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Article ; Online: Holliday junction branch migration driven by AAA+ ATPase motors.

Wald, Jiri / Marlovits, Thomas C

2023 Volume 82, Page(s) 102650

Abstract: Holliday junctions are key intermediate DNA structures during genetic recombination. One of the first Holliday junction-processing protein complexes to be discovered was the well conserved RuvAB branch migration complex present in bacteria that mediates ... ...

Abstract	Holliday junctions are key intermediate DNA structures during genetic recombination. One of the first Holliday junction-processing protein complexes to be discovered was the well conserved RuvAB branch migration complex present in bacteria that mediates an ATP-dependent movement of the Holliday junction (branch migration). Although the RuvAB complex served as a paradigm for the processing of the Holliday junction, due to technical limitations the detailed structure and underlying mechanism of the RuvAB branch migration complex has until now remained unclear. Recently, structures of a reconstituted RuvAB complex actively-processing a Holliday junction were resolved using time-resolved cryo-electron microscopy. These structures showed distinct conformational states at different stages of the migration process. These structures made it possible to propose an integrated model for RuvAB Holliday junction branch migration. Furthermore, they revealed unexpected insights into the highly coordinated and regulated mechanisms of the nucleotide cycle powering substrate translocation in the hexameric AAA+ RuvB ATPase. Here, we review these latest advances and describe areas for future research.
MeSH term(s)	DNA, Cruciform ; Cryoelectron Microscopy ; ATPases Associated with Diverse Cellular Activities ; Movement ; Nucleotides
Chemical Substances	DNA, Cruciform ; ATPases Associated with Diverse Cellular Activities (EC 3.6.4.-) ; Nucleotides
Language	English
Publishing date	2023-08-19
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2023.102650
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Article ; Online: Cryo-EM of the injectisome and type III secretion systems.

Bergeron, Julien R C / Marlovits, Thomas C

Current opinion in structural biology

2022 Volume 75, Page(s) 102403

Abstract: Double-membrane-spanning protein complexes, such as the T3SS, had long presented an intractable challenge for structural biology. As a consequence, until a few years ago, our molecular understanding of this fascinating complex was limited to composite ... ...

Abstract	Double-membrane-spanning protein complexes, such as the T3SS, had long presented an intractable challenge for structural biology. As a consequence, until a few years ago, our molecular understanding of this fascinating complex was limited to composite models, consisting of structures of isolated domains, positioned within the overall complex. Most of the membrane-embedded components remained completely uncharacterized. In recent years, the emergence of cryo-electron microscopy (cryo-EM) as a method for determining protein structures to high resolution, has be transformative to our capacity to understand the architecture of this complex, and its mechanism of substrate transport. In this review, we summarize the recent structures of the various T3SS components, determined by cryo-EM, and highlight the regions of the complex that remain to be characterized. We also discuss the recent structural insights into the mechanism of effector transport through the T3SS. Finally, we highlight some of the challenges that remain to be tackled.
MeSH term(s)	Cryoelectron Microscopy/methods ; Type III Secretion Systems/chemistry
Chemical Substances	Type III Secretion Systems
Language	English
Publishing date	2022-06-17
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2022.102403
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Article ; Online: Residue-level error detection in cryoelectron microscopy models.

Reggiano, Gabriella / Lugmayr, Wolfgang / Farrell, Daniel / Marlovits, Thomas C / DiMaio, Frank

Structure (London, England : 1993)

2023 Volume 31, Issue 7, Page(s) 860–869.e4

Abstract: Building accurate protein models into moderate resolution (3-5 Å) cryoelectron microscopy (cryo-EM) maps is challenging and error prone. We have developed MEDIC (Model Error Detection in Cryo-EM), a robust statistical model that identifies local backbone ...

Abstract	Building accurate protein models into moderate resolution (3-5 Å) cryoelectron microscopy (cryo-EM) maps is challenging and error prone. We have developed MEDIC (Model Error Detection in Cryo-EM), a robust statistical model that identifies local backbone errors in protein structures built into cryo-EM maps by combining local fit-to-density with deep-learning-derived structural information. MEDIC is validated on a set of 28 structures that were subsequently solved to higher resolutions, where we identify the differences between low- and high-resolution structures with 68% precision and 60% recall. We additionally use this model to fix over 100 errors in 12 deposited structures and to identify errors in 4 refined AlphaFold predictions with 80% precision and 60% recall. As modelers more frequently use deep learning predictions as a starting point for refinement and rebuilding, MEDIC's ability to handle errors in structures derived from hand-building and machine learning methods makes it a powerful tool for structural biologists.
MeSH term(s)	Protein Conformation ; Cryoelectron Microscopy/methods ; Models, Molecular ; Proteins/chemistry ; Machine Learning
Chemical Substances	Proteins
Language	English
Publishing date	2023-05-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2023.05.002
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Zs.A 4141: Show issues

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Article ; Online: PickYOLO: Fast deep learning particle detector for annotation of cryo electron tomograms.

Genthe, Erik / Miletic, Sean / Tekkali, Indira / Hennell James, Rory / Marlovits, Thomas C / Heuser, Philipp

Journal of structural biology

2023 Volume 215, Issue 3, Page(s) 107990

Abstract: Particle localization (picking) in digital tomograms is a laborious and time-intensive step in cryogenic electron tomography (cryoET) analysis often requiring considerable user involvement, thus becoming a bottleneck for automated cryoET subtomogram ... ...

Abstract	Particle localization (picking) in digital tomograms is a laborious and time-intensive step in cryogenic electron tomography (cryoET) analysis often requiring considerable user involvement, thus becoming a bottleneck for automated cryoET subtomogram averaging (STA) pipelines. In this paper, we introduce a deep learning framework called PickYOLO to tackle this problem. PickYOLO is a super-fast, universal particle detector based on the deep-learning real-time object recognition system YOLO (You Only Look Once), and tested on single particles, filamentous structures, and membrane-embedded particles. After training with the centre coordinates of a few hundred representative particles, the network automatically detects additional particles with high yield and reliability at a rate of 0.24-3.75 s per tomogram. PickYOLO can automatically detect number of particles comparable to those manually selected by experienced microscopists. This makes PickYOLO a valuable tool to substantially reduce the time and manual effort needed to analyse cryoET data for STA, greatly aiding in high-resolution cryoET structure determination.
MeSH term(s)	Deep Learning ; Electrons ; Reproducibility of Results ; Cryoelectron Microscopy/methods ; Electron Microscope Tomography/methods ; Image Processing, Computer-Assisted/methods
Language	English
Publishing date	2023-06-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2023.107990
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Zs.A 1428: Show issues

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Article ; Online: Structural basis for subversion of host cell actin cytoskeleton during

Yuan, Biao / Scholz, Jonas / Wald, Jiri / Thuenauer, Roland / Hennell James, Rory / Ellenberg, Irina / Windhorst, Sabine / Faix, Jan / Marlovits, Thomas C

Science advances

2023 Volume 9, Issue 49, Page(s) eadj5777

Abstract: Secreted bacterial type III secretion system (T3SS) proteins are essential for successful infection by many human pathogens. Both T3SS translocator SipC and effector SipA are critical ... ...

Abstract	Secreted bacterial type III secretion system (T3SS) proteins are essential for successful infection by many human pathogens. Both T3SS translocator SipC and effector SipA are critical for
MeSH term(s)	Humans ; Actins/metabolism ; Cryoelectron Microscopy ; Bacterial Proteins/metabolism ; Actin Cytoskeleton/metabolism ; Salmonella Infections
Chemical Substances	Actins ; N-succinimidyl-5-iodo-3-pyridinecarboxylic acid (131865-61-7) ; Bacterial Proteins
Language	English
Publishing date	2023-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adj5777
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The Structure of the Type III Secretion System Needle Complex.

Miletic, Sean / Goessweiner-Mohr, Nikolaus / Marlovits, Thomas C

Current topics in microbiology and immunology

2019 Volume 427, Page(s) 67–90

Abstract: The type III secretion system (T3SS) is an essential virulence factor of many pathogenic bacterial species including Salmonella, Yersinia, Shigella and enteropathogenic Escherichia coli (EPEC). It is an intricate molecular machine that spans the ... ...

Abstract	The type III secretion system (T3SS) is an essential virulence factor of many pathogenic bacterial species including Salmonella, Yersinia, Shigella and enteropathogenic Escherichia coli (EPEC). It is an intricate molecular machine that spans the bacterial membranes and injects effector proteins into target host cells, enabling bacterial infection. The T3SS needle complex comprises of proteinaceous rings supporting a needle filament which extends out into the extracellular environment. It serves as the central conduit for translocating effector proteins. Multiple laboratories have dedicated a remarkable effort to decipher the structure and function of the needle complex. A combination of structural biology techniques such as cryo-electron microscopy (cryoEM), X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and computer modelling have been utilized to study different structural components at progressively higher resolutions. This chapter will provide an overview of the structural details of the T3SS needle complex, shedding light on this essential component of this fascinating bacterial system.
MeSH term(s)	Bacterial Proteins ; Computer Simulation ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Nuclear Magnetic Resonance, Biomolecular ; Type III Secretion Systems/chemistry ; Type III Secretion Systems/ultrastructure ; Virulence Factors
Chemical Substances	Bacterial Proteins ; Type III Secretion Systems ; Virulence Factors
Language	English
Publishing date	2019-10-30
Publishing country	Germany
Document type	Journal Article ; Review
ISSN	0070-217X
ISSN	0070-217X
DOI	10.1007/82_2019_178
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structural snapshots of human PepT1 and PepT2 reveal mechanistic insights into substrate and drug transport across epithelial membranes.

Killer, Maxime / Wald, Jiri / Pieprzyk, Joanna / Marlovits, Thomas C / Löw, Christian

Science advances

2021 Volume 7, Issue 45, Page(s) eabk3259

Abstract: The uptake of peptides in mammals plays a crucial role in nutrition and inflammatory diseases. This process is mediated by promiscuous transporters of the solute carrier family 15, which form part of the major facilitator superfamily. Besides the uptake ... ...

Abstract	The uptake of peptides in mammals plays a crucial role in nutrition and inflammatory diseases. This process is mediated by promiscuous transporters of the solute carrier family 15, which form part of the major facilitator superfamily. Besides the uptake of short peptides, peptide transporter 1 (PepT1) is a highly abundant drug transporter in the intestine and represents a major route for oral drug delivery. PepT2 also allows renal drug reabsorption from ultrafiltration and brain-to-blood efflux of neurotoxic compounds. Here, we present cryogenic electron microscopy (cryo-EM) structures of human PepT1 and PepT2 captured in four different states throughout the transport cycle. The structures reveal the architecture of human peptide transporters and provide mechanistic insights into substrate recognition and conformational transitions during transport. This may support future drug design efforts to increase the bioavailability of different drugs in the human body.
Language	English
Publishing date	2021-11-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.abk3259
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Helical reconstruction of

Kotov, Vadim / Lunelli, Michele / Wald, Jiri / Kolbe, Michael / Marlovits, Thomas C

Biochemistry and biophysics reports

2021 Volume 27, Page(s) 101039

Abstract: 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 ... ...

Abstract	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
Language	English
Publishing date	2021-06-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2831046-9
ISSN	2405-5808 ; 2405-5808
ISSN (online)	2405-5808
ISSN	2405-5808
DOI	10.1016/j.bbrep.2021.101039
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration.

Wald, Jiri / Fahrenkamp, Dirk / Goessweiner-Mohr, Nikolaus / Lugmayr, Wolfgang / Ciccarelli, Luciano / Vesper, Oliver / Marlovits, Thomas C

Nature

2022 Volume 609, Issue 7927, Page(s) 630–639

Abstract: The Holliday junction is a key intermediate formed during DNA recombination across all kingdoms of ... ...

Abstract	The Holliday junction is a key intermediate formed during DNA recombination across all kingdoms of life
MeSH term(s)	ATPases Associated with Diverse Cellular Activities/chemistry ; ATPases Associated with Diverse Cellular Activities/metabolism ; ATPases Associated with Diverse Cellular Activities/ultrastructure ; Adenosine Triphosphate/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Bacterial Proteins/ultrastructure ; Cryoelectron Microscopy ; DNA Helicases/chemistry ; DNA Helicases/metabolism ; DNA Helicases/ultrastructure ; DNA, Cruciform/chemistry ; DNA, Cruciform/metabolism ; DNA, Cruciform/ultrastructure ; DNA, Single-Stranded/chemistry ; DNA, Single-Stranded/metabolism ; DNA, Single-Stranded/ultrastructure ; Homologous Recombination ; Hydrolysis ; Multienzyme Complexes/chemistry ; Multienzyme Complexes/metabolism ; Multienzyme Complexes/ultrastructure ; Nucleotides ; Protein Conformation ; Rotation
Chemical Substances	Bacterial Proteins ; DNA, Cruciform ; DNA, Single-Stranded ; Multienzyme Complexes ; Nucleotides ; RuvB protein, Bacteria ; Adenosine Triphosphate (8L70Q75FXE) ; ATPases Associated with Diverse Cellular Activities (EC 3.6.4.-) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2022-08-24
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-022-05121-1
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Zs.A 26: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement.

Lugmayr, Wolfgang / Kotov, Vadim / Goessweiner-Mohr, Nikolaus / Wald, Jiri / DiMaio, Frank / Marlovits, Thomas C

Nature protocols

2022 Volume 18, Issue 1, Page(s) 239–264

Abstract: Cryogenic electron microscopy (cryo-EM) data represent density maps of macromolecular systems at atomic or near-atomic resolution. However, building and refining 3D atomic models by using data from cryo-EM maps is not straightforward and requires ... ...

Abstract	Cryogenic electron microscopy (cryo-EM) data represent density maps of macromolecular systems at atomic or near-atomic resolution. However, building and refining 3D atomic models by using data from cryo-EM maps is not straightforward and requires significant hands-on experience and manual intervention. We recently developed StarMap, an easy-to-use interface between the popular structural display program ChimeraX and Rosetta, a powerful molecular modeling engine. StarMap offers a general approach for refining structural models of biological macromolecules into cryo-EM density maps by combining Monte Carlo sampling with local density-guided optimization, Rosetta-based all-atom refinement and real-space B-factor calculations in a straightforward workflow. StarMap includes options for structural symmetry, local refinements and independent model validation. The overall quality of the refinement and the structure resolution is then assessed via analytical outputs, such as magnification calibration (pixel size calibration) and Fourier shell correlations. Z-scores reported by StarMap provide an easily interpretable indicator of the goodness of fit for each residue and can be plotted to evaluate structural models and improve local residue refinements, as well as to identify flexible regions and potentially functional sites in large macromolecular complexes. The protocol requires general computer skills, without the need for coding expertise, because most parts of the workflow can be operated by clicking tabs within the ChimeraX graphical user interface. Time requirements for the model refinement depend on the size and quality of the input data; however, this step can typically be completed within 1 d. The analytical parts of the workflow are completed within minutes.
MeSH term(s)	Molecular Structure ; Workflow ; Cryoelectron Microscopy/methods ; Models, Molecular ; Protein Conformation ; Macromolecular Substances
Chemical Substances	Macromolecular Substances
Language	English
Publishing date	2022-11-02
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-022-00757-9
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