scholarly journals A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 Å resolution

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Xing Zhang ◽  
Huatao Guo ◽  
Lei Jin ◽  
Elizabeth Czornyj ◽  
Asher Hodes ◽  
...  
Keyword(s):  
Phage Display ◽  
Electrostatic Interactions ◽  
Whooping Cough ◽  
Atomic Structures ◽  
Complex Interactions ◽  
Cryo Electron Microscopy ◽  
Naturally Occurring ◽  
Feasible Alternative ◽  
Β Sheet ◽  
Cement Protein

Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like (‘Johnson’) for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. β-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering.

scholarly journals An Iterative Bézier Method for Fitting Beta-sheet Component of a Cryo-EM Density Map

2017 ◽  
Vol 5 (1) ◽  
pp. 31-39 ◽  
Author(s):  
Michael Poteat ◽  
Jing He
Keyword(s):  
Shape Representation ◽  
Molecular Complexes ◽  
Geometrical Shape ◽  
3 Dimensional ◽  
Atomic Structures ◽  
Cryo Electron Microscopy ◽  
Density Maps ◽  
Medium Resolution ◽  
Density Map ◽  
Β Sheet

AbstractCryo-electron microscopy (Cryo-EM) is a powerful technique to produce 3-dimensional density maps for large molecular complexes. Although many atomic structures have been solved from cryo-EM density maps, it is challenging to derive atomic structures when the resolution of density maps is not sufficiently high. Geometrical shape representation of secondary structural components in a medium-resolution density map enhances modeling of atomic structures.We compare two methods in producing surface representation of the β-sheet component of a density map. Given a 3-dimensional volume of β-sheet that is segmented from a density map, the performance of a polynomial fitting was compared with that of an iterative Bézier fitting. The results suggest that the iterative Bézier fitting is more suitable for β-sheets, since it provides more accurate representation of the corners that are naturally twisted in a β-sheet.

Cryo-EM Is a Powerful Tool, But Helical Applications Can Have Pitfalls

Soft Matter ◽  
2021 ◽  
Author(s):  
Edward Egelman ◽  
Fengbin Wang
Keyword(s):  
Electron Microscopy ◽  
Structural Biology ◽  
Macromolecular Complexes ◽  
Atomic Structures ◽  
Cryo Electron Microscopy ◽  
Main Technique

In structural biology, cryo-electron microscopy (cryo-EM) has emerged as the main technique for determining the atomic structures of macromolecular complexes. This has largely been due to the introduction of direct...

scholarly journals Isolation of Disease-relevant p53 for Cryo-Electron Microscopy Analysis

2021 ◽  
Author(s):  
Maria J. Solares ◽  
GM Jonaid ◽  
William Y. Luqiu ◽  
Yanping Liang ◽  
Madison C. Evans ◽  
...  
Keyword(s):  
P53 Protein ◽  
P53 Gene ◽  
Tp53 Gene ◽  
Tumor Suppressor Protein ◽  
Protein Assemblies ◽  
Cryo Electron Microscopy ◽  
Naturally Occurring ◽  
Imaging Protocols ◽  
Electron Microscopy Analysis ◽  
Microscopy Analysis

Abstract Tumor suppressor protein TP53 (p53) plays a multi-faceted role in all cells of thehuman body. Sadly, mutations in the TP53 gene are involved in nearly ~50% of tumors,spurring erratic cell growth and disease progression. Until recently, structural informationfor p53 remained incomplete and there are limited studies on native p53 produced inhuman tumors. Here, we present a highly reproducible and effective protocol to extract,enrich, and purify native p53 protein assemblies from cancer cells for downstreamstructural studies. This method does not introduce purification tags into the p53 gene andmaintains naturally occurring modifications. In conjunction with cryo-Electron Microscopytechniques, we determined new structures for p53 monomers (~50 kDa) and tetramers(~200 kDa) at spatial resolutions of ~4.8 Å and ~7 Å, respectively.1 These modelsrevealed new insights for flexible regions of p53 along with biologically-relevantubiquitination sites. Combining biochemical and structural imaging protocols, we aim tobuild a better understanding of native p53’s impact in cancer formation.

scholarly journals Atomic structures of the RNA end-healing 5′-OH kinase and 2′,3′-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor

2019 ◽  
Author(s):  
Ankan Banerjee ◽  
Yehuda Goldgur ◽  
Beate Schwer ◽  
Stewart Shuman
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Fungal Pathogens ◽  
Pathogenic Fungus ◽  
Atomic Structures ◽  
Polynucleotide Kinase ◽  
Phosphate Donor ◽  
Guanine Base ◽  
Conformational Switches ◽  
Β Sheet

Abstract Fungal tRNA ligase (Trl1) rectifies RNA breaks with 2′,3′-cyclic-PO4 and 5′-OH termini. Trl1 consists of three catalytic modules: an N-terminal ligase (LIG) domain; a central polynucleotide kinase (KIN) domain; and a C-terminal cyclic phosphodiesterase (CPD) domain. Trl1 enzymes found in all human fungal pathogens are untapped targets for antifungal drug discovery. Here we report a 1.9 Å crystal structure of Trl1 KIN-CPD from the pathogenic fungus Candida albicans, which adopts an extended conformation in which separate KIN and CPD domains are connected by an unstructured linker. CPD belongs to the 2H phosphotransferase superfamily by dint of its conserved central concave β sheet and interactions of its dual HxT motif histidines and threonines with phosphate in the active site. Additional active site motifs conserved among the fungal CPD clade of 2H enzymes are identified. We present structures of the Candida Trl1 KIN domain at 1.5 to 2.0 Å resolution—as apoenzyme and in complexes with GTP•Mg2+, IDP•PO4, and dGDP•PO4—that highlight conformational switches in the G-loop (which recognizes the guanine base) and lid-loop (poised over the nucleotide phosphates) that accompany nucleotide binding.

Heuristic theory in corpus compilation

2016 ◽  
Vol 5 (2) ◽  
Author(s):  
John Patkin
Keyword(s):  
Prior Experience ◽  
Trial And Error ◽  
Geographical Differences ◽  
Complex Interactions ◽  
Naturally Occurring ◽  
Software And Hardware

AbstractBuilding the Asian Corpus of English (ACE, 2014) involved complex interactions between researchers, participants, transcription conventions, software and hardware. The gathering and transcribing of naturally occurring conversations of English among Asian multilinguals was undertaken by a team of more than twenty researchers in nine locations across Asia. Modelled on the Vienna Oxford Corpus of English (VOICE), ACE faced unique challenges due to linguistic, cultural and geographical differences. These problems were solved through procedures and tools known as heuristics which were built on prior experience and also trial and error. The process of developing and categorising these skills are presented with experiences shared by ACE researchers and the author along with examples from the corpus.

scholarly journals Structural characterization of toxic oligomers that are kinetically trapped during α-synuclein fibril formation

2015 ◽  
Vol 112 (16) ◽  
pp. E1994-E2003 ◽  
Author(s):  
Serene W. Chen ◽  
Srdja Drakulic ◽  
Emma Deas ◽  
Myriam Ouberai ◽  
Francesco A. Aprile ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Self Assembly ◽  
Protein Misfolding ◽  
Amyloid Fibril ◽  
Amyloid Formation ◽  
Image Reconstruction Techniques ◽  
Cryo Electron Microscopy ◽  
Amyloid Oligomers ◽  
Β Sheet

We describe the isolation and detailed structural characterization of stable toxic oligomers of α-synuclein that have accumulated during the process of amyloid formation. Our approach has allowed us to identify distinct subgroups of oligomers and to probe their molecular architectures by using cryo-electron microscopy (cryoEM) image reconstruction techniques. Although the oligomers exist in a range of sizes, with different extents and nature of β-sheet content and exposed hydrophobicity, they all possess a hollow cylindrical architecture with similarities to certain types of amyloid fibril, suggesting that the accumulation of at least some forms of amyloid oligomers is likely to be a consequence of very slow rates of rearrangement of their β-sheet structures. Our findings reveal the inherent multiplicity of the process of protein misfolding and the key role the β-sheet geometry acquired in the early stages of the self-assembly process plays in dictating the kinetic stability and the pathological nature of individual oligomeric species.

scholarly journals Inhibition of the Self-Assembly of Aβ and of Tau by Polyphenols: Mechanistic Studies

Molecules ◽  
2019 ◽  
Vol 24 (12) ◽  
pp. 2316 ◽  
Author(s):  
Qiuchen Zheng ◽  
Micheal T. Kebede ◽  
Merc M. Kemeh ◽  
Saadman Islam ◽  
Bethany Lee ◽  
...  
Keyword(s):  
Self Assembly ◽  
Complex Disease ◽  
Red Wine ◽  
Amyloid Β ◽  
Amyloid Plaques ◽  
Therapeutic Agents ◽  
Mechanistic Studies ◽  
Naturally Occurring ◽  
Aβ Oligomerization ◽  
Β Sheet

The amyloid-β (Aβ) peptide and tau protein are thought to play key neuropathogenic roles in Alzheimer’s disease (AD). Both Aβ and tau self-assemble to form the two major pathological hallmarks of AD: amyloid plaques and neurofibrillary tangles, respectively. In this review, we show that naturally occurring polyphenols abundant in fruits, vegetables, red wine, and tea possess the ability to target pathways associated with the formation of assemblies of Aβ and tau. Polyphenols modulate the enzymatic processing of the amyloid-β precursor protein and inhibit toxic Aβ oligomerization by enhancing the clearance of Aβ42 monomer, modulating monomer–monomer interactions and remodeling oligomers to non-toxic forms. Additionally, polyphenols modulate tau hyperphosphorylation and inhibit tau β-sheet formation. The anti-Aβ-self-assembly and anti-tau-self-assembly effects of polyphenols increase their potential as preventive or therapeutic agents against AD, a complex disease that involves many pathological mechanisms.

Quantifying β-Sheet Stability by Phage Display

2002 ◽  
Vol 322 (1) ◽  
pp. 179-188 ◽  
Author(s):  
Mark D Distefano ◽  
Alan Zhong ◽  
Andrea G Cochran
Keyword(s):  
Phage Display ◽  
Β Sheet

scholarly journals Elucidation of AMPA receptor–stargazin complexes by cryo–electron microscopy

Science ◽  
2016 ◽  
Vol 353 (6294) ◽  
pp. 83-86 ◽  
Author(s):  
Edward C. Twomey ◽  
Maria V. Yelshanskaya ◽  
Robert A. Grassucci ◽  
Joachim Frank ◽  
Alexander I. Sobolevsky
Keyword(s):  
Electron Microscopy ◽  
Cognitive Processes ◽  
Electrostatic Interactions ◽  
Structural Basis ◽  
Cryo Electron Microscopy ◽  
Activated State ◽  
Ampar Trafficking ◽  
Excitatory Neurotransmission ◽  
Binding Interfaces ◽  
The Brain

AMPA-subtype ionotropic glutamate receptors (AMPARs) mediate fast excitatory neurotransmission and contribute to high cognitive processes such as learning and memory. In the brain, AMPAR trafficking, gating, and pharmacology is tightly controlled by transmembrane AMPAR regulatory proteins (TARPs). Here, we used cryo–electron microscopy to elucidate the structural basis of AMPAR regulation by one of these auxiliary proteins, TARP γ2, or stargazin (STZ). Our structures illuminate the variable interaction stoichiometry of the AMPAR-TARP complex, with one or two TARP molecules binding one tetrameric AMPAR. Analysis of the AMPAR-STZ binding interfaces suggests that electrostatic interactions between the extracellular domains of AMPAR and STZ play an important role in modulating AMPAR function through contact surfaces that are conserved across AMPARs and TARPs. We propose a model explaining how TARPs stabilize the activated state of AMPARs and how the interactions between AMPARs and their auxiliary proteins control fast excitatory synaptic transmission.

scholarly journals Antibody-Based Affinity Cryo-Electron Microscopy at 2.6 Å Resolution

2016 ◽  
Author(s):  
Guimei Yu ◽  
Kunpeng Li ◽  
Pengwei Huang ◽  
Xi Jiang ◽  
Wen Jiang
Keyword(s):  
Electron Microscopy ◽  
Sample Preparation ◽  
High Concentration ◽  
Low Concentration ◽  
Atomic Structures ◽  
Cryo Electron Microscopy ◽  
Grid Approach ◽  
Reconstruction Quality ◽  
Tulane Virus ◽  
Quantitative Analyses

AbstractThe affinity cryo-electron microscopy (cryo-EM) approach has been explored in recent years to simplify and improve the sample preparation for cryo-EM. Despite the demonstrated successes for low-concentration and unpurified specimens, the lack of near-atomic structures using this approach has led to a common perception of affinity cryo-EM as a niche technique incapable of reaching high resolutions. Here, we report a ~2.6 Å structure solved using the antibody-based affinity grid approach with a Tulane virus sample of low concentration. This is the first near-atomic structure solved using the affinity cryo-EM approach. Quantitative analyses of the structure indicate data and reconstruction quality comparable to conventional grid preparation method using samples at high concentration. With the shifting of bottlenecks of cryo-EM structural studies to sample grid preparation, our demonstration of the sub-3 Å capability of affinity cryo-EM approach indicates its potential in revolutionizing cryo-EM sample preparation for a broader spectrum of specimens.

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