Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging

Science ◽  
2013 ◽  
Vol 341 (6146) ◽  
pp. 655-658 ◽  
Author(s):  
Anna Szymborska ◽  
Alex de Marco ◽  
Nathalie Daigle ◽  
Volker C. Cordes ◽  
John A. G. Briggs ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Super Resolution ◽  
Molecular Organization ◽  
Nuclear Pore ◽  
Protein Assemblies ◽  
Large Protein ◽  
Whole Cells ◽  
Molecular Machinery ◽  
Scaffold Structure ◽  
Super Resolution Microscopy

Much of life’s essential molecular machinery consists of large protein assemblies that currently pose challenges for structure determination. A prominent example is the nuclear pore complex (NPC), for which the organization of its individual components remains unknown. By combining stochastic super-resolution microscopy, to directly resolve the ringlike structure of the NPC, with single particle averaging, to use information from thousands of pores, we determined the average positions of fluorescent molecular labels in the NPC with a precision well below 1 nanometer. Applying this approach systematically to the largest building block of the NPC, the Nup107-160 subcomplex, we assessed the structure of the NPC scaffold. Thus, light microscopy can be used to study the molecular organization of large protein complexes in situ in whole cells.

scholarly journals Dictyostelium discoideum and autophagy – a perfect pair

2019 ◽  
Vol 63 (8-9-10) ◽  
pp. 485-495 ◽  
Author(s):  
Sarah Fischer ◽  
Ludwig Eichinger
Keyword(s):  
Dictyostelium Discoideum ◽  
Membrane Vesicles ◽  
Model Organisms ◽  
Protein Assemblies ◽  
Large Protein ◽  
Complex Dynamic ◽  
The Social ◽  
Wide Range ◽  
Molecular Machinery ◽  
Chaperone Mediated Autophagy

Autophagy is subdivided into chaperone-mediated autophagy, microautophagy and macroautophagy and is a highly conserved intracellular degradative pathway. It is crucial for cellular homeostasis and also serves as a response to different stresses. Here we focus on macroautophagy, which targets damaged organelles and large protein assemblies, as well as pathogenic intracellular microbes for destruction. During this process, cytosolic material becomes enclosed in newly generated double-membrane vesicles, the so-called autophagosomes. Upon maturation, the autophagosome fuses with the lysosome for degradation of the cargo. The basic molecular machinery that controls macroautophagy works in a sequential order and consists of the ATG1 complex, the PtdIns3K complex, the membrane delivery system, two ubiquitin-like conjugation systems, and autophagy adaptors and receptors. Since the different stages of macroautophagy from initiation to final degradation of cargo are tightly regulated and highly conserved across eukaryotes, simple model organisms in combination with a wide range of techniques contributed significantly to advance our understanding of this complex dynamic process. Here, we present the social amoeba Dictyostelium discoideum as an advantageous and relevant experimental model system for the analysis of macroautophagy.

scholarly journals 429 Nanoscale molecular organization of the desmosome as revealed by super-resolution microscopy

2016 ◽  
Vol 136 (5) ◽  
pp. S76
Author(s):  
S.N. Stahley ◽  
E.I. Bartle ◽  
C.E. Atkinson ◽  
A.P. Kowalczyk ◽  
A.L. Mattheyses
Keyword(s):  
Super Resolution ◽  
Molecular Organization ◽  
Super Resolution Microscopy

scholarly journals Annotating precision for integrative structural models using deep learning

2021 ◽  
Author(s):  
Nikhil Kasukurthi ◽  
Shruthi Viswanath
Keyword(s):  
Deep Learning ◽  
High Precision ◽  
Protein Complexes ◽  
Source Code ◽  
Structural Models ◽  
Protein Assemblies ◽  
Large Protein ◽  
Single Precision ◽  
Input Information ◽  
Gradient Based

Motivation: Integrative modeling of macromolecular structures usually results in an ensemble of models that satisfy the input information. The model precision, or variability among these models is estimated globally, i.e., a single precision value is reported for the model. However, it would be useful to identify regions of high and low precision. For instance, low-precision regions can suggest where the next experiments could be performed and high-precision regions can be used for further analysis, e.g., suggesting mutations. Results: We develop PrISM (Precision for Integrative Structural Models), using autoencoders to efficiently and accurately annotate precision for integrative models. The method is benchmarked and tested on five examples of binary protein complexes and five examples of large protein assemblies. The annotated precision is shown to be consistent with, and more informative than localization densities. The generated networks are also interpreted by gradient-based attention analysis. Availability: Source code is at https://github.com/isblab/prism.

Optical super-resolution microscopy unravels the molecular composition of functional protein complexes

Nanoscale ◽  
2019 ◽  
Vol 11 (39) ◽  
pp. 17981-17991 ◽  
Author(s):  
Marina S. Dietz ◽  
Mike Heilemann
Keyword(s):  
Single Molecule ◽  
Protein Complexes ◽  
Super Resolution ◽  
Molecular Composition ◽  
Functional Protein ◽  
Super Resolution Microscopy

The molecular composition of functional protein complexes can be determined from single-molecule super-resolution images.

scholarly journals ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Leonid Andronov ◽  
Igor Orlov ◽  
Yves Lutz ◽  
Jean-Luc Vonesch ◽  
Bruno P. Klaholz
Keyword(s):  
Protein Complexes ◽  
Voronoi Tessellation ◽  
Super Resolution ◽  
Super Resolution Microscopy

scholarly journals Super-resolution Microscopy of Clickable Amino Acids Reveals the Effects of Fluorescent Protein Tagging on Protein Assemblies

ACS Nano ◽  
2015 ◽  
Vol 9 (11) ◽  
pp. 11034-11041 ◽  
Author(s):  
Ingrid C. Vreja ◽  
Ivana Nikić ◽  
Fabian Göttfert ◽  
Mark Bates ◽  
Katharina Kröhnert ◽  
...  
Keyword(s):  
Amino Acids ◽  
Fluorescent Protein ◽  
Super Resolution ◽  
Protein Assemblies ◽  
Super Resolution Microscopy ◽  
Protein Tagging

scholarly journals Super-resolution microscopy reveals arrangement of inner membrane protein complexes in mammalian mitochondria

2021 ◽  
Author(s):  
Catherine S. Palmer ◽  
Jieqiong Lou ◽  
Betty Kouskousis ◽  
Elvis Pandzic ◽  
Alexander J. Anderson ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Protein Complexes ◽  
Super Resolution ◽  
Bimodal Distribution ◽  
Complex Iv ◽  
Inner Membrane ◽  
Mitochondrial Inner Membrane ◽  
Cellular Context ◽  
Inner Membrane Protein ◽  
Super Resolution Microscopy

The mitochondrial inner membrane is a protein rich environment containing large multimeric complexes including complexes of the mitochondrial electron transport chain, mitochondrial translocases and quality control machineries. Although the inner membrane is highly proteinaceous, with 40–60% of all mitochondrial proteins localised to this compartment, little is known about the spatial distribution and organisation of complexes in this environment. We set out to survey the arrangement of inner membrane complexes using stochastic optical reconstruction microscopy (STORM). We show subunits of the TIM23 Complex, Tim23 and Tim44, and the Complex IV subunit COXIV form organised clusters and show distinct properties to the outer membrane protein Tom20. Density based cluster analysis indicated a bimodal distribution of Tim44 that is distinct from Tim23, suggesting distinct TIM23 subcomplexes. COXIV is arranged in larger clusters, that are disrupted upon disruption of Complex IV assembly. Thus, STORM super-resolution microscopy is a powerful approach to examine the nanoscale distribution of mitochondrial inner membrane complexes, providing a “visual” approach to obtaining pivotal information on how mitochondrial complexes exist in a cellular context.

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