scholarly journals Mechanisms of strain diversity of disease-associated in-register parallel β-sheet amyloids and implications about prion strains

2018 ◽  
Author(s):  
Yuzuru Taguchi ◽  
Hiroki Otaki ◽  
Noriyuki Nishida
Keyword(s):  
Electron Microscopy ◽  
The Other ◽  
Resonance Spectroscopy ◽  
Post Translational Modifications ◽  
Local Structures ◽  
Strain Diversity ◽  
Cryo Electron Microscopy ◽  
Prion Strains ◽  
Dynamics Simulations ◽  
Β Sheet

AbstractThe mechanism of strain diversity of prions still remains unsolved, because the investigation of inheritance and diversification of the protein-based pathogenic information demands identification of the detailed structures of abnormal isoform of prion protein (PrPSc), while it is difficult to purify for analysis without affecting the infectious nature. On the other hand, the similar prion-like properties are recognized also in other disease-associated in-register parallel β-sheet amyloids including Tau and α-synuclein (αSyn) amyloids. Investigations into structures of those amyloids by solid-state nuclear magnetic resonance spectroscopy and cryo-electron microscopy recently made remarkable advances, because of their relatively small sizes and lack of post-translational modifications. We review the advances on those pathogenic amyloids, particularly Tau and αSyn, and discuss their implications about strain diversity mechanisms of prion/PrPSc from the viewpoint that PrPSc is an in-register parallel β-sheet amyloid. We also present our recent data of molecular dynamics simulations of αSyn amyloid, which suggest significance of compatibility between β-sheet propensities of the substrate and local structures of the template for stability of the amyloid structures. Detailed structures of the αSyn and Tau amyloids are good surrogate models of pathogenic amyloids including PrPSc to elucidate not only the strain diversity but also their pathogenic mechanisms.

scholarly journals Mechanisms of Strain Diversity of Disease-Associated in-Register Parallel β-Sheet Amyloids and Implications About Prion Strains

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 110 ◽  
Author(s):  
Yuzuru Taguchi ◽  
Hiroki Otaki ◽  
Noriyuki Nishida
Keyword(s):  
Electron Microscopy ◽  
Resonance Spectroscopy ◽  
Post Translational Modifications ◽  
Prion Strain ◽  
Local Structures ◽  
Strain Diversity ◽  
Cryo Electron Microscopy ◽  
Prion Strains ◽  
Dynamics Simulations ◽  
Β Sheet

The mechanism of prion strain diversity remains unsolved. Investigation of inheritance and diversification of protein-based pathogenic information demands the identification of the detailed structures of abnormal isoforms of the prion protein (PrPSc); however, achieving purification is difficult without affecting infectivity. Similar prion-like properties are recognized also in other disease-associated in-register parallel β-sheet amyloids including Tau and α-synuclein (αSyn) amyloids. Investigations into structures of those amyloids via solid-state nuclear magnetic resonance spectroscopy and cryo-electron microscopy recently made remarkable advances due to their relatively small sizes and lack of post-translational modifications. Herein, we review advances regarding pathogenic amyloids, particularly Tau and αSyn, and discuss implications about strain diversity mechanisms of prion/PrPSc from the perspective that PrPSc is an in-register parallel β-sheet amyloid. Additionally, we present our recent data of molecular dynamics simulations of αSyn amyloid, which suggest significance of compatibility between β-sheet propensities of the substrate and local structures of the template for stability of amyloid structures. Detailed structures of αSyn and Tau amyloids are excellent models of pathogenic amyloids, including PrPSc, to elucidate strain diversity and pathogenic mechanisms.

Structure of anchorless RML prion reveals motif variation between strains

2021 ◽  
Author(s):  
Forrest Hoyt ◽  
Heidi G. Standke ◽  
Efrosini Artikis ◽  
Cindi L. Schwartz ◽  
Bryan Hansen ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Structural Basis ◽  
Structural Motifs ◽  
Prion Strain ◽  
Cryo Electron Microscopy ◽  
Prion Strains ◽  
Scrapie Strain ◽  
Strain Determination ◽  
Β Sheet

Little is known about the structural basis of prion strains. Here we provide a high (3.0 Å) resolution cryo-electron microscopy-based structure of brain-derived fibrils of the mouse anchorless RML scrapie strain which, like the recently determined hamster 263K strain, has a parallel in-register β-sheet-based core. However, detailed comparisons reveal that variations in shared structural motifs provide a basis for prion strain determination.

scholarly journals Cryo–electron microscopy structure of the antidiuretic hormone arginine-vasopressin V2 receptor signaling complex

2021 ◽  
Vol 7 (21) ◽  
pp. eabg5628
Author(s):  
Julien Bous ◽  
Hélène Orcel ◽  
Nicolas Floquet ◽  
Cédric Leyrat ◽  
Joséphine Lai-Kee-Him ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Antidiuretic Hormone ◽  
Arginine Vasopressin ◽  
Molecular Mechanisms ◽  
Particle Analysis ◽  
Resonance Spectroscopy ◽  
Gpcr Signaling ◽  
Signaling Complex ◽  
Cryo Electron Microscopy ◽  
V2 Receptor

The antidiuretic hormone arginine-vasopressin (AVP) forms a signaling complex with the V2 receptor (V2R) and the Gs protein, promoting kidney water reabsorption. Molecular mechanisms underlying activation of this critical G protein–coupled receptor (GPCR) signaling system are still unknown. To fill this gap of knowledge, we report here the cryo–electron microscopy structure of the AVP-V2R-Gs complex. Single-particle analysis revealed the presence of three different states. The two best maps were combined with computational and nuclear magnetic resonance spectroscopy constraints to reconstruct two structures of the ternary complex. These structures differ in AVP and Gs binding modes. They reveal an original receptor-Gs interface in which the Gαs subunit penetrates deep into the active V2R. The structures help to explain how V2R R137H or R137L/C variants can lead to two severe genetic diseases. Our study provides important structural insights into the function of this clinically relevant GPCR signaling complex.

scholarly journals A strategy to study intrinsically mixed folded proteins: The structure in solution of ataxin-3

2018 ◽  
Author(s):  
A. Sicorello ◽  
G. Kelly ◽  
A. Oregioni ◽  
J. Nováček ◽  
V. Sklenář ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Nuclear Magnetic Resonance ◽  
Low Complexity ◽  
Structural Features ◽  
Resonance Spectroscopy ◽  
Cryo Electron Microscopy ◽  
Per Se ◽  
Folded Proteins ◽  
First Time ◽  
Structure In Solution

AbstractIt has increasingly become clear over the last two decades that proteins can contain both globular domains and intrinsically unfolded regions which both can contribute to function. While equally interesting, the disordered regions are difficult to study because they usually do not crystallize unless bound to partners and are not easily amenable to cryo-electron microscopy studies. Nuclear magnetic resonance spectroscopy remains the best technique to capture the structural features of intrinsically mixed folded proteins and describe their dynamics. These studies rely on the successful assignment of the spectrum, task not easy per se given the limited spread of the resonances of the disordered residues. Here, we describe assignment of the spectrum of ataxin-3, the protein responsible for the neurodegenerative Machado-Joseph disease. We used a 42 kDa construct containing a globular N-terminal josephin domain and a C-terminal tail which comprises thirteen polyglutamine repeats within a low-complexity region. We developed a strategy which allowed us to achieve 87% assignment of the spectrum. We show that the C-terminal tail is flexible with extended helical regions and interacts only marginally with the rest of the protein. We could also, for the first time, deduce the structure of the polyglutamine repeats within the context of the full-length protein and show that it has a strong helical propensity stabilized by the preceding region.

scholarly journals F0-F1 coupling and symmetry mismatch in ATP synthase resolved in every F0 rotation step

2021 ◽  
Author(s):  
Shintaroh Kubo ◽  
Toru Niina ◽  
Shoji Takada
Keyword(s):  
Electron Microscopy ◽  
Atp Synthase ◽  
Energy Production ◽  
Comprehensive Understanding ◽  
Cellular Energy ◽  
Cryo Electron Microscopy ◽  
Rotary Motors ◽  
Elastic Distortion ◽  
Dynamics Simulations ◽  
Symmetric Structures

The F0F1 ATP synthase, essential for cellular energy production, is composed of the F0 and F1 rotary motors. While both F0 and F1 have pseudo-symmetric structures, their symmetries do not match. How the symmetry mismatch is solved remains elusive due to missing intermediate structures of rotational steps. Here, for ATP synthases with 3- and 10-fold symmetries in F1 and F0, respectively, we uncovered the mechanical couplings between F0 and F1 at every 36° rotation step via molecular dynamics simulations and comparison of cryo-electron microscopy structures from three species. We found that the frustration is shared by several elements. The F1 stator partially rotates relative to the F0 stator via elastic distortion of the b-subunits. The rotor can be distorted. The c-ring rotary angles can be deviated from symmetric ones. Additionally, the F1 motor may take non-canonical structures relieving stronger frustration. Together, we provide comprehensive understanding to solve the symmetry mismatch.

scholarly journals Structural basis for backtracking by the SARS-CoV-2 replication–transcription complex

2021 ◽  
Vol 118 (19) ◽  
pp. e2102516118
Author(s):  
Brandon Malone ◽  
James Chen ◽  
Qi Wang ◽  
Eliza Llewellyn ◽  
Young Joo Choi ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Structural Basis ◽  
Nucleoside Triphosphate ◽  
Cross Linking ◽  
Rna Dependent Rna Polymerase ◽  
Present Evidence ◽  
Cryo Electron Microscopy ◽  
Dynamics Simulations ◽  
Transcription And Replication

Backtracking, the reverse motion of the transcriptase enzyme on the nucleic acid template, is a universal regulatory feature of transcription in cellular organisms but its role in viruses is not established. Here we present evidence that backtracking extends into the viral realm, where backtracking by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) may aid viral transcription and replication. Structures of SARS-CoV-2 RdRp bound to the essential nsp13 helicase and RNA suggested the helicase facilitates backtracking. We use cryo-electron microscopy, RNA–protein cross-linking, and unbiased molecular dynamics simulations to characterize SARS-CoV-2 RdRp backtracking. The results establish that the single-stranded 3′ segment of the product RNA generated by backtracking extrudes through the RdRp nucleoside triphosphate (NTP) entry tunnel, that a mismatched nucleotide at the product RNA 3′ end frays and enters the NTP entry tunnel to initiate backtracking, and that nsp13 stimulates RdRp backtracking. Backtracking may aid proofreading, a crucial process for SARS-CoV-2 resistance against antivirals.

scholarly journals The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Ahmad Abdelzaher Zaki Khalifa ◽  
Muneyoshi Ichikawa ◽  
Daniel Dai ◽  
Shintaroh Kubo ◽  
Corbin Steven Black ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Tetrahymena Thermophila ◽  
Building Blocks ◽  
Post Translational Modifications ◽  
Ciliary Beating ◽  
Cryo Electron Microscopy ◽  
The Stability ◽  
And Function ◽  
Β Tubulin ◽  
Junction Proteins

Microtubules are cytoskeletal structures involved in stability, transport and organization in the cell. The building blocks, the α- and β-tubulin heterodimers, form protofilaments that associate laterally into the hollow microtubule. Microtubule also exists as highly stable doublet microtubules in the cilia where stability is needed for ciliary beating and function. The doublet microtubule maintains its stability through interactions at its inner and outer junctions where its A- and B-tubules meet. Here, using cryo-electron microscopy, bioinformatics and mass spectrometry of the doublets of Chlamydomonas reinhardtii and Tetrahymena thermophila, we identified two new inner junction proteins, FAP276 and FAP106, and an inner junction-associated protein, FAP126, thus presenting the complete answer to the inner junction identity and localization. Our structural study of the doublets shows that the inner junction serves as an interaction hub that involves tubulin post-translational modifications. These interactions contribute to the stability of the doublet and hence, normal ciliary motility.

scholarly journals Remodeling and activation mechanisms of outer arm dynein revealed by cryo-EM

2020 ◽  
Author(s):  
Shintaroh Kubo ◽  
Shun Kai Yang ◽  
Corbin Black ◽  
Daniel Dai ◽  
Melissa Valente ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
High Frequency ◽  
Complex Structure ◽  
Eukaryotic Cells ◽  
Native State ◽  
Ciliary Beating ◽  
Cryo Electron Microscopy ◽  
Activation Mechanisms ◽  
Dynein Arms ◽  
Dynamics Simulations

Cilia are thin microtubule-based protrusions of eukaryotic cells, beating at high frequency to propel the cell in sperms or clear mucus in the respiratory tract. The ciliary beating is driven by the outer arm dynein arms (ODAs) which anchor on the doublet microtubules. Here, we report the ODA complex structure from the native doublet microtubules by cryo-electron microscopy. Our structure reveals how the ODA complex is attached to the doublet microtubule via the docking complex in its native state. Combined with molecular dynamics simulations, we present a model of how the attachment of the ODA complex to the doublet microtubule induces rearrangements and activation mechanisms within the ODA complex.

scholarly journals In silico evidence of unique behaviors of methionine in an in-register parallel beta-sheet amyloid, suggestive of its possible contribution to strain diversity of amyloids

2019 ◽  
Author(s):  
Hiroki Otaki ◽  
Yuzuru Taguchi ◽  
Noriyuki Nishida
Keyword(s):  
Md Simulation ◽  
Genetic Material ◽  
Side Chain ◽  
Critical Position ◽  
Local Structures ◽  
Strain Diversity ◽  
Hydrophobic Amino Acids ◽  
Α Helix ◽  
Species Specific ◽  
Β Sheet

AbstractMechanism of strain diversity of prions is a long-standing conundrum, because prions consist solely of abnormal isoform of prion protein (PrPSc) devoid of genetic material. Pathogenic properties of prions are determined by conformations of the constituent PrPScaccording to the protein-only hypothesis, and alterations to even a single residue can drastically change the properties when the residue is located at a critical position for the structure of PrPSc. Interestingly, methionine (Met) is often recognized as the polymorphic or species-specific residues responsible for species/strain barriers of prions, implying its unique influences on the structures of PrPSc. However, how it is unique is difficult to demonstrate due to lack of the detailed structures of PrPSc. Here we analyzed influences of Met substitutions on structures of an in-register parallel β-sheet amyloid of α-synuclein (αSyn) by molecular dynamics (MD) simulation, to extrapolate the results to PrPSc. The MD simulation revealed that Met uniquely stabilized a U-shaped β-arch of the Greek-key αSyn amyloid, whereas other hydrophobic amino acids tended to destabilize it. The stabilizing effect of Met was attributable to the long side chain without Cβ branching. Our findings exemplify specifically how and in what structure of an in-register parallel β-sheet amyloid Met can uniquely behave, and are suggestive of its influences on structures of PrPScand strain diversity of prions. We also discuss about relations between α-helix propensity and local structures of in-register parallel amyloids.

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