307 results on '"Edward H Egelman"'
Search Results
2. Molecular architecture of the assembly of Bacillus spore coat protein GerQ revealed by cryo-EM
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Yijia Cheng, Mark A. B. Kreutzberger, Jianting Han, Edward H. Egelman, and Qin Cao
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Science - Abstract
Abstract Protein filaments are ubiquitous in nature and have diverse biological functions. Cryo-electron microscopy (cryo-EM) enables the determination of atomic structures, even from native samples, and is capable of identifying previously unknown filament species through high-resolution cryo-EM maps. In this study, we determine the structure of an unreported filament species from a cryo-EM dataset collected from Bacillus amyloiquefaciens biofilms. These filaments are composed of GerQ, a spore coat protein known to be involved in Bacillus spore germination. GerQ assembles into a structurally stable architecture consisting of rings containing nine subunits, which stacks to form filaments. Molecular dockings and model predictions suggest that this nine-subunit structure is suitable for binding CwlJ, a protein recruited by GerQ and essential for Ca2+-DPA induced spore germination. While the assembly state of GerQ within the spores and the direct interaction between GerQ and CwlJ have yet to be validated through further experiments, our findings provide valuable insights into the self-assembly of GerQ and enhance our understanding of its role in spore germination.
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- 2024
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3. Two distinct archaeal type IV pili structures formed by proteins with identical sequence
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Junfeng Liu, Gunnar N. Eastep, Virginija Cvirkaite-Krupovic, Shane T. Rich-New, Mark A. B. Kreutzberger, Edward H. Egelman, Mart Krupovic, and Fengbin Wang
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Science - Abstract
Abstract Type IV pili (T4P) represent one of the most common varieties of surface appendages in archaea. These filaments, assembled from small pilin proteins, can be many microns long and serve diverse functions, including adhesion, biofilm formation, motility, and intercellular communication. Here, we determine atomic structures of two distinct adhesive T4P from Saccharolobus islandicus via cryo-electron microscopy (cryo-EM). Unexpectedly, both pili were assembled from the same pilin polypeptide but under different growth conditions. One filament, denoted mono-pilus, conforms to canonical archaeal T4P structures where all subunits are equivalent, whereas in the other filament, the tri-pilus, the same polypeptide exists in three different conformations. The three conformations in the tri-pilus are very different from the single conformation found in the mono-pilus, and involve different orientations of the outer immunoglobulin-like domains, mediated by a very flexible linker. Remarkably, the outer domains rotate nearly 180° between the mono- and tri-pilus conformations. Both forms of pili require the same ATPase and TadC-like membrane pore for assembly, indicating that the same secretion system can produce structurally very different filaments. Our results show that the structures of archaeal T4P appear to be less constrained and rigid than those of the homologous archaeal flagellar filaments that serve as helical propellers.
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- 2024
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4. Profile of Edward H. Egelman
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Sandeep Ravindran
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Multidisciplinary ,media_common.quotation_subject ,Industrial scale ,Biophysics ,Media studies ,Opposition (politics) ,History, 20th Century ,Racism ,Social justice ,Structure and function ,Actin Cytoskeleton ,Microscopy, Electron ,Vietnam War ,Profile ,Sociology ,media_common - Abstract
Edward H. Egelman has had a long and distinguished career as a biophysicist, but he took a fairly circuitous path into science. Egelman graduated high school in 1968, a particularly tumultuous year for the United States. “This was the peak of the Vietnam war and my main interests at that point were focused on opposition to the Vietnam war and issues of social justice, racism, and inequality,” he says. After starting an undergraduate degree at Brandeis University, Egelman dropped out and was actively involved in the antiwar movement. Edward H. Egelman. Image credit: UVA Health/Kay Taylor. When Egelman eventually went back to Brandeis, an interest in philosophy led him to pursue a degree in physics. “I thought that maybe physics held the answer to all these interesting philosophical questions,” he says. After completing a physics major within a year and a half and graduating in 1976, Egelman started a doctorate in experimental high-energy physics at Harvard University. “I quickly became pretty disillusioned with that type of physics; it was sort of industrial scale with [dozens of] authors on each paper,” he says. As he considered his next steps, Egelman recalled enjoying his undergraduate honors research project with David DeRosier, whose work lay at the intersection of physics and biology. “I had so much fun doing that project, and I thought perhaps biophysics might be as much fun,” he says. Egelman returned to Brandeis to work with DeRosier for his doctorate in biophysics. “In biophysics, a person could do something on a benchtop that was both interesting and potentially relevant to public health,” says Egelman. “Everything I’ve done since then is sort of a continuation of that work,” he says. During his career, Egelman has deciphered the structure and function of protein polymers and has made key contributions to the use …
- Published
- 2020
5. An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano
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Ravi R. Sonani, Lee K. Palmer, Nathaniel C. Esteves, Abigail A. Horton, Amanda L. Sebastian, Rebecca J. Kelly, Fengbin Wang, Mark A. B. Kreutzberger, William K. Russell, Petr G. Leiman, Birgit E. Scharf, and Edward H. Egelman
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Science - Abstract
Abstract A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, contraction of an external sheath powers the motion of an inner tube through the membrane. The structure, energetics, and mechanism of the machinery imply rigidity and straightness. The contractile tail of Agrobacterium tumefaciens bacteriophage Milano is flexible and bent to varying degrees, which sets it apart from other contractile tail-like systems. Here, we report structures of the Milano tail including the sheath-tube complex, baseplate, and putative receptor-binding proteins. The flexible-to-rigid transformation of the Milano tail upon contraction can be explained by unique electrostatic properties of the tail tube and sheath. All components of the Milano tail, including sheath subunits, are crosslinked by disulfides, some of which must be reduced for contraction to occur. The putative receptor-binding complex of Milano contains a tailspike, a tail fiber, and at least two small proteins that form a garland around the distal ends of the tailspikes and tail fibers. Despite being flagellotropic, Milano lacks thread-like tail filaments that can wrap around the flagellum, and is thus likely to employ a different binding mechanism.
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- 2024
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6. Neck and capsid architecture of the robust Agrobacterium phage Milano
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Ravi R. Sonani, Nathaniel C. Esteves, Abigail A. Horton, Rebecca J. Kelly, Amanda L. Sebastian, Fengbin Wang, Mark A. B. Kreutzberger, Petr G. Leiman, Birgit E. Scharf, and Edward H. Egelman
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Biology (General) ,QH301-705.5 - Abstract
Abstract Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the “neck” region, where the DNA-filled capsid is connected to the host-recognizing tail remains poorly understood. We describe cryo-EM structures of the neck, the neck-capsid and neck-tail junctions, and capsid of the Agrobacterium phage Milano. The Milano neck 1 protein connects the 12-fold symmetrical neck to a 5-fold vertex of the icosahedral capsid. Comparison of Milano neck 1 homologs leads to four proposed classes, likely evolved from the simplest one in siphophages to more complex ones in myo- and podophages. Milano neck is surrounded by the atypical collar, which covalently crosslinks the tail sheath to neck 1. The Milano capsid is decorated with three types of proteins, a minor capsid protein (mCP) and two linking proteins crosslinking the mCP to the major capsid protein. The extensive network of disulfide bonds within and between neck, collar, capsid and tail provides an exceptional structural stability to Milano.
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- 2023
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7. The mating pilus of E. coli pED208 acts as a conduit for ssDNA during horizontal gene transfer
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Leticia Beltrán, Holly Torsilieri, Jonasz B. Patkowski, Jie E. Yang, James Casanova, Tiago R. D. Costa, Elizabeth R. Wright, and Edward H. Egelman
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cryo-EM ,conjugation pilus ,horizontal gene transfer ,Microbiology ,QR1-502 - Abstract
ABSTRACTBacterial conjugation, a process of horizontal gene transfer, plays a key role in promoting the spread of antimicrobial resistance among human pathogens. The mechanism of conjugation involves the development of a conjugative pilus that forms a physical bridge between two bacterial cells and the subsequent unidirectional transfer of single-stranded DNA (ssDNA) complexed with a protein from the donor to the recipient cell. Atomic structures exist for many of the components of the type IV secretion system (T4SS), responsible for the nucleoprotein secretion, but little is known about the events preceding gene transfer, specifically what is the extent of the participation of the conjugative pilus in ssDNA transfer? There has been a longstanding debate about whether its main role is to bring a donor and a recipient cell into physical juxtaposition and form a mating junction that allows for ssDNA transfer via the T4SS machinery complex or whether ssDNA is actually transferred through the lumen of the pilus. Here, through a combination of maleimide labeling of the conjugative pilus and SeqA-YFP labeling of the transferred ssDNA, we visualize the process of bacterial conjugation in real time. We discover that the conjugative pilus is capable of transferring the ssDNA at a distance, between physically separated cells, and thus conclude that a physical mating junction is not essential for conjugative gene transfer.IMPORTANCEBacteria are constantly exchanging DNA, which constitutes horizontal gene transfer. While some of these occurs by a non-specific process called natural transformation, some occurs by a specific mating between a donor and a recipient cell. In specific conjugation, the mating pilus is extended from the donor cell to make contact with the recipient cell, but whether DNA is actually transferred through this pilus or by another mechanism involving the type IV secretion system complex without the pilus has been an open question. Using Escherichia coli, we show that DNA can be transferred through this pilus between a donor and a recipient cell that has not established a tight mating junction, providing a new picture for the role of this pilus.
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- 2024
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8. Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery
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Leticia C. Beltran, Virginija Cvirkaite-Krupovic, Jessalyn Miller, Fengbin Wang, Mark A. B. Kreutzberger, Jonasz B. Patkowski, Tiago R. D. Costa, Stefan Schouten, Ilya Levental, Vincent P. Conticello, Edward H. Egelman, and Mart Krupovic
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Science - Abstract
Bacteria can exchange DNA through extracellular appendages (‘mating pili’) in a process known as conjugation. Here, Beltran et al. determine atomic structures by cryo-electron microscopy of a bacterial conjugative pilus and two archaeal pili, showing that the archaeal pili are homologous to bacterial mating pili.
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- 2023
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9. An unbroken network of interactions connecting flagellin domains is required for motility in viscous environments.
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Marko Nedeljković, Mark A B Kreutzberger, Sandra Postel, Daniel Bonsor, Yingying Xing, Neil Jacob, William J Schuler, Edward H Egelman, and Eric J Sundberg
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Immunologic diseases. Allergy ,RC581-607 ,Biology (General) ,QH301-705.5 - Abstract
In its simplest form, bacterial flagellar filaments are composed of flagellin proteins with just two helical inner domains, which together comprise the filament core. Although this minimal filament is sufficient to provide motility in many flagellated bacteria, most bacteria produce flagella composed of flagellin proteins with one or more outer domains arranged in a variety of supramolecular architectures radiating from the inner core. Flagellin outer domains are known to be involved in adhesion, proteolysis and immune evasion but have not been thought to be required for motility. Here we show that in the Pseudomonas aeruginosa PAO1 strain, a bacterium that forms a ridged filament with a dimerization of its flagellin outer domains, motility is categorically dependent on these flagellin outer domains. Moreover, a comprehensive network of intermolecular interactions connecting the inner domains to the outer domains, the outer domains to one another, and the outer domains back to the inner domain filament core, is required for motility. This inter-domain connectivity confers PAO1 flagella with increased stability, essential for its motility in viscous environments. Additionally, we find that such ridged flagellar filaments are not unique to Pseudomonas but are, instead, present throughout diverse bacterial phyla.
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- 2023
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10. Flagellin outer domain dimerization modulates motility in pathogenic and soil bacteria from viscous environments
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Mark A. B. Kreutzberger, Richard C. Sobe, Amber B. Sauder, Sharanya Chatterjee, Alejandro Peña, Fengbin Wang, Jorge A. Giron, Volker Kiessling, Tiago R. D. Costa, Vincent P. Conticello, Gad Frankel, Melissa M. Kendall, Birgit E. Scharf, and Edward H. Egelman
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Science - Abstract
It has been suggested that the outer domains of bacterial flagellins are not needed for motility. Here, the authors show that flagellar filament outer domains from some bacteria have unique structures which can alter the motility of the bacteria.
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- 2022
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11. Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times
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Fengbin Wang, Chi Ho Chan, Victor Suciu, Khawla Mustafa, Madeline Ammend, Dong Si, Allon I Hochbaum, Edward H Egelman, and Daniel R Bond
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geobacter sulfurreducens ,cryo-EM ,long range electron transfer ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
While early genetic and low-resolution structural observations suggested that extracellular conductive filaments on metal-reducing organisms such as Geobacter were composed of type IV pili, it has now been established that bacterial c-type cytochromes can polymerize to form extracellular filaments capable of long-range electron transport. Atomic structures exist for two such cytochrome filaments, formed from the hexaheme cytochrome OmcS and the tetraheme cytochrome OmcE. Due to the highly conserved heme packing within the central OmcS and OmcE cores, and shared pattern of heme coordination between subunits, it has been suggested that these polymers have a common origin. We have now used cryo-electron microscopy (cryo-EM) to determine the structure of a third extracellular filament, formed from the Geobacter sulfurreducens octaheme cytochrome, OmcZ. In contrast to the linear heme chains in OmcS and OmcE from the same organism, the packing of hemes, heme:heme angles, and between-subunit heme coordination is quite different in OmcZ. A branched heme arrangement within OmcZ leads to a highly surface exposed heme in every subunit, which may account for the formation of conductive biofilm networks, and explain the higher measured conductivity of OmcZ filaments. This new structural evidence suggests that conductive cytochrome polymers arose independently on more than one occasion from different ancestral multiheme proteins.
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- 2022
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12. Distinct axial and lateral interactions within homologous filaments dictate the signaling specificity and order of the AIM2-ASC inflammasome
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Mariusz Matyszewski, Weili Zheng, Jacob Lueck, Zachary Mazanek, Naveen Mohideen, Albert Y. Lau, Edward H. Egelman, and Jungsan Sohn
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Science - Abstract
AIM2-ASC inflammasomes are filamentous signalling platforms that play a central role in host innate defence. Here, the authors present the filament cryo-EM structure of the inflammasome receptor AIM2, which is very similar to the adaptor ASC filament structure. By employing Rosetta and Molecular Dynamics simulations the authors provide further insights into the directionality and recognition mechanisms of the individual AIM2 and ASC filaments, which is further validated with biochemical and cellular experiments.
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- 2021
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13. Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials
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Fengbin Wang, Ordy Gnewou, Charles Modlin, Leticia C. Beltran, Chunfu Xu, Zhangli Su, Puneet Juneja, Gevorg Grigoryan, Edward H. Egelman, and Vincent P. Conticello
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Science - Abstract
Peptide-based filamentous assemblies are successfully used for generation of structurally ordered materials, but their de novo design and structural characterization is challenging. Here, the authors provide a strategy for the design of self-assembling peptide nanotubes based on modifications of an arginine clasp interaction motif, and report the cryo-EM structures of seven designed nanotubes.
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- 2021
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14. The structures of two archaeal type IV pili illuminate evolutionary relationships
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Fengbin Wang, Diana P. Baquero, Zhangli Su, Leticia C. Beltran, David Prangishvili, Mart Krupovic, and Edward H. Egelman
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Science - Abstract
Archaeal type IV pili (T4P) mediate adhesion to surfaces and are receptors for hyperthermophilic archaeal viruses. Here, the authors present the cryo-EM structures of two archaeal T4P from Pyrobaculum arsenaticum and Saccharolobus solfataricus and discuss evolutionary relationships between bacterial T4P, archaeal T4P and archaeal flagellar filaments.
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- 2020
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15. The AAA + ATPase TorsinA polymerizes into hollow helical tubes with 8.5 subunits per turn
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F. Esra Demircioglu, Weili Zheng, Alexander J. McQuown, Nolan K. Maier, Nicki Watson, Iain M. Cheeseman, Vladimir Denic, Edward H. Egelman, and Thomas U. Schwartz
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Science - Abstract
Torsins are unusual AAA + ATPases of unknown function that reside in the endoplasmic reticulum of all animals. Here the authors report that TorsinA forms tubular helical filaments with an unusual periodicity and that filamentous TorsinA directly interacts with membranes to form tubular protrusions.
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- 2019
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16. Photorhabdus luminescens TccC3 Toxin Targets the Dynamic Population of F-Actin and Impairs Cell Cortex Integrity
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Songyu Dong, Weili Zheng, Nicholas Pinkerton, Jacob Hansen, Svetlana B. Tikunova, Jonathan P. Davis, Sarah M. Heissler, Elena Kudryashova, Edward H. Egelman, and Dmitri S. Kudryashov
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TccC3 ,actin ,ADP-ribosylation ,bacterial toxin ,calponin-homology domain ,actin dynamics ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Due to its essential role in cellular processes, actin is a common target for bacterial toxins. One such toxin, TccC3, is an effector domain of the ABC-toxin produced by entomopathogenic bacteria of Photorhabdus spp. Unlike other actin-targeting toxins, TccC3 uniquely ADP-ribosylates actin at Thr-148, resulting in the formation of actin aggregates and inhibition of phagocytosis. It has been shown that the fully modified F-actin is resistant to depolymerization by cofilin and gelsolin, but their effects on partially modified actin were not explored. We found that only F-actin unprotected by tropomyosin is the physiological TccC3 substrate. Yet, ADP-ribosylated G-actin can be produced upon cofilin-accelerated F-actin depolymerization, which was only mildly inhibited in partially modified actin. The affinity of TccC3-ADP-ribosylated G-actin for profilin and thymosin-β4 was weakened moderately but sufficiently to potentiate spontaneous polymerization in their presence. Interestingly, the Arp2/3-mediated nucleation was also potentiated by T148-ADP-ribosylation. Notably, even partially modified actin showed reduced bundling by plastins and α-actinin. In agreement with the role of these and other tandem calponin-homology domain actin organizers in the assembly of the cortical actin network, TccC3 induced intense membrane blebbing in cultured cells. Overall, our data suggest that TccC3 imposes a complex action on the cytoskeleton by affecting F-actin nucleation, recycling, and interaction with actin-binding proteins involved in the integration of actin filaments with each other and cellular elements.
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- 2022
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17. Microbial nanowires: type IV pili or cytochrome filaments?
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Fengbin Wang, Lisa Craig, Xing Liu, Christopher Rensing, and Edward H. Egelman
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Microbiology (medical) ,Infectious Diseases ,Virology ,Microbiology - Abstract
A dynamic field of study has emerged involving long-range electron transport by extracellular filaments in anaerobic bacteria, with Geobacter sulfurreducens being used as a model system. The interest in this topic stems from the potential uses of such systems in bioremediation, energy generation, and new bio-based nanotechnology for electronic devices. These conductive extracellular filaments were originally thought, based upon low-resolution observations of dried samples, to be type IV pili (T4P). However, the recently published atomic structure for the T4P from G. sulfurreducens, obtained by cryo-electron microscopy (cryo-EM), is incompatible with the numerous models that have been put forward for electron conduction. As with all high-resolution structures of T4P, the G. sulfurreducens T4P structure shows a partial melting of the α-helix that substantially impacts the aromatic residue positions such that they are incompatible with conductivity. Furthermore, new work using high-resolution cryo-EM shows that conductive filaments thought to be T4P are actually polymerized cytochromes, with stacked heme groups forming a continuous conductive wire, or extracellular DNA. Recent atomic structures of three different cytochrome filaments from G. sulfurreducens suggest that such polymers evolved independently on multiple occasions. The expectation is that such polymerized cytochromes may be found emanating from other anaerobic organisms.
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- 2023
18. Cryo-EM of Helical Polymers
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Fengbin Wang, Ordy Gnewou, Armin Solemanifar, Vincent P. Conticello, and Edward H. Egelman
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Macromolecular Substances ,Polymers ,Cryoelectron Microscopy ,Viruses ,General Chemistry - Abstract
While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.
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- 2023
19. Artificial Intracellular Filaments
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Zhaoqianqi Feng, Huaimin Wang, Fengbin Wang, Younghoon Oh, Cristina Berciu, Qiang Cui, Edward H. Egelman, and Bing Xu
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intracellular ,filaments ,peptides ,self-assembly ,cryo-EM ,enzyme ,Physics ,QC1-999 - Abstract
Summary: Intracellular protein filaments are ubiquitous for cellular functions, but forming bona fide biomimetic intracellular filaments of small molecules in living cells remains elusive. Here, we report the in situ formation of self-limiting intracellular filaments of a small peptide via enzymatic morphological transition of a phosphorylated and trimethylated heterochiral tetrapeptide. Enzymatic dephosphorylation reduces repulsive intermolecular electrostatic interactions and converts the peptidic nanoparticles into filaments, which exhibit distinct types of cross-β structures with either C7 or C2 symmetries, with the hydrophilic C-terminal residues at the periphery of the helix. Macromolecular crowding promotes the peptide filaments to form bundles, which extend from the plasma membrane to nuclear membrane and hardly interact with endogenous components, including cytoskeletons. Stereochemistry and post-translational modification (PTM) of peptides are critical for generating the intracellular bundles. This work may offer a way to gain lost functions or to provide molecular insights for understanding normal and aberrant intracellular filaments.
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- 2020
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20. Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile
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Ying Liu, Tomasz Osinski, Fengbin Wang, Mart Krupovic, Stefan Schouten, Peter Kasson, David Prangishvili, and Edward H. Egelman
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Science - Abstract
Only a few archaeal filamentous viruses have been structurally characterized. Here the authors describe the membrane-enveloped Sulfolobus filamentous virus 1 that infects Sulfolobus shibatae and present its 3.7 Å resolution cryo-EM structure, which reveals that major coat proteins are structurally conserved among archaeal filamentous viruses.
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- 2018
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21. Structural basis for high-affinity actin binding revealed by a β-III-spectrin SCA5 missense mutation
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Adam W. Avery, Michael E. Fealey, Fengbin Wang, Albina Orlova, Andrew R. Thompson, David D. Thomas, Thomas S. Hays, and Edward H. Egelman
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Science - Abstract
The disease causing L253P mutation in the actin-binding domain (ABD) of β-III-spectrin drastically increases actin-binding affinity. Here, the authors present the cryo-EM structure of F-actin complexed with the ABD mutant and double electron–electron resonance measurements show how the mutation affects the ABD conformational state.
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- 2017
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22. Enzyme Responsive Rigid-Rod Aromatics Target 'Undruggable' Phosphatases to Kill Cancer Cells in a Mimetic Bone Microenvironment
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Meihui Yi, Fengbin Wang, Weiyi Tan, Jer-Tsong Hsieh, Edward H. Egelman, and Bing Xu
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Male ,Colloid and Surface Chemistry ,Tumor Microenvironment ,Humans ,Prostatic Neoplasms ,General Chemistry ,Phosphorylation ,Alkaline Phosphatase ,Endoplasmic Reticulum ,Biochemistry ,Catalysis ,Phosphoric Monoester Hydrolases - Abstract
Bone metastasis remains a challenge in cancer treatment. Here we show enzymatic responsive rigid-rod aromatics acting as the substrates of "undruggable" phosphatases to kill cancer cells in a mimetic bone microenvironment. By phosphorylation and conjugating nitrobenzoxadiazole (NBD) to hydroxybiphenylcarboxylate (BP), we obtained pBP-NBD (
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- 2023
23. Cell spheroid creation by transcytotic intercellular gelation
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Jiaqi Guo, Fengbin Wang, Yimeng Huang, Hongjian He, Weiyi Tan, Meihui Yi, Edward H. Egelman, and Bing Xu
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Biomedical Engineering ,General Materials Science ,Bioengineering ,Electrical and Electronic Engineering ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics - Published
- 2023
24. Hierarchical assembly of intrinsically disordered short peptides
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Jiaqi Guo, Shane T. Rich-New, Chen Liu, Yimeng Huang, Weiyi Tan, Hongjian He, Meihui Yi, Xixiang Zhang, Edward H. Egelman, Fengbin Wang, and Bing Xu
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General Chemical Engineering ,Biochemistry (medical) ,Materials Chemistry ,Environmental Chemistry ,General Chemistry ,Biochemistry - Published
- 2023
25. A structural model of flagellar filament switching across multiple bacterial species
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Fengbin Wang, Andrew M. Burrage, Sandra Postel, Reece E. Clark, Albina Orlova, Eric J. Sundberg, Daniel B. Kearns, and Edward H. Egelman
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Science - Abstract
Bacterial flagellar filaments are composed almost entirely of a single protein—flagellin—which can switch between different supercoiled states in a highly cooperative manner. Here the authors present near-atomic resolution cryo-EM structures of nine flagellar filaments, and begin to shed light on the molecular basis of filament switching.
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- 2017
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26. DNA-guided lattice remodeling of carbon nanotubes
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Zhiwei Lin, Leticia C. Beltrán, Zeus A. De los Santos, Yinong Li, Tehseen Adel, Jeffrey A Fagan, Angela R. Hight Walker, Edward H. Egelman, and Ming Zheng
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Multidisciplinary - Abstract
Covalent modification of carbon nanotubes is a promising strategy for engineering their electronic structures. However, keeping modification sites in registration with a nanotube lattice is challenging. We report a solution using DNA-directed, guanine (G)-specific cross-linking chemistry. Through DNA screening we identify a sequence, C 3 GC 7 GC 3 , whose reaction with an (8,3) enantiomer yields minimum disorder-induced Raman mode intensities and photoluminescence Stokes shift, suggesting ordered defect array formation. Single-particle cryo–electron microscopy shows that the C 3 GC 7 GC 3 functionalized (8,3) has an ordered helical structure with a 6.5 angstroms periodicity. Reaction mechanism analysis suggests that the helical periodicity arises from an array of G-modified carbon-carbon bonds separated by a fixed distance along an armchair helical line. Our findings may be used to remodel nanotube lattices for novel electronic properties.
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- 2022
27. Models are useful until high-resolution structures are available
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Fengbin Wang, Lisa Craig, Xing Liu, Christopher Rensing, and Edward H. Egelman
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Microbiology (medical) ,Infectious Diseases ,Virology ,Microbiology - Published
- 2023
28. Structure of the Neisseria meningitidis Type IV pilus
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Subramania Kolappan, Mathieu Coureuil, Xiong Yu, Xavier Nassif, Edward H. Egelman, and Lisa Craig
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Science - Abstract
Type IV pili are present on a wide range of bacterial pathogens and mediate diverse functions. Here the authors report a high resolution crystal structure of the pilin subunit PilE, and a cryoEM reconstruction of the Type IV pilus filament from N. meningitidisthat offer insight into pilus assembly and functions.
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- 2016
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29. Mutate or die: Atomic structures explain bacterial SOS induction
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Edward H. Egelman
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Multidisciplinary - Published
- 2023
30. Archaeal bundling pili of
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Fengbin, Wang, Virginija, Cvirkaite-Krupovic, Mart, Krupovic, and Edward H, Egelman
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Archaeal Proteins ,Biofilms ,Fimbriae, Bacterial ,Cryoelectron Microscopy ,Pyrobaculum ,Protein Conformation, beta-Strand - Abstract
While biofilms formed by bacteria have received great attention due to their importance in pathogenesis, much less research has been focused on the biofilms formed by archaea. It has been known that extracellular filaments in archaea, such as type IV pili, hami, and cannulae, play a part in the formation of archaeal biofilms. We have used cryo-electron microscopy to determine the atomic structure of a previously uncharacterized class of archaeal surface filaments from hyperthermophilic
- Published
- 2022
31. Editor's evaluation: Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub
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Edward H Egelman
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- 2022
32. Editor's evaluation: A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0
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Edward H Egelman
- Published
- 2022
33. Functional role of the type 1 pilus rod structure in mediating host-pathogen interactions
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Caitlin N Spaulding, Henry Louis Schreiber IV, Weili Zheng, Karen W Dodson, Jennie E Hazen, Matt S Conover, Fengbin Wang, Pontus Svenmarker, Areli Luna-Rico, Olivera Francetic, Magnus Andersson, Scott Hultgren, and Edward H Egelman
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Chaperone-usher pathway pili ,CUP pili ,type 1 pili ,cryo-EM ,UPEC ,UTI ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Uropathogenic E. coli (UPEC), which cause urinary tract infections (UTI), utilize type 1 pili, a chaperone usher pathway (CUP) pilus, to cause UTI and colonize the gut. The pilus rod, comprised of repeating FimA subunits, provides a structural scaffold for displaying the tip adhesin, FimH. We solved the 4.2 Å resolution structure of the type 1 pilus rod using cryo-electron microscopy. Residues forming the interactive surfaces that determine the mechanical properties of the rod were maintained by selection based on a global alignment of fimA sequences. We identified mutations that did not alter pilus production in vitro but reduced the force required to unwind the rod. UPEC expressing these mutant pili were significantly attenuated in bladder infection and intestinal colonization in mice. This study elucidates an unappreciated functional role for the molecular spring-like property of type 1 pilus rods in host-pathogen interactions and carries important implications for other pilus-mediated diseases.
- Published
- 2018
- Full Text
- View/download PDF
34. Author response: Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times
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Fengbin Wang, Chi Ho Chan, Victor Suciu, Khawla Mustafa, Madeline Ammend, Dong Si, Allon I Hochbaum, Edward H Egelman, and Daniel R Bond
- Published
- 2022
35. Convergent evolution in the supercoiling of prokaryotic flagellar filaments
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Mark A.B. Kreutzberger, Ravi R. Sonani, Junfeng Liu, Sharanya Chatterjee, Fengbin Wang, Amanda L. Sebastian, Priyanka Biswas, Cheryl Ewing, Weili Zheng, Frédéric Poly, Gad Frankel, B.F. Luisi, Chris R. Calladine, Mart Krupovic, Birgit E. Scharf, Edward H. Egelman, Luisi, Ben [0000-0003-1144-9877], and Apollo - University of Cambridge Repository
- Subjects
Protein Subunits ,motility ,Bacteria ,helical symmetry ,Flagella ,Fimbriae, Bacterial ,Cryoelectron Microscopy ,cryo-EM ,Keywords ,Archaea ,General Biochemistry, Genetics and Molecular Biology ,Flagellin - Abstract
The supercoiling of bacterial and archaeal flagellar filaments is required for motility. Archaeal flagellar filaments have no homology to their bacterial counterparts and are instead homologs of bacterial type IV pili. How these prokaryotic flagellar filaments, each composed of thousands of copies of identical subunits, can form stable supercoils under torsional stress is a fascinating puzzle for which structural insights have been elusive. Advances in cryoelectron microscopy (cryo-EM) make it now possible to directly visualize the basis for supercoiling, and here, we show the atomic structures of supercoiled bacterial and archaeal flagellar filaments. For the bacterial flagellar filament, we identify 11 distinct protofilament conformations with three broad classes of inter-protomer interface. For the archaeal flagellar filament, 10 protofilaments form a supercoil geometry supported by 10 distinct conformations, with one inter-protomer discontinuity creating a seam inside of the curve. Our results suggest that convergent evolution has yielded stable superhelical geometries that enable microbial locomotion.
- Published
- 2022
- Full Text
- View/download PDF
36. Model for a novel membrane envelope in a filamentous hyperthermophilic virus
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Peter Kasson, Frank DiMaio, Xiong Yu, Soizick Lucas-Staat, Mart Krupovic, Stefan Schouten, David Prangishvili, and Edward H Egelman
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archaea ,cryo-electron microscopy ,membranes ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Biological membranes create compartments, and are usually formed by lipid bilayers. However, in hyperthermophilic archaea that live optimally at temperatures above 80°C the membranes are monolayers which resemble fused bilayers. Many double-stranded DNA viruses which parasitize such hosts, including the filamentous virus AFV1 of Acidianus hospitalis, are enveloped with a lipid-containing membrane. Using cryo-EM, we show that the membrane in AFV1 is a ~2 nm-thick monolayer, approximately half the expected membrane thickness, formed by host membrane-derived lipids which adopt a U-shaped ‘horseshoe’ conformation. We hypothesize that this unusual viral envelope structure results from the extreme curvature of the viral capsid, as ‘horseshoe’ lipid conformations favor such curvature and host membrane lipids that permit horseshoe conformations are selectively recruited into the viral envelope. The unusual envelope found in AFV1 also has many implications for biotechnology, since this membrane can survive the most aggressive conditions involving extremes of temperature and pH.
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- 2017
- Full Text
- View/download PDF
37. Editor's evaluation: Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for label-free detection of molecules across entire cell sections
- Author
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Edward H Egelman
- Published
- 2022
38. Structure of
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Fengbin, Wang, Chi Ho, Chan, Victor, Suciu, Khawla, Mustafa, Madeline, Ammend, Dong, Si, Allon I, Hochbaum, Edward H, Egelman, and Daniel R, Bond
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Electron Transport ,Bacterial Proteins ,Polymers ,Cryoelectron Microscopy ,Cytochromes ,Heme ,Geobacter ,Oxidation-Reduction - Abstract
While early genetic and low-resolution structural observations suggested that extracellular conductive filaments on metal-reducing organisms such as
- Published
- 2022
39. DeepTracer ID: De Novo Protein Identification from Cryo-EM Maps
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Luca Chang, Fengbin Wang, Kiernan Connolly, Hanze Meng, Zhangli Su, Virginija Cvirkaite-Krupovic, Mart Krupovic, Edward H. Egelman, Dong Si, University of Washington-Bothell, University of Virginia, University of Washington [Seattle], University of Alabama at Birmingham [ Birmingham] (UAB), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), The cryo-EM imaging was done at the Molecular Electron Microscopy Core Facility at the University of Virginia, which is supported by the School of Medicine and built with NIH grant G20-RR31199. This work was supported by NIH grant GM122510 (E.H.E.), K99GM138756 (F.W.), K99CA259526 (Z.S.), NSF grant 2030381 (D.S.), the SRCP Seed Grant at the University of Washington Bothell (D.S.), and l’Agence Nationale de la Recherche grant ANR-21-CE11-0001-01 (M.K.)., and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
- Subjects
Models, Molecular ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Protein Conformation ,Cryoelectron Microscopy ,Biophysics ,Proteins ,Software - Abstract
The recent revolution in cryo-electron microscopy has made it possible to determine macromolecular structures directly from cell extracts. However, identifying the correct protein from the cryo-EM map is still challenging and often needs additional sequence information from other techniques, such as tandem mass spectrometry and/or bioinformatics. Here, we present DeepTracer-ID, a server-based approach to identify the candidate protein in a user-provided organism de novo from a cryo-EM map, without the need for additional information. Our method first uses DeepTracer to generate a protein backbone model that best represents the cryo-EM map, and this model is then searched against the library of AlphaFold2 predictions for all proteins in the given organism. This method is highly accurate and robust: in all 13 experimental maps tested blindly, DeepTracer-ID identified the correct proteins as the top candidates. Eight of the maps were of known structures, while the other five unpublished maps were validated by prior protein annotation and careful inspection of the model refined into the map. The program also showed promising results for both homomeric and heteromeric protein complexes. This platform is possible because of the recent breakthroughs in large-scale protein 3D structure prediction.Statement of SignificanceWhile it has now become routine for cryo-EM maps of proteins to reach a near-atomic resolution, potentially allowing for reliable atomic models to be built, there are a growing number of instances where the protein identity may not be known. Without knowing the protein sequence, it is impossible to build an atomic model. DeepTracer-ID is a server-based approach to surmount this problem by identifying the proteins in a given organism that are found in the cryo-EM map. A free web service for global academic access is provided.
- Published
- 2022
40. Editor's evaluation: Filamentation modulates allosteric regulation of PRPS
- Author
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Edward H Egelman
- Published
- 2022
41. Phenol-soluble modulins PSMα3 and PSMβ2 form nanotubes that are cross-α amyloids
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Mark A. B. Kreutzberger, Shengyuan Wang, Leticia C. Beltran, Abraham Tuachi, Xiaobing Zuo, Edward H. Egelman, and Vincent P. Conticello
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Amyloid ,Staphylococcus aureus ,Nanotubes ,Multidisciplinary ,Bacterial Toxins ,Cryoelectron Microscopy ,Humans ,Peptides - Abstract
Phenol-soluble modulins (PSMs) are peptide-based virulence factors that play significant roles in the pathogenesis of staphylococcal strains in community-associated and hospital-associated infections. In addition to cytotoxicity, PSMs display the propensity to self-assemble into fibrillar species, which may be mediated through the formation of amphipathic conformations. Here, we analyze the self-assembly behavior of two PSMs, PSMα3 and PSMβ2, which are derived from peptides expressed by methicillin-resistant Staphylococcus aureus (MRSA), a significant human pathogen. In both cases, we observed the formation of a mixture of self-assembled species including twisted filaments, helical ribbons, and nanotubes, which can reversibly interconvert in vitro. Cryo–electron microscopy structural analysis of three PSM nanotubes, two derived from PSMα3 and one from PSMβ2, revealed that the assemblies displayed remarkably similar structures based on lateral association of cross-α amyloid protofilaments. The amphipathic helical conformations of PSMα3 and PSMβ2 enforced a bilayer arrangement within the protofilaments that defined the structures of the respective PSMα3 and PSMβ2 nanotubes. We demonstrate that, similar to amyloids based on cross-β protofilaments, cross-α amyloids derived from these PSMs display polymorphism, not only in terms of the global morphology (e.g., twisted filament, helical ribbon, and nanotube) but also with respect to the number of protofilaments within a given peptide assembly. These results suggest that the folding landscape of PSM derivatives may be more complex than originally anticipated and that the assemblies are able to sample a wide range of supramolecular structural space.
- Published
- 2022
42. Domesticated conjugation machinery promotes DNA exchange in hyperthermophilic archaea
- Author
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Leticia Beltran, Virginija Cvirkaite-Krupovic, Jessalyn Roberts, Fengbin Wang, Mark A. Kreutzberger, Tiago Costa, Ilya Levental, Vincent Conticello, Edward H. Egelman, and Mart Krupovic
- Subjects
Biophysics - Published
- 2023
43. How SipA, a toxin from Salmonella, increases stability of F-actin
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Ewa Niedzialkowska, Lucas Runyan, Dmitri S. Kudryashov, and Edward H. Egelman
- Subjects
Biophysics - Published
- 2023
44. Microbial nanowires: Cytochrome filaments in Geobacter and more
- Author
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Diana Baquero, Virginija Cvirkaite-Krupovic, Khawla Mustafa, Chiho Chan, Allon Hochbaum, Daniel Bond, Edward H. Egelman, Mart Krupovic, and Fengbin Wang
- Subjects
Biophysics - Published
- 2023
45. Stimuli responsive hierarchical assembly of supramolecular conductive fibers from coiled-coil building blocks
- Author
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Adam Grosvirt-Dramen, Zachary Urbach, Fengbin Wang, Yuanming Song, Douglas J. Tobias, Edward H. Egelman, and Allon Hochbaum
- Subjects
Biophysics - Published
- 2023
46. Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome
- Author
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Fengbin Wang, Virginija Cvirkaite-Krupovic, Matthijn Vos, Leticia C. Beltran, Mark A.B. Kreutzberger, Jean-Marie Winter, Zhangli Su, Jun Liu, Stefan Schouten, Mart Krupovic, Edward H. Egelman, University of Virginia, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Yale University [New Haven], Royal Netherlands Institute for Sea Research (NIOZ), This work was supported by NIH grant GM122510 (E.H.E.) and K99GM138756 (F.W.). The work in the M.K. laboratory was supported by grants from l’Agence Nationale de la Recherche (ANR-17-CE15-0005-01, ANR-20-CE20-009-02, and ANR-21-CE11-0001-01) and Ville de Paris (Emergence(s) project MEMREMA). We are grateful to Youssef Ghorbal for the help with data transfer, to Caglar Yildiz for support in the lipid analysis, and to the Ultrastructural BioImaging unit of Institut Pasteur for access to electron microscopes., We are grateful to Dr. Xu Peng (University of Copenhagen) for the kind gift of SMV1 and its host, Saccharolobus islandicus ΔC1C2. Part of the cryo-EM imaging of SMV1 was done at the Molecular Electron Microscopy Core Facility at the University of Virginia, which is supported by the School of Medicine. Part of the Cryo-EM and the cryo-ET imaging were done at the Nano-Imaging Core Facility at Institut Pasteur, created with the help of a grant from the French Government’s Investissements d’avenir program (EQUIPEX CACSICE - Centre d’analyse de systèmes complexes dans les environnements complexes, ANR-11-EQPX-0008)., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), ANR-11-EQPX-0008,CACSICE,Centre d'analyse de systèmes complexes dans les environnements complexes(2011), and ANR-21-CE11-0001,ArcFus,Protéines de classe II de fusion membranaire chez les archées(2021)
- Subjects
Archaeal Viruses ,helical polymers ,viruses ,Virion ,Genome, Viral ,Article ,General Biochemistry, Genetics and Molecular Biology ,capsids ,extremeophiles ,viral evolution ,Capsid ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,cryo-EM ,Capsid Proteins - Abstract
International audience; Spindle- or lemon-shaped viruses infect archaea in diverse environments. Due to the highly pleomorphic nature of these virions, which can be found with cylindrical tails emanating from the spindle-shaped body, structural studies of these capsids have been challenging. We have determined the atomic structure of the capsid of Sulfolobus monocaudavirus 1, a virus that infects hosts living in nearly boiling acid. A highly hydrophobic protein, likely integrated into the host membrane before the virions assemble, forms 7 strands that slide past each other in both the tails and the spindle body. We observe the discrete steps that occur as the tail tubes expand, and these are due to highly conserved quasiequivalent interactions with neighboring subunits maintained despite significant diameter changes. Our results show how helical assemblies can vary their diameters, becoming nearly spherical to package a larger genome and suggest how all spindle-shaped viruses have evolved from archaeal rod-like viruses.
- Published
- 2022
47. Decision letter: Assembly of recombinant tau into filaments identical to those of Alzheimer’s disease and chronic traumatic encephalopathy
- Author
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Edward H Egelman, Fengbin Wang, and Louise C Serpell
- Published
- 2022
48. Editor's evaluation: Assembly of recombinant tau into filaments identical to those of Alzheimer’s disease and chronic traumatic encephalopathy
- Author
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Edward H Egelman
- Published
- 2022
49. Bacterial flagellar capping proteins adopt diverse oligomeric states
- Author
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Sandra Postel, Daniel Deredge, Daniel A Bonsor, Xiong Yu, Kay Diederichs, Saskia Helmsing, Aviv Vromen, Assaf Friedler, Michael Hust, Edward H Egelman, Dorothy Beckett, Patrick L Wintrode, and Eric J Sundberg
- Subjects
Pseudomonas ,flagella ,X-ray crystallography ,hydrogen-deuterium exchange ,analytical ultracentrifugation ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Flagella are crucial for bacterial motility and pathogenesis. The flagellar capping protein (FliD) regulates filament assembly by chaperoning and sorting flagellin (FliC) proteins after they traverse the hollow filament and exit the growing flagellum tip. In the absence of FliD, flagella are not formed, resulting in impaired motility and infectivity. Here, we report the 2.2 Å resolution X-ray crystal structure of FliD from Pseudomonas aeruginosa, the first high-resolution structure of any FliD protein from any bacterium. Using this evidence in combination with a multitude of biophysical and functional analyses, we find that Pseudomonas FliD exhibits unexpected structural similarity to other flagellar proteins at the domain level, adopts a unique hexameric oligomeric state, and depends on flexible determinants for oligomerization. Considering that the flagellin filaments on which FliD oligomers are affixed vary in protofilament number between bacteria, our results suggest that FliD oligomer stoichiometries vary across bacteria to complement their filament assemblies.
- Published
- 2016
- Full Text
- View/download PDF
50. Atomic structure of the Campylobacter jejuni flagellar filament reveals how ε Proteobacteria escaped Toll-like receptor 5 surveillance
- Author
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Fengbin Wang, Frédéric Poly, Edward H. Egelman, Cheryl P. Ewing, and Mark A. B. Kreutzberger
- Subjects
Toll-like receptor ,Multidisciplinary ,Glycosylation ,biology ,Chemistry ,Protein subunit ,Flagellum ,biology.organism_classification ,Campylobacter jejuni ,Epitope ,Cell biology ,chemistry.chemical_compound ,TLR5 ,biology.protein ,Flagellin - Abstract
Vertebrates, from zebra fish to humans, have an innate immune recognition of many bacterial flagellins. This involves a conserved eight-amino acid epitope in flagellin recognized by the Toll-like receptor 5 (TLR5). Several important human pathogens, such as Helicobacter pylori and Campylobacter jejuni, have escaped TLR5 activation by mutations in this epitope. When such mutations were introduced into Salmonella flagellin, motility was abolished. It was previously argued, using very low-resolution cryoelectron microscopy (cryo-EM), that C. jejuni accommodated these mutations by forming filaments with 7 protofilaments, rather than the 11 found in other bacteria. We have now determined the atomic structure of the C. jejuni G508A flagellar filament from a 3.5-A-resolution cryo-EM reconstruction, and show that it has 11 protofilaments. The residues in the C. jejuni TLR5 epitope have reduced contacts with the adjacent subunit compared to other bacterial flagellar filament structures. The weakening of the subunit-subunit interface introduced by the mutations in the TLR5 epitope is compensated for by extensive interactions between the outer domains of the flagellin subunits. In other bacteria, these outer domains can be nearly absent or removed without affecting motility. Furthermore, we provide evidence for the stabilization of these outer domain interactions through glycosylation of key residues. These results explain the essential role of glycosylation in C. jejuni motility, and show how the outer domains have evolved to play a role not previously found in other bacteria.
- Published
- 2020
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