scholarly journals Molecular architecture of the SYCP3 fibre and its interaction with DNA

Open Biology ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 190094 ◽  
Author(s):  
Daniel Bollschweiler ◽  
Laura Radu ◽  
Luay Joudeh ◽  
Jürgen M. Plitzko ◽  
Robert M. Henderson ◽  
...  
Keyword(s):  
Dna Binding ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Local Geometry ◽  
Molecular Architecture ◽  
Lateral Element ◽  
Force Microscopy ◽  
Intrinsically Disordered ◽  
Atomic Force ◽  
Chromosome Axis

The synaptonemal complex (SC) keeps homologous chromosomes in close alignment during meiotic recombination. A hallmark of the SC is the presence of its constituent protein SYCP3 on the chromosome axis. During SC assembly, SYCP3 is deposited on both axes of the homologue pair, forming axial elements that fuse into the lateral element (LE) in the tripartite structure of the mature SC. We have used cryo-electron tomography and atomic force microscopy to study the mechanism of assembly and DNA binding of the SYCP3 fibre. We find that the three-dimensional architecture of the fibre is built on a highly irregular arrangement of SYCP3 molecules displaying very limited local geometry. Interaction between SYCP3 molecules is driven by the intrinsically disordered tails of the protein, with no contact between the helical cores, resulting in a flexible fibre assembly. We demonstrate that the SYCP3 fibre can engage in extensive interactions with DNA, indicative of an efficient mechanism for incorporation of DNA within the fibre. Our findings suggest that SYCP3 deposition on the chromosome axis might take place by polymerization into a fibre that is fastened to the chromosome surface via DNA binding.

scholarly journals Reconstitution of a flexible SYCP3-DNA fibre suggests a mechanism for SYCP3 coating of the meiotic chromosome axis

2018 ◽  
Author(s):  
Daniel Bollschweiler ◽  
Laura Radu ◽  
Jürgen M. Plitzko ◽  
Robert M. Henderson ◽  
Ioanna Mela ◽  
...  
Keyword(s):  
Dna Binding ◽  
Electron Tomography ◽  
Meiotic Chromosome ◽  
Three Dimensional ◽  
Structural Basis ◽  
Local Geometry ◽  
Lateral Element ◽  
Force Microscopy ◽  
Intrinsically Disordered ◽  
Chromosome Axis

The synaptonemal complex (SC) keeps homologous chromosomes in close alignment during meiotic crossover. A hallmark of SC formation is the presence of its protein component SYCP3 on the chromosome axis. As SC assembly progresses, SYCP3 is deposited on both axes of the homologue pair, forming the lateral element (LE) in the tripartite structure of the mature SC. We have used cryo-electron tomography and atomic force microscopy to study the mechanism of assembly and DNA binding of the SYCP3 fibre. We find that the three-dimensional architecture of the fibre is built on a highly irregular arrangement of SYCP3 molecules displaying very limited local geometry. Interaction between SYCP3 molecules is driven by the intrinsically disordered tails of the protein, with no contact between the helical cores, resulting in a flexible fibre assembly. We demonstrate that the SYCP3 fibre can engage in extensive interactions with DNA, indicative of an efficient mechanism for incorporation of DNA within the fibre. Taken together, our findings suggest that, upon deposition on the chromosome axis, SYCP3 spreads by polymerising into a fibre that is fastened to the chromosome surface via DNA binding. The resulting layer of SYCP3 coating the chromosome axis might provide a structural basis for LE assembly in meiotic prophase.

scholarly journals Acoustic subsurface-atomic force microscopy: Three-dimensional imaging at the nanoscale

2021 ◽  
Vol 129 (3) ◽  
pp. 030901
Author(s):  
Hossein J. Sharahi ◽  
Mohsen Janmaleki ◽  
Laurene Tetard ◽  
Seonghwan Kim ◽  
Hamed Sadeghian ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Three Dimensional ◽  
Three Dimensional Imaging ◽  
Force Microscopy ◽  
Atomic Force

scholarly journals Membrane fusion studied by colloidal probes

2021 ◽  
Vol 50 (2) ◽  
pp. 223-237 ◽  
Author(s):  
Hannes Witt ◽  
Filip Savić ◽  
Sarah Verbeek ◽  
Jörn Dietz ◽  
Gesa Tarantola ◽  
...  
Keyword(s):  
Membrane Fusion ◽  
Optical Tweezers ◽  
Three Dimensional ◽  
Biological Processes ◽  
Supported Membranes ◽  
Supported Bilayers ◽  
Force Microscopy ◽  
Advantages And Disadvantages ◽  
Atomic Force ◽  
Colloidal Probes

AbstractMembrane-coated colloidal probes combine the benefits of solid-supported membranes with a more complex three-dimensional geometry. This combination makes them a powerful model system that enables the visualization of dynamic biological processes with high throughput and minimal reliance on fluorescent labels. Here, we want to review recent applications of colloidal probes for the study of membrane fusion. After discussing the advantages and disadvantages of some classical vesicle-based fusion assays, we introduce an assay using optical detection of fusion between membrane-coated glass microspheres in a quasi two-dimensional assembly. Then, we discuss free energy considerations of membrane fusion between supported bilayers, and show how colloidal probes can be combined with atomic force microscopy or optical tweezers to access the fusion process with even greater detail.

Probing protein–peptide–protein molecular architecture by atomic force microscopy and surface plasmon resonance

The Analyst ◽  
2000 ◽  
Vol 125 (2) ◽  
pp. 245-250 ◽  
Author(s):  
Molly M. Stevens ◽  
Stephanie Allen ◽  
Martyn C. Davies ◽  
Clive J. Roberts ◽  
Saul J. B. Tendler ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Surface Plasmon Resonance ◽  
Surface Plasmon ◽  
Plasmon Resonance ◽  
Molecular Architecture ◽  
Force Microscopy ◽  
Atomic Force

scholarly journals Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm

2017 ◽  
Vol 23 (3) ◽  
pp. 661-667 ◽  
Author(s):  
Yue Li ◽  
Di Zhang ◽  
Ilker Capoglu ◽  
Karl A. Hujsak ◽  
Dhwanil Damania ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Density Distribution ◽  
Scanning Transmission Electron Microscopy ◽  
Mass Density ◽  
Three Dimensional ◽  
Force Microscopy ◽  
Statistical Measures ◽  
Atomic Force ◽  
Transmission Electron ◽  
Scanning Transmission

AbstractEssentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass–density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass–density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass–density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass–density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass–density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.

Asphaltenes: Fundamental Principles to Oilfield Applications

2021 ◽  
Author(s):  
Oliver Mullins ◽  
Andrew Pomerantz ◽  
Yunlong Zhang
Keyword(s):  
Scanning Tunneling ◽  
Quasi Equilibrium ◽  
Molecular Architecture ◽  
Tunneling Microscopy ◽  
Force Microscopy ◽  
Viscous Oil ◽  
Atomic Force ◽  
Fluid Process ◽  
Onset Pressure ◽  
Reservoir Connectivity

Abstract The sophisticated molecular imaging methods, atomic force microscopy (AFM) and scanning tunneling microscopy (STM), have been utilized to image individual asphaltene molecules, both their atoms and bonds, and their electronic structure. The stunning images have confirmed previous results and have all but resolved the long-standing uncertainties regarding asphaltene molecular architecture. Asphaltenes are also known to have a strong propensity to aggregate. The dominante asphaltene molecular structure and hierarchical nanocolloidal structures have been resolved and codified in the Yen-Mullins model. Use of this model in a simple polymer solution theory has given the first equation of state (EoS) for asphaltene gradients in oilfield reservoirs, the Flory-Huggins-Zuo EoS. With this EoS it is now possible to address reservoir connectivity in new ways; equilibrated asphaltenes imply reservoir connectivity. For reservoirs with disequilibrium of contained fluids, there is often a fluid process occurring in geologic time that precludes equilibrium. The collection of processes leading to equilibrium and those that preclude equilibrium constitute a new technical discipline, reservoir fluid geodynamics (RFG). Several reservoirs are reviewed employing RFG evaluation of connectivity via asphaltene thermodynamics. RFG processes in reservoris often include diffusion, RFG models incorporating simple solution to the diffusion equation coupled with quasi-equilibrium with the FHZ EoS are shown to apply for timelines up to 50 million years, the age of charge in a reservoir. When gas (or condensates) diffuse into oil, the asphaltenes are destabilized and can convect to the base of the reservoir. Increasing asphaltene onset pressure as well as viscous oil and tar mats can be consequences. Depending on specifics of the process, either gooey tar or coal-like asphaltene deposits can form. In addition, the asphaltene structures illuminated by AFM are now being used to account for interfacial properties using simple thermodynamics. At long last, asphaltenes are no longer the enigmatic component of crude oil, instead the resolution of asphaltene structures and dynamics has led to new thermodynamic applications in reservoirs, the new discipline RFG, and a new understanding of tar mats.

High-resolution transmission electron microscopic investigations of molybdenum thin films on faceted α-Al2O3

2005 ◽  
Vol 38 (2) ◽  
pp. 260-265 ◽  
Author(s):  
Leonore Wiehl ◽  
Jens Oster ◽  
Michael Huth
Keyword(s):  
High Resolution ◽  
Three Dimensional ◽  
Epitaxial Relationship ◽  
Electron Microscopic ◽  
Force Microscopy ◽  
Atomic Force ◽  
Transmission Electron ◽  
High Resolution Images ◽  
Α Al2o3 ◽  
Relationship Of

Epitaxially grown Mo films on a faceted corundum (α-Al2O3)mplane were investigated by transmission electron microscopy. Low- and high-resolution images were taken from a cross-section specimen cut perpendicular to the facets. It was possible to identify unambiguously the crystallographic orientation of these facets and explain the considerable deviation (∼10°) of the experimental interfacet angle, as measured with atomic force microscopy (AFM), from the expected value. For the first time, proof is given for a smooth \{10\bar{1}1\} facet and a curvy facet with orientation near to \{10\bar{1}\bar{2}\}. Moreover, the three-dimensional epitaxial relationship of an Mo film on a faceted corundummsurface was determined.

scholarly journals Planar Boronic Graphene and Nitrogenized Graphene Heterostructure for Protein Stretch and Confinement

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1756
Author(s):  
Xuchang Su ◽  
Zhi He ◽  
Lijun Meng ◽  
Hong Liang ◽  
Ruhong Zhou
Keyword(s):  
Single Molecule ◽  
Intrinsically Disordered Proteins ◽  
Electron Tunneling ◽  
Amyloid Β ◽  
Protein Sequencing ◽  
Disordered Proteins ◽  
Force Microscopy ◽  
Intrinsically Disordered ◽  
Atomic Force ◽  
Dynamics Simulations

Single-molecule techniques such as electron tunneling and atomic force microscopy have attracted growing interests in protein sequencing. For these methods, it is critical to refine and stabilize the protein sample to a “suitable mode” before applying a high-fidelity measurement. Here, we show that a planar heterostructure comprising boronic graphene (BC3) and nitrogenized graphene (C3N) sandwiched stripe (BC3/C3N/BC3) is capable of the effective stretching and confinement of three types of intrinsically disordered proteins (IDPs), including amyloid-β (1–42), polyglutamine (Q42), and α-Synuclein (61–95). Our molecular dynamics simulations demonstrate that the protein molecules interact more strongly with the C3N stripe than the BC3 one, which leads to their capture, elongation, and confinement along the center C3N stripe of the heterostructure. The conformational fluctuations of IDPs are substantially reduced after being stretched. This design may serve as a platform for single-molecule protein analysis with reduced thermal noise.

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