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  1. Article ; Online: Structural biology of microbial gas vesicles: historical milestones and current knowledge.

    Huber, Stefan T / Jakobi, Arjen J

    Biochemical Society transactions

    2024  Volume 52, Issue 1, Page(s) 205–215

    Abstract: Gas vesicles mediate buoyancy-based motility in aquatic bacteria and archaea and are the only protein-based structures known to enclose a gas-filled volume. Their unique physicochemical properties and ingenious architecture rank them among the most ... ...

    Abstract Gas vesicles mediate buoyancy-based motility in aquatic bacteria and archaea and are the only protein-based structures known to enclose a gas-filled volume. Their unique physicochemical properties and ingenious architecture rank them among the most intriguing macromolecular assemblies characterised to date. This review covers the 60-year journey in quest for a high-resolution structural model of gas vesicles, first highlighting significant strides made in establishing the detailed ultrastructure of gas vesicles through transmission electron microscopy, X-ray fibre diffraction, atomic force microscopy, and NMR spectroscopy. We then survey the recent progress in cryogenic electron microscopy studies of gas vesicles, which eventually led to a comprehensive atomic model of the mature assembly. Synthesising insight from these structures, we examine possible mechanisms of gas vesicle biogenesis and growth, presenting a testable model to guide future experimental work. We conclude by discussing future directions in the structural biology of gas vesicles, particularly considering advancements in AI-driven structure prediction.
    MeSH term(s) Proteins/chemistry ; Bacteria ; Archaea ; Biology
    Chemical Substances Proteins
    Language English
    Publishing date 2024-02-08
    Publishing country England
    Document type Review ; Journal Article
    ZDB-ID 184237-7
    ISSN 1470-8752 ; 0300-5127
    ISSN (online) 1470-8752
    ISSN 0300-5127
    DOI 10.1042/BST20230396
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  2. Article ; Online: Electron scattering properties of biological macromolecules and their use for cryo-EM map sharpening.

    Bharadwaj, Alok / Jakobi, Arjen J

    Faraday discussions

    2022  Volume 240, Page(s) 168–183

    Abstract: Resolution-dependent loss of contrast in cryo-EM maps may obscure features at high resolution that are critical for map interpretation. Post-processing of cryo-EM maps can improve the interpretability by adjusting the resolution-dependence of structure ... ...

    Abstract Resolution-dependent loss of contrast in cryo-EM maps may obscure features at high resolution that are critical for map interpretation. Post-processing of cryo-EM maps can improve the interpretability by adjusting the resolution-dependence of structure factor amplitudes through map sharpening. Traditionally this has been done by rescaling the relative contribution of low and high-resolution frequencies globally. More recently, the realisation that molecular motion and heterogeneity cause non-uniformity of resolution throughout the map has inspired the development of techniques that optimise sharpening locally. We previously developed
    MeSH term(s) Cryoelectron Microscopy/methods ; Models, Molecular ; Electrons ; Protein Conformation
    Language English
    Publishing date 2022-11-08
    Publishing country England
    Document type Review ; Journal Article
    ISSN 1364-5498
    ISSN (online) 1364-5498
    DOI 10.1039/d2fd00078d
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  3. Article ; Online: Cryo-EM structure of gas vesicles for buoyancy-controlled motility.

    Huber, Stefan T / Terwiel, Dion / Evers, Wiel H / Maresca, David / Jakobi, Arjen J

    Cell

    2023  Volume 186, Issue 5, Page(s) 975–986.e13

    Abstract: Gas vesicles are gas-filled nanocompartments that allow a diverse group of bacteria and archaea to control their buoyancy. The molecular basis of their properties and assembly remains unclear. Here, we report the 3.2 Å cryo-EM structure of the gas ... ...

    Abstract Gas vesicles are gas-filled nanocompartments that allow a diverse group of bacteria and archaea to control their buoyancy. The molecular basis of their properties and assembly remains unclear. Here, we report the 3.2 Å cryo-EM structure of the gas vesicle shell made from the structural protein GvpA that self-assembles into hollow helical cylinders closed off by cone-shaped tips. Two helical half shells connect through a characteristic arrangement of GvpA monomers, suggesting a mechanism of gas vesicle biogenesis. The fold of GvpA features a corrugated wall structure typical for force-bearing thin-walled cylinders. Small pores enable gas molecules to diffuse across the shell, while the exceptionally hydrophobic interior surface effectively repels water. Comparative structural analysis confirms the evolutionary conservation of gas vesicle assemblies and demonstrates molecular features of shell reinforcement by GvpC. Our findings will further research into gas vesicle biology and facilitate molecular engineering of gas vesicles for ultrasound imaging.
    MeSH term(s) Cryoelectron Microscopy ; Biological Evolution ; Archaea ; Engineering ; Reinforcement, Psychology
    Language English
    Publishing date 2023-03-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2023.01.041
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  4. Article ; Online: Roodmus: A toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions

    Joosten, Maarten / Greer, Joel / Parkhurst, James / Burnley, Tom / Jakobi, Arjen J.

    bioRxiv

    Abstract: Conformational heterogeneity of biological macromolecules is a challenge in single particle averaging (SPA). Current standard practice is to employ classification and filtering methods which may allow a discrete number of conformational states to be ... ...

    Abstract Conformational heterogeneity of biological macromolecules is a challenge in single particle averaging (SPA). Current standard practice is to employ classification and filtering methods which may allow a discrete number of conformational states to be reconstructed. However, the conformation space accessible to these molecules is continuous and therefore explored incompletely by a small number of discrete classes. Recently developed heterogeneous reconstruction algorithms (HRAs) to analyse continuous heterogeneity rely on machine learning methods employing low-dimensional latent space representations. The non-linear nature of many of these methods pose challenges to their validation and interpretation, and to identifying functionally relevant conformational trajectories. We believe these methods would benefit from in-depth benchmarking using high quality synthetic data and concomitant ground truth information. Here we present a framework for the simulation and subsequent analysis with respect to ground-truth of cryo-EM micrographs containing conformationally heterogeneous particles whose conformational heterogeneity is sourced from molecular dynamics (MD) simulations. This synthetic data can then be processed as if it were experimental data allowing aspects of standard SPA workflows, as well as heterogeneous reconstruction methods, to be compared with known ground-truth using available utilities. We demonstrate the simulation and analysis of several such datasets and present an initial investigation into HRAs.
    Keywords covid19
    Language English
    Publishing date 2024-04-30
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.04.29.590932
    Database COVID19

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  5. Article ; Online: Nanofluidic chips for cryo-EM structure determination from picoliter sample volumes.

    Huber, Stefan T / Sarajlic, Edin / Huijink, Roeland / Weis, Felix / Evers, Wiel H / Jakobi, Arjen J

    eLife

    2022  Volume 11

    Abstract: Cryogenic electron microscopy has become an essential tool for structure determination of biological macromolecules. In practice, the difficulty to reliably prepare samples with uniform ice thickness still represents a barrier for routine high-resolution ...

    Abstract Cryogenic electron microscopy has become an essential tool for structure determination of biological macromolecules. In practice, the difficulty to reliably prepare samples with uniform ice thickness still represents a barrier for routine high-resolution imaging and limits the current throughput of the technique. We show that a nanofluidic sample support with well-defined geometry can be used to prepare cryo-EM specimens with reproducible ice thickness from picoliter sample volumes. The sample solution is contained in electron-transparent nanochannels that provide uniform thickness gradients without further optimisation and eliminate the potentially destructive air-water interface. We demonstrate the possibility to perform high-resolution structure determination with three standard protein specimens. Nanofabricated sample supports bear potential to automate the cryo-EM workflow, and to explore new frontiers for cryo-EM applications such as time-resolved imaging and high-throughput screening.
    MeSH term(s) Cryoelectron Microscopy/instrumentation ; Cryoelectron Microscopy/methods ; Microfluidics/instrumentation ; Microfluidics/methods ; Proteasome Endopeptidase Complex ; Protein Array Analysis/methods ; Specimen Handling/instrumentation ; Specimen Handling/methods ; Water/chemistry
    Chemical Substances Water (059QF0KO0R) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
    Language English
    Publishing date 2022-01-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.72629
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  6. Article ; Online: Robust Local Thickness Estimation of Sub-Micrometer Specimen by 4D-STEM.

    Skoupý, Radim / Boltje, Daan B / Slouf, Miroslav / Mrázová, Kateřina / Láznička, Tomáš / Taisne, Clémence M / Krzyžánek, Vladislav / Hoogenboom, Jacob P / Jakobi, Arjen J

    Small methods

    2023  Volume 7, Issue 9, Page(s) e2300258

    Abstract: A quantitative four-dimensional scanning transmission electron microscopy (4D-STEM) imaging technique (q4STEM) for local thickness estimation across amorphous specimen such as obtained by focused ion beam (FIB)-milling of lamellae for (cryo-)TEM analysis ...

    Abstract A quantitative four-dimensional scanning transmission electron microscopy (4D-STEM) imaging technique (q4STEM) for local thickness estimation across amorphous specimen such as obtained by focused ion beam (FIB)-milling of lamellae for (cryo-)TEM analysis is presented. This study is based on measuring spatially resolved diffraction patterns to obtain the angular distribution of electron scattering, or the ratio of integrated virtual dark and bright field STEM signals, and their quantitative evaluation using Monte Carlo simulations. The method is independent of signal intensity calibrations and only requires knowledge of the detector geometry, which is invariant for a given instrument. This study demonstrates that the method yields robust thickness estimates for sub-micrometer amorphous specimen using both direct detection and light conversion 2D-STEM detectors in a coincident FIB-SEM and a conventional SEM. Due to its facile implementation and minimal dose reauirements, it is anticipated that this method will find applications for in situ thickness monitoring during lamella fabrication of beam-sensitive materials.
    Language English
    Publishing date 2023-05-30
    Publishing country Germany
    Document type Journal Article
    ISSN 2366-9608
    ISSN (online) 2366-9608
    DOI 10.1002/smtd.202300258
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  7. Article: Thresholding of cryo-EM density maps by false discovery rate control.

    Beckers, Maximilian / Jakobi, Arjen J / Sachse, Carsten

    IUCrJ

    2019  Volume 6, Issue Pt 1, Page(s) 18–33

    Abstract: Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation ... ...

    Abstract Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and
    Language English
    Publishing date 2019-01-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252518014434
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  8. Article ; Online: Model-based local density sharpening of cryo-EM maps.

    Jakobi, Arjen J / Wilmanns, Matthias / Sachse, Carsten

    eLife

    2017  Volume 6

    Abstract: Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic ... ...

    Abstract Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement.
    MeSH term(s) Cryoelectron Microscopy/methods ; Image Processing, Computer-Assisted/methods ; Models, Molecular
    Language English
    Publishing date 2017-10-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.27131
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  9. Article ; Online: Author Correction: Multivalent interactions facilitate motor-dependent protein accumulation at growing microtubule plus-ends.

    Maan, Renu / Reese, Louis / Volkov, Vladimir A / King, Matthew R / van der Sluis, Eli O / Andrea, Nemo / Evers, Wiel H / Jakobi, Arjen J / Dogterom, Marileen

    Nature cell biology

    2023  Volume 25, Issue 4, Page(s) 626

    Language English
    Publishing date 2023-03-16
    Publishing country England
    Document type Published Erratum
    ZDB-ID 1474722-4
    ISSN 1476-4679 ; 1465-7392
    ISSN (online) 1476-4679
    ISSN 1465-7392
    DOI 10.1038/s41556-023-01124-w
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  10. Article ; Online: A rapid cloning method employing orthogonal end protection.

    Jakobi, Arjen J / Huizinga, Eric G

    PloS one

    2012  Volume 7, Issue 6, Page(s) e37617

    Abstract: We describe a novel in vitro cloning strategy that combines standard tools in molecular biology with a basic protecting group concept to create a versatile framework for the rapid and seamless assembly of modular DNA building blocks into functional open ... ...

    Abstract We describe a novel in vitro cloning strategy that combines standard tools in molecular biology with a basic protecting group concept to create a versatile framework for the rapid and seamless assembly of modular DNA building blocks into functional open reading frames. Analogous to chemical synthesis strategies, our assembly design yields idempotent composite synthons amenable to iterative and recursive split-and-pool reaction cycles. As an example, we illustrate the simplicity, versatility and efficiency of the approach by constructing an open reading frame composed of tandem arrays of a human fibronectin type III (FNIII) domain and the von Willebrand Factor A2 domain (VWFA2), as well as chimeric (FNIII)(n)-VWFA2-(FNIII)(n) constructs. Although we primarily designed this strategy to accelerate assembly of repetitive constructs for single-molecule force spectroscopy, we anticipate that this approach is equally applicable to the reconstitution and modification of complex modular sequences including structural and functional analysis of multi-domain proteins, synthetic biology or the modular construction of episomal vectors.
    MeSH term(s) Amino Acid Sequence ; Base Sequence ; Biomarkers, Tumor/chemistry ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Calcium-Binding Proteins ; Cloning, Molecular/methods ; DNA/genetics ; Fibronectins/chemistry ; Fibronectins/genetics ; Fibronectins/metabolism ; HEK293 Cells ; Humans ; Models, Genetic ; Molecular Sequence Data ; Open Reading Frames/genetics ; Plasmids/genetics ; Recombinant Fusion Proteins/chemistry ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Reproducibility of Results ; Transition Temperature
    Chemical Substances Biomarkers, Tumor ; Calcium-Binding Proteins ; Fibronectins ; Recombinant Fusion Proteins ; VWA2 protein, human ; DNA (9007-49-2)
    Language English
    Publishing date 2012-06-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0037617
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