1
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Hughes J, Winkler A. New Insight Into Phytochromes: Connecting Structure to Function. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:153-183. [PMID: 39038250 DOI: 10.1146/annurev-arplant-070623-110636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Red and far-red light-sensing phytochromes are widespread in nature, occurring in plants, algae, fungi, and prokaryotes. Despite at least a billion years of evolution, their photosensory modules remain structurally and functionally similar. Conversely, nature has found remarkably different ways of transmitting light signals from the photosensor to diverse physiological responses. We summarize key features of phytochrome structure and function and discuss how these are correlated, from how the bilin environment affects the chromophore to how light induces cellular signals. Recent advances in the structural characterization of bacterial and plant phytochromes have resulted in paradigm changes in phytochrome research that we discuss in the context of present-day knowledge. Finally, we highlight questions that remain to be answered and suggest some of the benefits of understanding phytochrome structure and function.
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Affiliation(s)
- Jon Hughes
- Department of Plant Physiology, Justus Liebig University, Giessen, Germany;
- Department of Physics, Free University of Berlin, Berlin, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Graz, Austria;
- BioTechMed-Graz, Graz, Austria
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2
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Kolesiński P, McGowan M, Botteaux A, Smeesters PR, Ghosh P. Conservation of C4BP-binding sequence patterns in Streptococcus pyogenes M and Enn proteins. J Biol Chem 2024; 300:107478. [PMID: 38879009 PMCID: PMC11292367 DOI: 10.1016/j.jbc.2024.107478] [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: 04/23/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/25/2024] Open
Abstract
Antigenically sequence variable M proteins of the major bacterial pathogen Streptococcus pyogenes (Strep A) are responsible for recruiting human C4b-binding protein (C4BP) to the bacterial surface, which enables Strep A to evade destruction by the immune system. The most sequence divergent portion of M proteins, the hypervariable region (HVR), is responsible for binding C4BP. Structural evidence points to the conservation of two C4BP-binding sequence patterns (M2 and M22) in the HVR of numerous M proteins, with this conservation applicable to vaccine immunogen design. These two patterns, however, only partially explain C4BP binding by Strep A. Here, we identified several M proteins that lack these patterns but still bind C4BP and determined the structures of two, M68 and M87 HVRs, in complex with a C4BP fragment. Mutagenesis of these M proteins led to the identification of amino acids that are crucial for C4BP binding, enabling formulation of new C4BP-binding patterns. Mutagenesis was also carried out on M2 and M22 proteins to refine or generate experimentally grounded C4BP-binding patterns. The M22 pattern was the most prevalent among M proteins, followed by the M87 and M2 patterns, while the M68 pattern was rare. These patterns, except for M68, were also evident in numerous M-like Enn proteins. Binding of C4BP via these patterns to Enn proteins was verified. We conclude that C4BP-binding patterns occur frequently in Strep A strains of differing M types, being present in their M or Enn proteins, or frequently both, providing further impetus for their use as vaccine immunogens.
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Affiliation(s)
- Piotr Kolesiński
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, California, USA
| | - Matthew McGowan
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, California, USA
| | - Anne Botteaux
- Molecular Bacteriology Laboratory, European Plotkin Institute for Vaccinology, ULB, Brussels, Belgium
| | - Pierre R Smeesters
- Molecular Bacteriology Laboratory, European Plotkin Institute for Vaccinology, ULB, Brussels, Belgium; Department of Paediatrics, Brussels University Hospital, Academic Children Hospital Queen Fabiola, Université libre de Bruxelles, Brussels, Belgium
| | - Partho Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, California, USA.
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3
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Kolesiński P, McGowan M, Botteaux A, Smeesters PR, Ghosh P. Conservation of C4BP-binding Sequence Patterns in Streptococcus pyogenes M and Enn Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590534. [PMID: 38712057 PMCID: PMC11071373 DOI: 10.1101/2024.04.22.590534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Antigenically sequence variable M proteins of the major bacterial pathogen Streptococcus pyogenes (Strep A) are responsible for recruiting human C4b-binding protein (C4BP) to the bacterial surface, which enables Strep A to evade destruction by the immune system. The most sequence divergent portion of M proteins, the hypervariable region (HVR), is responsible for binding C4BP. Structural evidence points to the conservation of two C4BP-binding sequence patterns (M2 and M22) in the HVR of numerous M proteins, with this conservation applicable to vaccine immunogen design. These two patterns, however, only partially explain C4BP-binding by Strep A. Here, we identified several M proteins that lack these patterns but still bind C4BP, and determined the structures of two, M68 and M87 HVRs, in complex with a C4BP fragment. Mutagenesis of these M proteins led to identification of amino acids that are crucial for C4BP-binding, enabling formulation of new C4BP-binding patterns. Mutagenesis was also carried out on M2 and M22 proteins to refine or generate experimentally grounded C4BP-binding patterns. The M22 pattern was the most populated among M proteins, followed by the M87 and M2 patterns, while the M68 pattern was rare. These patterns, except for M68, were also evident in numerous M-like Enn proteins. Binding of C4BP via these patterns to Enn proteins was verified. We conclude that C4BP-binding patterns occur frequently in Strep A strains of differing M types, being present in their M or Enn proteins, or frequently both, providing further impetus for their use as vaccine immunogens.
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4
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Proctor EJ, Frost HR, Satapathy S, Botquin G, Urbaniec J, Gorman J, De Oliveira DMP, McArthur J, Davies MR, Botteaux A, Smeesters P, Sanderson-Smith M. Molecular characterization of the interaction between human IgG and the M-related proteins from Streptococcus pyogenes. J Biol Chem 2024; 300:105623. [PMID: 38176650 PMCID: PMC10844976 DOI: 10.1016/j.jbc.2023.105623] [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: 10/24/2023] [Revised: 12/04/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
Group A Streptococcal M-related proteins (Mrps) are dimeric α-helical-coiled-coil cell membrane-bound surface proteins. During infection, Mrp recruit the fragment crystallizable region of human immunoglobulin G via their A-repeat regions to the bacterial surface, conferring upon the bacteria enhanced phagocytosis resistance and augmented growth in human blood. However, Mrps show a high degree of sequence diversity, and it is currently not known whether this diversity affects the Mrp-IgG interaction. Herein, we report that diverse Mrps all bind human IgG subclasses with nanomolar affinity, with differences in affinity which ranged from 3.7 to 11.1 nM for mixed IgG. Using surface plasmon resonance, we confirmed Mrps display preferential IgG-subclass binding. All Mrps were found to have a significantly weaker affinity for IgG3 (p < 0.05) compared to all other IgG subclasses. Furthermore, plasma pulldown assays analyzed via Western blotting revealed that all Mrp were able to bind IgG in the presence of other serum proteins at both 25 °C and 37 °C. Finally, we report that dimeric Mrps bind to IgG with a 1:1 stoichiometry, enhancing our understanding of this important host-pathogen interaction.
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Affiliation(s)
- Emma-Jayne Proctor
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Hannah R Frost
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Sandeep Satapathy
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia; The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gwenaëlle Botquin
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Joanna Urbaniec
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Jody Gorman
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - David M P De Oliveira
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, QLD, Australia
| | - Jason McArthur
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
| | - Anne Botteaux
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Pierre Smeesters
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Martina Sanderson-Smith
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.
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5
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Wang KC, Kuliyev E, Nizet V, Ghosh P. A conserved 3D pattern in a Streptococcus pyogenes M protein immunogen elicits M-type crossreactivity. J Biol Chem 2023; 299:104980. [PMID: 37390991 PMCID: PMC10400905 DOI: 10.1016/j.jbc.2023.104980] [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: 02/04/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023] Open
Abstract
Coiled coil-forming M proteins of the widespread and potentially deadly bacterial pathogen Streptococcus pyogenes (strep A) are immunodominant targets of opsonizing antibodies. However, antigenic sequence variability of M proteins into >220 M types, as defined by their hypervariable regions (HVRs), is considered to limit M proteins as vaccine immunogens because of type specificity in the antibody response. Surprisingly, a multi-HVR immunogen in clinical vaccine trials was shown to elicit M-type crossreactivity. The basis for this crossreactivity is unknown but may be due in part to antibody recognition of a 3D pattern conserved in many M protein HVRs that confers binding to human complement C4b-binding protein (C4BP). To test this hypothesis, we investigated whether a single M protein immunogen carrying the 3D pattern would elicit crossreactivity against other M types carrying the 3D pattern. We found that a 34-amino acid sequence of S. pyogenes M2 protein bearing the 3D pattern retained full C4BP-binding capacity when fused to a coiled coil-stabilizing sequence from the protein GCN4. We show that this immunogen, called M2G, elicited cross-reactive antibodies against a number of M types that carry the 3D pattern but not against those that lack the 3D pattern. We further show that the M2G antiserum-recognized M proteins displayed natively on the strep A surface and promoted the opsonophagocytic killing of strep A strains expressing these M proteins. As C4BP binding is a conserved virulence trait of strep A, we propose that targeting the 3D pattern may prove advantageous in vaccine design.
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Affiliation(s)
- Kuei-Chen Wang
- Department of Chemistry & Biochemistry, University of California, San Diego, California, USA
| | - Eziz Kuliyev
- Department of Chemistry & Biochemistry, University of California, San Diego, California, USA
| | - Victor Nizet
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, California, USA
| | - Partho Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, California, USA.
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6
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Kolesinski P, Wang KC, Hirose Y, Nizet V, Ghosh P. An M protein coiled coil unfurls and exposes its hydrophobic core to capture LL-37. eLife 2022; 11:e77989. [PMID: 35726694 PMCID: PMC9212996 DOI: 10.7554/elife.77989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/28/2022] [Indexed: 01/11/2023] Open
Abstract
Surface-associated, coiled-coil M proteins of Streptococcus pyogenes (Strep A) disable human immunity through interaction with select proteins. However, coiled coils lack features typical of protein-protein interaction sites, and it is therefore challenging to understand how M proteins achieve specific binding, for example, with the human antimicrobial peptide LL-37, leading to its neutralization. The crystal structure of a complex of LL-37 with M87 protein, an antigenic M protein variant from a strain that is an emerging threat, revealed a novel interaction mode. The M87 coiled coil unfurled and asymmetrically exposed its hydrophobic core to capture LL-37. A single LL-37 molecule was bound by M87 in the crystal, but in solution additional LL-37 molecules were recruited, consistent with a 'protein trap' neutralization mechanism. The interaction mode visualized crystallographically was verified to contribute significantly to LL-37 resistance in an M87 Strep A strain and was identified to be conserved in a number of other M protein types that are prevalent in human populations. Our results provide specific detail for therapeutic inhibition of LL-37 neutralization by M proteins.
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Affiliation(s)
- Piotr Kolesinski
- Department of Chemistry & Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Kuei-Chen Wang
- Department of Chemistry & Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Yujiro Hirose
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Victor Nizet
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoLa JollaUnited States
| | - Partho Ghosh
- Department of Chemistry & Biochemistry, University of California, San DiegoLa JollaUnited States
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7
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Rafei R, Al Iaali R, Osman M, Dabboussi F, Hamze M. A global snapshot on the prevalent macrolide-resistant emm types of Group A Streptococcus worldwide, their phenotypes and their resistance marker genotypes during the last two decades: A systematic review. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105258. [PMID: 35219865 DOI: 10.1016/j.meegid.2022.105258] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 12/29/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Watchful epidemiological surveillance of macrolide-resistant Group A Streptococcus (MRGAS) clones is important owing to the evolutionary and epidemiological dynamic of GAS. Meanwhile, data on the global distribution of MRGAS emm types according to macrolide resistance phenotypes and genotypes are scant and need to be updated. For this, the present systematic review analyses a global set of extensively characterized MRGAS isolates from patients of diverse ages and clinical presentations over approximately two decades (2000 to 2020) and recaps the peculiar epidemiological features of the dominant MRGAS clones. Based on the inclusion and exclusion criteria, 53 articles (3593 macrolide-resistant and 15,951 susceptible isolates) distributed over 23 countries were dissected with a predominance of high-income countries over low-income ones. Although macrolide resistance in GAS is highly variable in different countries, its within-GAS distribution seems not to be random. emm pattern E, 13 major emm types (emm12, 4, 28, 77, 75, 11, 22, 92, 58, 60, 94, 63, 114) and 4 emm clusters (A-C4, E1, E6, and E2) were significantly associated with macrolide resistance. emm patterns A-C and D, 14 major emm types (emm89, 3, 6, 2, 44, 82, 87, 118, 5, 49, 81, 59, 227, 78) and 3 well-defined emm clusters (A-C5, E3, and D4) were significantly associated with macrolide susceptibility. Scrutinizing the tendency of each MRGAS emm type to be significantly associated with specific macrolide resistance phenotype or genotype, interesting vignettes are also unveiled. The 30-valent vaccine covers ~95% of MRGAS isolates. The presented data urge the importance of comprehensive nationwide sustained surveillance of MRGAS circulating clones particularly in Low and Middle income countries where sampling bias is high and GAS epidemiology is obfuscated and needs to be demystified.
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Affiliation(s)
- Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
| | - Rayane Al Iaali
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon; Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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8
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Clopés J, Shin J, Jahnel M, Grill SW, Zaburdaev V. Thermal fluctuations assist mechanical signal propagation in coiled-coil proteins. Phys Rev E 2021; 104:054403. [PMID: 34942783 DOI: 10.1103/physreve.104.054403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/18/2021] [Indexed: 11/07/2022]
Abstract
Recently, it has been shown that the long coiled-coil membrane tether protein early endosome antigen 1 (EEA1) switches from a rigid to a flexible conformation upon binding of a signaling protein to its free end. This flexibility switch represents a motorlike activity, allowing EEA1 to generate a force that moves vesicles closer to the membrane they will fuse with. It was hypothesized that the binding-induced signal could propagate along the coiled coil and lead to conformational changes through the localized domains of the protein chain that deviate from a perfect coiled-coil structure. To elucidate, if upon binding of a single protein the corresponding mechanical signal could propagate through the whole 200-nm-long chain, we propose a simplified description of the coiled coil as a one-dimensional Frenkel-Kontorova chain. Using numerical simulations, we find that an initial perturbation of the chain can propagate along its whole length in the presence of thermal fluctuations. This may enable the change of the configuration of the entire molecule and thereby affect its stiffness. Our work sheds light on intramolecular communication and force generation in long coiled-coil proteins.
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Affiliation(s)
- Judit Clopés
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany
| | - Jaeoh Shin
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany.,Department of Chemistry, Rice University, Houston, Texas 77005, USA
| | - Marcus Jahnel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,Biotechnology Center, Technical University Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,Biotechnology Center, Technical University Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany.,Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
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9
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Abstract
Streptococcus pyogenes is known to cause both mucosal and systemic infections in humans. In this study, we used a combination of quantitative and structural mass spectrometry techniques to determine the composition and structure of the interaction network formed between human plasma proteins and the surfaces of different S. pyogenes serotypes. Quantitative network analysis revealed that S. pyogenes forms serotype-specific interaction networks that are highly dependent on the domain arrangement of the surface-attached M protein. Subsequent structural mass spectrometry analysis and computational modeling of one of the M proteins, M28, revealed that the network structure changes across different host microenvironments. We report that M28 binds secretory IgA via two separate binding sites with high affinity in saliva. During vascular leakage mimicked by increasing plasma concentrations in saliva, the binding of secretory IgA was replaced by the binding of monomeric IgA and C4b-binding protein (C4BP). This indicates that an upsurge of C4BP in the local microenvironment due to damage to the mucosal membrane drives the binding of C4BP and monomeric IgA to M28. These results suggest that S. pyogenes has evolved to form microenvironment-dependent host-pathogen protein complexes to combat human immune surveillance during both mucosal and systemic infections. IMPORTANCEStreptococcus pyogenes (group A Streptococcus [GAS]), is a human-specific Gram-positive bacterium. Each year, the bacterium affects 700 million people globally, leading to 160,000 deaths. The clinical manifestations of S. pyogenes are diverse, ranging from mild and common infections like tonsillitis and impetigo to life-threatening systemic conditions such as sepsis and necrotizing fasciitis. S. pyogenes expresses multiple virulence factors on its surface to localize and initiate infections in humans. Among all these expressed virulence factors, the M protein is the most important antigen. In this study, we perform an in-depth characterization of the human protein interactions formed around one of the foremost human pathogens. This strategy allowed us to decipher the protein interaction networks around different S. pyogenes strains on a global scale and to compare and visualize how such interactions are mediated by M proteins.
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10
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Upadhyay T, Potteth US, Karekar VV, Saraogi I. A Stutter in the Coiled-Coil Domain of Escherichia coli Co-chaperone GrpE Connects Structure with Function. Biochemistry 2021; 60:1356-1367. [PMID: 33881310 DOI: 10.1021/acs.biochem.1c00110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In bacteria, the co-chaperone GrpE acts as a nucleotide exchange factor and plays an important role in controlling the chaperone cycle of DnaK. The functional form of GrpE is an asymmetric dimer, consisting of a non-ideal coiled coil. Partial unfolding of this region during heat stress results in reduced nucleotide exchange and disrupts protein folding by DnaK. In this study, we elucidate the role of non-ideality in the coiled-coil domain of Escherichia coli GrpE in controlling its co-chaperone activity. The presence of a four-residue stutter introduces nonheptad periodicity in the GrpE coiled coil, resulting in global structural changes in GrpE and regulating its interaction with DnaK. Introduction of hydrophobic residues at the stutter core increased the structural stability of the protein. Using an in vitro FRET assay, we show that the enhanced stability of GrpE resulted in an increased affinity for DnaK. However, these mutants were unable to support bacterial growth at 42°C in a grpE-deleted E. coli strain. This work provides valuable insights into the functional role of a stutter in GrpE in regulating the DnaK-chaperone cycle during heat stress. More generally, our findings illustrate how stutters in a coiled-coil domain regulate structure-function trade-off in proteins.
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Affiliation(s)
- Tulsi Upadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India
| | - Upasana S Potteth
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India
| | - Vaibhav V Karekar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India
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11
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Structural resolution of switchable states of a de novo peptide assembly. Nat Commun 2021; 12:1530. [PMID: 33750792 PMCID: PMC7943578 DOI: 10.1038/s41467-021-21851-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 12/18/2022] Open
Abstract
De novo protein design is advancing rapidly. However, most designs are for single states. Here we report a de novo designed peptide that forms multiple α-helical-bundle states that are accessible and interconvertible under the same conditions. Usually in such designs amphipathic α helices associate to form compact structures with consolidated hydrophobic cores. However, recent rational and computational designs have delivered open α-helical barrels with functionalisable cavities. By placing glycine judiciously in the helical interfaces of an α-helical barrel, we obtain both open and compact states in a single protein crystal. Molecular dynamics simulations indicate a free-energy landscape with multiple and interconverting states. Together, these findings suggest a frustrated system in which steric interactions that maintain the open barrel and the hydrophobic effect that drives complete collapse are traded-off. Indeed, addition of a hydrophobic co-solvent that can bind within the barrel affects the switch between the states both in silico and experimentally. So far most of the de novo designed proteins are for single states only. Here, the authors present the de novo design and crystal structure determination of a coiled-coil peptide that assembles into multiple, distinct conformational states under the same conditions and further characterise its properties with biophysical experiments, NMR and MD simulations.
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12
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Arora S, Gordon J, Hook M. Collagen Binding Proteins of Gram-Positive Pathogens. Front Microbiol 2021; 12:628798. [PMID: 33613497 PMCID: PMC7893114 DOI: 10.3389/fmicb.2021.628798] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Collagens are the primary structural components of mammalian extracellular matrices. In addition, collagens regulate tissue development, regeneration and host defense through interaction with specific cellular receptors. Their unique triple helix structure, which requires a glycine residue every third amino acid, is the defining structural feature of collagens. There are 28 genetically distinct collagens in humans. In addition, several other unrelated human proteins contain a collagen domain. Gram-positive bacteria of the genera Staphylococcus, Streptococcus, Enterococcus, and Bacillus express cell surface proteins that bind to collagen. These proteins of Gram-positive pathogens are modular proteins that can be classified into different structural families. This review will focus on the different structural families of collagen binding proteins of Gram-positive pathogen. We will describe how these proteins interact with the triple helix in collagens and other host proteins containing a collagenous domain and discuss how these interactions can contribute to the pathogenic processes.
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Affiliation(s)
- Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, United States
| | - Jay Gordon
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, United States
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, United States
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13
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Adamczyk M, Lewicka E, Szatkowska R, Nieznanska H, Ludwiczak J, Jasiński M, Dunin-Horkawicz S, Sitkiewicz E, Swiderska B, Goch G, Jagura-Burdzy G. Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins. BMC Microbiol 2021; 21:32. [PMID: 33482722 PMCID: PMC7821693 DOI: 10.1186/s12866-020-02079-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/20/2020] [Indexed: 01/22/2023] Open
Abstract
Background DNA binding KfrA-type proteins of broad-host-range bacterial plasmids belonging to IncP-1 and IncU incompatibility groups are characterized by globular N-terminal head domains and long alpha-helical coiled-coil tails. They have been shown to act as transcriptional auto-regulators. Results This study was focused on two members of the growing family of KfrA-type proteins encoded by the broad-host-range plasmids, R751 of IncP-1β and RA3 of IncU groups. Comparative in vitro and in silico studies on KfrAR751 and KfrARA3 confirmed their similar biophysical properties despite low conservation of the amino acid sequences. They form a wide range of oligomeric forms in vitro and, in the presence of their cognate DNA binding sites, they polymerize into the higher order filaments visualized as “threads” by negative staining electron microscopy. The studies revealed also temperature-dependent changes in the coiled-coil segment of KfrA proteins that is involved in the stabilization of dimers required for DNA interactions. Conclusion KfrAR751 and KfrARA3 are structural homologues. We postulate that KfrA type proteins have moonlighting activity. They not only act as transcriptional auto-regulators but form cytoskeletal structures, which might facilitate plasmid DNA delivery and positioning in the cells before cell division, involving thermal energy. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02079-w.
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Affiliation(s)
- M Adamczyk
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Noakowskiego 3, 00-664, Warsaw, Poland.
| | - E Lewicka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - R Szatkowska
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - H Nieznanska
- Nencki Institute of Experimental Biology PAS, Laboratory of Electron Microscopy, Pasteura 3, 02-093, Warsaw, Poland
| | - J Ludwiczak
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland.,Nencki Institute of Experimental Biology, Laboratory of Bioinformatics, Pasteura 3, 02-093, Warsaw, Poland
| | - M Jasiński
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland
| | - S Dunin-Horkawicz
- University of Warsaw, Centre of New Technologies, Laboratory of Structural Bioinformatics, 02-097, Warsaw, Poland
| | - E Sitkiewicz
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - B Swiderska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - G Goch
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - G Jagura-Burdzy
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
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14
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Karami Y, Saighi P, Vanderhaegen R, Gerlier D, Longhi S, Laine E, Carbone A. Predicting substitutions to modulate disorder and stability in coiled-coils. BMC Bioinformatics 2020; 21:573. [PMID: 33349244 PMCID: PMC7751101 DOI: 10.1186/s12859-020-03867-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/09/2020] [Indexed: 11/20/2022] Open
Abstract
Background Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disordered regions in proteins are characterized by lack of stable secondary and tertiary structure under physiological conditions in vitro. They are increasingly recognized as important for protein function. However, characterizing their behaviour in solution and determining precisely the extent of disorder of a protein region remains challenging, both experimentally and computationally. Results In this work, we propose a computational framework to quantify the extent of disorder within a coiled-coil in solution and to help design substitutions modulating such disorder. Our method relies on the analysis of conformational ensembles generated by relatively short all-atom Molecular Dynamics (MD) simulations. We apply it to the phosphoprotein multimerisation domains (PMD) of Measles virus (MeV) and Nipah virus (NiV), both forming tetrameric left-handed coiled-coils. We show that our method can help quantify the extent of disorder of the C-terminus region of MeV and NiV PMDs from MD simulations of a few tens of nanoseconds, and without requiring an extensive exploration of the conformational space. Moreover, this study provided a conceptual framework for the rational design of substitutions aimed at modulating the stability of the coiled-coils. By assessing the impact of four substitutions known to destabilize coiled-coils, we derive a set of rules to control MeV PMD structural stability and cohesiveness. We therefore design two contrasting substitutions, one increasing the stability of the tetramer and the other increasing its flexibility. Conclusions Our method can be considered as a platform to reason about how to design substitutions aimed at regulating flexibility and stability.
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Affiliation(s)
- Yasaman Karami
- CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France. .,Institute of Computing and Data Sciences (ISCD), Sorbonne Université, 75005, Paris, France.
| | - Paul Saighi
- CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France
| | - Rémy Vanderhaegen
- CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Sonia Longhi
- CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille University, Marseille, France
| | - Elodie Laine
- CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France.
| | - Alessandra Carbone
- CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France. .,Institut Universitaire de France, 75005, Paris, France.
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15
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Yuan Y, Ayinuola YA, Singh D, Ayinuola O, Mayfield JA, Quek A, Whisstock JC, Law RHP, Lee SW, Ploplis VA, Castellino FJ. Solution structural model of the complex of the binding regions of human plasminogen with its M-protein receptor from Streptococcus pyogenes. J Struct Biol 2019; 208:18-29. [PMID: 31301349 PMCID: PMC6983471 DOI: 10.1016/j.jsb.2019.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/01/2019] [Accepted: 07/09/2019] [Indexed: 11/22/2022]
Abstract
VEK50 is a truncated peptide from a Streptococcal pyogenes surface human plasminogen (hPg) binding M-protein (PAM). VEK50 contains the full A-domain of PAM, which is responsible for its low nanomolar binding to hPg. The interaction of VEK50 with kringle 2, the PAM-binding domain in hPg (K2hPg), has been studied by high-resolution NMR spectroscopy. The data show that each VEK50 monomer in solution contains two tight binding sites for K2hPg, one each in the a1- (RH1; R17H18) and a2- (RH2; R30H31) repeats within the A-domain of VEK50. Two mutant forms of VEK50, viz., VEK50[RH1/AA] (VEK50ΔRH1) and VEK50[RH2/AA] (VEK50ΔRH2), were designed by replacing each RH with AA, thus eliminating one of the K2hPg binding sites within VEK50, and allowing separate study of each binding site. Using 13C- and 15N-labeled peptides, NMR-derived solution structures of VEK50 in its complex with K2hPg were solved. We conclude that the A-domain of PAM can accommodate two molecules of K2hPg docked within a short distance of each other, and the strength of the binding is slightly different for each site. The solution structure of the VEK50/K2hPg, complex, which is a reductionist model of the PAM/hPg complex, provides insights for the binding mechanism of PAM to a host protein, a process that is critical to S. pyogenes virulence.
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Affiliation(s)
- Yue Yuan
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Yetunde A Ayinuola
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Damini Singh
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Olawole Ayinuola
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jeffrey A Mayfield
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Adam Quek
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800 VIC, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800 VIC, Australia
| | - Ruby H P Law
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800 VIC, Australia
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Victoria A Ploplis
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Francis J Castellino
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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16
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Structural diversity of coiled coils in protein fibers of the bacterial cell envelope. Int J Med Microbiol 2019; 309:351-358. [PMID: 31182277 DOI: 10.1016/j.ijmm.2019.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/14/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023] Open
Abstract
The cell envelope of bacteria shows great diversity in architecture and composition, to a large extent due to its proteome. Proteins localized to the cell envelope, whether integrally embedded in the membrane, membrane-anchored, or peripherally associated as part of a macromolecular complex, often form elongated fibers, in which coiled coils represent a prominent structural element. These coiled-coil segments show a surprising degree of structural variability, despite being shaped by a small number of simple biophysical rules, foremost being their geometry of interaction referred to as 'knobs-into-holes'. Here we will review this diversity, particularly as it has emerged over the last decade.
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17
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Bloyet LM, Schramm A, Lazert C, Raynal B, Hologne M, Walker O, Longhi S, Gerlier D. Regulation of measles virus gene expression by P protein coiled-coil properties. SCIENCE ADVANCES 2019; 5:eaaw3702. [PMID: 31086822 PMCID: PMC6506246 DOI: 10.1126/sciadv.aaw3702] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 05/18/2023]
Abstract
The polymerase of negative-stranded RNA viruses consists of the large protein (L) and the phosphoprotein (P), the latter serving both as a chaperon and a cofactor for L. We mapped within measles virus (MeV) P the regions responsible for binding and stabilizing L and showed that the coiled-coil multimerization domain (MD) of P is required for gene expression. MeV MD is kinked as a result of the presence of a stammer. Both restoration of the heptad regularity and displacement of the stammer strongly decrease or abrogate activity in a minigenome assay. By contrast, P activity is rather tolerant of substitutions within the stammer. Single substitutions at the "a" or "d" hydrophobic anchor positions with residues of variable hydrophobicity revealed that P functionality requires a narrow range of cohesiveness of its MD. Results collectively indicate that, beyond merely ensuring P oligomerization, the MD finely tunes viral gene expression through its cohesiveness.
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Affiliation(s)
- Louis-Marie Bloyet
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Antoine Schramm
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Carine Lazert
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Bertrand Raynal
- Institut Pasteur, Plateforme de Biophysique Moléculaire, Paris, France
| | - Maggy Hologne
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon 1, Lyon France
| | - Olivier Walker
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon 1, Lyon France
| | - Sonia Longhi
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
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18
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Qiu C, Yuan Y, Liang Z, Lee SW, Ploplis VA, Castellino FJ. Variations in the secondary structures of PAM proteins influence their binding affinities to human plasminogen. J Struct Biol 2019; 206:193-203. [PMID: 30880082 DOI: 10.1016/j.jsb.2019.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 11/25/2022]
Abstract
M-proteins (M-Prts) are major virulence determinants of Group A Streptococcus pyogenes (GAS) that are covalently anchored to the cell wall at their conserved COOH-termini while the NH2-terminal regions extend through the capsule into extracellular space. Functional M-Prts are also secreted and/or released from GAS cells where they exist as helical coiled-coil dimers in solution. Certain GAS strains (Pattern D) uniquely express an M-protein (plasminogen-binding group A streptococcal M-protein; PAM) that directly interacts with human plasminogen (hPg), a process strongly implicated in the virulence of these strains. M-Prt expressed by the emm gene is employed to serotype over 250 known strains of GAS, ∼20 of which are hitherto found to express PAMs. We have developed a modular structural model of the PAM dimer that describes the roles of different domains of this protein in various functions. While the helical COOH-terminal domains of PAM are essential for dimerization in solution, regions of its NH2-terminal domains also exhibit a weak potential to dimerize. We find that temperature controls the open (unwound) or closed (wound) states of the functional NH2-terminal domains of PAM. As temperature increases, α-helices are dramatically reduced, which concomitantly destabilizes the helical coiled-coil PAM dimers. PAMs with two a-repeats within the variable NH2-terminal A-domain (class I/III) bind to hPg tightly, but natural PAM isolates with a single a-repeat in this domain (class II) display dramatic changes in hPg binding with temperature. We conclude that coexistence of two a-repeats in PAM is critical to achieve optimal binding to hPg, especially in its monomeric form, at the biologically relevant temperature.
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Affiliation(s)
- Cunjia Qiu
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Yue Yuan
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Zhong Liang
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Victoria A Ploplis
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Francis J Castellino
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States.
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19
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Gomez D, Gavrilov Y, Levy Y. Sliding Mechanism at a Coiled-Coil Interface. Biophys J 2019; 116:1228-1238. [PMID: 30904175 DOI: 10.1016/j.bpj.2019.02.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/16/2019] [Accepted: 02/26/2019] [Indexed: 12/15/2022] Open
Abstract
The α-helical coiled coil (CC) is a common protein motif that because of the simplicity of its sequence/structure relationship, it has been studied extensively to address fundamental questions in protein science as well as to develop strategies for designing protein with novel architectures. Nevertheless, a complete understanding of CC structures and their dynamics is still far from achieved. Particularly, spontaneous sliding at interfaces of CC proteins was observed for some systems, but its mechanism and usage as an intrinsic conformational change at CCs in protein-protein interfaces is unclear. Using coarse-grained and atomistic simulations, we study various sequences of homodimeric CC, in both parallel and antiparallel configurations. Both the strength of the hydrophobic core and the existence of salt bridges at the periphery of the interface affect sliding dynamics at the CC interface. Although the energy landscape for sliding along a CC interface is different for parallel and antiparallel configurations, both are characterized by a free energy of 1-1.5 kcal/mol, depending on the residues that constitute the CC interface. These barrier heights suggest that sliding kinetics is relatively slow in CC systems and are not expected to be of long length scale, yet they can be involved in functional motions. Our study explains the sliding that has been experimentally observed for the antiparallel CC of the dynein stalk region and the nuclear pore complex and suggests that this one-dimensional motion is an intrinsic feature in CC systems that can be involved in other CC systems.
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Affiliation(s)
- David Gomez
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yulian Gavrilov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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20
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Controlling the dynamics of the Nek2 leucine zipper by engineering of "kinetic" disulphide bonds. PLoS One 2019; 14:e0210352. [PMID: 30707691 PMCID: PMC6358272 DOI: 10.1371/journal.pone.0210352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/20/2018] [Indexed: 12/25/2022] Open
Abstract
Nek2 is a dimeric serine/ threonine protein kinase that belongs to the family of NIMA-related kinases (Neks). Its N-terminal catalytic domain and its C-terminal regulatory region are bridged by a leucine zipper, which plays an important role in the activation of Nek2's catalytic activity. Unusual conformational dynamics on the intermediary/slow timescale has thwarted all attempts so far to determine the structure of the Nek2 leucine zipper by means of X-ray crystallography and Nuclear Magnetic Resonance (NMR). Disulfide engineering, the strategic placement of non-native disulfide bonds into flexible regions flanking the coiled coil, was used to modulate the conformational exchange dynamics of this important dimerization domain. The resulting reduction in exchange rate leads to substantial improvements of important features in NMR spectra, such as line width, coherence transfer leakage and relaxation. These effects were comprehensively analyzed for the wild type protein, two single disulfide bond-bearing mutants and another double disulfide bonds-carrying mutant. Furthermore, exchange kinetics were measured across a wide temperature range, allowing for a detailed analysis of activation energy (ΔG‡) and maximal rate constant (k'ex). For one mutant carrying a disulfide bond at its C-terminus, a full backbone NMR assignment could be obtained for both conformers, demonstrating the benefits of the disulfide engineering. Our study demonstrates the first successful application of 'kinetic' disulfide bonds for the purpose of controlling the adverse effects of protein dynamics. Firstly, this provides a promising, robust platform for the full structural and functional investigation of the Nek2 leucine zipper in the future. Secondly, this work broadens the toolbox of protein engineering by disulfide bonds through the addition of a kinetic option in addition to the well-established thermodynamic uses of disulfide bonds.
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21
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Qiu C, Yuan Y, Zajicek J, Liang Z, Balsara RD, Brito-Robionson T, Lee SW, Ploplis VA, Castellino FJ. Contributions of different modules of the plasminogen-binding Streptococcus pyogenes M-protein that mediate its functional dimerization. J Struct Biol 2018; 204:151-164. [PMID: 30071314 PMCID: PMC6544907 DOI: 10.1016/j.jsb.2018.07.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/26/2018] [Accepted: 07/28/2018] [Indexed: 10/28/2022]
Abstract
Group A Streptococcus pyogenes (GAS) is a causative agent of pharyngeal and dermal infections in humans. A major virulence determinant of GAS is its dimeric signature fibrillar M-protein (M-Prt), which is evolutionarily designed in modules, ranging from a hypervariable extracellular N-terminal region to a progressively more highly conserved C-terminus that is covalently anchored to the cell wall. Of the >250 GAS isolates classified, only the subset of skin-trophic Pattern D strains expresses a specific serotype of M-Prt, PAM, that directly binds to host human plasminogen (hPg) via its extracellular NH2-terminal variable A-domain region. This interaction allows these GAS strains to accumulate components of the host fibrinolytic system on their surfaces to serve extracellular functions. While structure-function studies have been accomplished on M-Prts from Pattern A-C GAS isolates with different direct ligand binding properties compared to PAM, much less is known regarding the structure-function relationships of PAM-type M-Prts, particularly their dimerization determinants. To examine these questions, PAMs from seven GAS strains with sequence variations in the NH2-terminal ligand binding domains, as well as truncated versions of PAM, were designed and studied. The results from bioinformatic and biophysical analyses show that the different domains of PAM are disparately engaged in dimerization. From these data, we propose an experimentally-based model for PAM secondary and quaternary structures that is highly dependent on the conserved helical C-terminal C-D-domains. In addition, while the N-terminal regions of PAMs are variable in sequence, the binding properties of hPg and its activated product, plasmin, to the A-domain, remain intact.
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Affiliation(s)
- Cunjia Qiu
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Yue Yuan
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Jaroslav Zajicek
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Zhong Liang
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Rashna D Balsara
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Teresa Brito-Robionson
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Shaun W Lee
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Victoria A Ploplis
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Francis J Castellino
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States.
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Bessen DE, Smeesters PR, Beall BW. Molecular Epidemiology, Ecology, and Evolution of Group A Streptococci. Microbiol Spectr 2018; 6. [PMID: 30191802 DOI: 10.1128/microbiolspec.cpp3-0009-2018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Indexed: 12/27/2022] Open
Abstract
The clinico-epidemiological features of diseases caused by group A streptococci (GAS) is presented through the lens of the ecology, population genetics, and evolution of the organism. The serological targets of three typing schemes (M, T, SOF) are themselves GAS cell surface proteins that have a myriad of virulence functions and a diverse array of structural forms. Horizontal gene transfer expands the GAS antigenic cell surface repertoire by generating numerous combinations of M, T, and SOF antigens. However, horizontal gene transfer of the serotype determinant genes is not unconstrained, and therein lies a genetic organization that may signify adaptations to a narrow ecological niche, such as the primary tissue reservoirs of the human host. Adaptations may be further shaped by selection pressures such as herd immunity. Understanding the molecular evolution of GAS on multiple levels-short, intermediate, and long term-sheds insight on mechanisms of host-pathogen interactions, the emergence and spread of new clones, rational vaccine design, and public health interventions.
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Affiliation(s)
- Debra E Bessen
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY 10595
| | - Pierre R Smeesters
- Department of Pediatrics, Queen Fabiola Children's University Hospital, and Molecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, 1020, Belgium
| | - Bernard W Beall
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333
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23
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Song C, Mroginski MA, Lang C, Kopycki J, Gärtner W, Matysik J, Hughes J. 3D Structures of Plant Phytochrome A as Pr and Pfr From Solid-State NMR: Implications for Molecular Function. FRONTIERS IN PLANT SCIENCE 2018; 9:498. [PMID: 29740459 PMCID: PMC5928327 DOI: 10.3389/fpls.2018.00498] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/03/2018] [Indexed: 05/25/2023]
Abstract
We present structural information for oat phyA3 in the far-red-light-absorbing (Pfr) signaling state, to our knowledge the first three-dimensional (3D) information for a plant phytochrome as Pfr. Solid-state magic-angle spinning (MAS) NMR was used to detect interatomic contacts in the complete photosensory module [residues 1-595, including the NTE (N-terminal extension), PAS (Per/Arnt/Sim), GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) and PHY (phytochrome-specific) domains but with the C-terminal PAS repeat and transmitter-like module deleted] auto-assembled in vitro with 13C- and 15N-labeled phycocyanobilin (PCB) chromophore. Thereafter, quantum mechanics/molecular mechanics (QM/MM) enabled us to refine 3D structural models constrained by the NMR data. We provide definitive atomic assignments for all carbon and nitrogen atoms of the chromophore, showing the Pfr chromophore geometry to be periplanar ZZEssa with the D -ring in a β-facial disposition incompatible with many earlier notions regarding photoconversion yet supporting circular dichroism (CD) data. The Y268 side chain is shifted radically relative to published Pfr crystal structures in order to accommodate the β-facial ring D . Our findings support a photoconversion sequence beginning with Pr photoactivation via an anticlockwise D -ring Za→Ea photoflip followed by significant shifts at the coupling of ring A to the protein, a B -ring propionate partner swap from R317 to R287, changes in the C -ring propionate hydrogen-bonding network, breakage of the D272-R552 salt bridge accompanied by sheet-to-helix refolding of the tongue region stabilized by Y326-D272-S554 hydrogen bonding, and binding of the NTE to the hydrophobic side of ring A . We discuss phyA photoconversion, including the possible roles of mesoscopic phase transitions and protonation dynamics in the chromophore pocket. We also discuss possible associations between structural changes and translocation and signaling processes within the cell.
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Affiliation(s)
- Chen Song
- Institut für Analytische Chemie, Universität Leipzig, Leipzig, Germany
- Leids Instituut voor Chemisch Onderzoek, Universiteit Leiden, Leiden, Netherlands
| | | | - Christina Lang
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Giessen, Germany
| | - Jakub Kopycki
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Giessen, Germany
| | - Wolfgang Gärtner
- Institut für Analytische Chemie, Universität Leipzig, Leipzig, Germany
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Leipzig, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Giessen, Germany
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24
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Khazina E, Weichenrieder O. Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p. eLife 2018; 7:34960. [PMID: 29565245 PMCID: PMC5940361 DOI: 10.7554/elife.34960] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/21/2018] [Indexed: 12/22/2022] Open
Abstract
LINE-1 (L1) is an autonomous retrotransposon, which acted throughout mammalian evolution and keeps contributing to human genotypic diversity, genetic disease and cancer. L1 encodes two essential proteins: L1ORF1p, a unique RNA-binding protein, and L1ORF2p, an endonuclease and reverse transcriptase. L1ORF1p contains an essential, but rapidly evolving N-terminal portion, homo-trimerizes via a coiled coil and packages L1RNA into large assemblies. Here, we determined crystal structures of the entire coiled coil domain of human L1ORF1p. We show that retrotransposition requires a non-ideal and metastable coiled coil structure, and a strongly basic L1ORF1p amino terminus. Human L1ORF1p therefore emerges as a highly calibrated molecular machine, sensitive to mutation but functional in different hosts. Our analysis rationalizes the locally rapid L1ORF1p sequence evolution and reveals striking mechanistic parallels to coiled coil-containing membrane fusion proteins. It also suggests how trimeric L1ORF1p could form larger meshworks and indicates critical novel steps in L1 retrotransposition. Almost half of the human genome consists of DNA strings that have been copied and pasted from one part of the genome to another many thousands of times. These strings of DNA are called mobile genetic elements. Mobile elements can disrupt important genes, causing disease and cancer, but they can also drive evolution. Presently, only one type of mobile element, called LINE-1, is active in the human genome and able to multiply without help from other mobile elements. LINE-1 DNA is ‘transcribed’ to form molecules of LINE-1 RNA, which can then be ‘translated’ into two distinct proteins. These bind to LINE-1 RNA, which then gets back-transcribed into DNA and inserted as a new LINE-1 element in a new region of the genome. One of the two proteins, called L1ORF1p, forms complexes where three copies of the protein come together. These ‘trimers’ cover and protect LINE-1 RNA and are required for LINE-1 mobility. Different versions of L1ORF1p are found in different animals. Part of the protein is the same across all mammals, and this ‘conserved’ part controls the ability of L1ORF1p to bind to RNA. The non-conserved part of L1ORF1p differs even between humans and their closest animal relatives and little was known about its structure or role. However, this rapidly evolving part of L1ORF1p is essential for LINE-1 mobility. Using X-ray crystallography, Khazina and Weichenrieder obtained a molecular snapshot of the part of L1ORF1p that interacts with other copies of the protein to form trimers. Combined with earlier snapshots of L1ORF1p’s conserved part, this generated a complete structural model of the L1ORF1p trimer. Additional biophysical characterizations suggest that L1ORF1p trimers form a semi-stable structure that can partially open up, indicating how trimers could form larger assemblies of L1ORF1p on LINE-1 RNA. Indeed, the need to maintain a semi-stable structure could explain why L1ORF1p is evolving so rapidly. A second important finding is that the beginning of L1ORF1p needs to be positively charged – a requirement that warrants further exploration. The structural and mechanistic insight into L1ORF1p points to critical new steps in LINE-1 mobilization. It will help to design inhibitor molecules with the goal to halt the mobilization process at various points and to dissect such steps in great detail. Understanding how to control LINE-1 mobility could help to improve stem cell therapies and reproduction assistance techniques, due to the fact that LINE-1 mobility is a potential source of mutation in stem cells, egg and sperm cells, and newly formed embryos.
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Affiliation(s)
- Elena Khazina
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
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25
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Raynes JM, Young PG, Proft T, Williamson DA, Baker EN, Moreland NJ. Protein adhesins as vaccine antigens for Group A Streptococcus. Pathog Dis 2018; 76:4919728. [DOI: 10.1093/femspd/fty016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/01/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- J M Raynes
- School of Medical Sciences, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - P G Young
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
- School of Biological Sciences, University of Auckland, 5 Symonds Street, Auckland 1010, New Zealand
| | - T Proft
- School of Medical Sciences, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - D A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - E N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
- School of Biological Sciences, University of Auckland, 5 Symonds Street, Auckland 1010, New Zealand
| | - N J Moreland
- School of Medical Sciences, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
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26
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Zhang Y, Gao W, Chen Y, Escajadillo T, Fang RH, Nizet V, Zhang L. Self-Assembled Colloidal Gel Using Cell Membrane-Coated Nanosponges as Building Blocks. ACS NANO 2017; 11:11923-11930. [PMID: 29116753 PMCID: PMC6336496 DOI: 10.1021/acsnano.7b06968] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Colloidal gels consisting of oppositely charged nanoparticles are increasingly utilized for drug delivery and tissue engineering. Meanwhile, cell membrane-coated nanoparticles are becoming a compelling biomimetic system for innovative therapeutics. Here, we demonstrate the successful use of cell membrane-coated nanoparticles as building blocks to formulate a colloidal gel that gelates entirely based on material self-assembly without chemical cross-linking. Specifically, we prepare red blood cell membrane-coated nanosponges and mix them with an appropriate amount of cationic nanoparticles, resulting in a spontaneously formed gel-like complex. Rheological test shows that the nanosponge colloidal gel has pronounced shear-thinning property, which makes it an injectable formulation. The gel formulation not only preserves the nanosponges' toxin neutralization capability but also greatly prolongs their retention time after subcutaneous injection into mouse tissue. When tested in a mouse model of subcutaneous group A Streptococcus infection, the nanosponge colloidal gel shows significant antibacterial efficacy by markedly reducing skin lesion development. Overall, the nanosponge colloidal gel system is promising as an injectable formulation for therapeutic applications such as antivirulence treatment for local bacterial infections.
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Affiliation(s)
- Yue Zhang
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Weiwei Gao
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Yijie Chen
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Tamara Escajadillo
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Ronnie H. Fang
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Victor Nizet
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Liangfang Zhang
- Department of Nanoengineering, University of California San Diego, La Jolla, California 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
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27
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Ghosh P. Variation, Indispensability, and Masking in the M protein. Trends Microbiol 2017; 26:132-144. [PMID: 28867148 DOI: 10.1016/j.tim.2017.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/26/2017] [Accepted: 08/08/2017] [Indexed: 11/17/2022]
Abstract
The M protein is the major surface-associated virulence factor of group A Streptococcus (GAS) and an antigenically variable target of host immunity. How selection pressures to escape immune recognition, maintain indispensable functions, and mask vulnerabilities have shaped the sequences of the >220M protein types is unclear. Recent experiments have shed light on this question by showing that, hidden within the antigenic variability of many M protein types, are sequence patterns conserved for recruiting human C4b-binding protein (C4BP). Other host factors may be recruited in a similar manner by conserved but hidden sequence patterns in the M protein. The identification of such patterns may be applicable to the development of a GAS vaccine.
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Affiliation(s)
- Partho Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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28
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Group A streptococcal M protein activates the NLRP3 inflammasome. Nat Microbiol 2017; 2:1425-1434. [PMID: 28784982 DOI: 10.1038/s41564-017-0005-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 07/04/2017] [Indexed: 12/17/2022]
Abstract
Group A Streptococcus (GAS) is among the top ten causes of infection-related mortality in humans. M protein is the most abundant GAS surface protein, and M1 serotype GAS strains are associated with invasive infections, including necrotizing fasciitis and toxic shock syndrome. Here, we report that released, soluble M1 protein triggers programmed cell death in macrophages (Mϕ). M1 served as a second signal for caspase-1-dependent NLRP3 inflammasome activation, inducing maturation and release of proinflammatory cytokine interleukin-1β (IL-1β) and macrophage pyroptosis. The structurally dynamic B-repeat domain of M1 was critical for inflammasome activation, which involved K+ efflux and M1 protein internalization by clathrin-mediated endocytosis. Mouse intraperitoneal challenge showed that soluble M1 was sufficient and specific for IL-1β activation, which may represent an early warning to activate host immunity against the pathogen. Conversely, in systemic infection, hyperinflammation associated with M1-mediated pyroptosis and IL-1β release could aggravate tissue injury.
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29
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Gourinchas G, Etzl S, Göbl C, Vide U, Madl T, Winkler A. Long-range allosteric signaling in red light-regulated diguanylyl cyclases. SCIENCE ADVANCES 2017; 3:e1602498. [PMID: 28275738 PMCID: PMC5336353 DOI: 10.1126/sciadv.1602498] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/10/2017] [Indexed: 05/06/2023]
Abstract
Nature has evolved an astonishingly modular architecture of covalently linked protein domains with diverse functionalities to enable complex cellular networks that are critical for cell survival. The coupling of sensory modules with enzymatic effectors allows direct allosteric regulation of cellular signaling molecules in response to diverse stimuli. We present molecular details of red light-sensing bacteriophytochromes linked to cyclic dimeric guanosine monophosphate-producing diguanylyl cyclases. Elucidation of the first crystal structure of a full-length phytochrome with its enzymatic effector, in combination with the characterization of light-induced changes in conformational dynamics, reveals how allosteric light regulation is fine-tuned by the architecture and composition of the coiled-coil sensor-effector linker and also the central helical spine. We anticipate that consideration of molecular principles of sensor-effector coupling, going beyond the length of the characteristic linker, and the appreciation of dynamically driven allostery will open up new directions for the design of novel red light-regulated optogenetic tools.
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Affiliation(s)
- Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Stefan Etzl
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Christoph Göbl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Uršula Vide
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Tobias Madl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
- Corresponding author.
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