The sweet coat of living cells – from supramolecular structure and dynamics to biological function

The endoplasmic reticulum (ER) is composed of interconnected membrane sheets and tubules. Superresolution microscopy recently revealed densely packed, rapidly moving ER tubules mistaken for sheets by conventional light microscopy, highlighting the importance of revisiting classical views of ER structure with high spatiotemporal resolution in living cells. In this study, we use live-cell stimulated emission depletion (STED) microscopy to survey the architecture of the ER at 50-nm resolution. We determine the nanoscale dimensions of ER tubules and sheets for the first time in living cells. We demonstrate that ER sheets contain highly dynamic, subdiffraction-sized holes, which we call nanoholes, that coexist with uniform sheet regions. Reticulon family members localize to curved edges of holes within sheets and are required for their formation. The luminal tether Climp63 and microtubule cytoskeleton modulate their nanoscale dynamics and organization. Thus, by providing the first quantitative analysis of ER membrane structure and dynamics at the nanoscale, our work reveals that the ER in living cells is not limited to uniform sheets and tubules; instead, we suggest the ER contains a continuum of membrane structures that includes dynamic nanoholes in sheets as well as clustered tubules.

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Characterizing Locus Specific Chromatin Structure and Dynamics with Correlative Conventional and Super Resolution imaging in living cells

10.1101/2021.03.16.435731 ◽

2021 ◽

Author(s):

Dushyant Mehra ◽

Santosh Adhikari ◽

Chiranjib Banerjee ◽

Elias M. Puchner

Keyword(s):

Single Molecule ◽

Chromatin Structure ◽

Spatial Organization ◽

Super Resolution ◽

Living Cells ◽

Diffraction Limit ◽

Optical Diffraction ◽

Acquisition Time ◽

Structure And Dynamics ◽

Chromatin Structure And Dynamics

The dynamic rearrangement of chromatin is critical for gene regulation, but mapping both the spatial organization of chromatin and its dynamics remains a challenge. Many structural conformations are too small to be resolved via conventional fluorescence microscopy and the long acquisition time of super-resolution PALM imaging precludes the structural characterization of chromatin below the optical diffraction limit in living cells due to chromatin motion. Here we develop a correlative conventional fluorescence and PALM imaging approach to quantitatively map time-averaged chromatin structure and dynamics below the optical diffraction limit in living cells. By assigning localizations to a locus as it moves, we reliably discriminate between bound and searching dCas9 molecules, whose mobility overlap. Our approach accounts for changes in DNA mobility and relates local chromatin motion to larger scale domain movement. In our experimental system, we show that compacted telomeres have a higher density of bound dCas9 molecules, but the relative motion of those molecules is more restricted than in less compacted telomeres. Correlative conventional and PALM imaging therefore improves the ability to analyze the mobility and time-averaged nanoscopic structural features of locus specific chromatin with single molecule precision and yields unprecedented insights across length and time scales.

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Fibrin membrane endowed with biological function. III. Fixing living cells in fibrin gel without impairing their functions

Cellular and Molecular Life Sciences ◽

10.1007/bf01922366 ◽

1977 ◽

Vol 33 (9) ◽

pp. 1257-1258 ◽

Cited By ~ 8

Author(s):

Y. Inada ◽

S. Hirose ◽

A. Matsushima ◽

H. Mihama ◽

Y. Hiramoto

Keyword(s):

Biological Function ◽

Living Cells ◽

Fibrin Gel ◽

Fibrin Membrane

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Single molecule fluorescence spectroscopy: approaches toward quantitative investigations of structure and dynamics in living cells

10.1117/12.646407 ◽

2006 ◽

Cited By ~ 2

Author(s):

Daniel Siegberg ◽

Christian Michael Roth ◽

Dirk-Peter Herten

Keyword(s):

Fluorescence Spectroscopy ◽

Single Molecule ◽

Living Cells ◽

Single Molecule Fluorescence ◽

Structure And Dynamics ◽

Single Molecule Fluorescence Spectroscopy

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Fibrin Membrane Endowed With Biological Function: Immobilization Of Enzymes And Living Cells

10.1055/s-0038-1652276 ◽

1981 ◽

Author(s):

Y Inada ◽

H Hagiwara ◽

Y Saito ◽

A Matsushima

Keyword(s):

Biological Function ◽

Urea Cycle ◽

Glyoxylic Acid ◽

Coagulation Factor ◽

Immobilized Enzymes ◽

Living Cells ◽

Inorganic Pyrophosphatase ◽

Multienzyme System ◽

Immobilization Of Enzymes ◽

Fibrin Membrane

Fibrin membrane formed from fibrinogen with thrombin and blood coagulation factor XIII was a superior matrix for preparing immobilized enzymes and living cells. Enzymes such as asparaginase, chloroplast ATPase or catalase and living cells such as Chlorella cells or sea urchin eggs were embedded in fibrin membrane without imparing their functions. The enzymes participating in degradation of purine bases(uric acid), uricase, allantoinase and allantoicase together with catalase were embedded simultaneously in matrices of fibrin molecules. The multienzyme complex thus prepared had an ability to degrade urate to glyoxylic acid and urea via allantoin and allantoic acid. Four enzymes in urea cycle, ornithine carbamoyltransferase, argininosuccinate synthetase, argininosuccinate lyase and orginase together with inorganic pyrophosphatase, were immobilized into matrices of fibrin molecules. The immobilized multienzyme system not only had an ability to carry out urea cycle continuously at least over several hours, but also had a greately improved efficiency over the corresponding soluble system. To the best of our knowledge this is the first report to show an immobilization of efficient cyclic enzyme system.

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A spotlight on chromatin choreography

The Journal of Cell Biology ◽

10.1083/jcb.2102fta ◽

2015 ◽

Vol 210 (2) ◽

pp. 176-176 ◽

Cited By ~ 1

Author(s):

Caitlin Sedwick

Keyword(s):

Chromatin Structure ◽

Living Cells ◽

Structure And Dynamics ◽

Chromatin Structure And Dynamics

In 1996, Robinett et al. developed a way to visualize chromatin structure and dynamics in living cells.

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Photochemical and Magnetic Resonance Investigations of the Supramolecular Structure and Dynamics of Molecules and Reactive Radicals on the External and Internal Surface of MFI Zeolites§

Journal of the American Chemical Society ◽

10.1021/ja001712s ◽

2000 ◽

Vol 122 (47) ◽

pp. 11649-11659 ◽

Cited By ~ 13

Author(s):

Nicholas J. Turro ◽

Xue-Gong Lei ◽

Wei Li ◽

Zhiqiang Liu ◽

Ann McDermott ◽

...

Keyword(s):

Magnetic Resonance ◽

Supramolecular Structure ◽

Internal Surface ◽

Structure And Dynamics ◽

Reactive Radicals ◽

Mfi Zeolites

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A Survey of Computational Treatments of Biomolecules by Robotics-Inspired Methods Modeling Equilibrium Structure and Dynamic

Journal of Artificial Intelligence Research ◽

10.1613/jair.5040 ◽

2016 ◽

Vol 57 ◽

pp. 509-572 ◽

Cited By ~ 17

Author(s):

Amarda Shehu ◽

Erion Plaku

Keyword(s):

Molecular Mechanisms ◽

Biological Function ◽

Equilibrium Structure ◽

Critical Discussion ◽

Molecular Processes ◽

Biomolecular Structure ◽

Large Molecules ◽

Physiological Conditions ◽

Cellular Processes ◽

Structure And Dynamics

More than fifty years of research in molecular biology have demonstrated that the ability of small and large molecules to interact with one another and propagate the cellular processes in the living cell lies in the ability of these molecules to assume and switch between specific structures under physiological conditions. Elucidating biomolecular structure and dynamics at equilibrium is therefore fundamental to furthering our understanding of biological function, molecular mechanisms in the cell, our own biology, disease, and disease treatments. By now, there is a wealth of methods designed to elucidate biomolecular structure and dynamics contributed from diverse scientific communities. In this survey, we focus on recent methods contributed from the Robotics community that promise to address outstanding challenges regarding the disparate length and time scales that characterize dynamic molecular processes in the cell. In particular, we survey robotics-inspired methods designed to obtain efficient representations of structure spaces of molecules in isolation or in assemblies for the purpose of characterizing equilibrium structure and dynamics. While an exhaustive review is an impossible endeavor, this survey balances the description of important algorithmic contributions with a critical discussion of outstanding computational challenges. The objective is to spur further research to address outstanding challenges in modeling equilibrium biomolecular structure and dynamics.

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