scholarly journals Structural analysis of the Sulfolobus solfataricus TF55β chaperonin by cryo-electron microscopy

2021 ◽  
Vol 77 (3) ◽  
pp. 79-84
Author(s):  
Yi Cheng Zeng ◽  
Meghna Sobti ◽  
Alastair G. Stewart
Keyword(s):  
Electron Microscopy ◽  
Protein Folding ◽  
Structural Analysis ◽  
Sulfolobus Solfataricus ◽  
Nucleotide Exchange ◽  
Cryo Electron Microscopy ◽  
Biomolecular Complexes ◽  
Group Ii ◽  
Group Ii Chaperonin ◽  
Archaeal Genus

Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. Using cryo-electron microscopy, structures of the β-only complex of S. solfataricus TF55 (TF55β) were determined to 3.6–4.2 Å resolution. The structures of the TF55β complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle.

scholarly journals Structural Analysis of a Filamentous Chaperonin from Sulfolobus solfataricus

2020 ◽  
Author(s):  
Yi C. Zeng ◽  
Meghna Sobti ◽  
Alastair G. Stewart
Keyword(s):  
Dependent Manner ◽  
Filament Formation ◽  
Temperature Dependent ◽  
Filamentous Form ◽  
Cold Shock Response ◽  
Cryo Electron Microscopy ◽  
Dodecyl Maltoside ◽  
Biomolecular Complexes ◽  
Group Ii Chaperonin ◽  
Archaeal Genus

SUMMARY/AbstractChaperonins are biomolecular complexes that assist protein folding. Thermophilic Factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus and which undergoes changes in modular subunit composition in a temperature-dependent manner. TF55 can form filamentous assemblies that may be a component of the archaeal cytoskeleton or sequester inactive chaperonin. Using cryo-electron microscopy, we have determined the structure of the β-only complex of S. solfataricus TF55 complexes to 3.6 Å resolution and its filamentous form to 5.2 Å resolution. Filament formation can be induced when the protein is enriched in solution or in the presence of the detergent dodecyl maltoside. Helical protrusions in the apical domain facilitate end-on-end interactions in the filamentous state. Our findings establish the molecular basis for forming chaperonin filaments in Sulfolobus and may suggest how filament formation could function as a cold-shock response and provides a background for generating tuneable protein nanowires.

Archaeal group II chaperonin mediates protein folding in the cis-cavity without a detachable GroES-like co-chaperonin11Edited by W. Baumeister

2002 ◽  
Vol 315 (1) ◽  
pp. 73-85 ◽  
Author(s):  
Takao Yoshida ◽  
Rika Kawaguchi ◽  
Hideki Taguchi ◽  
Masasuke Yoshida ◽  
Takuo Yasunaga ◽  
...  
Keyword(s):  
Protein Folding ◽  
Group Ii ◽  
Group Ii Chaperonin

scholarly journals Structural Analysis of Self-assembled Nanotubes of Bacteriophage T4 Capsid Protein gp23 by Cryo Electron Microscopy and Mass Spectrometry

2006 ◽  
Vol 12 (S02) ◽  
pp. 658-659
Author(s):  
BK Kaletas ◽  
E Van Duijn ◽  
AJ R Heck ◽  
RB J Geels ◽  
F De Haas ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Mass Spectrometry ◽  
Structural Analysis ◽  
Capsid Protein ◽  
Bacteriophage T4 ◽  
Cryo Electron Microscopy ◽  
Self Assembled

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2006

scholarly journals Structural identification of individual helical amyloid filaments by integration of cryo-electron microscopy-derived maps in comparative morphometric atomic force microscopy image analysis

2021 ◽  
Author(s):  
Liisa Lutter ◽  
Youssra Al-Hilaly ◽  
Christopher J. Serpell ◽  
Mick F. Tuite ◽  
Claude M. Wischik ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Atomic Force Microscopy ◽  
Image Analysis ◽  
Structural Analysis ◽  
Amyloid Fibrils ◽  
Structural Identification ◽  
Force Microscopy ◽  
Atomic Force ◽  
Cryo Electron Microscopy

The presence of amyloid fibrils is a hallmark of more than 50 human disorders, including neurodegenerative diseases and systemic amyloidoses. A key unresolved challenge in understanding the involvement of amyloid in disease is to explain the relationship between individual structural polymorphs of amyloid fibrils, in potentially mixed populations, and the specific pathologies with which they are associated. Although cryo-electron microscopy (cryo-EM) and solid-state nuclear magnetic resonance (ssNMR) spectroscopy methods have been successfully employed in recent years to determine the structures of amyloid fibrils with high resolution detail, they rely on ensemble averaging of fibril structures in the entire sample or significant subpopulations. Here, we report a method for structural identification of individual fibril structures imaged by atomic force microscopy (AFM) by integration of high-resolution maps of amyloid fibrils determined by cryo-EM in comparative AFM image analysis. This approach was demonstrated using the hitherto structurally unresolved amyloid fibrils formed in vitro from a fragment of tau (297-391), termed 'dGAE'. Our approach established unequivocally that dGAE amyloid fibrils bear no structural relationship to heparin-induced tau fibrils formed in vitro. Furthermore, our comparative analysis resulted in the prediction that dGAE fibrils are closely related structurally to the paired helical filaments (PHFs) isolated from Alzheimer's disease (AD) brain tissue characterised by cryo-EM. These results show the utility of individual particle structural analysis using AFM, provide a workflow of how cryo-EM data can be incorporated into AFM image analysis and facilitate an integrated structural analysis of amyloid polymorphism.

PB-13An Approach to Structural Analysis of a Small Membrane Protein KcsA by Cryo-electron Microscopy

Microscopy ◽  
2017 ◽  
Vol 66 (suppl_1) ◽  
pp. i39-i39
Author(s):  
Hiroko Takazaki ◽  
Hirofumi Shimizu ◽  
Naoko Kajimura ◽  
Kaoru Mitsuoka ◽  
Takuo Yasunaga
Keyword(s):  
Electron Microscopy ◽  
Structural Analysis ◽  
Membrane Protein ◽  
Cryo Electron Microscopy

scholarly journals GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting

2014 ◽  
Vol 169 ◽  
pp. 265-283 ◽  
Author(s):  
John E. Stone ◽  
Ryan McGreevy ◽  
Barry Isralewitz ◽  
Klaus Schulten
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Hybrid Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Interactive Computation ◽  
Biomolecular Complexes ◽  
Quality Of Fit

Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular interest today such as viruses or for long molecular dynamics trajectories as they arise in protein folding. We present new data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-of-fit metrics linking all-atom structures and molecular dynamics trajectories to experimentally-determined density maps obtained from cryo-electron microscopy or X-ray crystallography. We evaluate the performance and accuracy of the new quality-of-fit analysis algorithmsvis-à-visexisting tools, examine algorithm performance on GPU-accelerated desktop workstations and supercomputers, and describe new visualization techniques for results of hybrid structure fitting methods.

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