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Affiliation(s)
- Ji-Hye Yun
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Sunggeon Ko
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Chung-Kyung Lee
- Division of Magnetic Resonance, Korea Basic Science Institute (KBSI), Ochang, Cheongwon, Chungbuk, Korea
| | - Hae-Kap Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute (KBSI), Ochang, Cheongwon, Chungbuk, Korea
| | - Chaejoon Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute (KBSI), Ochang, Cheongwon, Chungbuk, Korea
| | - Jong-Bok Yoon
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
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32
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Garcia BL, Summers BJ, Ramyar KX, Tzekou A, Lin Z, Ricklin D, Lambris JD, Laity JH, Geisbrecht BV. A structurally dynamic N-terminal helix is a key functional determinant in staphylococcal complement inhibitor (SCIN) proteins. J Biol Chem 2013; 288:2870-81. [PMID: 23233676 PMCID: PMC3554951 DOI: 10.1074/jbc.m112.426858] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Complement is a network of interacting circulatory and cell surface proteins that recognizes, marks, and facilitates clearance of microbial invaders. To evade complement attack, the pathogenic organism Staphylococcus aureus expresses a number of secreted proteins that interfere with activation and regulation of the complement cascade. Staphylococcal complement inhibitors (SCINs) are one important class of these immunomodulators and consist of three active members (SCIN-A/-B/-C). SCINs inhibit a critical enzymatic complex, the alternative pathway C3 convertase, by targeting a functional "hot spot" on the central opsonin of complement, C3b. Although N-terminal truncation mutants of SCINs retain complement inhibitory properties, they are significantly weaker binders of C3b. To provide a structural basis for this observation, we undertook a series of crystallographic and NMR dynamics studies on full-length SCINs. This work reveals that N-terminal SCIN domains are characterized by a conformationally dynamic helical motif. C3b binding and functional experiments further demonstrate that this sequence-divergent N-terminal region of SCINs is both functionally important and context-dependent. Finally, surface plasmon resonance data provide evidence for the formation of inhibitor·enzyme·substrate complexes ((SCIN·C3bBb)·C3). Similar to the (SCIN·C3bBb)(2) pseudodimeric complexes, ((SCIN·C3bBb)·C3) interferes with the interaction of complement receptors and C3b. This activity provides an additional mechanism by which SCIN couples convertase inhibition to direct blocking of phagocytosis. Together, these data suggest that tethering multi-host protein complexes by small modular bacterial inhibitors may be a global strategy of immune evasion used by S. aureus. The work presented here provides detailed structure-activity relationships and improves our understanding of how S. aureus circumvents human innate immunity.
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Affiliation(s)
- Brandon L Garcia
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri, Kansas City, Missouri 64110, USA
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33
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Oka O, Waters LC, Strong SL, Dosanjh NS, Veverka V, Muskett FW, Renshaw PS, Klempnauer KH, Carr MD. Interaction of the transactivation domain of B-Myb with the TAZ2 domain of the coactivator p300: molecular features and properties of the complex. PLoS One 2012; 7:e52906. [PMID: 23300815 PMCID: PMC3534135 DOI: 10.1371/journal.pone.0052906] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 11/23/2012] [Indexed: 01/15/2023] Open
Abstract
The transcription factor B-Myb is a key regulator of the cell cycle in vertebrates, with activation of transcription involving the recognition of specific DNA target sites and the recruitment of functional partner proteins, including the coactivators p300 and CBP. Here we report the results of detailed studies of the interaction between the transactivation domain of B-Myb (B-Myb TAD) and the TAZ2 domain of p300. The B-Myb TAD was characterized using circular dichroism, fluorescence and NMR spectroscopy, which revealed that the isolated domain exists as a random coil polypeptide. Pull-down and spectroscopic experiments clearly showed that the B-Myb TAD binds to p300 TAZ2 to form a moderately tight (K(d) ~1.0-10 µM) complex, which results in at least partial folding of the B-Myb TAD. Significant changes in NMR spectra of p300 TAZ2 suggest that the B-Myb TAD binds to a relatively large patch on the surface of the domain (~1200 Å(2)). The apparent B-Myb TAD binding site on p300 TAZ2 shows striking similarity to the surface of CBP TAZ2 involved in binding to the transactivation domain of the transcription factor signal transducer and activator of transcription 1 (STAT1), which suggests that the structure of the B-Myb TAD-p300 TAZ2 complex may share many features with that reported for STAT1 TAD-p300 TAZ2.
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Affiliation(s)
- Ojore Oka
- Department of Biochemistry, University of Leicester, Henry Wellcome Building, Leicester, United Kingdom
| | - Lorna C. Waters
- Department of Biochemistry, University of Leicester, Henry Wellcome Building, Leicester, United Kingdom
| | - Sarah L. Strong
- Department of Biochemistry, University of Leicester, Henry Wellcome Building, Leicester, United Kingdom
| | - Nuvjeevan S. Dosanjh
- Department of Biochemistry, University of Leicester, Henry Wellcome Building, Leicester, United Kingdom
| | - Vaclav Veverka
- Department of Biochemistry, University of Leicester, Henry Wellcome Building, Leicester, United Kingdom
| | - Frederick W. Muskett
- Department of Biochemistry, University of Leicester, Henry Wellcome Building, Leicester, United Kingdom
| | - Philip S. Renshaw
- Department of Biochemistry, University of Leicester, Henry Wellcome Building, Leicester, United Kingdom
| | | | - Mark D. Carr
- Department of Biochemistry, University of Leicester, Henry Wellcome Building, Leicester, United Kingdom
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34
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Leonard PG, Bezar IF, Sidote DJ, Stock AM. Identification of a hydrophobic cleft in the LytTR domain of AgrA as a locus for small molecule interactions that inhibit DNA binding. Biochemistry 2012. [PMID: 23181972 DOI: 10.1021/bi3011785] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The AgrA transcription factor regulates the quorum-sensing response in Staphylococcus aureus, controlling the production of hemolysins and other virulence factors. AgrA binds to DNA via its C-terminal LytTR domain, a domain not found in humans but common in many pathogenic bacteria, making it a potential target for antimicrobial development. We have determined the crystal structure of the apo AgrA LytTR domain and screened a library of 500 fragment compounds to find inhibitors of AgrA DNA binding activity. Using nuclear magnetic resonance, the binding site for five compounds has been mapped to a common locus at the C-terminal end of the LytTR domain, a site known to be important for DNA binding activity. Three of these compounds inhibit AgrA DNA binding. These results provide the first evidence that LytTR domains can be targeted by small organic compounds.
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Affiliation(s)
- Paul G Leonard
- Center for Advanced Biotechnology and Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, NJ 08854-5635, USA
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35
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Sun S, Yan S, Guo C, Li M, Hoch JC, Williams JC, Polenova T. A time-saving strategy for MAS NMR spectroscopy by combining nonuniform sampling and paramagnetic relaxation assisted condensed data collection. J Phys Chem B 2012; 116:13585-96. [PMID: 23094591 DOI: 10.1021/jp3005794] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present a time-saving strategy for acquiring 3D magic angle spinning NMR spectra for chemical shift assignments in proteins and protein assemblies in the solid state. By simultaneous application of nonuniform sampling (NUS) and paramagnetic-relaxation-assisted condensed data collection (PACC), we can attain 16-fold time reduction in the 3D experiments without sacrificing the signal-to-noise ratio or the resolution. We demonstrate that with appropriate concentration of paramagnetic dopant introduced into the sample the overwhelming majority of chemical shifts are not perturbed, with the exception of a limited number of shifts corresponding to residues located at the surface of the protein, which exhibit small perturbations. This approach enables multidimensional MAS spectroscopy in samples of intrinsically low sensitivity and/or high spectral congestion where traditional experiments fail, and is especially beneficial for structural and dynamics studies of large proteins and protein assemblies.
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Affiliation(s)
- Shangjin Sun
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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36
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Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein. PLoS One 2012; 7:e43820. [PMID: 22937103 PMCID: PMC3427171 DOI: 10.1371/journal.pone.0043820] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/26/2012] [Indexed: 01/30/2023] Open
Abstract
Split-protein systems have emerged as a powerful tool for detecting biomolecular interactions and reporting biological reactions. However, reliable methods for identifying viable split sites are still unavailable. In this study, we demonstrated the feasibility that valid circular permutation (CP) sites in proteins have the potential to act as split sites and that CP prediction can be used to search for internal permissive sites for creating new split proteins. Using a protein ligase, intein, as a model, CP predictor facilitated the creation of circular permutants in which backbone opening imposes the least detrimental effects on intein folding. We screened a series of predicted intein CPs and identified stable and native-fold CPs. When the valid CP sites were introduced as split sites, there was a reduction in folding enthalpy caused by the new backbone opening; however, the coincident loss in entropy was sufficient to be compensated, yielding a favorable free energy for self-association. Since split intein is exploited in protein semi-synthesis, we tested the related protein trans-splicing (PTS) activities of the corresponding split inteins. Notably, a novel functional split intein composed of the N-terminal 36 residues combined with the remaining C-terminal fragment was identified. Its PTS activity was shown to be better than current reported two-piece intein with a short N-terminal segment. Thus, the incorporation of in silico CP prediction facilitated the design of split intein as well as circular permutants.
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37
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Zhong D, Lefebre M, Kaur K, McDowell MA, Gdowski C, Jo S, Wang Y, Benedict SH, Lea SM, Galan JE, De Guzman RN. The Salmonella type III secretion system inner rod protein PrgJ is partially folded. J Biol Chem 2012; 287:25303-11. [PMID: 22654099 DOI: 10.1074/jbc.m112.381574] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The type III secretion system (T3SS) is essential in the pathogenesis of many bacteria. The inner rod is important in the assembly of the T3SS needle complex. However, the atomic structure of the inner rod protein is currently unknown. Based on computational methods, others have suggested that the Salmonella inner rod protein PrgJ is highly helical, forming a folded 3 helix structure. Here we show by CD and NMR spectroscopy that the monomeric form of PrgJ lacks a tertiary structure, and the only well-structured part of PrgJ is a short α-helix at the C-terminal region from residues 65-82. Disruption of this helix by glycine or proline mutation resulted in defective assembly of the needle complex, rendering bacteria incapable of secreting effector proteins. Likewise, CD and NMR data for the Shigella inner rod protein MxiI indicate this protein lacks a tertiary structure as well. Our results reveal that the monomeric forms of the T3SS inner rod proteins are partially folded.
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Affiliation(s)
- Dalian Zhong
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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38
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Estrada DF, Conner M, Jeor SC, Guzman RND. The Structure of the Hantavirus Zinc Finger Domain is Conserved and Represents the Only Natively Folded Region of the Gn Cytoplasmic Tail. Front Microbiol 2011; 2:251. [PMID: 22203819 PMCID: PMC3243910 DOI: 10.3389/fmicb.2011.00251] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 11/27/2011] [Indexed: 11/25/2022] Open
Abstract
Hantaviruses, of the family Bunyaviridae, are present throughout the world and cause a variety of infections ranging from the asymptomatic to mild and severe hemorrhagic fevers. Hantaviruses are enveloped anti-sense RNA viruses that contain three genomic segments that encode for a nucleocapsid protein, two membrane glycoproteins (Gn and Gc), and an RNA polymerase. Recently, the pathogenicity of hantaviruses has been mapped to the carboxyl end of the 150 residue Gn cytoplasmic tail. The Gn tail has also been shown to play a role in binding the ribonucleoprotein (RNP), a step critical for virus assembly. In this study, we use NMR spectroscopy to compare the structure of a Gn tail zinc finger domain of both a pathogenic (Andes) and a non-pathogenic (Prospect Hill) hantavirus. We demonstrate that despite a stark difference in the virulence of both of these viruses, the structure of the Gn core zinc finger domain is largely conserved in both strains. We also use NMR backbone relaxation studies to demonstrate that the regions of the Andes virus Gn tail immediately outside the zinc finger domain, sites known to bind the RNP, are disordered and flexible, thus intimating that the zinc finger domain is the only structured region of the Gn tail. These structural observations provide further insight into the role of the Gn tail during viral assembly as well as its role in pathogenesis.
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Affiliation(s)
- D Fernando Estrada
- Department of Molecular Biosciences, University of Kansas Lawrence, KS, USA
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39
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Skasko M, Wang Y, Tian Y, Tokarev A, Munguia J, Ruiz A, Stephens EB, Opella SJ, Guatelli J. HIV-1 Vpu protein antagonizes innate restriction factor BST-2 via lipid-embedded helix-helix interactions. J Biol Chem 2011; 287:58-67. [PMID: 22072710 DOI: 10.1074/jbc.m111.296772] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Vpu protein of HIV-1 antagonizes BST-2 (tetherin), a broad spectrum effector of the innate immune response to viral infection, by an intermolecular interaction that maps genetically to the α-helical transmembrane domains (TMDs) of each protein. Here we utilize NMR spectroscopy to describe key features of the helix-helix pairing that underlies this interaction. The antagonism of BST-2 involves a sequence of three alanines and a tryptophan spaced at four residue intervals within the Vpu TMD helix. Responsiveness to Vpu involves bulky hydrophobic residues in the C-terminal region of the BST-2 TMD helix that likely fit between the alanines on the interactive face of Vpu. These aspects of Vpu and BST-2 form an anti-parallel, lipid-embedded helix-helix interface. Changes in human BST-2 that mimic sequences found in nonhuman primate orthologs unresponsive to Vpu change the tilt angle of the TMD in the lipid bilayer without abrogating its intrinsic ability to interact with Vpu. These data explain the mechanism by which HIV-1 evades a key aspect of innate immunity and the species specificity of Vpu using an anti-parallel helix-helix packing model.
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Affiliation(s)
- Mark Skasko
- Department of Medicine, University of California, San Diego, La Jolla, California, 92093
| | - Yan Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093
| | - Ye Tian
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093
| | - Andrey Tokarev
- Department of Medicine, University of California, San Diego, La Jolla, California, 92093
| | - Jason Munguia
- Department of Medicine, University of California, San Diego, La Jolla, California, 92093
| | - Autumn Ruiz
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Edward B Stephens
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093.
| | - John Guatelli
- Department of Medicine, University of California, San Diego, La Jolla, California, 92093; San Diego Veterans Affairs Healthcare System, San Diego, California 92161.
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40
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Desjardins A, Yang A, Bouvette J, Omichinski JG, Legault P. Importance of the NCp7-like domain in the recognition of pre-let-7g by the pluripotency factor Lin28. Nucleic Acids Res 2011; 40:1767-77. [PMID: 22013165 PMCID: PMC3287177 DOI: 10.1093/nar/gkr808] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The pluripotency factor Lin28 is a highly conserved protein comprising a unique combination of RNA-binding motifs, an N-terminal cold-shock domain and a C-terminal region containing two retroviral-type CCHC zinc-binding domains. An important function of Lin28 is to inhibit the biogenesis of the let-7 family of microRNAs through a direct interaction with let-7 precursors. Here, we systematically characterize the determinants of the interaction between Lin28 and pre-let-7g by investigating the effect of protein and RNA mutations on in vitro binding. We determine that Lin28 binds with high affinity to the extended loop of pre-let-7g and that its C-terminal domain contributes predominantly to the affinity of this interaction. We uncover remarkable similarities between this C-terminal domain and the NCp7 protein of HIV-1, not only in terms of primary structure but also in their modes of RNA binding. This NCp7-like domain of Lin28 recognizes a G-rich bulge within pre-let-7g, which is adjacent to one of the Dicer cleavage sites. We hypothesize that the NCp7-like domain initiates RNA binding and partially unfolds the RNA. This partial unfolding would then enable multiple copies of Lin28 to bind the extended loop of pre-let-7g and protect the RNA from cleavage by the pre-microRNA processing enzyme Dicer.
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Affiliation(s)
- Alexandre Desjardins
- Département de Biochimie, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
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41
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Adén J, Wallgren M, Storm P, Weise CF, Christiansen A, Schröder WP, Funk C, Wolf-Watz M. Extraordinary μs-ms backbone dynamics in Arabidopsis thaliana peroxiredoxin Q. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1880-90. [PMID: 21798375 DOI: 10.1016/j.bbapap.2011.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/27/2011] [Accepted: 07/12/2011] [Indexed: 11/29/2022]
Abstract
Peroxiredoxin Q (PrxQ) isolated from Arabidopsis thaliana belongs to a family of redox enzymes called peroxiredoxins, which are thioredoxin- or glutaredoxin-dependent peroxidases acting to reduce peroxides and in particular hydrogen peroxide. PrxQ cycles between an active reduced state and an inactive oxidized state during its catalytic cycle. The catalytic mechanism involves a nucleophilic attack of the catalytic cysteine on hydrogen peroxide to generate a sulfonic acid intermediate with a concerted release of a water molecule. This intermediate is subsequently relaxed by the reaction of a second cysteine, denoted the resolving cysteine, generating an intramolecular disulfide bond and release of a second water molecule. PrxQ is recycled to the active state by a thioredoxin-dependent reduction. Previous structural studies of PrxQ homologues have provided the structural basis for the switch between reduced and oxidized conformations. Here, we have performed a detailed study of the activity, structure and dynamics of PrxQ in both the oxidized and reduced states. Reliable and experimentally validated structural models of PrxQ in both oxidation states were generated using homology based modeling. Analysis of NMR spin relaxation rates shows that PrxQ is monomeric in both oxidized and reduced states. As evident from R(2) relaxation rates the reduced form of PrxQ undergoes unprecedented dynamics on the slow μs-ms timescale. The ground state of this conformational dynamics is likely the stably folded reduced state as implied by circular dichroism spectroscopy. We speculate that the extensive dynamics is intimately related to the catalytic function of PrxQ.
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Affiliation(s)
- Jörgen Adén
- Department of Chemistry, Umea University, Umea, Sweden
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42
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Estrada DF, De Guzman RN. Structural characterization of the Crimean-Congo hemorrhagic fever virus Gn tail provides insight into virus assembly. J Biol Chem 2011; 286:21678-86. [PMID: 21507948 DOI: 10.1074/jbc.m110.216515] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA virus that causes the Crimean Congo Hemorrhagic Fever (CCHF) is a tick-borne pathogen of the Nairovirus genus, family Bunyaviridae. Unlike many zoonotic viruses that are only passed between animals and humans, the CCHF virus can also be transmitted from human to human with an overall mortality rate approaching 30%. Currently, there are no atomic structures for any CCHF virus proteins or for any Nairovirus proteins. A critical component of the virus is the envelope Gn glycoprotein, which contains a C-terminal cytoplasmic tail. In other Bunyaviridae viruses, the Gn tail has been implicated in host-pathogen interaction and viral assembly. Here we report the NMR structure of the CCHF virus Gn cytoplasmic tail, residues 729-805. The structure contains a pair of tightly arranged dual ββα zinc fingers similar to those found in the Hantavirus genus, with which it shares about 12% sequence identity. Unlike Hantavirus zinc fingers, however, the CCHF virus zinc fingers bind viral RNA and contain contiguous clusters of conserved surface electrostatics. Our results provide insight into a likely role of the CCHF virus Gn zinc fingers in Nairovirus assembly.
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Affiliation(s)
- D Fernando Estrada
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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43
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Ko S, Kim H, Yun J, Yee A, Arrowsmith CH, Cheong C, Lee W. Solution structure of MTH1821, a putative structure homologue to RNA polymerase α subunit from Methanobacterium thermoautotrophicum. Proteins 2011; 79:1347-51. [PMID: 21387412 DOI: 10.1002/prot.22956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/04/2010] [Accepted: 11/16/2010] [Indexed: 11/10/2022]
Affiliation(s)
- Sunggeon Ko
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
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44
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Mangels C, Kellner R, Einsiedel J, Weiglmeier PR, Rosch P, Gmeiner P, Schwarzinger S. The therapeutically anti-prion active antibody-fragment scFv-W226: paramagnetic relaxation-enhanced NMR spectroscopy aided structure elucidation of the paratope-epitope interface. J Biomol Struct Dyn 2010; 28:13-22. [PMID: 20476792 DOI: 10.1080/07391102.2010.10507340] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antibodies have become indispensable reagents with numerous applications in biological and biotechnical analysis, in diagnostics as well as in therapy. In all cases, selective interaction with an epitope is crucial and depends on the conformation of the paratope. While epitopes are routinely mapped at high throughput, methods revealing structural insights on a rather short timescale are rare. We here demonstrate paramagnetic relaxation-enhanced (PRE) NMR spectroscopy to be a powerful tool unraveling structural information about epitope-orientation in a groove spanned by the complementary determining regions. In particular, we utilize the spin label TOAC, which is fused to the peptidic epitope using standard solid-phase chemistry and which is characterized by a reduced mobility compared to, e.g., spin labels attached to the side-chain functionalities of cysteine or lysine residues. We apply the method to determine the orientation of helix 1 of the prion protein, which is the epitope for the therapeutically anti-prion active scF(v) fragment W226.
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Affiliation(s)
- Christian Mangels
- Department of Biopolymers, Universitat Bayreuth, Universitatsstrasse 30, 95440 Bayreuth, Germany
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45
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Protein refolding is required for assembly of the type three secretion needle. Nat Struct Mol Biol 2010; 17:788-92. [PMID: 20543831 DOI: 10.1038/nsmb.1822] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Accepted: 04/01/2010] [Indexed: 12/30/2022]
Abstract
Pathogenic Gram-negative bacteria use a type three secretion system (TTSS) to deliver virulence factors into host cells. Although the order in which proteins incorporate into the growing TTSS is well described, the underlying assembly mechanisms are still unclear. Here we show that the TTSS needle protomer refolds spontaneously to extend the needle from the distal end. We developed a functional mutant of the needle protomer from Shigella flexneri and Salmonella typhimurium to study its assembly in vitro. We show that the protomer partially refolds from alpha-helix into beta-strand conformation to form the TTSS needle. Reconstitution experiments show that needle growth does not require ATP. Thus, like the structurally related flagellar systems, the needle elongates by subunit polymerization at the distal end but requires protomer refolding. Our studies provide a starting point to understand the molecular assembly mechanisms and the structure of the TTSS at atomic level.
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46
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Gu X, Harmon BJ, Wang DI. Site- and branch-specific sialylation of recombinant human interferon-gamma in Chinese hamster ovary cell culture. Biotechnol Bioeng 2010; 55:390-8. [PMID: 18636497 DOI: 10.1002/(sici)1097-0290(19970720)55:2<390::aid-bit16>3.0.co;2-l] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Since sialic acid content is known to be a critical determinant of the biological properties of glycoproteins, it is essential to characterize and monitor sialylation patterns of recombinant glycoproteins intended for therapeutic use. This study reports site- and branch-specific differences in sialylation of human interferon-gamma (IFN-gamma) derived from Chinese hamster ovary (CHO) cell culture. Sialylation profiles were quantitated by reversed-phase HPLC separations of the site-specific pools of tryptic glycopeptides representing IFN-gamma's two potential N-linked glycosylation sites (i.e., Asn(25) and Asn(97)). Although sialylation at each glycosylation site was found to be incomplete, glycans of Asn(25) were more heavily sialylated than those of Asn(97). Furthermore, Man(alpha1-3) arms of the predominant complex biantennary structures were more favorably sialylated than Man(alpha1-6) branches at each glycosylation site. When the sialylation profile was analyzed throughout a suspension batch culture, sialic acid content at each site and branch was found to be relatively constant until a steady decrease in sialylation was observed coincident with loss of cell viability. The introduction of a competitive inhibitor of sialidase into the culture supernatant prevented the loss of sialic acid after the onset of cell death but did not affect sialylation prior to cell death. This finding indicated that incomplete sialylation prior to loss of cell viability could be attributed to incomplete intracellular sialylation while the reduction in sialylation following loss of cell viability was due to extracellular sialidase activity resulting from cell lysis. Thus, both intracellular and extracellular processes defined the sialic acid content of the final product. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 390-398, 1977.
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Affiliation(s)
- X Gu
- Biotechnology Process Engineering Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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47
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Prischi F, Pastore C, Carroni M, Iannuzzi C, Adinolfi S, Temussi P, Pastore A. Of the vulnerability of orphan complex proteins: the case study of the E. coli IscU and IscS proteins. Protein Expr Purif 2010; 73:161-6. [PMID: 20471481 DOI: 10.1016/j.pep.2010.05.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 05/01/2010] [Accepted: 05/03/2010] [Indexed: 11/18/2022]
Abstract
IscS and IscU, the two central protein components of the iron sulfur cluster assembly machinery, form a complex that is still relatively poorly characterized. In an attempt to standardize the purification of these proteins for structural studies we have developed a protocol to produce them individually in high concentration and purity. We show that IscS is a rather robust protein as long as it is produced in a PLP loaded form and that this co-factor is essential for fold stability and enzyme activity. In contrast to previous evidence, we also propose that, in contrast with previous evidence, IscU is a thermodynamically stable protein with a well defined fold but, when produced in isolation, is a 'complex-orphan protein' that is prone to unfolding if not stabilised by a co-factor or a protein partner. Our work will facilitate further structural and functional studies of these proteins and eventually lead to a better understanding of the whole machinery.
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Affiliation(s)
- Filippo Prischi
- MRC National Institute for Medical research, The Ridgeway, London NW7 1AA, UK
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48
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Lyon AM, Reveal BS, Macdonald PM, Hoffman DW. Bruno protein contains an expanded RNA recognition motif. Biochemistry 2010; 48:12202-12. [PMID: 19919093 DOI: 10.1021/bi900624j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The RNA recognition motif (or RRM) is a ubiquitous RNA-binding module present in approximately 2% of the proteins encoded in the human genome. This work characterizes an expanded RRM, which is present in the Drosophila Bruno protein, and targets regulatory elements in the oskar mRNA through which Bruno controls translation. In this Bruno RRM, the deletion of 40 amino acids prior to the N-terminus of the canonical RRM resulted in a significantly decreased affinity of the protein for its RNA target. NMR spectroscopy showed that the expanded Bruno RRM contains the familiar RRM fold of four antiparallel beta-strands and two alpha-helices, preceded by a 10-residue loop that contacts helix alpha(1) and strand beta(2); additional amino acids at the N-terminus of the domain are relatively flexible in solution. NMR results also showed that a truncated form of the Bruno RRM, lacking the flexible N-terminal amino acids, forms a stable and complete canonical RRM, so that the loss of RNA binding activity cannot be attributed to disruption of the RRM fold. This expanded Bruno RRM provides a new example of the features that are important for RNA recognition by an RRM-containing protein.
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Affiliation(s)
- Angeline M Lyon
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
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49
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Doddapaneni K, Mahler B, Pavlovicz R, Haushalter A, Yuan C, Wu Z. Solution structure of RCL, a novel 2'-deoxyribonucleoside 5'-monophosphate N-glycosidase. J Mol Biol 2009; 394:423-34. [PMID: 19720067 DOI: 10.1016/j.jmb.2009.08.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 08/20/2009] [Accepted: 08/22/2009] [Indexed: 11/16/2022]
Abstract
RCL is an enzyme that catalyzes the N-glycosidic bond cleavage of purine 2'-deoxyribonucleoside 5'-monophosphates, a novel enzymatic reaction reported only recently. In this work, we determined the solution structure by multidimensional NMR and provide a structural framework to elucidate its mechanism with computational simulation. RCL is a symmetric homodimer, with each monomer consisting of a five-stranded parallel beta-sheet sandwiched between five alpha-helices. Three of the helices form the dimer interface, allowing two monomers to pack side by side. The overall architecture featuring a Rossmann fold is topologically similar to that of deoxyribosyltransferases, with major differences observed in the putative substrate binding pocket and the C-terminal tail. The latter is seemingly flexible and projecting away from the core structure in RCL, but loops back and is positioned at the bottom of the neighboring active site in the transferases. This difference may bear functional implications in the context of nucleobase recognition involving the C-terminal carboxyl group, which is only required in the reverse reaction by the transferases. It was also noticed that residues around the putative active site show significant conformational variation, suggesting that protein dynamics may play an important role in the enzymatic function of apo-RCL. Overall, the work provides invaluable insight into the mechanism of a novel N-glycosidase from the structural point of view, which in turn will allow rational anti-tumor and anti-angiogenesis drug design.
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Affiliation(s)
- Kiran Doddapaneni
- Biochemistry Department, Ohio State University, Columbus, OH 43210, USA
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Ko S, Ahn KE, Lee YM, Ahn HC, Lee W. Structural basis of the auto-inhibition mechanism of nonreceptor tyrosine kinase PTK6. Biochem Biophys Res Commun 2009; 384:236-42. [PMID: 19401189 DOI: 10.1016/j.bbrc.2009.04.103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 04/21/2009] [Indexed: 11/27/2022]
Abstract
Protein tyrosine kinase 6 (PTK6) is composed of SH3, SH2, and Kinase domains, with a linker region (Linker) between the SH2 and Kinase domains. Here, we report the structural basis of the SH3-Linker interaction that results in auto-inhibition of PTK6. The solution structures of the SH3 domain and SH3/Linker complex were determined by NMR spectroscopy. The structure of the SH3 domain forms a conventional beta-barrel with two beta-sheets comprised of five beta-strands. However, the molecular topology and charge distribution of PTK6-SH3 slightly differs from that of the other SH3 domains. The structure of the N-terminal Linker within the complex showed that the proline-rich region (P175-P187) of the Linker forms a compact hairpin structure through hydrophobic interactions. The structure of the SH3/Linker complex revealed intra-molecular interaction between the amino acid pairs R22/E190, W44/W184, N65/P177, and Y66/P179. Mutations in PTK6 at R22, W44, N65, and Y66 residues in the SH3 domain increased catalytic activity compared with wild-type protein, implying that specific interactions between hydrophobic residues in the proline-rich linker region and hydrophobic residues in the SH3 domain are mainly responsible for down-regulating the catalytic activity of PTK6.
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Affiliation(s)
- Sunggeon Ko
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
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