1
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Ali MG, Wahba HM, Igelmann S, Cyr N, Ferbeyre G, Omichinski JG. Structural and functional characterization of the role of acetylation on the interactions of the human Atg8-family proteins with the autophagy receptor TP53INP2/DOR. Autophagy 2024; 20:1948-1967. [PMID: 38726830 PMCID: PMC11346521 DOI: 10.1080/15548627.2024.2353443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 04/20/2024] [Accepted: 05/05/2024] [Indexed: 05/29/2024] Open
Abstract
The Atg8-family proteins (MAP1LC3/LC3A, LC3B, LC3C, GABARAP, GABARAPL1 and GABARAPL2) play a pivotal role in macroautophagy/autophagy through their ability to help form autophagosomes. Although autophagosomes form in the cytoplasm, nuclear levels of the Atg8-family proteins are significant. Recently, the nuclear/cytoplasmic shuttling of LC3B was shown to require deacetylation of two Lys residues (K49 and K51 in LC3B), which are conserved in Atg8-family proteins. To exit the nucleus, deacetylated LC3B must bind TP53INP2/DOR (tumor protein p53 inducible nuclear protein 2) through interaction with the LC3-interacting region (LIR) of TP53INP2 (TP53INP2LIR). To examine their selectivity for TP53INP2 and the role of the conserved Lys residues in Atg8-family proteins, we prepared the six human Atg8-family proteins and acetylated variants of LC3A and GABARAP for biophysical and structural characterization of their interactions with the TP53INP2LIR. Isothermal titration calorimetry (ITC) experiments demonstrate that this LIR binds preferentially to GABARAP subfamily proteins, and that only acetylation of the second Lys residue reduces binding to GABARAP and LC3A. Crystal structures of complexes with GABARAP and LC3A (acetylated and deacetylated) define a β-sheet in the TP53INP2LIR that determines the GABARAP selectivity and establishes the importance of acetylation at the second Lys. The in vitro results were confirmed in cells using acetyl-mimetic variants of GABARAP and LC3A to examine nuclear/cytoplasmic shuttling and colocalization with TP53INP2. Together, the results demonstrate that TP53INP2 shows selectivity to the GABARAP subfamily and acetylation at the second Lys of GABARAP and LC3A disrupts key interactions with TP53INP2 required for their nuclear/cytoplasmic shuttling.
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Affiliation(s)
- Mohamed G. Ali
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Department of Biochemistry, Beni-Suef University, Beni-Suef, Egypt
| | - Haytham M. Wahba
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Department of Biochemistry, Beni-Suef University, Beni-Suef, Egypt
| | - Sebastian Igelmann
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Normand Cyr
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Gerardo Ferbeyre
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - James G. Omichinski
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
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2
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Velasco‐Carneros L, Bernardo‐Seisdedos G, Maréchal J, Millet O, Moro F, Muga A. Pseudophosphorylation of single residues of the J-domain of DNAJA2 regulates the holding/folding balance of the Hsc70 system. Protein Sci 2024; 33:e5105. [PMID: 39012012 PMCID: PMC11249846 DOI: 10.1002/pro.5105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/20/2024] [Accepted: 06/23/2024] [Indexed: 07/17/2024]
Abstract
The Hsp70 system is essential for maintaining protein homeostasis and comprises a central Hsp70 and two accessory proteins that belong to the J-domain protein (JDP) and nucleotide exchange factor families. Posttranslational modifications offer a means to tune the activity of the system. We explore how phosphorylation of specific residues of the J-domain of DNAJA2, a class A JDP, regulates Hsc70 activity using biochemical and structural approaches. Among these residues, we find that pseudophosphorylation of Y10 and S51 enhances the holding/folding balance of the Hsp70 system, reducing cochaperone collaboration with Hsc70 while maintaining the holding capacity. Truly phosphorylated J domains corroborate phosphomimetic variant effects. Notably, distinct mechanisms underlie functional impacts of these DNAJA2 variants. Pseudophosphorylation of Y10 induces partial disordering of the J domain, whereas the S51E substitution weakens essential DNAJA2-Hsc70 interactions without a large structural reorganization of the protein. S51 phosphorylation might be class-specific, as all cytosolic class A human JDPs harbor a phosphorylatable residue at this position.
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Affiliation(s)
- Lorea Velasco‐Carneros
- Instituto Biofisika (UPV/EHU, CSIC)University of Basque CountryLeioaSpain
- Department of Biochemistry and Molecular Biology, Faculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Ganeko Bernardo‐Seisdedos
- Precision Medicine and Metabolism LabCIC bioGUNEDerioSpain
- Department of Medicine, Faculty of Health SciencesUniversity of DeustoBilbaoSpain
| | - Jean‐Didier Maréchal
- Insilichem, Departament de QuímicaUniversitat Autònoma de Barcelona (UAB)Bellaterra (Barcelona)Spain
| | - Oscar Millet
- Precision Medicine and Metabolism LabCIC bioGUNEDerioSpain
| | - Fernando Moro
- Instituto Biofisika (UPV/EHU, CSIC)University of Basque CountryLeioaSpain
- Department of Biochemistry and Molecular Biology, Faculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Arturo Muga
- Instituto Biofisika (UPV/EHU, CSIC)University of Basque CountryLeioaSpain
- Department of Biochemistry and Molecular Biology, Faculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
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3
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Rios T, Maximiano MR, Fernandes FC, Amorim GC, Porto WF, Buccini DF, Nieto Marín V, Feitosa GC, Freitas CDP, Barra JB, Alonso A, Grossi de Sá MF, Lião LM, Franco OL. Anti-Staphy Peptides Rationally Designed from Cry10Aa Bacterial Protein. ACS OMEGA 2024; 9:29159-29174. [PMID: 39005792 PMCID: PMC11238290 DOI: 10.1021/acsomega.3c07455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 07/16/2024]
Abstract
Bacterial infections pose a significant threat to human health, constituting a major challenge for healthcare systems. Antibiotic resistance is particularly concerning in the context of treating staphylococcal infections. In addressing this challenge, antimicrobial peptides (AMPs), characterized by their hydrophobic and cationic properties, unique mechanism of action, and remarkable bactericidal and immunomodulatory capabilities, emerge as promising alternatives to conventional antibiotics for tackling bacterial multidrug resistance. This study focuses on the Cry10Aa protein as a template for generating AMPs due to its membrane-penetrating ability. Leveraging the Joker algorithm, six peptide variants were derived from α-helix 3 of Cry10Aa, known for its interaction with lipid bilayers. In vitro, antimicrobial assays determined the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) required for inhibiting the growth of Staphylococcus aureus, Escherichia coli, Acinetobacter baummanii, Enterobacter cloacae, Enterococcus facallis, Klebsiella pneumonia, and Pseudomonas aeruginosa. Time-kill kinetics were performed using the parental peptide AMPCry10Aa, as well as AMPCry10Aa_1 and AMPCry10Aa_5, against E. coli ATCC, S. aureus 111 and S. aureus ATCC strains showing that AMPCry10Aa_1 and AMPCry10Aa_5 peptides can completely reduce the initial bacterial load with less than 2 h of incubation. AMPCry10Aa_1 and AMPCry 10Aa_5 present stability in human serum and activity maintenance up to 37 °C. Cytotoxicity assays, conducted using the MTT method, revealed that all of the tested peptides exhibited cell viability >50% (IC50). The study also encompassed evaluations of the structure and physical-chemical properties. The three-dimensional structures of AMPCry10Aa and AMPCry10Aa_5 were determined through nuclear magnetic resonance (NMR) spectroscopy, indicating the adoption of α-helical segments. Electron paramagnetic resonance (EPR) spectroscopy elucidated the mechanism of action, demonstrating that AMPCry10Aa_5 enters the outer membranes of E. coli and S. aureus, causing substantial increases in lipid fluidity, while AMPCry10Aa slightly increases lipid fluidity in E. coli. In conclusion, the results obtained underscore the potential of Cry10Aa as a source for developing antimicrobial peptides as alternatives to conventional antibiotics, offering a promising avenue in the battle against antibiotic resistance.
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Affiliation(s)
- Thuanny
Borba Rios
- S-Inova
Biotech, Programa de Pós-Graduação
em Biotecnologia Universidade Católica Dom Bosco, Av. Tamandaré, 6000—Jardim
Seminario, Campo Grande, MS 79117-900, Brazil
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
| | - Mariana Rocha Maximiano
- S-Inova
Biotech, Programa de Pós-Graduação
em Biotecnologia Universidade Católica Dom Bosco, Av. Tamandaré, 6000—Jardim
Seminario, Campo Grande, MS 79117-900, Brazil
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
| | - Fabiano Cavalcanti Fernandes
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
| | - Gabriella Cavalcante Amorim
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
- Embrapa
Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte—Asa Norte, Brasília, DF 70770-917, Brazil
| | | | - Danieli Fernanda Buccini
- S-Inova
Biotech, Programa de Pós-Graduação
em Biotecnologia Universidade Católica Dom Bosco, Av. Tamandaré, 6000—Jardim
Seminario, Campo Grande, MS 79117-900, Brazil
| | - Valentina Nieto Marín
- S-Inova
Biotech, Programa de Pós-Graduação
em Biotecnologia Universidade Católica Dom Bosco, Av. Tamandaré, 6000—Jardim
Seminario, Campo Grande, MS 79117-900, Brazil
| | - Gabriel Cidade Feitosa
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
- Pós-Graduação
em Patologia Molecular, Universidade de
Brasília, Campus
Darcy Ribeiro, Brasília, DF 70910-900, Brazil
| | | | - Juliana Bueno Barra
- Laboratório
de RMN, Instituto de Química, Universidade
Federal de Goiás, Goiânia, GO 74690-900, Brazil
| | - Antonio Alonso
- Instituto
de Física, Universidade Federal de
Goiás, Goiânia, GO 74690-900, Brazil
| | - Maria Fátima Grossi de Sá
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
- Embrapa
Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte—Asa Norte, Brasília, DF 70770-917, Brazil
| | - Luciano Morais Lião
- Laboratório
de RMN, Instituto de Química, Universidade
Federal de Goiás, Goiânia, GO 74690-900, Brazil
| | - Octávio Luiz Franco
- S-Inova
Biotech, Programa de Pós-Graduação
em Biotecnologia Universidade Católica Dom Bosco, Av. Tamandaré, 6000—Jardim
Seminario, Campo Grande, MS 79117-900, Brazil
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
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4
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Vilas Boas LCP, Buccini DF, Berlanda RLA, Santos BDPO, Maximiano MR, Lião LM, Gonçalves S, Santos NC, Franco OL. Antiviral Activities of Mastoparan-L-Derived Peptides against Human Alphaherpesvirus 1. Viruses 2024; 16:948. [PMID: 38932240 PMCID: PMC11209138 DOI: 10.3390/v16060948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Human alphaherpesvirus 1 (HSV-1) is a significantly widespread viral pathogen causing recurrent infections that are currently incurable despite available treatment protocols. Studies have highlighted the potential of antimicrobial peptides sourced from Vespula lewisii venom, particularly those belonging to the mastoparan family, as effective against HSV-1. This study aimed to demonstrate the antiviral properties of mastoparans, including mastoparan-L [I5, R8], mastoparan-MO, and [I5, R8] mastoparan, against HSV-1. Initially, Vero cell viability was assessed in the presence of these peptides, followed by the determination of antiviral activity, mechanism of action, and dose-response curves through plaque assays. Structural analyses via circular dichroism and nuclear magnetic resonance were conducted, along with evaluating membrane fluidity changes induced by [I5, R8] mastoparan using fluorescence-labeled lipid vesicles. Cytotoxic assays revealed high cell viability (>80%) at concentrations of 200 µg/mL for mastoparan-L and mastoparan-MO and 50 µg/mL for [I5, R8] mastoparan. Mastoparan-MO and [I5, R8] mastoparan exhibited over 80% HSV-1 inhibition, with up to 99% viral replication inhibition, particularly in the early infection stages. Structural analysis indicated an α-helical structure for [I5, R8] mastoparan, suggesting effective viral particle disruption before cell attachment. Mastoparans present promising prospects for HSV-1 infection control, although further investigation into their mechanisms is warranted.
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Affiliation(s)
- Liana Costa Pereira Vilas Boas
- Pós-Graduação em Patologia Molecular, Campus Darcy Ribeiro, Universidade de Brasília, Brasília 70910-900, DF, Brazil
- Centro de Análises Bioquímicas e Proteômicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 70790-760, DF, Brazil
| | - Danieli Fernanda Buccini
- Centro de Análises Bioquímicas e Proteômicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 70790-760, DF, Brazil
- Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, MS, Brazil
| | - Rhayfa Lorrayne Araújo Berlanda
- Pós-Graduação em Patologia Molecular, Campus Darcy Ribeiro, Universidade de Brasília, Brasília 70910-900, DF, Brazil
- Centro de Análises Bioquímicas e Proteômicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 70790-760, DF, Brazil
| | - Bruno de Paula Oliveira Santos
- Laboratório de Ressonância Magnética Nuclear, Instituto de Química, Universidade Federal de Goiás, Goiânia 74690-900, GO, Brazil
| | - Mariana Rocha Maximiano
- Centro de Análises Bioquímicas e Proteômicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 70790-760, DF, Brazil
- Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, MS, Brazil
| | - Luciano Morais Lião
- Laboratório de Ressonância Magnética Nuclear, Instituto de Química, Universidade Federal de Goiás, Goiânia 74690-900, GO, Brazil
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal (N.C.S.)
| | - Nuno C. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal (N.C.S.)
| | - Octávio Luiz Franco
- Pós-Graduação em Patologia Molecular, Campus Darcy Ribeiro, Universidade de Brasília, Brasília 70910-900, DF, Brazil
- Centro de Análises Bioquímicas e Proteômicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 70790-760, DF, Brazil
- Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, MS, Brazil
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5
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Kang M, Otani Y, Guo Y, Yan J, Goult BT, Howe AK. The focal adhesion protein talin is a mechanically gated A-kinase anchoring protein. Proc Natl Acad Sci U S A 2024; 121:e2314947121. [PMID: 38513099 PMCID: PMC10990152 DOI: 10.1073/pnas.2314947121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024] Open
Abstract
Protein kinase A (PKA) is a ubiquitous, promiscuous kinase whose activity is specified through subcellular localization mediated by A-kinase anchoring proteins (AKAPs). PKA has complex roles as both an effector and a regulator of integrin-mediated cell adhesion to extracellular matrix (ECM). Recent observations demonstrate that PKA is an active component of focal adhesions (FA), suggesting the existence of one or more FA AKAPs. Using a promiscuous biotin ligase fused to PKA type-IIα regulatory (RIIα) subunits and subcellular fractionation, we identify the archetypal FA protein talin1 as an AKAP. Talin is a large, mechanosensitive scaffold that directly links integrins to actin filaments and promotes FA assembly by recruiting additional components in a force-dependent manner. The rod region of talin1 consists of 62 α-helices bundled into 13 rod domains, R1 to R13. Direct binding assays and NMR spectroscopy identify helix41 in the R9 subdomain of talin as the PKA binding site. PKA binding to helix41 requires unfolding of the R9 domain, which requires the linker region between R9 and R10. Experiments with single molecules and in cells manipulated to alter actomyosin contractility demonstrate that the PKA-talin interaction is regulated by mechanical force across the talin molecule. Finally, talin mutations that disrupt PKA binding also decrease levels of total and phosphorylated PKA RII subunits as well as phosphorylation of VASP, a known PKA substrate, within FA. These observations identify a mechanically gated anchoring protein for PKA, a force-dependent binding partner for talin1, and a potential pathway for adhesion-associated mechanotransduction.
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Affiliation(s)
- Mingu Kang
- Department of Pharmacology, University of Vermont Larner College of Medicine, Burlington, VT05405
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT05405
- University of Vermont Cancer Center, Burlington, VT05405
| | - Yasumi Otani
- School of Biosciences, University of Kent, Canterbury, KentCT2 7NJ, United Kingdom
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, LiverpoolL69 7ZB, United Kingdom
| | - Yanyu Guo
- Department of Physics, Mechanobiology Institute, National University of Singapore, Singapore117542, Singapore
| | - Jie Yan
- Department of Physics, Mechanobiology Institute, National University of Singapore, Singapore117542, Singapore
| | - Benjamin T. Goult
- School of Biosciences, University of Kent, Canterbury, KentCT2 7NJ, United Kingdom
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, LiverpoolL69 7ZB, United Kingdom
| | - Alan K. Howe
- Department of Pharmacology, University of Vermont Larner College of Medicine, Burlington, VT05405
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT05405
- University of Vermont Cancer Center, Burlington, VT05405
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6
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Oshiro KGN, Freitas CDP, Rezende SB, Orozco RMQ, Chan LY, Lawrence N, Lião LM, Macedo MLR, Craik DJ, Cardoso MH, Franco OL. Deciphering the structure and mechanism of action of computer-designed mastoparan peptides. FEBS J 2024; 291:865-883. [PMID: 37997610 DOI: 10.1111/febs.17010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/05/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
Mastoparans are cationic peptides with multifunctional pharmacological properties. Mastoparan-R1 and mastoparan-R4 were computationally designed based on native mastoparan-L from wasps and have improved therapeutic potential for the control of bacterial infections. Here, we evaluated whether these peptides maintain their activity against Escherichia coli strains under a range of salt concentrations. We found that mastoparan-R1 and mastoparan-R4 preserved their activity under the conditions tested, including having antibacterial activities at physiological salt concentrations. The overall structure of the peptides was investigated using circular dichroism spectroscopy in a range of solvents. No significant changes in secondary structure were observed (random coil in aqueous solutions and α-helix in hydrophobic and anionic environments). The three-dimensional structures of mastoparan-R1 and mastoparan-R4 were elucidated through nuclear magnetic resonance spectroscopy, revealing amphipathic α-helical segments for Leu3-Ile13 (mastoparan-R1) and Leu3-Ile14 (mastoparan-R4). Possible membrane-association mechanisms for mastoparan-R1 and mastoparan-R4 were investigated through surface plasmon resonance and leakage studies with synthetic POPC and POPC/POPG (4:1) lipid bilayers. Mastoparan-L had the highest affinity for both membrane systems, whereas the two analogs had weaker association, but improved selectivity for lysing anionic membranes. This finding was also supported by molecular dynamics simulations, in which mastoparan-R1 and mastoparan-R4 were found to have greater interactions with bacteria-like membranes compared with model mammalian membranes. Despite having a few differences in their functional and structural profiles, the mastoparan-R1 analog stood out with the highest activity, greater bacteriostatic potential, and selectivity for lysing anionic membranes. This study reinforces the potential of mastoparan-R1 as a drug candidate.
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Affiliation(s)
- Karen G N Oshiro
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
| | - Carlos D P Freitas
- Laboratório de RMN, Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil
| | - Samilla B Rezende
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
| | - Raquel M Q Orozco
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
| | - Lai Y Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Luciano M Lião
- Laboratório de RMN, Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil
| | - Maria L R Macedo
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Marlon H Cardoso
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
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7
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Low KE, Gheorghita AA, Tammam SD, Whitfield GB, Li YE, Riley LM, Weadge JT, Caldwell SJ, Chong PA, Walvoort MTC, Kitova EN, Klassen JS, Codée JDC, Howell PL. Pseudomonas aeruginosa AlgF is a protein-protein interaction mediator required for acetylation of the alginate exopolysaccharide. J Biol Chem 2023; 299:105314. [PMID: 37797696 PMCID: PMC10641220 DOI: 10.1016/j.jbc.2023.105314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
Enzymatic modifications of bacterial exopolysaccharides enhance immune evasion and persistence during infection. In the Gram-negative opportunistic pathogen Pseudomonas aeruginosa, acetylation of alginate reduces opsonic killing by phagocytes and improves reactive oxygen species scavenging. Although it is well known that alginate acetylation in P. aeruginosa requires AlgI, AlgJ, AlgF, and AlgX, how these proteins coordinate polymer modification at a molecular level remains unclear. Here, we describe the structural characterization of AlgF and its protein interaction network. We characterize direct interactions between AlgF and both AlgJ and AlgX in vitro and demonstrate an association between AlgF and AlgX, as well as AlgJ and AlgI, in P. aeruginosa. We determine that AlgF does not exhibit acetylesterase activity and is unable to bind to polymannuronate in vitro. Therefore, we propose that AlgF functions to mediate protein-protein interactions between alginate acetylation enzymes, forming the periplasmic AlgJFXK (AlgJ-AlgF-AlgX-AlgK) acetylation and export complex required for robust biofilm formation.
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Affiliation(s)
- Kristin E Low
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andreea A Gheorghita
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie D Tammam
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gregory B Whitfield
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yancheng E Li
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Laura M Riley
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joel T Weadge
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shane J Caldwell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - P Andrew Chong
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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8
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Hu W, Jing H, Fu W, Wang Z, Zhou J, Zhang N. Conversion to Trimolecular G-Quadruplex by Spontaneous Hoogsteen Pairing-Based Strand Displacement Reaction between Bimolecular G-Quadruplex and Double G-Rich Probes. J Am Chem Soc 2023; 145:18578-18590. [PMID: 37553999 DOI: 10.1021/jacs.3c05617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Bimolecular or tetramolecular G-quadruplexes (GQs) are predominantly self-assembled by the same sequence-identical G-rich oligonucleotides and usually remain inert to the strand displacement reaction (SDR) with other short G-rich invading fragments of DNA or RNA. Appealingly, in this study, we demonstrate that a parallel homomeric bimolecular GQ target of Tub10 d(CAGGGAGGGT) as the starting reactant, although completely folded in K+ solution and sufficiently stable (melting temperature of 57.7 °C), can still spontaneously accept strand invasion by a pair of short G-rich invading probes of P1 d(TGGGA) near room temperature. The final SDR product is a novel parallel heteromeric trimolecular GQ (tri-GQ) of Tub10/2P1 reassembled between one Tub10 strand and two P1 strands. Here we present, to the best of our knowledge, the first NMR solution structure of such a discrete heteromeric tri-GQ and unveil a unique mode of two probes vs one target in mutual recognition among G-rich canonical DNA oligomers. As a model system, the short invading probe P1 can spontaneously trap G-rich target Tub10 from a Watson-Crick duplex completely hybridized between Tub10 and its fully complementary strand d(ACCCTCCCTG). The Tub10 sequence of d(CAGGGAGGGT) is a fragment from the G-rich promoter region of the human β2-tubulin gene. Our findings provide new insights into the Hoogsteen pairing-based SDR between a GQ target and double invading probes of short G-rich DNA fragments and are expected to grant access to increasingly complex architectures in GQ-based DNA nanotechnology.
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Affiliation(s)
- Wenxuan Hu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Wenqiang Fu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Zengrong Wang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Jiang Zhou
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Na Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Key Laboratory of Anhui Province for High Field Magnetic Resonance Imaging, Hefei 230031, China
- High Magnetic Field Laboratory of Anhui Province, Hefei 230031, China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
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9
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Kang M, Otani Y, Guo Y, Yan J, Goult BT, Howe AK. The focal adhesion protein talin is a mechanically-gated A-kinase anchoring protein (AKAP). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.20.554038. [PMID: 37645895 PMCID: PMC10462126 DOI: 10.1101/2023.08.20.554038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The cAMP-dependent protein kinase (Protein Kinase A; PKA) is a ubiquitous, promiscuous kinase whose activity is focused and specified through subcellular localization mediated by A-kinase anchoring proteins (AKAPs). PKA has complex roles as both an effector and a regulator of integrin-mediated cell adhesion to the extracellular matrix (ECM). Recent observations demonstrate that PKA is an active component of focal adhesions (FA), intracellular complexes coupling ECM-bound integrins to the actin cytoskeleton, suggesting the existence of one or more FA AKAPs. Using a combination of a promiscuous biotin ligase fused to PKA type-IIα regulatory (RIIα) subunits and subcellular fractionation, we identify the archetypal FA protein talin1 as an AKAP. Talin is a large, mechanosensitive scaffold that directly links integrins to actin filaments and promotes FA assembly by recruiting additional components in a force-dependent manner. The rod region of talin1 consists of 62 α-helices bundled into 13 rod domains, R1-R13. Direct binding assays and nuclear magnetic resonance spectroscopy identify helix41 in the R9 subdomain of talin as the PKA binding site. PKA binding to helix41 requires unfolding of the R9 domain, which requires the linker region between R9 and R10. Finally, single-molecule experiments with talin1 and PKA, and experiments in cells manipulated to alter actomyosin contractility demonstrate that the PKA-talin interaction is regulated by mechanical force across the talin molecule. These observations identify the first mechanically-gated anchoring protein for PKA, a new force-dependent binding partner for talin1, and thus a new mechanism for coupling cellular tension and signal transduction.
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10
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Sulekha A, Osborne MJ, Gasiorek J, Borden KLB. 1H, 13C, 15N Backbone and sidechain chemical shift assignments of the C-terminal domain of human UDP-glucuronosyltransferase 2B17 (UGT2B17-C). BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:67-73. [PMID: 36757531 DOI: 10.1007/s12104-023-10122-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/01/2023] [Indexed: 06/02/2023]
Abstract
UDP-glucuronosyltransferases are the principal enzymes involved in the glucuronidation of metabolites and xenobiotics for physiological clearance in humans. Though glucuronidation is an indispensable process in the phase II metabolic pathway, UGT-mediated glucuronidation of most prescribed drugs (> 55%) and clinical evidence of UGT-associated drug resistance are major concerns for therapeutic development. While UGTs are highly conserved enzymes, they manifest unique substrate and inhibitor specificity which is poorly understood given the dearth of experimentally determined full-length structures. Such information is important not only to conceptualize their specificity but is central to the design of inhibitors specific to a given UGT in order to avoid toxicity associated with pan-UGT inhibitors. Here, we provide the 1H, 13C and 15N backbone (~ 90%) and sidechain (~ 62%) assignments for the C-terminal domain of UGT2B17, which can be used to determine the molecular binding sites of inhibitor and substrate, and to understand the atomic basis for inhibitor selectivity between UGT2B17 and other members of the UGT2B subfamily. Given the physiological relevance of UGT2B17 in the elimination of hormone-based cancer drugs, these assignments will contribute towards dissecting the structural basis for substrate specificity, selective inhibitor recognition and other aspects of enzyme activity with the goal of selectively overcoming glucuronidation-based drug resistance.
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Affiliation(s)
- Anamika Sulekha
- Department of Pathology and Cell Biology and Institute of Research in Immunology and Cancer (IRIC), Université de Montréal, Pavilion Marcelle‑Coutu, Chemin Polytechnique, Montreal, QC, Canada
| | - Michael J Osborne
- Department of Pathology and Cell Biology and Institute of Research in Immunology and Cancer (IRIC), Université de Montréal, Pavilion Marcelle‑Coutu, Chemin Polytechnique, Montreal, QC, Canada
| | - Jadwiga Gasiorek
- Department of Pathology and Cell Biology and Institute of Research in Immunology and Cancer (IRIC), Université de Montréal, Pavilion Marcelle‑Coutu, Chemin Polytechnique, Montreal, QC, Canada
| | - Katherine L B Borden
- Department of Pathology and Cell Biology and Institute of Research in Immunology and Cancer (IRIC), Université de Montréal, Pavilion Marcelle‑Coutu, Chemin Polytechnique, Montreal, QC, Canada.
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11
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Gallego-Paez LM, Edwards WJS, Chanduri M, Guo Y, Koorman T, Lee CY, Grexa N, Derksen P, Yan J, Schwartz MA, Mauer J, Goult BT. TLN1 contains a cancer-associated cassette exon that alters talin-1 mechanosensitivity. J Cell Biol 2023; 222:213923. [PMID: 36880935 PMCID: PMC9997659 DOI: 10.1083/jcb.202209010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/08/2023] [Accepted: 02/17/2023] [Indexed: 03/08/2023] Open
Abstract
Talin-1 is the core mechanosensitive adapter protein linking integrins to the cytoskeleton. The TLN1 gene is comprised of 57 exons that encode the 2,541 amino acid TLN1 protein. TLN1 was previously considered to be expressed as a single isoform. However, through differential pre-mRNA splicing analysis, we discovered a cancer-enriched, non-annotated 51-nucleotide exon in TLN1 between exons 17 and 18, which we refer to as exon 17b. TLN1 is comprised of an N-terminal FERM domain, linked to 13 force-dependent switch domains, R1-R13. Inclusion of exon 17b introduces an in-frame insertion of 17 amino acids immediately after Gln665 in the region between R1 and R2 which lowers the force required to open the R1-R2 switches potentially altering downstream mechanotransduction. Biochemical analysis of this isoform revealed enhanced vinculin binding, and cells expressing this variant show altered adhesion dynamics and motility. Finally, we showed that the TGF-β/SMAD3 signaling pathway regulates this isoform switch. Future studies will need to consider the balance of these two TLN1 isoforms.
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Affiliation(s)
| | | | - Manasa Chanduri
- Departments of Internal Medicine (Cardiology) and Yale Cardiovascular Research Center , New Haven, CT, USA
| | - Yanyu Guo
- Mechanobiology Institute, National University of Singapore , Singapore, Singapore
| | - Thijs Koorman
- Department of Pathology, University Medical Center Utrecht , Utrecht, Netherlands
| | | | - Nina Grexa
- Biomed X Institute (GmbH) , Heidelberg, Germany
| | - Patrick Derksen
- Department of Pathology, University Medical Center Utrecht , Utrecht, Netherlands
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore , Singapore, Singapore.,Department of Physics, National University of Singapore , Singapore, Singapore
| | - Martin A Schwartz
- Departments of Internal Medicine (Cardiology) and Yale Cardiovascular Research Center , New Haven, CT, USA.,Departments of Cell Biology and Biomedical Engineering, Yale School of Medicine , New Haven, CT, USA
| | - Jan Mauer
- Biomed X Institute (GmbH) , Heidelberg, Germany.,Department of Immunology, Novartis Institutes for BioMedical Research, Basel, Switzerland
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12
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Viana de Freitas T, Karmakar U, Vasconcelos AG, Santos MA, Oliveira do Vale Lira B, Costa SR, Barbosa EA, Cardozo-Fh J, Correa R, Ribeiro DJS, Prates MV, Magalhães KG, Soller Ramada MH, Roberto de Souza Almeida Leite J, Bloch C, Lima de Oliveira A, Vendrell M, Brand GD. Release of immunomodulatory peptides at bacterial membrane interfaces as a novel strategy to fight microorganisms. J Biol Chem 2023; 299:103056. [PMID: 36822328 PMCID: PMC10074799 DOI: 10.1016/j.jbc.2023.103056] [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: 09/23/2022] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023] Open
Abstract
Cationic and amphiphilic peptides can be used as homing devices to accumulate conjugated antibiotics to bacteria-enriched sites and promote efficient microbial killing. However, just as important as tackling bacterial infections, is the modulation of the immune response in this complex microenvironment. In the present report, we designed a peptide chimaera called Chim2, formed by a membrane-active module, an enzyme hydrolysis site and a formyl peptide receptor 2 (FPR2) agonist. This molecule was designed to adsorb onto bacterial membranes, promote their lysis, and upon hydrolysis by local enzymes, release the FPR2 agonist sequence for activation and recruitment of immune cells. We synthesized the isolated peptide modules of Chim2 and characterized their biological activities independently and as a single polypeptide chain. We conducted antimicrobial assays, along with other tests aiming at the analyses of the cellular and immunological responses. In addition, assays using vesicles as models of eukaryotic and prokaryotic membranes were conducted and solution structures of Chim2 were generated by 1H NMR. Chim2 is antimicrobial, adsorbs preferentially to negatively charged vesicles while adopting an α-helix structure and exposes its disorganized tail to the solvent, which facilitates hydrolysis by tryptase-like enzymes, allowing the release of the FPR2 agonist fragment. This fragment was shown to induce accumulation of the cellular activation marker, lipid bodies, in mouse macrophages and the release of immunomodulatory interleukins. In conclusion, these data demonstrate that peptides with antimicrobial and immunomodulatory activities can be considered for further development as drugs.
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Affiliation(s)
- Thiago Viana de Freitas
- Universidade de Brasília, Instituto de Química, Laboratório de Síntese e Análise de Biomoléculas, LSAB, Brasília, Distrito Federal, Brasil
| | - Utsa Karmakar
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh, UK
| | - Andreanne G Vasconcelos
- Universidade de Brasília, Faculdade de Medicina, Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Brasília, Distrito Federal, Brasil
| | - Michele A Santos
- Universidade de Brasília, Instituto de Química, Laboratório de Síntese e Análise de Biomoléculas, LSAB, Brasília, Distrito Federal, Brasil; Universidade de Brasília, Instituto de Química, Laboratório de Ressonância Magnética Nuclear, LRMN, Brasília, Distrito Federal, Brasil
| | - Bianca Oliveira do Vale Lira
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brasil; Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brasil
| | - Samuel Ribeiro Costa
- Universidade de Brasília, Instituto de Química, Laboratório de Síntese e Análise de Biomoléculas, LSAB, Brasília, Distrito Federal, Brasil
| | - Eder Alves Barbosa
- Universidade de Brasília, Instituto de Química, Laboratório de Síntese e Análise de Biomoléculas, LSAB, Brasília, Distrito Federal, Brasil
| | - José Cardozo-Fh
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brasil
| | - Rafael Correa
- Universidade de Brasília, Instituto de Biologia, Laboratório de Imunologia e Inflamação, LIMI, Brasília, Distrito Federal, Brasil
| | - Dalila J S Ribeiro
- Universidade de Brasília, Instituto de Biologia, Laboratório de Imunologia e Inflamação, LIMI, Brasília, Distrito Federal, Brasil
| | - Maura Vianna Prates
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brasil
| | - Kelly G Magalhães
- Universidade de Brasília, Instituto de Biologia, Laboratório de Imunologia e Inflamação, LIMI, Brasília, Distrito Federal, Brasil
| | - Marcelo Henrique Soller Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brasil; Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brasil
| | - José Roberto de Souza Almeida Leite
- Universidade de Brasília, Faculdade de Medicina, Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Brasília, Distrito Federal, Brasil
| | - Carlos Bloch
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brasil
| | - Aline Lima de Oliveira
- Universidade de Brasília, Instituto de Química, Laboratório de Ressonância Magnética Nuclear, LRMN, Brasília, Distrito Federal, Brasil
| | - Marc Vendrell
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh, UK
| | - Guilherme Dotto Brand
- Universidade de Brasília, Instituto de Química, Laboratório de Síntese e Análise de Biomoléculas, LSAB, Brasília, Distrito Federal, Brasil.
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13
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Parijat P, Ponnam S, Attili S, Campbell KS, El-Mezgueldi M, Pfuhl M, Kampourakis T. Discovery of novel cardiac troponin activators using fluorescence polarization-based high throughput screening assays. Sci Rep 2023; 13:5216. [PMID: 36997544 PMCID: PMC10063609 DOI: 10.1038/s41598-023-32476-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The large unmet demand for new heart failure therapeutics is widely acknowledged. Over the last decades the contractile myofilaments themselves have emerged as an attractive target for the development of new therapeutics for both systolic and diastolic heart failure. However, the clinical use of myofilament-directed drugs has been limited, and further progress has been hampered by incomplete understanding of myofilament function on the molecular level and screening technologies for small molecules that accurately reproduce this function in vitro. In this study we have designed, validated and characterized new high throughput screening platforms for small molecule effectors targeting the interactions between the troponin C and troponin I subunits of the cardiac troponin complex. Fluorescence polarization-based assays were used to screen commercially available compound libraries, and hits were validated using secondary screens and orthogonal assays. Hit compound-troponin interactions were characterized using isothermal titration calorimetry and NMR spectroscopy. We identified NS5806 as novel calcium sensitizer that stabilizes active troponin. In good agreement, NS5806 greatly increased the calcium sensitivity and maximal isometric force of demembranated human donor myocardium. Our results suggest that sarcomeric protein-directed screening platforms are suitable for the development of compounds that modulate cardiac myofilament function.
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Affiliation(s)
- Priyanka Parijat
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- British Heart Foundation Centre of Research Excellence, King's College London, London, SE1 1UL, UK
| | - Saraswathi Ponnam
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- British Heart Foundation Centre of Research Excellence, King's College London, London, SE1 1UL, UK
| | - Seetharamaiah Attili
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- British Heart Foundation Centre of Research Excellence, King's College London, London, SE1 1UL, UK
| | - Kenneth S Campbell
- Division of Cardiovascular Medicine and Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Mohammed El-Mezgueldi
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- British Heart Foundation Centre of Research Excellence, King's College London, London, SE1 1UL, UK
| | - Mark Pfuhl
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- British Heart Foundation Centre of Research Excellence, King's College London, London, SE1 1UL, UK
| | - Thomas Kampourakis
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK.
- British Heart Foundation Centre of Research Excellence, King's College London, London, SE1 1UL, UK.
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14
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Bhattacharya A, Shukla VK, Kachariya N, Preeti, Sehrawat P, Kumar A. Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly. J Mol Biol 2022; 434:167830. [PMID: 36116539 DOI: 10.1016/j.jmb.2022.167830] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 08/20/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022]
Abstract
Skp1(S-phase kinase-associated protein 1 - Homo sapiens) is an adapter protein of the SCF(Skp1-Cullin1-Fbox) complex, which links the constant components (Cul1-RBX) and the variable receptor (F-box proteins) in Ubiquitin E3 ligase. It is intriguing how Skp1 can recognise and bind to a variety of structurally different F-box proteins. For practical reasons, previous efforts have used truncated Skp1, and thus it has not been possible to track the crucial aspects of the substrate recognition process. In this background, we report the solution structure of the full-length Skp1 protein determined by NMR spectroscopy for the first time and investigate the sequence-dependent dynamics in the protein. The solution structure reveals that Skp1 has an architecture: β1-β2-H1-H2-L1-H3-L2-H4-H5-H6-H7(partially formed) and a long tail-like disordered C-terminus. Structural analysis using DALI (Distance Matrix Alignment) reveals conserved domain structure across species for Skp1. Backbone dynamics investigated using NMR relaxation suggest substantial variation in the motional timescales along the length of the protein. The loops and the C-terminal residues are highly flexible, and the (R2/R1) data suggests μs-ms timescale motions in the helices as well. Further, the dependence of amide proton chemical shift on temperature and curved profiles of their residuals indicate that the residues undergo transitions between native state and excited state. The curved profiles for several residues across the length of the protein suggest that there are native-like low-lying excited states, particularly for several C-terminal residues. Our results provide a rationale for how the protein can adapt itself, bind, and get functionally associated with other proteins in the SCF complex by utilising its flexibility and conformational sub-states.
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Affiliation(s)
- Amrita Bhattacharya
- Lab No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Vaibhav Kumar Shukla
- Biophysical Chemistry & Structural Biology Laboratory, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai 400098, India. https://twitter.com/bhu_vaibhav
| | - Nitin Kachariya
- Lab No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Preeti
- Lab No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Parveen Sehrawat
- Lab No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ashutosh Kumar
- Lab No. 606, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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15
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Harman JL, Reardon PN, Costello SM, Warren GD, Phillips SR, Connor PJ, Marqusee S, Harms MJ. Evolution avoids a pathological stabilizing interaction in the immune protein S100A9. Proc Natl Acad Sci U S A 2022; 119:e2208029119. [PMID: 36194634 PMCID: PMC9565474 DOI: 10.1073/pnas.2208029119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/07/2022] [Indexed: 01/03/2023] Open
Abstract
Stability constrains evolution. While much is known about constraints on destabilizing mutations, less is known about the constraints on stabilizing mutations. We recently identified a mutation in the innate immune protein S100A9 that provides insight into such constraints. When introduced into human S100A9, M63F simultaneously increases the stability of the protein and disrupts its natural ability to activate Toll-like receptor 4. Using chemical denaturation, we found that M63F stabilizes a calcium-bound conformation of hS100A9. We then used NMR to solve the structure of the mutant protein, revealing that the mutation distorts the hydrophobic binding surface of hS100A9, explaining its deleterious effect on function. Hydrogen-deuterium exchange (HDX) experiments revealed stabilization of the region around M63F in the structure, notably Phe37. In the structure of the M63F mutant, the Phe37 and Phe63 sidechains are in contact, plausibly forming an edge-face π-stack. Mutating Phe37 to Leu abolished the stabilizing effect of M63F as probed by both chemical denaturation and HDX. It also restored the biological activity of S100A9 disrupted by M63F. These findings reveal that Phe63 creates a molecular staple with Phe37 that stabilizes a nonfunctional conformation of the protein, thus disrupting function. Using a bioinformatic analysis, we found that S100A9 proteins from different organisms rarely have Phe at both positions 37 and 63, suggesting that avoiding a pathological stabilizing interaction indeed constrains S100A9 evolution. This work highlights an important evolutionary constraint on stabilizing mutations, namely, that they must avoid inappropriately stabilizing nonfunctional protein conformations.
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Affiliation(s)
- Joseph L. Harman
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Patrick N. Reardon
- College of Science, NMR Facility, Oregon State University, Corvallis, OR 97331
| | - Shawn M. Costello
- Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720
| | - Gus D. Warren
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Sophia R. Phillips
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Patrick J. Connor
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Michael J. Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
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16
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Leighton GO, Irvin EM, Kaur P, Liu M, You C, Bhattaram D, Piehler J, Riehn R, Wang H, Pan H, Williams DC. Densely methylated DNA traps Methyl-CpG-binding domain protein 2 but permits free diffusion by Methyl-CpG-binding domain protein 3. J Biol Chem 2022; 298:102428. [PMID: 36037972 PMCID: PMC9520026 DOI: 10.1016/j.jbc.2022.102428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 10/29/2022] Open
Abstract
The methyl-CpG-binding domain 2 and 3 proteins (MBD2 and MBD3) provide structural and DNA-binding function for the Nucleosome Remodeling and Deacetylase (NuRD) complex. The two proteins form distinct NuRD complexes and show different binding affinity and selectivity for methylated DNA. Previous studies have shown that MBD2 binds with high affinity and selectivity for a single methylated CpG dinucleotide while MBD3 does not. However, the NuRD complex functions in regions of the genome that contain many CpG dinucleotides (CpG islands). Therefore, in this work, we investigate the binding and diffusion of MBD2 and MBD3 on more biologically relevant DNA templates that contain a large CpG island or limited CpG sites. Using a combination of single-molecule and biophysical analyses, we show that both MBD2 and MBD3 diffuse freely and rapidly across unmethylated CpG-rich DNA. In contrast, we found methylation of large CpG islands traps MBD2 leading to stable and apparently static binding on the CpG island while MBD3 continues to diffuse freely. In addition, we demonstrate both proteins bend DNA, which is augmented by methylation. Together, these studies support a model in which MBD2-NuRD strongly localizes to and compacts methylated CpG islands while MBD3-NuRD can freely mobilize nucleosomes independent of methylation status.
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Affiliation(s)
- Gage O Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Ming Liu
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Dhruv Bhattaram
- Department of Biomedical Engineering, Georgia Institute of Technology & Emory University of Medicine, Atlanta, Georgia, USA
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, North Carolina, USA; Department of Physics, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Hai Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
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17
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Azizi L, Varela L, Turkki P, Mykuliak VV, Korpela S, Ihalainen TO, Church J, Hytönen VP, Goult BT. Talin variant P229S compromises integrin activation and associates with multifaceted clinical symptoms. Hum Mol Genet 2022; 31:4159-4172. [PMID: 35861643 PMCID: PMC9759328 DOI: 10.1093/hmg/ddac163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/13/2022] [Accepted: 07/12/2022] [Indexed: 01/21/2023] Open
Abstract
Adhesion of cells to the extracellular matrix (ECM) must be exquisitely coordinated to enable development and tissue homeostasis. Cell-ECM interactions are regulated by multiple signalling pathways that coordinate the activation state of the integrin family of ECM receptors. The protein talin is pivotal in this process, and talin's simultaneous interactions with the cytoplasmic tails of the integrins and the plasma membrane are essential to enable robust, dynamic control of integrin activation and cell-ECM adhesion. Here, we report the identification of a de novo heterozygous c.685C>T (p.Pro229Ser) variant in the TLN1 gene from a patient with a complex phenotype. The mutation is located in the talin head region at the interface between the F2 and F3 domains. The characterization of this novel p.P229S talin variant reveals the disruption of adhesion dynamics that result from disturbance of the F2-F3 domain interface in the talin head. Using biophysical, computational and cell biological techniques, we find that the variant perturbs the synergy between the integrin-binding F3 and the membrane-binding F2 domains, compromising integrin activation, adhesion and cell migration. Whilst this remains a variant of uncertain significance, it is probable that the dysregulation of adhesion dynamics we observe in cells contributes to the multifaceted clinical symptoms of the patient and may provide insight into the multitude of cellular processes dependent on talin-mediated adhesion dynamics.
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Affiliation(s)
| | | | | | - Vasyl V Mykuliak
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sanna Korpela
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Teemu O Ihalainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Joseph Church
- To whom correspondence should be addressed. (Benjamin T. Goult), (Vesa P. Hytönen), (Joe Church)
| | - Vesa P Hytönen
- To whom correspondence should be addressed. (Benjamin T. Goult), (Vesa P. Hytönen), (Joe Church)
| | - Benjamin T Goult
- To whom correspondence should be addressed. (Benjamin T. Goult), (Vesa P. Hytönen), (Joe Church)
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18
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Noll NA, Riley LA, Moore CS, Zhong L, Bersi MR, West JD, Zent R, Merryman WD. Loss of talin in cardiac fibroblasts results in augmented ventricular cardiomyocyte hypertrophy in response to pressure overload. Am J Physiol Heart Circ Physiol 2022; 322:H857-H866. [PMID: 35333120 PMCID: PMC9018049 DOI: 10.1152/ajpheart.00632.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/22/2022]
Abstract
Pressure overload of the heart is characterized by concentric hypertrophy and interstitial fibrosis. Cardiac fibroblasts (CFs) in the ventricular wall become activated during injury and synthesize and compact the extracellular matrix, which causes interstitial fibrosis and stiffening of the ventricular heart walls. Talin1 (Tln1) and Talin2 (Tln2) are mechanosensitive proteins that participate in focal adhesion transmission of signals from the extracellular environment to the actin cytoskeleton of CFs. The aim of the present study was to determine whether the removal of Tln1 and Tln2 from CFs would reduce interstitial fibrosis and cardiac hypertrophy. Twelve-week-old male and female Tln2-null (Tln2-/-) and Tln2-null, CF-specific Tln1 knockout (Tln2-/-;Tln1CF-/-) mice were given angiotensin-II (ANG II) (1.5 mg/kg/day) or saline through osmotic pumps for 8 wk. Cardiomyocyte area and measures of heart thickness were increased in the male ANG II-infused Tln2-/-;Tln1CF-/- mice, whereas there was no increase in interstitial fibrosis. Systolic blood pressure was increased in the female Tln2-/-;Tln1CF-/- mice after ANG II infusion compared with the Tln2-/- mice. However, there was no increase in cardiac hypertrophy in the Tln2-/-;Tln1CF-/- mice, which was seen in the Tln2-/- mice. Collectively, these data indicate that in male mice, the absence of Tln1 and Tln2 in CFs leads to cardiomyocyte hypertrophy in response to ANG II, whereas it results in a hypertrophy-resistant phenotype in female mice. These findings have important implications for the role of mechanosensitive proteins in CFs and their impact on cardiomyocyte function in the pathogenesis of hypertension and cardiac hypertrophy.NEW & NOTEWORTHY The role of talins has been previously studied in cardiomyocytes; however, these mechanotransductive proteins that are members of the focal adhesion complex have not been examined in cardiac fibroblasts previously. We hypothesized that loss of talins in cardiac fibroblasts would reduce interstitial fibrosis in the heart with a pressure overload model. However, we found that although loss of talins did not alter fibrosis, it did result in cardiomyocyte and ventricular hypertrophy.
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Affiliation(s)
- Natalie A Noll
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Lance A Riley
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Christy S Moore
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lin Zhong
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mathew R Bersi
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - James D West
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Roy Zent
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - W David Merryman
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
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19
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Mukundan A, Byeon CH, Hinck CS, Cunningham K, Campion T, Smyth DJ, Maizels RM, Hinck AP. Convergent evolution of a parasite-encoded complement control protein-scaffold to mimic binding of mammalian TGF-β to its receptors, TβRI and TβRII. J Biol Chem 2022; 298:101994. [PMID: 35500648 PMCID: PMC9163516 DOI: 10.1016/j.jbc.2022.101994] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 11/02/2022] Open
Abstract
The mouse intestinal helminth Heligmosomoides polygyrus modulates host immune responses by secreting a transforming growth factor (TGF)-β mimic (TGM), to expand the population of Foxp3+ Tregs. TGM comprises five complement control protein (CCP)-like domains, designated D1-D5. Though lacking homology to TGF-β, TGM binds directly to the TGF-β receptors TβRI and TβRII and stimulates the differentiation of naïve T-cells into Tregs. However, the molecular determinants of binding are unclear. Here, we used surface plasmon resonance, isothermal calorimetry, NMR spectroscopy, and mutagenesis to investigate how TGM binds the TGF-β receptors. We demonstrate that binding is modular, with D1-D2 binding to TβRI and D3 binding to TβRII. D1-D2 and D3 were further shown to compete with TGF-β(TβRII)2 and TGF-β for binding to TβRI and TβRII, respectively. The solution structure of TGM-D3 revealed that TGM adopts a CCP-like fold but is also modified to allow the C-terminal strand to diverge, leading to an expansion of the domain and opening potential interaction surfaces. TGM-D3 also incorporates a long structurally ordered hypervariable loop, adding further potential interaction sites. Through NMR shift perturbations and binding studies of TGM-D3 and TβRII variants, TGM-D3 was shown to occupy the same site of TβRII as bound by TGF-β using both a novel interaction surface and the hypervariable loop. These results, together with the identification of other secreted CCP-like proteins with immunomodulatory activity in H. polygyrus, suggest that TGM is part of a larger family of evolutionarily plastic parasite effector molecules that mediate novel interactions with their host.
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Affiliation(s)
- Ananya Mukundan
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania USA
| | - Chang-Hyeock Byeon
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania USA
| | - Cynthia S Hinck
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania USA
| | - Kyle Cunningham
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Tiffany Campion
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Danielle J Smyth
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Rick M Maizels
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Andrew P Hinck
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania USA.
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20
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Lan H, Abualrous ET, Sticht J, Fernandez LMA, Werk T, Weise C, Ballaschk M, Schmieder P, Loll B, Freund C. Exchange catalysis by tapasin exploits conserved and allele-specific features of MHC-I molecules. Nat Commun 2021; 12:4236. [PMID: 34244493 PMCID: PMC8271027 DOI: 10.1038/s41467-021-24401-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/18/2021] [Indexed: 11/29/2022] Open
Abstract
The repertoire of peptides presented by major histocompatibility complex class I (MHC-I) molecules on the cell surface is tailored by the ER-resident peptide loading complex (PLC), which contains the exchange catalyst tapasin. Tapasin stabilizes MHC-I molecules and promotes the formation of stable peptide-MHC-I (pMHC-I) complexes that serve as T cell antigens. Exchange of suboptimal by high-affinity ligands is catalyzed by tapasin, but the underlying mechanism is still elusive. Here we analyze the tapasin-induced changes in MHC-I dynamics, and find the catalyst to exploit two essential features of MHC-I. First, tapasin recognizes a conserved allosteric site underneath the α2-1-helix of MHC-I, ‘loosening’ the MHC-I F-pocket region that accomodates the C-terminus of the peptide. Second, the scoop loop11–20 of tapasin relies on residue L18 to target the MHC-I F-pocket, enabling peptide exchange. Meanwhile, tapasin residue K16 plays an accessory role in catalysis of MHC-I allotypes bearing an acidic F-pocket. Thus, our results provide an explanation for the observed allele-specificity of catalyzed peptide exchange. Tapasin is part of the peptide loading complex necessary for presenting antigenic peptides on MHC-I for the induction of adaptive immunity. Here the authors show that tapasin interacts with MHC-I in both conserved and allele-specific regions to promote antigen presentation, with tapasin L18 and K16 residues both implicated in this molecular interaction.
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Affiliation(s)
- Huan Lan
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Esam T Abualrous
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.,Artificial Intelligence for the Sciences, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Jana Sticht
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.,Core Facility BioSupraMol, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Laura Maria Arroyo Fernandez
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Tamina Werk
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christoph Weise
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.,Core Facility BioSupraMol, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Martin Ballaschk
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Bernhard Loll
- Laboratory of Structural Biology, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute for Chemistry & Biochemistry, Freie Universität Berlin, Berlin, Germany.
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21
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Gough RE, Jones MC, Zacharchenko T, Le S, Yu M, Jacquemet G, Muench SP, Yan J, Humphries JD, Jørgensen C, Humphries MJ, Goult BT. Talin mechanosensitivity is modulated by a direct interaction with cyclin-dependent kinase-1. J Biol Chem 2021; 297:100837. [PMID: 34118235 PMCID: PMC8260872 DOI: 10.1016/j.jbc.2021.100837] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Talin (TLN1) is a mechanosensitive component of adhesion complexes that directly couples integrins to the actin cytoskeleton. In response to force, talin undergoes switch-like behavior of its multiple rod domains that modulate interactions with its binding partners. Cyclin-dependent kinase-1 (CDK1) is a key regulator of the cell cycle, exerting its effects through synchronized phosphorylation of a large number of protein targets. CDK1 activity maintains adhesion during interphase, and its inhibition is a prerequisite for the tightly choreographed changes in cell shape and adhesion that are required for successful mitosis. Using a combination of biochemical, structural, and cell biological approaches, we demonstrate a direct interaction between talin and CDK1 that occurs at sites of integrin-mediated adhesion. Mutagenesis demonstrated that CDK1 contains a functional talin-binding LD motif, and the binding site within talin was pinpointed to helical bundle R8. Talin also contains a consensus CDK1 phosphorylation motif centered on S1589, a site shown to be phosphorylated by CDK1 in vitro. A phosphomimetic mutant of this site within talin lowered the binding affinity of the cytoskeletal adaptor KANK and weakened the response of this region to force as measured by single molecule stretching, potentially altering downstream mechanotransduction pathways. The direct binding of the master cell cycle regulator CDK1 to the primary integrin effector talin represents a coupling of cell proliferation and cell adhesion machineries and thereby indicates a mechanism by which the microenvironment can control cell division in multicellular organisms.
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Affiliation(s)
| | - Matthew C Jones
- Faculty of Biology, Medicine & Health, Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Thomas Zacharchenko
- Faculty of Biology, Medicine & Health, Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Shimin Le
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Miao Yu
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Guillaume Jacquemet
- Faculty of Science and Engineering, Cell Biology Department, Åbo Akademi University, Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ste P Muench
- School of Biomedical Sciences, Astbury Centre for Structural Biology, University of Leeds, Leeds, UK
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore; Department of Physics, National University of Singapore, Singapore
| | - Jonathan D Humphries
- Faculty of Biology, Medicine & Health, Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Claus Jørgensen
- Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Martin J Humphries
- Faculty of Biology, Medicine & Health, Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
| | - Benjamin T Goult
- School of Biosciences, University of Kent, Canterbury, Kent, UK.
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22
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Solution NMR Structure of Titin N2A Region Ig Domain I83 and Its Interaction with Metal Ions. J Mol Biol 2021; 433:166977. [PMID: 33811919 DOI: 10.1016/j.jmb.2021.166977] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 11/21/2022]
Abstract
Titin, the largest single chain protein known so far, has long been known to play a critical role in passive muscle function but recent studies have highlighted titin's role in active muscle function. One of the key elements in this role is the Ca2+-dependent interaction between titin's N2A region and the thin filament. An important element in this interaction is I83, the terminal immunoglobulin domain in the N2A region. There is limited structural information about this domain, but experimental evidence suggests that it plays a critical role in the N2A-actin binding interaction. We now report the solution NMR structure of I83 and characterize its dynamics and metal binding properties in detail. Its structure shows interesting relationships to other I-band Ig domains. Metal binding and dynamics data point towards the way the domain is evolutionarily optimized to interact with neighbouring domains. We also identify a calcium binding site on the N-terminal side of I83, which is expected to impact the interdomain interaction with the I82 domain. Together these results provide a first step towards a better understanding of the physiological effects associated with deletion of most of the I83 domain, as occurs in the mdm mouse model, as well as for future investigations of the N2A region.
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23
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Jing H, Fu W, Hu W, Xu S, Xu X, He M, Liu Y, Zhang N. NMR structural study on the self-trimerization of d(GTTAGG) into a dynamic trimolecular G-quadruplex assembly preferentially in Na+ solution with a moderate K+ tolerance. Nucleic Acids Res 2021; 49:2306-2316. [PMID: 33524157 PMCID: PMC7913680 DOI: 10.1093/nar/gkab028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/05/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
Vast G-quadruplexes (GQs) are primarily folded by one, two, or four G-rich oligomers, rarely with an exception. Here, we present the first NMR solution structure of a trimolecular GQ (tri-GQ) that is solely assembled by the self-trimerization of d(GTTAGG), preferentially in Na+ solution tolerant to an equal amount of K+ cation. Eight guanines from three asymmetrically folded strands of d(GTTAGG) are organized into a two-tetrad core, which features a broken G-column and two width-irregular grooves. Fast strand exchanges on a timescale of second at 17°C spontaneously occur between folded tri-GQ and unfolded single-strand of d(GTTAGG) that both species coexist in dynamic equilibrium. Thus, this tri-GQ is not just simply a static assembly but rather a dynamic assembly. Moreover, another minor tetra-GQ that has putatively tetrameric (2+2) antiparallel topology becomes noticeable only at an extremely high strand concentration above 18 mM. The major tri-GQ and minor tetra-GQ are considered to be mutually related, and their reversible interconversion pathways are proposed accordingly. The sequence d(GTTAGG) could be regarded as either a reading frame shifted single repeat of human telomeric DNA or a 1.5 repeat of Bombyx mori telomeric DNA. Overall, our findings provide new insight into GQs and expect more functional applications.
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Affiliation(s)
- Haitao Jing
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Wenqiang Fu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Wenxuan Hu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Suping Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Xiaojuan Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Miao He
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Yangzhong Liu
- University of Science and Technology of China, Hefei 230026, China
| | - Na Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of Anhui Province for High Field Magnetic Resonance Imaging, Hefei 230031, China.,High Magnetic Field Laboratory of Anhui Province, Hefei 230031, China
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24
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Mariano G, Gomes de Sá L, Carmo da Silva E, Santos M, Cardozo Fh J, Lira B, Barbosa E, Araujo A, Leite J, Ramada M, Bloch Jr. C, Oliveira A, Chaker J, Brand G. Characterization of novel human intragenic antimicrobial peptides, incorporation and release studies from ureasil-polyether hybrid matrix. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 119:111581. [DOI: 10.1016/j.msec.2020.111581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/25/2022]
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25
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Abstract
More than 250 proteins are associated with the formation of integrin adhesion complexes involving a vast number of complex interactions between them. These interactions enable adhesions to serve as dynamic and diverse mechanosignaling centers. Our laboratory focuses on the biochemical and structural study of these interactions to help unpick this complex network. Here, we describe the general pipeline of biochemical assays and methods we use. The chapter is split into two sections: (1) protein production and characterization and (2) biochemical assays for the characterization of binding between full-length proteins and/or specific regions of proteins with other proteins, peptides, and phospholipids. The suite of assays we use routinely includes circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy for sample quality assessment, prior to biochemical analysis using NMR, fluorescence polarization (FP), microscale thermophoresis (MST), size-exclusion chromatography multiangle light scattering (SEC-MALS), and pulldown/cosedimentation-based approaches. The results of our analysis feed into in vivo studies that allow for the elucidation of the biological role of each interaction.
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26
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Krishnarjuna B, Sunanda P, Villegas-Moreno J, Csoti A, A V Morales R, Wai DCC, Panyi G, Prentis P, Norton RS. A disulfide-stabilised helical hairpin fold in acrorhagin I: An emerging structural motif in peptide toxins. J Struct Biol 2020; 213:107692. [PMID: 33387653 DOI: 10.1016/j.jsb.2020.107692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/14/2020] [Accepted: 12/24/2020] [Indexed: 12/22/2022]
Abstract
Acrorhagin I (U-AITX-Aeq5a) is a disulfide-rich peptide identified in the aggressive organs (acrorhagi) of the sea anemone Actinia equina. Previous studies (Toxicon 2005, 46:768-74) found that the peptide is toxic in crabs, although the structural and functional properties of acrorhagin I have not been reported. In this work, an Escherichia coli (BL21 strain) expression system was established for the preparation of 13C,15N-labelled acrorhagin I, and the solution structure was determined using NMR spectroscopy. Structurally, acrorhagin I is similar to B-IV toxin from the marine worm Cerebratulus lacteus (PDB id 1VIB), with a well-defined helical hairpin structure stabilised by four intramolecular disulfide bonds. The recombinant peptide was tested in patch-clamp electrophysiology assays against voltage-gated potassium and sodium channels, and in bacterial and fungal growth inhibitory assays and haemolytic assays. Acrorhagin I was not active against any of the ion channels tested and showed no activity in functional assays, indicating that this peptide may possess a different biological function. Metal ion interaction studies using NMR spectroscopy showed that acrorhagin I bound zinc and nickel, suggesting that its function might be modulated by metal ions or that it may be involved in regulating metal ion levels and their transport. The similarity between the structure of acrorhagin I and that of B-IV toxin from a marine worm suggests that this fold may prove to be a recurring motif in disulfide-rich peptides from marine organisms.
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Affiliation(s)
- Bankala Krishnarjuna
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Punnepalli Sunanda
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Jessica Villegas-Moreno
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Agota Csoti
- Department of Biophysics and Cell Biology, University of Debrecen, 4032 Debrecen, Hungary; MTA-DE-NAP B Ion Channel Structure-Function Research Group, RCMM, University of Debrecen, 4032 Debrecen, Hungary
| | - Rodrigo A V Morales
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Dorothy C C Wai
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, University of Debrecen, 4032 Debrecen, Hungary; MTA-DE-NAP B Ion Channel Structure-Function Research Group, RCMM, University of Debrecen, 4032 Debrecen, Hungary
| | - Peter Prentis
- School of Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Australia; Institute for Future Environments, Queensland University of Technology, Brisbane, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria 3052, Australia.
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27
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Allain F, Mareuil F, Ménager H, Nilges M, Bardiaux B. ARIAweb: a server for automated NMR structure calculation. Nucleic Acids Res 2020; 48:W41-W47. [PMID: 32383755 PMCID: PMC7319541 DOI: 10.1093/nar/gkaa362] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/14/2020] [Accepted: 04/28/2020] [Indexed: 11/13/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a method of choice to study the dynamics and determine the atomic structure of macromolecules in solution. The standalone program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and structure calculation is well established in the NMR community. To ultimately provide a perfectly transparent and easy to use service, we designed an online user interface to ARIA with additional functionalities. Data conversion, structure calculation setup and execution, followed by interactive visualization of the generated 3D structures are all integrated in ARIAweb and freely accessible at https://ariaweb.pasteur.fr.
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Affiliation(s)
- Fabrice Allain
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, Institut Pasteur, Paris, 75015, France
| | - Fabien Mareuil
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, CNRS USR 3756, Institut Pasteur, Paris, 75015, France
| | - Hervé Ménager
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, CNRS USR 3756, Institut Pasteur, Paris, 75015, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, Institut Pasteur, Paris, 75015, France
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, Institut Pasteur, Paris, 75015, France
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28
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Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. Expanding the space of protein geometries by computational design of de novo fold families. Science 2020; 369:1132-1136. [PMID: 32855341 DOI: 10.1126/science.abc0881] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/14/2020] [Indexed: 01/03/2023]
Abstract
Naturally occurring proteins vary the precise geometries of structural elements to create distinct shapes optimal for function. We present a computational design method, loop-helix-loop unit combinatorial sampling (LUCS), that mimics nature's ability to create families of proteins with the same overall fold but precisely tunable geometries. Through near-exhaustive sampling of loop-helix-loop elements, LUCS generates highly diverse geometries encompassing those found in nature but also surpassing known structure space. Biophysical characterization showed that 17 (38%) of 45 tested LUCS designs encompassing two different structural topologies were well folded, including 16 with designed non-native geometries. Four experimentally solved structures closely matched the designs. LUCS greatly expands the designable structure space and offers a new paradigm for designing proteins with tunable geometries that may be customizable for novel functions.
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Affiliation(s)
- Xingjie Pan
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. .,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA
| | - Michael C Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Yang Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Lin Liu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. .,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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29
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Elliott AG, Huang JX, Neve S, Zuegg J, Edwards IA, Cain AK, Boinett CJ, Barquist L, Lundberg CV, Steen J, Butler MS, Mobli M, Porter KM, Blaskovich MAT, Lociuro S, Strandh M, Cooper MA. An amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria. Nat Commun 2020; 11:3184. [PMID: 32576824 PMCID: PMC7311426 DOI: 10.1038/s41467-020-16950-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/03/2020] [Indexed: 11/09/2022] Open
Abstract
Peptide antibiotics are an abundant and synthetically tractable source of molecular diversity, but they are often cationic and can be cytotoxic, nephrotoxic and/or ototoxic, which has limited their clinical development. Here we report structure-guided optimization of an amphipathic peptide, arenicin-3, originally isolated from the marine lugworm Arenicola marina. The peptide induces bacterial membrane permeability and ATP release, with serial passaging resulting in a mutation in mlaC, a phospholipid transport gene. Structure-based design led to AA139, an antibiotic with broad-spectrum in vitro activity against multidrug-resistant and extensively drug-resistant bacteria, including ESBL, carbapenem- and colistin-resistant clinical isolates. The antibiotic induces a 3–4 log reduction in bacterial burden in mouse models of peritonitis, pneumonia and urinary tract infection. Cytotoxicity and haemolysis of the progenitor peptide is ameliorated with AA139, and the ‘no observable adverse effect level’ (NOAEL) dose in mice is ~10-fold greater than the dose generally required for efficacy in the infection models. Peptide antibiotics often display a very narrow therapeutic index. Here, the authors present an optimized peptide antibiotic with broad-spectrum in vitro activities, in vivo efficacy in multiple disease models against multidrug-resistant Gram-negative infections, and reduced toxicity.
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Affiliation(s)
- Alysha G Elliott
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Johnny X Huang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia.,School of Life Science and Technology, Weifang Medical University, Weifang, 261053, China
| | - Søren Neve
- Orphazyme, Ole Maaloesvej 3, 2200, Copenhagen, Denmark
| | - Johannes Zuegg
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Ingrid A Edwards
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Amy K Cain
- Wellcome Sanger Institute, Hinxton, UK.,Department of Molecular Sciences, Macquarie University, NSW, 2109, Australia
| | | | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | | | - Jason Steen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Queensland, Qld, Australia
| | - Mark S Butler
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, Queensland, Qld, Australia
| | - Kaela M Porter
- Adenium Biotech ApS, Ole Maaloesvej 3, 2200, Copenhagen, Denmark
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia
| | - Sergio Lociuro
- BioVersys AG, Hochbergerstrasse 60C, Technology Park, 4057, Basel, Switzerland
| | - Magnus Strandh
- Adenium Biotech ApS, Ole Maaloesvej 3, 2200, Copenhagen, Denmark
| | - Matthew A Cooper
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Queensland, QLD, 4072, Australia. .,Trinity College Dublin, Dublin, Ireland.
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30
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Wang L, Rowe RG, Jaimes A, Yu C, Nam Y, Pearson DS, Zhang J, Xie X, Marion W, Heffron GJ, Daley GQ, Sliz P. Small-Molecule Inhibitors Disrupt let-7 Oligouridylation and Release the Selective Blockade of let-7 Processing by LIN28. Cell Rep 2019; 23:3091-3101. [PMID: 29874593 PMCID: PMC6511231 DOI: 10.1016/j.celrep.2018.04.116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 02/27/2018] [Accepted: 04/26/2018] [Indexed: 12/29/2022] Open
Abstract
LIN28 is an RNA-binding protein that regulates the maturation of the let-7 family of microRNAs by bipartite interactions with let-7 precursors through its two distinct cold shock and zinc-knuckle domains. Through inhibition of let-7 biogenesis, LIN28 functions as a pluripotency factor, as well as a driver of tumorigenesis. Here, we report a fluorescence polarization assay to identify small-molecule inhibitors for both domains of LIN28 involved in let-7 interactions. Of 101,017 compounds screened, six inhibit LIN28:let-7 binding and impair LIN28-mediated let-7 oligouridylation. Upon further characterization, we demonstrate that the LIN28 inhibitor TPEN destabilizes the zinc-knuckle domain of LIN28, while LI71 binds the cold shock domain to suppress LIN28's activity against let-7 in leukemia cells and embryonic stem cells. Our results demonstrate selective pharmacologic inhibition of individual domains of LIN28 and provide a foundation for therapeutic inhibition of the let-7 biogenesis pathway in LIN28-driven diseases.
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Affiliation(s)
- Longfei Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - R Grant Rowe
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adriana Jaimes
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Chunxiao Yu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yunsun Nam
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Jin Zhang
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Xiangyu Xie
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - William Marion
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Gregory J Heffron
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - George Q Daley
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA; Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA; Manton Center for Orphan Disease Research, Boston, MA, USA
| | - Piotr Sliz
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
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31
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Brand GD, Ramada MHS, Manickchand JR, Correa R, Ribeiro DJS, Santos MA, Vasconcelos AG, Abrão FY, Prates MV, Murad AM, Cardozo Fh JL, Leite JRSA, Magalhães KG, Oliveira AL, Bloch C. Intragenic antimicrobial peptides (IAPs) from human proteins with potent antimicrobial and anti-inflammatory activity. PLoS One 2019; 14:e0220656. [PMID: 31386688 PMCID: PMC6684085 DOI: 10.1371/journal.pone.0220656] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/19/2019] [Indexed: 11/20/2022] Open
Abstract
Following the treads of our previous works on the unveiling of bioactive peptides encrypted in plant proteins from diverse species, the present manuscript reports the occurrence of four proof-of-concept intragenic antimicrobial peptides in human proteins, named Hs IAPs. These IAPs were prospected using the software Kamal, synthesized by solid phase chemistry, and had their interactions with model phospholipid vesicles investigated by differential scanning calorimetry and circular dichroism. Their antimicrobial activity against bacteria, yeasts and filamentous fungi was determined, along with their cytotoxicity towards erythrocytes. Our data demonstrates that Hs IAPs are capable to bind model membranes while attaining α-helical structure, and to inhibit the growth of microorganisms at concentrations as low as 1μM. Hs02, a novel sixteen residue long internal peptide (KWAVRIIRKFIKGFIS-NH2) derived from the unconventional myosin 1h protein, was further investigated in its capacity to inhibit lipopolysaccharide-induced release of TNF-α in murine macrophages. Hs02 presented potent anti-inflammatory activity, inhibiting the release of TNF-α in LPS-primed cells at the lowest assayed concentration, 0.1 μM. A three-dimensional solution structure of Hs02 bound to DPC micelles was determined by Nuclear Magnetic Resonance. Our work exemplifies how the human genome can be mined for molecules with biotechnological potential in human health and demonstrates that IAPs are actual alternatives to antimicrobial peptides as pharmaceutical agents or in their many other putative applications.
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Affiliation(s)
- Guilherme D. Brand
- Laboratório de Síntese e Análise de Biomoléculas, LSAB, Instituto de Química, Universidade de Brasília, Brasília, DF, Brasil
- * E-mail:
| | - Marcelo H. S. Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brasil
- Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasília, DF, Brasil
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
| | - Júlia R. Manickchand
- Laboratório de Síntese e Análise de Biomoléculas, LSAB, Instituto de Química, Universidade de Brasília, Brasília, DF, Brasil
| | - Rafael Correa
- Laboratório de Imunologia e Inflamação, LIMI, Instituto de Biologia, Universidade de Brasília, Brasília, DF, Brasil
| | - Dalila J. S. Ribeiro
- Laboratório de Imunologia e Inflamação, LIMI, Instituto de Biologia, Universidade de Brasília, Brasília, DF, Brasil
| | - Michele A. Santos
- Laboratório de Ressonância Magnética Nuclear, LRMN, Instituto de Química, Universidade de Brasília, Brasília, DF, Brasil
| | - Andreanne G. Vasconcelos
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Campus Universitário Darcy Ribeiro, Universidade de Brasília, Brasília, DF, Brasil
| | | | - Maura V. Prates
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
| | - André M. Murad
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
| | - José L. Cardozo Fh
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
- Departamento de Fitopatologia, Instituto Mato-Grossense do Algodão, Primavera do Leste, MT, Brasil
| | - José Roberto S. A. Leite
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Campus Universitário Darcy Ribeiro, Universidade de Brasília, Brasília, DF, Brasil
| | - Kelly G. Magalhães
- Laboratório de Imunologia e Inflamação, LIMI, Instituto de Biologia, Universidade de Brasília, Brasília, DF, Brasil
| | - Aline L. Oliveira
- Laboratório de Ressonância Magnética Nuclear, LRMN, Instituto de Química, Universidade de Brasília, Brasília, DF, Brasil
| | - Carlos Bloch
- Laboratório de Espectrometria de Massa, LEM, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
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32
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Zhang AH, Edwards IA, Mishra BP, Sharma G, Healy MD, Elliott AG, Blaskovich MAT, Cooper MA, Collins BM, Jia X, Mobli M. Elucidating the Lipid Binding Properties of Membrane-Active Peptides Using Cyclised Nanodiscs. Front Chem 2019; 7:238. [PMID: 31058133 PMCID: PMC6477933 DOI: 10.3389/fchem.2019.00238] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/26/2019] [Indexed: 01/02/2023] Open
Abstract
The lipid composition of the cellular membrane plays an important role in a number of biological processes including the binding of membrane-active peptides. Characterization of membrane binding remains challenging, due to the technical limitations associated with the use of standard biophysical techniques and available membrane models. Here, we investigate the lipid binding properties of two membrane-active peptides, VSTx1, a well characterized ion-channel inhibitor, identified from spider venom, that preferentially binds to anionic lipid mixtures, and AA139 an antimicrobial β-hairpin peptide with uncharacterised lipid binding properties, currently in pre-clinical development. The lipid binding properties of these peptides are elucidated using nanodiscs formed by both linear and circularized (sortase-mediated) forms of a membrane scaffold protein (MSP1D1ΔH5). We find that nanodiscs formed by circularized MSPs—in contrast to those formed by linear MSPs—are sufficiently stable under sample conditions typically used for biophysical measurements (including lipid composition, a range of buffers, temperatures and concentrations). Using these circularized nanodiscs, we are able to extract detailed thermodynamic data using isothermal titration calorimetry (ITC) as well as atomic resolution mapping of the lipid binding interfaces of our isotope labeled peptides using solution-state, heteronuclear, nuclear magnetic resonance (NMR) spectroscopy. This represents a novel and general approach for elucidating the thermodynamics and molecular interface of membrane-active peptides toward flat lipid bilayers of variable composition. Our approach is validated by first determining the thermodynamic parameters and binding interface of VSTx1 toward the lipid bilayer, which shows good agreement with previous studies using lipid micelles and liposomes. The method is then applied to AA139, where the membrane binding properties are unknown. This characterization, involved solving the high-resolution structure of AA139 in solution using NMR spectroscopy and the development of a suitable expression system for isotope labeling. AA139 was found to bind exclusively to anionic membranes with moderate affinity (Kd~low μM), and was found to have a lipid binding interface involving the termini of the β-hairpin structure. The preference of AA139 for anionic lipids supports a role for membrane binding in the mode-of-action of this peptide, which is also consistent with its higher inhibitory activity against bacterial cells compared to mammalian cells. The described approach is a powerful method for investigation of the membrane binding properties of this important class of molecules.
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Affiliation(s)
- Alan H Zhang
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Ingrid A Edwards
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Biswa P Mishra
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Gagan Sharma
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Michael D Healy
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Alysha G Elliott
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Xinying Jia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
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33
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Camp D, Haage A, Solianova V, Castle WM, Xu QA, Lostchuck E, Goult BT, Tanentzapf G. Direct binding of Talin to Rap1 is required for cell-ECM adhesion in Drosophila. J Cell Sci 2018; 131:jcs.225144. [PMID: 30446511 DOI: 10.1242/jcs.225144] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022] Open
Abstract
Attachment of cells to the extracellular matrix (ECM) via integrins is essential for animal development and tissue maintenance. The cytoplasmic protein Talin (encoded by rhea in flies) is necessary for linking integrins to the cytoskeleton, and its recruitment is a key step in the assembly of the adhesion complex. However, the mechanisms that regulate Talin recruitment to sites of adhesion in vivo are still not well understood. Here, we show that Talin recruitment to, and maintenance at, sites of integrin-mediated adhesion requires a direct interaction between Talin and the GTPase Rap1. A mutation that blocks the direct binding of Talin to Rap1 abolished Talin recruitment to sites of adhesion and the resulting phenotype phenocopies that seen with null alleles of Talin. Moreover, we show that Rap1 activity modulates Talin recruitment to sites of adhesion via its direct binding to Talin. These results identify the direct Talin-Rap1 interaction as a key in vivo mechanism for controlling integrin-mediated cell-ECM adhesion.
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Affiliation(s)
- Darius Camp
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6T 1Z3
| | - Amanda Haage
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6T 1Z3
| | - Veronika Solianova
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6T 1Z3
| | - William M Castle
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Qinyuan A Xu
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6T 1Z3
| | - Emily Lostchuck
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6T 1Z3
| | - Benjamin T Goult
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Guy Tanentzapf
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6T 1Z3
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34
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Kock G, Dicks M, Yip KT, Kohl B, Pütz S, Heumann R, Erdmann KS, Stoll R. Molecular Basis of Class III Ligand Recognition by PDZ3 in Murine Protein Tyrosine Phosphatase PTPN13. J Mol Biol 2018; 430:4275-4292. [PMID: 30189200 DOI: 10.1016/j.jmb.2018.08.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/31/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022]
Abstract
Protein tyrosine phosphatase PTPN13, also known as PTP-BL in mice, represents a large multi-domain non-transmembrane scaffolding protein that contains five consecutive PDZ domains. Here, we report the solution structures of the extended murine PTPN13 PDZ3 domain in its apo form and in complex with its physiological ligand, the carboxy-terminus of protein kinase C-related kinase-2 (PRK2), determined by multidimensional NMR spectroscopy. Both in its ligand-free state and when complexed to PRK2, PDZ3 of PTPN13 adopts the classical compact, globular D/E fold. PDZ3 of PTPN13 binds five carboxy-terminal amino acids of PRK2 via a groove located between the EB-strand and the DB-helix. The PRK2 peptide resides in the canonical PDZ3 binding cleft in an elongated manner and the amino acid side chains in position P0 and P-2, cysteine and aspartate, of the ligand face the groove between EB-strand and DB-helix, whereas the PRK2 side chains of tryptophan and alanine located in position P-1 and P-3 point away from the binding cleft. These structures are rare examples of selective class III ligand recognition by a PDZ domain and now provide a basis for the detailed structural investigation of the promiscuous interaction between the PDZ domains of PTPN13 and their ligands. They will also lead to a better understanding of the proposed scaffolding function of these domains in multi-protein complexes assembled by PTPN13 and could ultimately contribute to low molecular weight antagonists that might even act on the PRK2 signaling pathway to modulate rearrangements of the actin cytoskeleton.
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Affiliation(s)
- Gerd Kock
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - Markus Dicks
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - King Tuo Yip
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - Bastian Kohl
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - Stefanie Pütz
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - Rolf Heumann
- Molecular Neurobiochemistry, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - Kai S Erdmann
- Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Raphael Stoll
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany.
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35
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Synthesis, folding, structure and activity of a predicted peptide from the sea anemone Oulactis sp. with an ShKT fold. Toxicon 2018; 150:50-59. [DOI: 10.1016/j.toxicon.2018.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/08/2018] [Accepted: 05/13/2018] [Indexed: 11/22/2022]
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36
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Martínez-Lumbreras S, Krysztofinska EM, Thapaliya A, Spilotros A, Matak-Vinkovic D, Salvadori E, Roboti P, Nyathi Y, Muench JH, Roessler MM, Svergun DI, High S, Isaacson RL. Structural complexity of the co-chaperone SGTA: a conserved C-terminal region is implicated in dimerization and substrate quality control. BMC Biol 2018; 16:76. [PMID: 29996828 PMCID: PMC6042327 DOI: 10.1186/s12915-018-0542-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/20/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Protein quality control mechanisms are essential for cell health and involve delivery of proteins to specific cellular compartments for recycling or degradation. In particular, stray hydrophobic proteins are captured in the aqueous cytosol by a co-chaperone, the small glutamine-rich, tetratricopeptide repeat-containing protein alpha (SGTA), which facilitates the correct targeting of tail-anchored membrane proteins, as well as the sorting of membrane and secretory proteins that mislocalize to the cytosol and endoplasmic reticulum-associated degradation. Full-length SGTA has an unusual elongated dimeric structure that has, until now, evaded detailed structural analysis. The C-terminal region of SGTA plays a key role in binding a broad range of hydrophobic substrates, yet in contrast to the well-characterized N-terminal and TPR domains, there is a lack of structural information on the C-terminal domain. In this study, we present new insights into the conformation and organization of distinct domains of SGTA and show that the C-terminal domain possesses a conserved region essential for substrate processing in vivo. RESULTS We show that the C-terminal domain region is characterized by α-helical propensity and an intrinsic ability to dimerize independently of the N-terminal domain. Based on the properties of different regions of SGTA that are revealed using cell biology, NMR, SAXS, Native MS, and EPR, we observe that its C-terminal domain can dimerize in the full-length protein and propose that this reflects a closed conformation of the substrate-binding domain. CONCLUSION Our results provide novel insights into the structural complexity of SGTA and provide a new basis for mechanistic studies of substrate binding and release at the C-terminal region.
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Affiliation(s)
| | - Ewelina M Krysztofinska
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, SE1 1DB, UK
| | - Arjun Thapaliya
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, SE1 1DB, UK
| | - Alessandro Spilotros
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany
| | - Dijana Matak-Vinkovic
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Enrico Salvadori
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, UK
| | - Peristera Roboti
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yvonne Nyathi
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Present Address: School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, LN6 7DL, UK
| | - Janina H Muench
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, SE1 1DB, UK
| | - Maxie M Roessler
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Rivka L Isaacson
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, SE1 1DB, UK.
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37
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Krishnarjuna B, Sugiki T, Morales RAV, Seow J, Fujiwara T, Wilde KL, Norton RS, MacRaild CA. Transient antibody-antigen interactions mediate the strain-specific recognition of a conserved malaria epitope. Commun Biol 2018; 1:58. [PMID: 30271940 PMCID: PMC6123721 DOI: 10.1038/s42003-018-0063-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 05/07/2018] [Indexed: 01/09/2023] Open
Abstract
Transient interactions in which binding partners retain substantial conformational disorder play an essential role in regulating biological networks, challenging the expectation that specificity demands structurally defined and unambiguous molecular interactions. The monoclonal antibody 6D8 recognises a completely conserved continuous nine-residue epitope within the intrinsically disordered malaria antigen, MSP2, yet it has different affinities for the two allelic forms of this antigen. NMR chemical shift perturbations, relaxation rates and paramagnetic relaxation enhancements reveal the presence of transient interactions involving polymorphic residues immediately C-terminal to the structurally defined epitope. A combination of these experimental data with molecular dynamics simulations shows clearly that the polymorphic C-terminal extension engages in multiple transient interactions distributed across much of the accessible antibody surface. These interactions are determined more by topographical features of the antibody surface than by sequence-specific interactions. Thus, specificity arises as a consequence of subtle differences in what are highly dynamic and essentially non-specific interactions.
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Affiliation(s)
- Bankala Krishnarjuna
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Toshihiko Sugiki
- Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Rodrigo A V Morales
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Jeffrey Seow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Toshimichi Fujiwara
- Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Karyn L Wilde
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Lucas Heights, Sydney, NSW, 2234, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
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38
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Sunanda P, Krishnarjuna B, Peigneur S, Mitchell ML, Estrada R, Villegas‐Moreno J, Pennington MW, Tytgat J, Norton RS. Identification, chemical synthesis, structure, and function of a new K
V
1 channel blocking peptide from
Oulactis
sp. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Punnepalli Sunanda
- Medicinal ChemistryMonash Institute of Pharmaceutical Sciences, Monash University, 381 Royal ParadeParkville, VIC 3052 Australia
| | - Bankala Krishnarjuna
- Medicinal ChemistryMonash Institute of Pharmaceutical Sciences, Monash University, 381 Royal ParadeParkville, VIC 3052 Australia
| | - Steve Peigneur
- Department of Toxicology and PharmacologyUniversity of Leuven, O&N 2, Herestraat 49, P.O. Box 922Leuven, 3000 Belgium
| | - Michela L. Mitchell
- Medicinal ChemistryMonash Institute of Pharmaceutical Sciences, Monash University, 381 Royal ParadeParkville, VIC 3052 Australia
| | | | - Jessica Villegas‐Moreno
- Medicinal ChemistryMonash Institute of Pharmaceutical Sciences, Monash University, 381 Royal ParadeParkville, VIC 3052 Australia
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de MorelosCuernavaca México
| | | | - Jan Tytgat
- Department of Toxicology and PharmacologyUniversity of Leuven, O&N 2, Herestraat 49, P.O. Box 922Leuven, 3000 Belgium
| | - Raymond S. Norton
- Medicinal ChemistryMonash Institute of Pharmaceutical Sciences, Monash University, 381 Royal ParadeParkville, VIC 3052 Australia
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39
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Bokhovchuk FM, Bate N, Kovalevskaya NV, Goult BT, Spronk CAEM, Vuister GW. The Structural Basis of Calcium-Dependent Inactivation of the Transient Receptor Potential Vanilloid 5 Channel. Biochemistry 2018; 57:2623-2635. [DOI: 10.1021/acs.biochem.7b01287] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fedir M. Bokhovchuk
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
| | - Neil Bate
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
| | - Nadezda V. Kovalevskaya
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
| | - Benjamin T. Goult
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
| | - Chris A. E. M. Spronk
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
- JSC Spronk, Vilnius, Lithuania
| | - Geerten W. Vuister
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
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40
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Abstract
NMR spectroscopy and other solution methods are increasingly being used to obtain novel insights into the mechanisms by which MAPK regulatory proteins bind and direct the activity of MAPKs. Here, we describe how interactions between the MAPK p38α and its regulatory proteins are studied using NMR spectroscopy, isothermal titration calorimetry, and small angle X-ray scattering (SAXS).
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Affiliation(s)
- Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, 02912, USA. .,Department of Chemistry, Brown University, Providence, RI, 02912, USA.
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
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41
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Krishnarjuna B, MacRaild CA, Sunanda P, Morales RAV, Peigneur S, Macrander J, Yu HH, Daly M, Raghothama S, Dhawan V, Chauhan S, Tytgat J, Pennington MW, Norton RS. Structure, folding and stability of a minimal homologue from Anemonia sulcata of the sea anemone potassium channel blocker ShK. Peptides 2018; 99:169-178. [PMID: 28993277 DOI: 10.1016/j.peptides.2017.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/03/2017] [Accepted: 10/05/2017] [Indexed: 01/01/2023]
Abstract
Peptide toxins elaborated by sea anemones target various ion-channel sub-types. Recent transcriptomic studies of sea anemones have identified several novel candidate peptides, some of which have cysteine frameworks identical to those of previously reported sequences. One such peptide is AsK132958, which was identified in a transcriptomic study of Anemonia sulcata and has a cysteine framework similar to that of ShK from Stichodactyla helianthus, but is six amino acid residues shorter. We have determined the solution structure of this novel peptide using NMR spectroscopy. The disulfide connectivities and structural scaffold of AsK132958 are very similar to those of ShK but the structure is more constrained. Toxicity assays were performed using grass shrimp (Palaemonetes sp) and Artemia nauplii, and patch-clamp electrophysiology assays were performed to assess the activity of AsK132958 against a range of voltage-gated potassium (KV) channels. AsK132958 showed no activity against grass shrimp, Artemia nauplii, or any of the KV channels tested, owing partly to the absence of a functional Lys-Tyr dyad. Three AsK132958 analogues, each containing a Tyr in the vicinity of Lys19, were therefore generated in an effort to restore binding, but none showed activity against any of KV channels tested. However, AsK132958 and its analogues are less susceptible to proteolysis than that of ShK. Our structure suggests that Lys19, which might be expected to occupy the pore of the channel, is not sufficiently accessible for binding, and therefore that AsK132958 must have a distinct functional role that does not involve KV channels.
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Affiliation(s)
- Bankala Krishnarjuna
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Punnepalli Sunanda
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Rodrigo A V Morales
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven, O&N 2, Herestraat 49, P.O. Box 922, 3000, Leuven, Belgium
| | - Jason Macrander
- Department of Evolution, Ecology, Organismal Biology, Ohio State University, 1315 Kinnear Rd, Columbus, OH 43212, USA; Department of Biology, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
| | - Heidi H Yu
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
| | - Marymegan Daly
- Department of Evolution, Ecology, Organismal Biology, Ohio State University, 1315 Kinnear Rd, Columbus, OH 43212, USA
| | | | - Vikas Dhawan
- Peptides International, Louisville, KY 40299, USA
| | | | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven, O&N 2, Herestraat 49, P.O. Box 922, 3000, Leuven, Belgium
| | | | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.
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42
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Wheeler LC, Anderson JA, Morrison AJ, Wong CE, Harms MJ. Conservation of Specificity in Two Low-Specificity Proteins. Biochemistry 2017; 57:684-695. [PMID: 29240404 DOI: 10.1021/acs.biochem.7b01086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Many regulatory proteins bind peptide regions of target proteins and modulate their activity. Such regulatory proteins can often interact with highly diverse target peptides. In many instances, it is not known if the peptide-binding interface discriminates targets in a biological context, or whether biological specificity is achieved exclusively through external factors such as subcellular localization. We used an evolutionary biochemical approach to distinguish these possibilities for two such low-specificity proteins: S100A5 and S100A6. We used isothermal titration calorimetry to study the binding of peptides with diverse sequence and biochemistry to human S100A5 and S100A6. These proteins bound distinct, but overlapping, sets of peptide targets. We then studied the peptide binding properties of orthologs sampled from across five amniote species. Binding specificity was conserved along all lineages, for the last 320 million years, despite the low specificity of each protein. We used ancestral sequence reconstruction to determine the binding specificity of the last common ancestor of the paralogs. The ancestor bound the entire set of peptides bound by modern S100A5 and S100A6 proteins, suggesting that paralog specificity evolved via subfunctionalization. To rule out the possibility that specificity is conserved because it is difficult to modify, we identified a single historical mutation that, when reverted in human S100A5, gave it the ability to bind an S100A6-specific peptide. These results reveal strong evolutionary constraints on peptide binding specificity. Despite being able to bind a large number of targets, the specificity of S100 peptide interfaces is likely important for the biology of these proteins.
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Affiliation(s)
- Lucas C Wheeler
- Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon , Eugene, Oregon 97403, United States
| | - Jeremy A Anderson
- Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon , Eugene, Oregon 97403, United States
| | - Anneliese J Morrison
- Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon , Eugene, Oregon 97403, United States
| | - Caitlyn E Wong
- Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon , Eugene, Oregon 97403, United States
| | - Michael J Harms
- Department of Chemistry and Biochemistry, University of Oregon , Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon , Eugene, Oregon 97403, United States
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43
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Pan H, Bilinovich SM, Kaur P, Riehn R, Wang H, Williams DC. CpG and methylation-dependent DNA binding and dynamics of the methylcytosine binding domain 2 protein at the single-molecule level. Nucleic Acids Res 2017. [PMID: 28637186 PMCID: PMC5587734 DOI: 10.1093/nar/gkx548] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The methylcytosine-binding domain 2 (MBD2) protein recruits the nucleosome remodeling and deacetylase complex (NuRD) to methylated DNA to modify chromatin and regulate transcription. Importantly, MBD2 functions within CpG islands that contain 100s to 1000s of potential binding sites. Since NuRD physically rearranges nucleosomes, the dynamic mobility of this complex is directly related to function. In these studies, we use NMR and single-molecule atomic force microscopy and fluorescence imaging to study DNA binding dynamics of MBD2. Single-molecule fluorescence tracking on DNA tightropes containing regions with CpG-rich and CpG-free regions reveals that MBD2 carries out unbiased 1D diffusion on CpG-rich DNA but subdiffusion on CpG-free DNA. In contrast, the protein stably and statically binds to methylated CpG (mCpG) regions. The intrinsically disordered region (IDR) on MBD2 both reduces exchange between mCpG sites along the DNA as well as the dissociation from DNA, acting like an anchor that restricts the dynamic mobility of the MBD domain. Unexpectedly, MBD2 binding to methylated CpGs induces DNA bending that is augmented by the IDR region of the protein. These results suggest that MBD2 targets NuRD to unmethylated or methylated CpG islands where its distinct dynamic binding modes help maintain open or closed chromatin, respectively.
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Affiliation(s)
- Hai Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Stephanie M Bilinovich
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Hong Wang
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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44
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Dydecka A, Bloch S, Rizvi A, Perez S, Nejman-Falenczyk B, Topka G, Gasior T, Necel A, Wegrzyn G, Donaldson LW, Wegrzyn A. Bad Phages in Good Bacteria: Role of the Mysterious orf63 of λ and Shiga Toxin-Converting Φ24 B Bacteriophages. Front Microbiol 2017; 8:1618. [PMID: 28890713 PMCID: PMC5575149 DOI: 10.3389/fmicb.2017.01618] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/08/2017] [Indexed: 11/13/2022] Open
Abstract
Lambdoid bacteriophages form a group of viruses that shares a common schema of genome organization and lifecycle. Some of them can play crucial roles in creating the pathogenic profiles of Escherichia coli strains. For example, Shiga toxin-producing E. coli (STEC) acquired stx genes, encoding Shiga toxins, via lambdoid prophages (Stx phages). The results obtained so far present the evidence for the relation between the exo-xis region of the phage genome and lambdoid phage development, however molecular mechanisms of activities of the exo-xis genes' products are still unknown. In view of this, we decided to determine the influence of the uncharacterized open reading frame orf63 of the exo-xis region on lambdoid phages development using recombinant prophages, λ and Stx phage Φ24B. We have demonstrated that orf63 codes for a folded protein, thus, it is a functional gene. NMR spectroscopy and analytical gel filtration were used to extend this observation further. From backbone chemical shifts, Orf63 is oligomeric in solution, likely a trimer and consistent with its small size (63 aa.), is comprised of two helices, likely intertwined to form the oligomer. We observed that the deletion of phage orf63 does not impair the intracellular lambdoid phage lytic development, however delays the time and decreases the efficiency of prophage induction and in consequence results in increased survival of E. coli during phage lytic development. Additionally, the deletion of phage orf63 negatively influences expression of the major phage genes and open reading frames from the exo-xis region during prophage induction with hydrogen peroxide. We conclude, that lambdoid phage orf63 may have specific functions in the regulation of lambdoid phages development, especially at the stage of the lysis vs. lysogenization decision. Besides, orf63 probably participates in the regulation of the level of expression of essential phage genes and open reading frames from the exo-xis region during prophage induction.
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Affiliation(s)
- Aleksandra Dydecka
- Department of Molecular Biology, Faculty of Biology, University of GdanskGdansk, Poland
| | - Sylwia Bloch
- Department of Molecular Biology, Faculty of Biology, University of GdanskGdansk, Poland
| | - Ali Rizvi
- Department of Biology, York UniversityToronto, ON, Canada
| | - Shaili Perez
- Department of Biology, York UniversityToronto, ON, Canada
| | | | - Gracja Topka
- Department of Molecular Biology, Faculty of Biology, University of GdanskGdansk, Poland
| | - Tomasz Gasior
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Agnieszka Necel
- Department of Molecular Biology, Faculty of Biology, University of GdanskGdansk, Poland
| | - Grzegorz Wegrzyn
- Department of Molecular Biology, Faculty of Biology, University of GdanskGdansk, Poland
| | | | - Alicja Wegrzyn
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
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45
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NMR-based automated protein structure determination. Arch Biochem Biophys 2017; 628:24-32. [PMID: 28263718 DOI: 10.1016/j.abb.2017.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/18/2017] [Accepted: 02/28/2017] [Indexed: 11/21/2022]
Abstract
NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures.
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46
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Wiedemann C, Ohlenschläger O, Mrestani-Klaus C, Bordusa F. NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state. Phys Chem Chem Phys 2017; 19:24115-24125. [DOI: 10.1039/c7cp03295a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The impact of ionic liquids on the chemical shifts and the cis/trans equilibrium state of a model peptide was systematically investigated by NMR spectroscopy.
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Affiliation(s)
- Christoph Wiedemann
- Institute of Biochemistry and Biotechnology
- Martin-Luther-University Halle-Wittenberg
- D-06120 Halle
- Germany
| | | | - Carmen Mrestani-Klaus
- Institute of Biochemistry and Biotechnology
- Martin-Luther-University Halle-Wittenberg
- D-06120 Halle
- Germany
| | - Frank Bordusa
- Institute of Biochemistry and Biotechnology
- Martin-Luther-University Halle-Wittenberg
- D-06120 Halle
- Germany
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47
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Brown KA, Sharifi S, Hussain R, Donaldson L, Bayfield MA, Wilson DJ. Distinct Dynamic Modes Enable the Engagement of Dissimilar Ligands in a Promiscuous Atypical RNA Recognition Motif. Biochemistry 2016; 55:7141-7150. [PMID: 27959512 DOI: 10.1021/acs.biochem.6b00995] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational dynamics play a critical role in ligand binding, often conferring divergent activities and specificities even in species with highly similar ground-state structures. Here, we employ time-resolved electrospray ionization hydrogen-deuterium exchange (TRESI-HDX) to characterize the changes in dynamics that accompany oligonucleotide binding in the atypical RNA recognition motif (RRM2) in the C-terminal domain (CTD) of human La protein. Using this approach, which is uniquely capable of probing changes in the structure and dynamics of weakly ordered regions of proteins, we reveal that binding of RRM2 to a model 23-mer single-stranded RNA and binding of RRM2 to structured IRES domain IV of the hepatitis C viral (HCV) RNA are driven by fundamentally different dynamic processes. In particular, binding of the single-stranded RNA induces helical "unwinding" in a region of the CTD previously hypothesized to play an important role in La and La-related protein-associated RNA remodeling, while the same region becomes less dynamic upon engagement with the double-stranded HCV RNA. Binding of double-stranded RNA also involves less penetration into the RRM2 binding pocket and more engagement with the unstructured C-terminus of the La CTD. The complementarity between TRESI-HDX and Δδ nuclear magnetic resonance measurements for ligand binding analysis is also explored.
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Affiliation(s)
- Kerene A Brown
- Department of Chemistry, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University , Toronto, ON M3J 1P3, Canada
| | - Samel Sharifi
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
| | - Rawaa Hussain
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
| | - Logan Donaldson
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
| | - Mark A Bayfield
- Department of Biology, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Biomolecular Interactions, York University , Toronto, ON M3J 1P3, Canada
| | - Derek J Wilson
- Department of Chemistry, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University , Toronto, ON M3J 1P3, Canada
- Centre for Research in Biomolecular Interactions, York University , Toronto, ON M3J 1P3, Canada
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48
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Siu RCF, Smirnova E, Brown CA, Zoidl C, Spray DC, Donaldson LW, Zoidl G. Structural and Functional Consequences of Connexin 36 (Cx36) Interaction with Calmodulin. Front Mol Neurosci 2016; 9:120. [PMID: 27917108 PMCID: PMC5114276 DOI: 10.3389/fnmol.2016.00120] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/26/2016] [Indexed: 11/26/2022] Open
Abstract
Functional plasticity of neuronal gap junctions involves the interaction of the neuronal connexin36 with calcium/calmodulin-dependent kinase II (CaMKII). The important relationship between Cx36 and CaMKII must also be considered in the context of another protein partner, Ca2+ loaded calmodulin, binding an overlapping site in the carboxy-terminus of Cx36. We demonstrate that CaM and CaMKII binding to Cx36 is calcium-dependent, with Cx36 able to engage with CaM outside of the gap junction plaque. Furthermore, Ca2+ loaded calmodulin activates Cx36 channels, which is different to other connexins. The NMR solution structure demonstrates that CaM binds Cx36 in its characteristic compact state with major hydrophobic contributions arising from W277 at anchor position 1 and V284 at position 8 of Cx36. Our results establish Cx36 as a hub binding Ca2+ loaded CaM and they identify this interaction as a critical step with implications for functions preceding the initiation of CaMKII mediated plasticity at electrical synapses.
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Affiliation(s)
| | | | | | - Christiane Zoidl
- Biology Program, York University, TorontoON, Canada
- Psychology Program, York University, TorontoON, Canada
| | - David C. Spray
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New YorkNY, USA
| | | | - Georg Zoidl
- Biology Program, York University, TorontoON, Canada
- Psychology Program, York University, TorontoON, Canada
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49
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Thapaliya A, Nyathi Y, Martínez-Lumbreras S, Krysztofinska EM, Evans NJ, Terry IL, High S, Isaacson RL. SGTA interacts with the proteasomal ubiquitin receptor Rpn13 via a carboxylate clamp mechanism. Sci Rep 2016; 6:36622. [PMID: 27827410 PMCID: PMC5101480 DOI: 10.1038/srep36622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/18/2016] [Indexed: 11/17/2022] Open
Abstract
The fate of secretory and membrane proteins that mislocalize to the cytosol is decided by a collaboration between cochaperone SGTA (small, glutamine-rich, tetratricopeptide repeat protein alpha) and the BAG6 complex, whose operation relies on multiple transient and subtly discriminated interactions with diverse binding partners. These include chaperones, membrane-targeting proteins and ubiquitination enzymes. Recently a direct interaction was discovered between SGTA and the proteasome, mediated by the intrinsic proteasomal ubiquitin receptor Rpn13. Here, we structurally and biophysically characterize this binding and identify a region of the Rpn13 C-terminal domain that is necessary and sufficient to facilitate it. We show that the contact occurs through a carboxylate clamp-mediated molecular recognition event with the TPR domain of SGTA, and provide evidence that the interaction can mediate the association of Rpn13 and SGTA in a cellular context.
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Affiliation(s)
- Arjun Thapaliya
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, U.K
| | - Yvonne Nyathi
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, U.K
| | | | - Ewelina M. Krysztofinska
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, U.K
| | - Nicola J. Evans
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, U.K
| | - Isabelle L. Terry
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, U.K
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, U.K
| | - Rivka L. Isaacson
- Department of Chemistry, King’s College London, Britannia House, Trinity Street, London, SE1 1DB, U.K
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50
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Smirnova E, Kwan JJ, Siu R, Gao X, Zoidl G, Demeler B, Saridakis V, Donaldson LW. A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein. Cell Commun Signal 2016; 14:17. [PMID: 27549312 PMCID: PMC4994250 DOI: 10.1186/s12964-016-0140-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
Background CASKIN2 is a homolog of CASKIN1, a scaffolding protein that participates in a signaling network with CASK (calcium/calmodulin-dependent serine kinase). Despite a high level of homology between CASKIN2 and CASKIN1, CASKIN2 cannot bind CASK due to the absence of a CASK Interaction Domain and consequently, may have evolved undiscovered structural and functional distinctions. Results We demonstrate that the crystal structure of the Sterile Alpha Motif (SAM) domain tandem (SAM1-SAM2) oligomer from CASKIN2 is different than CASKIN1, with the minimal repeating unit being a dimer, rather than a monomer. Analytical ultracentrifugation sedimentation velocity methods revealed differences in monomer/dimer equilibria across a range of concentrations and ionic strengths for the wild type CASKIN2 SAM tandem and a structure-directed double mutant that could not oligomerize. Further distinguishing CASKIN2 from CASKIN1, EGFP-tagged SAM tandem proteins expressed in Neuro2a cells produced punctae that were distinct both in shape and size. Conclusions This study illustrates a new way in which neuronal SAM domains can assemble into large macromolecular assemblies that might concentrate and amplify synaptic responses. Electronic supplementary material The online version of this article (doi:10.1186/s12964-016-0140-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ekaterina Smirnova
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Jamie J Kwan
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Ryan Siu
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Xin Gao
- Division of Computer, Computational Bioscience Research Center, Electrical and Mathematical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Georg Zoidl
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.,Department of Psychology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7760 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Vivian Saridakis
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Logan W Donaldson
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.
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