2024-03-28T08:28:18Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/6210062019-08-30T11:35:39Zcom_10033_620736col_10033_620737
2017-07-11T13:09:44Z
urn:hdl:10033/621006
Cryo-electron Microscopy Study of the Genome Release of the Dicistrovirus Israeli Acute Bee Paralysis Virus.
Mullapudi, Edukondalu
Füzik, Tibor
Přidal, Antonín
Plevka, Pavel
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Viruses of the family Dicistroviridae can cause substantial economic damage by infecting agriculturally important insects. Israeli acute bee paralysis virus (IAPV) causes honeybee colony collapse disorder in the United States. High-resolution molecular details of the genome delivery mechanism of dicistroviruses are unknown. Here we present a cryo-electron microscopy analysis of IAPV virions induced to release their genomes in vitro We determined structures of full IAPV virions primed to release their genomes to a resolution of 3.3 Å and of empty capsids to a resolution of 3.9 Å. We show that IAPV does not form expanded A particles before genome release as in the case of related enteroviruses of the family Picornaviridae The structural changes observed in the empty IAPV particles include detachment of the VP4 minor capsid proteins from the inner face of the capsid and partial loss of the structure of the N-terminal arms of the VP2 capsid proteins. Unlike the case for many picornaviruses, the empty particles of IAPV are not expanded relative to the native virions and do not contain pores in their capsids that might serve as channels for genome release. Therefore, rearrangement of a unique region of the capsid is probably required for IAPV genome release.
2017-07-11T13:09:44Z
2017-07-11T13:09:44Z
2017-02-15
Article
Cryo-electron Microscopy Study of the Genome Release of the Dicistrovirus Israeli Acute Bee Paralysis Virus. 2017, 91 (4) J. Virol.
1098-5514
27928006
10.1128/JVI.02060-16
http://hdl.handle.net/10033/621006
Journal of virology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6219192019-08-30T11:24:30Zcom_10033_620736col_10033_620737
2019-08-26T11:18:32Z
urn:hdl:10033/621919
Molecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.
Bernal, Ivonne
Börnicke, Jonathan
Heidemann, Johannes
Svergun, Dmitri
Horstmann, Julia A
Erhardt, Marc
Tuukkanen, Anne
Uetrecht, Charlotte
Kolbe, Michael
CSSB, Centre for Structural Systembiologie, Notkestr.85, 22607 Hamburg. Germany.
Host–pathogen interaction
Salmonella enterica
native mass spectrometry
protein complex
small-angle X‐ray scattering (SAXS)
Many medically relevant Gram-negative bacteria use the type III secretion system (T3SS) to translocate effector proteins into the host for their invasion and intracellular survival. A multi-protein complex located at the cytosolic interface of the T3SS is proposed to act as a sorting platform by selecting and targeting substrates for secretion through the system. However, the precise stoichiometry and 3D organization of the sorting platform components are unknown. Here we reconstitute soluble complexes of the Salmonella Typhimurium sorting platform proteins including the ATPase InvC, the regulator OrgB, the protein SpaO and a recently identified subunit SpaOC, which we show to be essential for the solubility of SpaO. We establish domain-domain interactions, determine for the first time the stoichiometry of each subunit within the complexes by native mass spectrometry and gain insight into their organization using small-angle X-ray scattering. Importantly, we find that in solution the assembly of SpaO/SpaOC/OrgB/InvC adopts an extended L-shaped conformation resembling the sorting platform pods seen in in situ cryo-electron tomography, proposing that this complex is the core building block that can be conceivably assembled into higher oligomers to form the T3SS sorting platform. The determined molecular arrangements of the soluble complexes of the sorting platform provide important insights into its architecture and assembly.
2019-08-26T11:18:32Z
2019-08-26T11:18:32Z
2019-07-06
Article
J Mol Biol. 2019 Jul 6. pii: S0022-2836(19)30425-5. doi: 10.1016/j.jmb.2019.07.004.
1089-8638
31288030
10.1016/j.jmb.2019.07.004
http://hdl.handle.net/10033/621919
Journal of Molecular Biology
en
info:eu-repo/grantAgreement/EC/FP7/311374
http://creativecommons.org/licenses/by-nc-sa/4.0/
embargoedAccess
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier
Journal of molecular biology
oai:repository.helmholtz-hzi.de:10033/6219472019-09-19T01:30:55Zcom_10033_620736col_10033_620737
2019-09-18T08:30:52Z
urn:hdl:10033/621947
Structural analysis of ligand-bound states of the Salmonella type III secretion system ATPase InvC.
Bernal, Ivonne
Römermann, Jonas
Flacht, Lara
Lunelli, Michele
Uetrecht, Charlotte
Kolbe, Michael
CSSB, Centre for Structural Systembiologie, Notkestr.85, 22607 Hamburg. Germany.
Salmonella enterica
ATPase
bacterial pathogenesis
crystallography
multi-angle light scattering
native mass spectrometry
spectroscopy
type III secretion system (T3SS)
Translocation of virulence effector proteins through the type III secretion system (T3SS) is essential for the virulence of many medically relevant Gram‐negative bacteria. The T3SS ATPases are conserved components that specifically recognize chaperone–effector complexes and energize effector secretion through the system. It is thought that functional T3SS ATPases assemble into a cylindrical structure maintained by their N‐terminal domains. Using size‐exclusion chromatography coupled to multi‐angle light scattering and native mass spectrometry, we show that in the absence of the N‐terminal oligomerization domain the Salmonella T3SS ATPase InvC can form monomers and dimers in solution. We also present for the first time a 2.05 å resolution crystal structure of InvC lacking the oligomerization domain (InvCΔ79) and map the amino acids suggested for ATPase intersubunit interaction, binding to other T3SS proteins and chaperone–effector recognition. Furthermore, we validate the InvC ATP‐binding site by co‐crystallization of InvCΔ79 with ATPγS (2.65 å) and ADP (2.80 å). Upon ATP‐analogue recognition, these structures reveal remodeling of the ATP‐binding site and conformational changes of two loops located outside of the catalytic site. Both loops face the central pore of the predicted InvC cylinder and are essential for the function of the T3SS ATPase. Our results present a fine functional and structural correlation of InvC and provide further details of the homo‐oligomerization process and ATP‐dependent conformational changes underlying the T3SS ATPase activity.
2019-09-18T08:30:52Z
2019-09-18T08:30:52Z
2019-10-01
Article
Protein Sci. 2019 Oct;28(10):1888-1901. doi: 10.1002/pro.3704. Epub 2019 Aug 24.
1469-896X
31393998
10.1002/pro.3704
http://hdl.handle.net/10033/621947
Protein Science
en
info:eu-repo/grantAgreement/EC/FP7/ 311374
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley
Protein science : a publication of the Protein Society
oai:repository.helmholtz-hzi.de:10033/6220082019-11-08T02:20:59Zcom_10033_620736col_10033_620737
2019-11-07T10:38:31Z
urn:hdl:10033/622008
Role of flagellar hydrogen bonding in Salmonella motility and flagellar polymorphic transition.
Wang, Chu
Lunelli, Michele
Zschieschang, Erik
Bosse, Jens Bernhard
Thuenauer, Roland
Kolbe, Michael
CSSB, Centre for Structural Systembiologie, Notkestr.85, 22607 Hamburg. Germany.
Bacterial flagellar filaments are assembled by tens of thousands flagellin subunits, forming 11 helically arranged protofilaments. Each protofilament can take either of the two bistable forms L-type or R-type, having slightly different conformations and inter-protofilaments interactions. By mixing different ratios of L-type and R-type protofilaments, flagella adopt multiple filament polymorphs and promote bacterial motility. In this study, we investigated the hydrogen bonding networks at the flagellin crystal packing interface in Salmonella enterica serovar typhimurium (S. typhimurium) by site-directed mutagenesis of each hydrogen bonded residue. We identified three flagellin mutants D108A, N133A and D152A that were non-motile despite their fully assembled flagella. Mutants D108A and D152A trapped their flagellar filament into inflexible right-handed polymorphs, which resemble the previously predicted 3L/8R and 4L/7R helical forms in Calladine's model but have never been reported in vivo. Mutant N133A produces floppy flagella that transform flagellar polymorphs in a disordered manner, preventing the formation of flagellar bundles. Further, we found that the hydrogen bonding interactions around these residues are conserved and coupled to flagellin L/R transition. Therefore, we demonstrate that the hydrogen bonding networks formed around flagellin residues D108, N133 and D152 greatly contribute to flagellar bending, flexibility, polymorphisms and bacterial motility.
2019-11-07T10:38:31Z
2019-11-07T10:38:31Z
2019-08-23
Article
Mol Microbiol. 2019 Aug 23. doi: 10.1111/mmi.14377.
1365-2958
31444817
10.1111/mmi.14377
http://hdl.handle.net/10033/622008
Molecular Microbiology
en
info:eu-repo/grantAgreement/EC/FP7/311374
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley
Molecular microbiology
oai:repository.helmholtz-hzi.de:10033/6222332020-04-16T02:16:00Zcom_10033_620736col_10033_620737
2020-04-15T16:56:55Z
urn:hdl:10033/622233
Cryo-EM structure of the Shigella type III needle complex.
Lunelli, Michele
Kamprad, Antje
Bürger, Jörg
Mielke, Thorsten
Spahn, Christian M T
Kolbe, Michael
CSSB, Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany.
The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram-negative bacterial pathogens. This system is composed of a membrane-embedded basal body and an extracellular needle that deliver effector proteins into host cells. High-resolution structures of the T3SS from different organisms and infection stages are needed to understand the underlying molecular mechanisms of effector translocation. Here, we present the cryo-electron microscopy structure of the isolated Shigella T3SS needle complex. The inner membrane (IM) region of the basal body adopts 24-fold rotational symmetry and forms a channel system that connects the bacterial periplasm with the export apparatus cage. The secretin oligomer adopts a heterogeneous architecture with 16- and 15-fold cyclic symmetry in the periplasmic N-terminal connector and C-terminal outer membrane ring, respectively. Two out of three IM subunits bind the secretin connector via a β-sheet augmentation. The cryo-EM map also reveals the helical architecture of the export apparatus core, the inner rod, the needle and their intervening interfaces.
2020-04-15T16:56:55Z
2020-04-15T16:56:55Z
2020-02-24
Article
PLoS Pathog. 2020 Feb 24;16(2):e1008263. doi: 10.1371/journal.ppat.1008263. eCollection 2020 Feb.
32092125
10.1371/journal.ppat.1008263
http://hdl.handle.net/10033/622233
1553-7374
PLoS pathogens
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
PLOS
16
2
e1008263
PLoS pathogens
United States
oai:repository.helmholtz-hzi.de:10033/6226262020-12-02T01:41:45Zcom_10033_620736col_10033_620737
2020-12-01T15:57:52Z
urn:hdl:10033/622626
Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide.
Srivastava, Sukrit
Verma, Sonia
Kamthania, Mohit
Agarwal, Deepa
Saxena, Ajay Kumar
Kolbe, Michael
Singh, Sarman
Kotnis, Ashwin
Rathi, Brijesh
Nayar, Seema A
Shin, Ho-Joon
Vashisht, Kapil
Pandey, Kailash C
CSSB, Centre for Structural Systembiologie, Notkestr.85, 22607 Hamburg. Germany.
Ag-Patch (antigenic patch)
COVID-19
Coronavirus
Multi-Epitope Vaccine
Multi-Patch Vaccine
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
Toll-Like Receptor (TLR)
epitope
overlapping-epitope-clusters-to-patches
reverse epitomics
The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is responsible for the COVID-19 outbreak. The highly contagious COVID-19 disease has spread to 216 countries in less than six months. Though several vaccine candidates are being claimed, an effective vaccine is yet to come. A novel reverse epitomics approach, 'overlapping-epitope-clusters-to-patches' method is utilized to identify the antigenic regions from the SARS-CoV-2 proteome. These antigenic regions are named as 'Ag-Patch or Ag-Patches', for Antigenic Patch or Patches. The identification of Ag-Patches is based on the clusters of overlapping epitopes rising from SARS-CoV-2 proteins. Further, we have utilized the identified Ag-Patches to design Multi-Patch Vaccines (MPVs), proposing a novel method for the vaccine design. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties and cDNA constructs. We identified 73 CTL (Cytotoxic T-Lymphocyte) and 49 HTL (Helper T-Lymphocyte) novel Ag-Patches from the proteome of SARS-CoV-2. The identified Ag-Patches utilized to design MPVs cover 768 overlapping epitopes targeting 55 different HLA alleles leading to 99.98% of world human population coverage. The MPVs and Toll-Like Receptor ectodomain complex shows stable complex formation tendency. Further, the cDNA analysis favors high expression of the MPVs constructs in a human cell line. We identified highly immunogenic novel Ag-Patches from the entire proteome of SARS CoV-2 by a novel reverse epitomics approach and utilized them to design MPVs. We conclude that the novel MPVs could be a highly potential novel approach to combat SARS-CoV-2, with greater effectiveness, high specificity and large human population coverage worldwide.
2020-12-01T15:57:52Z
2020-12-01T15:57:52Z
2020-11-06
Article
J Biomol Struct Dyn. 2020 Nov 6:1-20. doi: 10.1080/07391102.2020.1838329. Epub ahead of print.
33155524
10.1080/07391102.2020.1838329
http://hdl.handle.net/10033/622626
1538-0254
Journal of biomolecular structure & dynamics
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Taylor & Francis
1
20
Journal of biomolecular structure & dynamics
England
oai:repository.helmholtz-hzi.de:10033/6228392021-04-23T01:43:57Zcom_10033_620736col_10033_620737
2021-04-22T13:28:25Z
urn:hdl:10033/622839
Novel Method for Quantifying AhR-Ligand Binding Affinities Using Microscale Thermophoresis.
Stinn, Anne
Furkert, Jens
Kaufmann, Stefan H E
Moura-Alves, Pedro
Kolbe, Michael
CSSB, Centre for Structural Systembiologie, Notkestr.85, 22607 Hamburg. Germany.
AhR
MST
high-throughput screening
ligand binding
recombinant expression
The aryl hydrocarbon receptor (AhR) is a highly conserved cellular sensor of a variety of environmental pollutants and dietary-, cell- and microbiota-derived metabolites with important roles in fundamental biological processes. Deregulation of the AhR pathway is implicated in several diseases, including autoimmune diseases and cancer, rendering AhR a promising target for drug development and host-directed therapy. The pharmacological intervention of AhR processes requires detailed information about the ligand binding properties to allow specific targeting of a particular signaling process without affecting the remaining. Here, we present a novel microscale thermophoresis-based approach to monitoring the binding of purified recombinant human AhR to its natural ligands in a cell-free system. This approach facilitates a precise identification and characterization of unknown AhR ligands and represents a screening strategy for the discovery of potential selective AhR modulators.
2021-04-22T13:28:25Z
2021-04-22T13:28:25Z
2021-02-24
Article
Biosensors (Basel). 2021 Feb 24;11(3):60. doi: 10.3390/bios11030060.
33668313
10.3390/bios11030060
http://hdl.handle.net/10033/622839
2079-6374
Biosensors
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
MDPI
11
3
Biosensors
Switzerland
oai:repository.helmholtz-hzi.de:10033/6228522021-05-01T01:44:30Zcom_10033_620736col_10033_620737
2021-04-30T13:18:28Z
urn:hdl:10033/622852
Structural Basis for Designing Multiepitope Vaccines Against COVID-19 Infection: In Silico Vaccine Design and Validation.
Srivastava, Sukrit
Verma, Sonia
Kamthania, Mohit
Kaur, Rupinder
Badyal, Ruchi Kiran
Saxena, Ajay Kumar
Shin, Ho-Joon
Kolbe, Michael
Pandey, Kailash C
CSSB, Centre for Structural Systembiologie, Notkestr.85, 22607 Hamburg. Germany.
COVID-19
coronavirus
epitope
human transporter associated with antigen processing (TAP)
immunoinformatics
molecular docking, molecular dynamics simulation
multiepitope vaccine
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
toll-like receptor (TLR)
Both designed MEVs are composed of CTL and HTL epitopes screened from 11 Open Reading Frame (ORF), structural and nonstructural proteins of the SARS-CoV-2 proteome. Both MEVs also carry potential B-cell linear and discontinuous epitopes as well as interferon gamma-inducing epitopes. To enhance the immune response of our vaccine design, truncated (residues 10-153) Onchocerca volvulus activation-associated secreted protein-1 was used as an adjuvant at the N termini of both MEVs. The tertiary models for both the designed MEVs were generated, refined, and further analyzed for stable molecular interaction with toll-like receptor 3. Codon-biased complementary DNA (cDNA) was generated for both MEVs and analyzed in silico for high level expression in a mammalian (human) host cell line.
2021-04-30T13:18:28Z
2021-04-30T13:18:28Z
2020-06-19
Article
JMIR Bioinform Biotech. 2020 Jun 19;1(1):e19371. doi: 10.2196/19371.
32776022
10.2196/19371
http://hdl.handle.net/10033/622852
2563-3570
JMIR bioinformatics and biotechnology
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
: JMIR Publications Inc.
1
1
e19371
JMIR bioinformatics and biotechnology
Canada
oai:repository.helmholtz-hzi.de:10033/6230592021-10-05T03:24:30Zcom_10033_620736col_10033_620737
2021-10-04T13:09:39Z
urn:hdl:10033/623059
Helical reconstruction of and needle filaments attached to type 3 basal bodies.
Kotov, Vadim
Lunelli, Michele
Wald, Jiri
Kolbe, Michael
Marlovits, Thomas C
CSSB, Centre for Structural Systembiologie, Notkestr.85, 22607 Hamburg. Germany.
Cryo electron microscopy
Helical reconstruction
Needle filament
Salmonella, host-pathogen interaction
Shigella
Type 3 secretion system
Gram-negative pathogens evolved a syringe-like nanomachine, termed type 3 secretion system, to deliver protein effectors into the cytoplasm of host cells. An essential component of this system is a long helical needle filament that protrudes from the bacterial surface and connects the cytoplasms of the bacterium and the eukaryotic cell. Previous structural research was predominantly focused on reconstituted type 3 needle filaments, which lacked the biological context. In this work we introduce a facile procedure to obtain high-resolution cryo-EM structure of needle filaments attached to the basal body of type 3 secretion systems. We validate our approach by solving the structure of Salmonella PrgI filament and demonstrate its utility by obtaining the first high-resolution cryo-EM reconstruction of Shigella MxiH filament. Our work paves the way to systematic structural characterization of attached type 3 needle filaments in the context of mutagenesis studies, protein structural evolution and drug development.
2021-10-04T13:09:39Z
2021-10-04T13:09:39Z
2021-06-27
Article
Biochem Biophys Rep. 2021 Jun 27;27:101039. doi: 10.1016/j.bbrep.2021.101039.
34258394
10.1016/j.bbrep.2021.101039
http://hdl.handle.net/10033/623059
2405-5808
Biochemistry and biophysics reports
en
http://creativecommons.org/licenses/by-nc-nd/4.0/
Attribution-NonCommercial-NoDerivatives 4.0 International
Elsevier
27
101039
Biochemistry and biophysics reports
Netherlands
oai:repository.helmholtz-hzi.de:10033/6231872022-05-07T01:56:52Zcom_10033_620736col_10033_620737
2022-05-06T13:32:15Z
urn:hdl:10033/623187
Functional homo- and heterodimeric actin capping proteins from the malaria parasite.
Bendes, Ábris Ádám
Chatterjee, Moon
Götte, Benjamin
Kursula, Petri
Kursula, Inari
Actin
Capping protein
Heterodimer
Homodimer
Malaria
Plasmodium
2022-05-06T13:32:15Z
2022-05-06T13:32:15Z
2020-03-02
2022-05-06
Article
Other
32139121
10.1016/j.bbrc.2020.02.119
http://hdl.handle.net/10033/623187
1090-2104
Biochemical and biophysical research communications
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
525
3
681
686
Biochemical and biophysical research communications
United States