scholarly journals The Structural Biology of Septins and Their Filaments: An Update

2021 ◽  
Vol 9 ◽  
Author(s):  
Italo A. Cavini ◽  
Diego A. Leonardo ◽  
Higor V. D. Rosa ◽  
Danielle K. S. V. Castro ◽  
Humberto D’Muniz Pereira ◽  
...  
Keyword(s):  
Structural Information ◽  
Three Dimensional ◽  
Higher Order ◽  
Coiled Coils ◽  
Cytoskeletal Proteins ◽  
Point Of View ◽  
The Individual ◽  
Molecular Components ◽  
Order Complexes ◽  
Order Structures

In order to fully understand any complex biochemical system from a mechanistic point of view, it is necessary to have access to the three-dimensional structures of the molecular components involved. Septins and their oligomers, filaments and higher-order complexes are no exception. Indeed, the spontaneous recruitment of different septin monomers to specific positions along a filament represents a fascinating example of subtle molecular recognition. Over the last few years, the amount of structural information available about these important cytoskeletal proteins has increased dramatically. This has allowed for a more detailed description of their individual domains and the different interfaces formed between them, which are the basis for stabilizing higher-order structures such as hexamers, octamers and fully formed filaments. The flexibility of these structures and the plasticity of the individual interfaces have also begun to be understood. Furthermore, recently, light has been shed on how filaments may bundle into higher-order structures by the formation of antiparallel coiled coils involving the C-terminal domains. Nevertheless, even with these advances, there is still some way to go before we fully understand how the structure and dynamics of septin assemblies are related to their physiological roles, including their interactions with biological membranes and other cytoskeletal components. In this review, we aim to bring together the various strands of structural evidence currently available into a more coherent picture. Although it would be an exaggeration to say that this is complete, recent progress seems to suggest that headway is being made in that direction.

scholarly journals Crystalline perfection of an aluminium single crystal determined by neutron diffraction

2011 ◽  
Vol 44 (4) ◽  
pp. 681-687
Author(s):  
Sabrina Metairon ◽  
Carlos Benedicto Ramos Parente ◽  
Vera Lucia Mazzocchi ◽  
Thierry Jacques Lemaire
Keyword(s):  
Neutron Diffraction ◽  
Single Crystal ◽  
Relative Intensity ◽  
Three Dimensional ◽  
Point Of View ◽  
Crystalline Perfection ◽  
Contour Map ◽  
The Individual ◽  
Crystalline Domains

In this work, a study of the crystalline perfection of an aluminium single crystal is presented. The study shows that, from three-dimensional neutron diffraction rocking curves, it is possible to characterize the individual crystalline domains of a multidomain crystal. From a macroscopic point of view, the determination of the domains allows an evaluation of the crystalline perfection of the crystal under study. Three-dimensional rocking curves have been obtained by neutron diffraction from a large mosaic aluminium crystal. Construction of a contour map of individual domains made it easier to determine the breadth and relative intensity of each domain. The angular distances between domains were also determined.

The role of Bni5 in the regulation of septin higher-order structure formation

2015 ◽  
Vol 396 (12) ◽  
pp. 1325-1337 ◽  
Author(s):  
Csilla Patasi ◽  
Jana Godočíková ◽  
Soňa Michlíková ◽  
Yan Nie ◽  
Radka Káčeriková ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Structural Changes ◽  
Higher Order ◽  
Cytoskeletal Proteins ◽  
Order Structure ◽  
Division Plane ◽  
Cellular Processes ◽  
Order Structures

Abstract Septins are a family of conserved cytoskeletal proteins playing an essential role in cytokinesis and in many other cellular processes in fungi and animals. In budding yeast Saccharomyces cerevisiae, septins form filaments and higher-order structures at the mother-bud neck depending on the particular stage of the cell cycle. Septin structures at the division plane serve as a scaffold to recruit the proteins required for particular cellular processes. The formation and localization of septin structures at particular stages of the cell cycle also determine functionality of these proteins. Many different proteins participate in regulating septin assembly. Despite recent developments, we are only beginning to understand how specific protein-protein interactions lead to changes in the polymerization of septin filaments or assembly of higher-order structures. Here, using fluorescence and electron microscopy, we found that Bni5 crosslinks septin filaments into networks by bridging pairs or multiple filaments, forming structures that resemble railways. Furthermore, Bni5 appears to be a substrate of the Elm1 protein kinase in vitro. Moreover, Elm1 induces in the presence of Bni5 disassembly of long septin filaments, suggesting that these proteins may participate in the hourglass to double ring transition. This work gives new insight into the regulatory role of Bni5 in the structural changes of septins.

Singular Behavior of Laminated Skew Composite Materials with Cross-Ply Stacking

2012 ◽  
Vol 538-541 ◽  
pp. 1640-1645 ◽  
Author(s):  
Jae Seok Ahn ◽  
Kwang Ik Son ◽  
Kwang Sung Woo ◽  
Young Shik Shin
Keyword(s):  
Composite Materials ◽  
Physical Meaning ◽  
Order Approximation ◽  
Three Dimensional ◽  
Laminated Composite ◽  
Higher Order ◽  
Point Of View ◽  
Shape Functions ◽  
Laminated Composite Materials ◽  
Dimensional Shape

This study deals with effects depending on skew angles in skewed-laminated composite materials in macroscopic point of view. Based on higher-order approximation of displacements, subparametric layer-wise finite elements are used to analyze skewed-laminated composite systems. The elements have higher-order shape functions derived from the Lobatto shape functions. The modes of the elements are classified into three groups such as vertex, side, and internal modes. The vertex modes have physical meaning, while side and internal modes with respect to the increase of order of the Lobatto shape functions do not have physical meaning but improve accuracy of analysis. Therefore, fixing mesh arrangement of present analysis, the quality of the analysis can be enhanced without re-meshing work. The approach based on p-version of finite element method is implemented with three-dimensional elasticity theory, while shape functions are developed by combination of one- and two-dimensional shape functions, not using three-dimensional shape functions. Using the accurate and practical proposed technique, macroscopic behavior of skewed-laminated composite materials is investigated.

scholarly journals SLAM-BASED BACKPACK LASER SCANNING FOR FOREST PLOT MAPPING

2020 ◽  
Vol V-2-2020 ◽  
pp. 267-271
Author(s):  
J. Shao ◽  
W. Zhang ◽  
L. Luo ◽  
S. Cai ◽  
H. Jiang
Keyword(s):  
Laser Scanning ◽  
Structural Information ◽  
Three Dimensional ◽  
Vertical Direction ◽  
Point Clouds ◽  
Forest Plot ◽  
Individual Tree ◽  
Forest Mapping ◽  
Localization And Mapping ◽  
The Individual

Abstract. Acquisition of three-dimensional (3D) structural information is significant for forest measurements. To achieve faster data collection in forests, we design a backpack laser scanning (BLS) system using a single mobile laser scanning (MLS) scanner and specific to forest environments. The simultaneous localization and mapping (SLAM) approach based on the natural geometric characteristics of trees is used for BLS-based forest mapping, in which the skeleton line of the individual tree is extracted for scan matching and the incremental maps are adopted for global optimization of all the BLS point clouds. The final experimental results show that the SLAM-based BLS system achieves accurate forest plots mapping and allows reaching low mapping errors, in which the mean errors are approximately 3 cm in the horizontal and 2 cm in the vertical direction.

Chromosome structure and dynamics as revealed by 3-D and 4-D imaging

1991 ◽  
Vol 49 ◽  
pp. 396-397
Author(s):  
Jason R. Swedlow ◽  
Yasushi Hiraoka ◽  
Michael R. Paddy ◽  
John W. Sedat ◽  
David A. Agard
Keyword(s):  
Data Collection ◽  
Chromosome Structure ◽  
State Of The Art ◽  
Three Dimensional ◽  
Higher Order ◽  
Structure And Dynamics ◽  
Complex Processes ◽  
Multi Wavelength ◽  
Cellular Dna ◽  
Order Structures

Cellular DNA is packaged into chromosomes through complex processes whereby the DNA becomes compacted up to 10,000-fold by assembly into higher-order structures. In spite of many decades of intense study, the details of this process are not known. In addition, there is little information describing the dynamics of these higher-order structures during DNA replication, transcription, and mitosis. The goal of our laboratory is to use state-of-the-art 3-D imaging methods to understand how DNA is arranged into chromosomes and how chromosomes are spatially and temporally organized in the nucleus.Towards this end, we have developed a fluorescence microscope workstation optimized for collecting three-dimensional multi-wavelength data from fixed and living specimens. The multiplewavelength capability of this system allows us to simultaneously examine the spatial relationships of different chromosomal components in 3-D. Fixed samples can be labelled with up to three different fluorophore-conjugated antibodies and a fluorescent DNA binding dye, DAPI. Three-dimensional multi-wavelength data collection proceeds by sequentially recording images of each color, changing the focus, and then repeating the process as many times as necessary.

scholarly journals The interpretation of structure from motion

1979 ◽  
Vol 203 (1153) ◽  
pp. 405-426 ◽  
Keyword(s):  
Structure From Motion ◽  
Three Dimensional ◽  
Point Of View ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Three Dimensional Structure ◽  
Structure And Motion ◽  
Rigid Objects ◽  
The Individual

The interpretation of structure from motion is examined from a computional point of view. The question addressed is how the three dimen­sional structure and motion of objects can be inferred from the two dimensional transformations of their projected images when no three dimensional information is conveyed by the individual projections. The following scheme is proposed: (i) divide the image into groups of four elements each; (ii) test each group for a rigid interpretation; (iii) combine the results obtained in (ii). It is shown that this scheme will correctly decompose scenes containing arbitrary rigid objects in motion, recovering their three dimensional structure and motion. The analysis is based primarily on the ʻstructure from motion’ theorem which states that the structure of four non-coplanar points is recoverable from three orthographic projections. The interpretation scheme is extended to cover perspective projections, and its psychological relevance is discussed.

Reconstructing a lost world: Ediacaran rangeomorphs from Spaniard's Bay, Newfoundland

2009 ◽  
Vol 83 (4) ◽  
pp. 503-523 ◽  
Author(s):  
Guy M. Narbonne ◽  
Marc Laflamme ◽  
Carolyn Greentree ◽  
Peter Trusler
Keyword(s):  
Three Dimensional ◽  
Higher Order ◽  
Morphological Features ◽  
Attachment Point ◽  
Architectural Elements ◽  
Order Branch ◽  
Central Stalk ◽  
Self Similar ◽  
The Individual ◽  
Avalon Peninsula

Ediacaran fronds at Spaniard's Bay on the Avalon Peninsula of Newfoundland exhibit exquisite, three-dimensional preservation with morphological features less than 0.05 mm in width visible on the best preserved specimens. Most of the nearly 100 specimens are juvenile rangeomorphs, an extinct Ediacaran clade that numerically dominated the early evolution of complex multicellular life. Spaniard's Bay rangeomorphs are characterized by cm-scale architectural elements exhibiting self-similar branching over several fractal scales that were used as modules in construction of larger structures. Four taxa of rangeomorph fronds are present – Avalofractus abaculus n. gen. et sp., Beothukis mistakensis Brasier and Antcliffe, Trepassia wardae (Narbonne and Gehling), and Charnia cf. C. masoni Ford. All of these taxa exhibit an alternate array of primary rangeomorph branches that pass off a central stalk or furrow that marks the midline of the petalodium. Avalofractus is remarkably self similar over at least four fractal scales, with each scale represented by double-sided rangeomorph elements that were constrained only at their attachment point with the higher-order branch and thus were free to rotate and pivot relative to other branches. Beothukis is similar in organization, but its primary branches show only one side of a typical rangeomorph element, probably due to longitudinal branch folding, and the position of the individual branches was moderately constrained. Trepassia shows only single-sided branches with both primary and secondary branches emanating from a central stalk or furrow; primary branches were capable of minor pivoting as reflected in bundles of secondary branches. Charnia shows only single-sided primary branches that branch from a zigzag central furrow and that were firmly constrained relative to each. This sequence provides a developmental linkage between Rangea-type and Charnia-type rangeomorphs. Avalonian assemblages show a wide array of rangeomorph constructions, but later Ediacaran assemblages contain a lower diversity of rangeomorphs represented mainly by well-constrained forms.

scholarly journals Three-dimensional topology of the SMC2/SMC4 subcomplex from chicken condensin I revealed by cross-linking and molecular modelling

Open Biology ◽  
2015 ◽  
Vol 5 (2) ◽  
pp. 150005 ◽  
Author(s):  
Helena Barysz ◽  
Ji Hun Kim ◽  
Zhuo Angel Chen ◽  
Damien F. Hudson ◽  
Juri Rappsilber ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Structural Information ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Dimensional Structure ◽  
Cross Linking ◽  
Mitotic Chromosomes ◽  
Essential Components

SMC proteins are essential components of three protein complexes that are important for chromosome structure and function. The cohesin complex holds replicated sister chromatids together, whereas the condensin complex has an essential role in mitotic chromosome architecture. Both are involved in interphase genome organization. SMC-containing complexes are large (more than 650 kDa for condensin) and contain long anti-parallel coiled-coils. They are thus difficult subjects for conventional crystallographic and electron cryomicroscopic studies. Here, we have used amino acid-selective cross-linking and mass spectrometry combined with structure prediction to develop a full-length molecular draft three-dimensional structure of the SMC2/SMC4 dimeric backbone of chicken condensin. We assembled homology-based molecular models of the globular heads and hinges with the lengthy coiled-coils modelled in fragments, using numerous high-confidence cross-links and accounting for potential irregularities. Our experiments reveal that isolated condensin complexes can exist with their coiled-coil segments closely apposed to one another along their lengths and define the relative spatial alignment of the two anti-parallel coils. The centres of the coiled-coils can also approach one another closely in situ in mitotic chromosomes. In addition to revealing structural information, our cross-linking data suggest that both H2A and H4 may have roles in condensin interactions with chromatin.

Mechanical Models of Cell Adhesion Incorporating Nonlinear Behavior and Stochastic Rupture of the Bonds

2011 ◽  
pp. 599-627
Author(s):  
Jean-François Ganghoffer
Keyword(s):  
Cell Membrane ◽  
Three Dimensional ◽  
Point Of View ◽  
Three Dimensional Model ◽  
Stochastic Field ◽  
Present Contribution ◽  
Ecm Extracellular Matrix ◽  
Mechanical Models ◽  
Distribution Of Power ◽  
The Individual

The rolling of a single biological cell is analysed using modelling of the local kinetics of successive attachment and detachment of bonds occurring at the interface between a single cell and the wall of an ECM (extracellular matrix). Those kinetics correspond to a succession of creations and ruptures of ligand-receptor molecular connections under the combined effects of mechanical, physical (both specific and non-specific), and chemical external interactions. A three-dimensional model of the interfacial molecular rupture and adhesion kinetic events is developed in the present contribution. From a mechanical point of view, this chapter works under the assumption that the cell-wall interface is composed of two elastic shells, namely the wall and the cell membrane, linked by rheological elements representing the molecular bonds. Both the time and space fluctuations of several parameters related to the mutual affinity of ligands and receptors are described by stochastic field theory; especially, the individual rupture limits of the bonds are modelled in Fourier space from the spectral distribution of power. The bonds are modelled as macromolecular chains undergoing a nonlinear elastic deformation according to the commonly used freely joined chains model, while the cell membrane facing the ECM wall is modelled as a linear elastic plate. The cell itself is represented by an equivalent constant rigidity. Numerical simulations predict the sequence of broken bonds, as well as the newly established connections on the ‘adhesive part’ of the interface. The interplay between adhesion and rupture entails a rolling phenomenon. In the last part of this chapter, a model of the deformation induced by the random fluctuation of the protrusion force resulting from the variation of affinity with chemiotactic sources is calculated, using stochastic finite element methods in combination with the theory of Gaussian random variables.

scholarly journals Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro

2020 ◽  
Vol 48 (12) ◽  
pp. 6458-6470
Author(s):  
Xiaonong Zhang ◽  
Yingqi Zhang ◽  
Wenke Zhang
Keyword(s):  
Single Molecule ◽  
Tandem Repeats ◽  
Structural Information ◽  
Higher Order ◽  
Single Wall Carbon Nanotubes ◽  
Order Structure ◽  
Telomeric Dna ◽  
Force Microscopy ◽  
Order Structures

Abstract The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.

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