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

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.

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 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.

scholarly journals ORANGE: A CRISPR/Cas9-based genome editing toolbox for epitope tagging of endogenous proteins in neurons

2019 ◽  
Author(s):  
Jelmer Willems ◽  
Arthur P.H. de Jong ◽  
Nicky Scheefhals ◽  
Harold D. MacGillavry
Keyword(s):  
Genome Editing ◽  
Cell Biology ◽  
Protein Complexes ◽  
Neuronal Cell ◽  
Super Resolution ◽  
Protein Distribution ◽  
Neuronal Processes ◽  
Endogenous Proteins ◽  
Fluorescent Tags ◽  
Super Resolution Microscopy

ABSTRACTThe correct subcellular distribution of protein complexes establishes the complex morphology of neurons and is fundamental to their functioning. Thus, determining the dynamic distribution of proteins is essential to understand neuronal processes. Fluorescence imaging, in particular super-resolution microscopy, has become invaluable to investigate subcellular protein distribution. However, these approaches suffer from the limited ability to efficiently and reliably label endogenous proteins. We developed ORANGE: an Open Resource for the Application of Neuronal Genome Editing, that mediates targeted genomic integration of fluorescent tags in neurons. This toolbox includes a knock-in library for in-depth investigation of endogenous protein distribution, and a detailed protocol explaining how knock-in can be developed for novel targets. In combination with super-resolution microscopy, ORANGE revealed the dynamic nanoscale organization of endogenous neuronal signaling molecules, synaptic scaffolding proteins, and neurotransmitter receptors. Thus, ORANGE enables quantitation of expression and distribution for virtually any protein in neurons at high resolution and will significantly further our understanding of neuronal cell biology.

scholarly journals Deformed Alignment of Super-Resolution Images for Semi-flexible Structures in 3D

2018 ◽  
Author(s):  
Xiaoyu Shi ◽  
Galo Garcia ◽  
Yina Wang ◽  
Jeremy Reiter ◽  
Bo Huang
Keyword(s):  
Single Molecule ◽  
Protein Complexes ◽  
Flexible Structures ◽  
Super Resolution ◽  
Computation Time ◽  
Structural Heterogeneity ◽  
Image Alignment ◽  
Stochastic Optical Reconstruction Microscopy ◽  
Optical Reconstruction ◽  
Super Resolution Microscopy

AbstractDue to low labeling efficiency and structural heterogeneity in fluorescence-based single-molecule localization microscopy (SMLM), image alignment and quantitative analysis is often required to make accurate conclusions on the spatial relationships between proteins. Cryo-electron microscopy (EM) image alignment procedures have been applied to average structures taken with super-resolution microscopy. However, unlike cryo-EM, the much larger cellular structures analyzed by super-resolution microscopy are often heterogeneous, resulting in misalignment. And the light-microscopy image library is much smaller, which makes classification not realistic. To overcome these two challenges, we developed a method to deform semi-flexible ring-shaped structures and then align the 3D structures without classification. These algorithms can register semi-flexible structures with an accuracy of several nanometers in short computation time and with greatly reduced memory requirements. We demonstrated our methods by aligning experimental Stochastic Optical Reconstruction Microscopy (STORM) images of ciliary distal appendages and simulated structures. Symmetries, dimensions, and locations of protein complexes in 3D are revealed by the alignment and averaging for heterogeneous, tilted, and under-labeled structures.

Super-Resolution Microscopy in Studying the Structure and Function of the Cell Nucleus

Acta Naturae ◽  
2017 ◽  
Vol 9 (4) ◽  
pp. 42-51
Author(s):  
S. S. Ryabichko ◽  
◽  
A. N. Ibragimov ◽  
L. A. Lebedeva ◽  
E. N. Kozlov ◽  
...  
Keyword(s):  
Cell Nucleus ◽  
Super Resolution ◽  
Structure And Function ◽  
And Function ◽  
Super Resolution Microscopy

Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins

2019 ◽  
Author(s):  
Jeffrey Chang ◽  
Matthew Romei ◽  
Steven Boxer
Keyword(s):  
Rational Design ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Super Resolution ◽  
Unit Cell Size ◽  
Chlorine Substituent ◽  
Gfp Chromophore ◽  
The One ◽  
Green Fluorescent ◽  
Super Resolution Microscopy

<p>Double-bond photoisomerization in molecules such as the green fluorescent protein (GFP) chromophore can occur either via a volume-demanding one-bond-flip pathway or via a volume-conserving hula-twist pathway. Understanding the factors that determine the pathway of photoisomerization would inform the rational design of photoswitchable GFPs as improved tools for super-resolution microscopy. In this communication, we reveal the photoisomerization pathway of a photoswitchable GFP, rsEGFP2, by solving crystal structures of <i>cis</i> and <i>trans</i> rsEGFP2 containing a monochlorinated chromophore. The position of the chlorine substituent in the <i>trans</i> state breaks the symmetry of the phenolate ring of the chromophore and allows us to distinguish the two pathways. Surprisingly, we find that the pathway depends on the arrangement of protein monomers within the crystal lattice: in a looser packing, the one-bond-flip occurs, whereas in a tighter packing (7% smaller unit cell size), the hula-twist occurs.</p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p> <p> </p>

Sign in / Sign up

Export Citation Format

Share Document