The Ribosome: A biochemist's mechano set

1985 ◽  
Vol 63 (5) ◽  
pp. 313-318 ◽  
Author(s):  
Ross N. Nazar
Keyword(s):  
Protein Synthesis ◽  
Complex Structure ◽  
Higher Order ◽  
Order Structure ◽  
Ribosomal Rnas ◽  
Experimental Approaches ◽  
Universal Structure ◽  
Order Structures

A ribosome, the cellular site for protein synthesis, is a very complex organelle composed of a myriad of macromolecular substructures. As models for this complex structure, we have been examining the structures and interactions of eukaryotic 5S and 5.8S rRNAs using adaptations of rapid RNA gel sequencing techniques. Estimates for their higher order structures have been proposed or evaluated, sites of interaction with other ribosomal components have been delineated, and the topography of these RNAs within the intact ribosome or 60S subunit have been examined. The results indicate that a universal structure for the ribosomal RNAs may only be present within the ribosome, that these molecules are probably present, at least in part, within the ribosomal interface, and that the bases for interactions with other ribosomal components are strongly dependent on their higher order structure. The experimental approaches which underlie these studies are considered in this review and the significance of the results with respect to the function and evolution of the ribosome are briefly discussed.

Importance of the determination of the higher order structure in the in-use stability studies of biopharmaceuticals

2020 ◽  
Vol 9 (2) ◽  
pp. 49-51
Author(s):  
Alian A Astier
Keyword(s):  
Analytical Methods ◽  
Higher Order ◽  
Order Structure ◽  
Spectroscopic Methods ◽  
Stability Studies ◽  
Structure Of Proteins ◽  
Order Structures

Knowledge of the higher order structure of proteins is important in biopharmacological studies, such as in biosimilar comparability studies. This paper describes the analytical methods available to determine higher order structures. It finds that, although other methods exist, spectroscopic methods remain most commonly used.

scholarly journals Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences

2018 ◽  
Vol 293 (44) ◽  
pp. 17033-17049 ◽  
Author(s):  
Hisao Masai ◽  
Naoko Kakusho ◽  
Rino Fukatsu ◽  
Yue Ma ◽  
Keisuke Iida ◽  
...  
Keyword(s):  
Replication Timing ◽  
Higher Order ◽  
Heat Denaturation ◽  
Order Structure ◽  
Molecular Architecture ◽  
Binding Assays ◽  
Dna Structures ◽  
Alternative Structures ◽  
Dna Strands ◽  
Order Structures

G-quadruplexes (G4s) are four-stranded DNA structures comprising stacks of four guanines, are prevalent in genomes, and have diverse biological functions in various chromosomal structures. A conserved protein, Rap1-interacting factor 1 (Rif1) from fission yeast (Schizosaccharomyces pombe), binds to Rif1-binding sequence (Rif1BS) and regulates DNA replication timing. Rif1BS is characterized by the presence of multiple G-tracts, often on both strands, and their unusual spacing. Although previous studies have suggested generation of G4-like structures on duplex Rif1BS, its precise molecular architecture remains unknown. Using gel-shift DNA binding assays and DNA footprinting with various nuclease probes, we show here that both of the Rif1BS strands adopt specific higher-order structures upon heat denaturation. We observed that the structure generated on the G-strand is consistent with a G4 having unusually long loop segments and that the structure on the complementary C-strand does not have an intercalated motif (i-motif). Instead, we found that the formation of the C-strand structure depends on the G4 formation on the G-strand. Thus, the higher-order structure generated at Rif1BS involved both DNA strands, and in some cases, G4s may form on both of these strands. The presence of multiple G-tracts permitted the formation of alternative structures when some G-tracts were mutated or disrupted by deazaguanine replacement, indicating the robust nature of DNA higher-order structures generated at Rif1BS. Our results provide general insights into DNA structures generated at G4-forming sequences on duplex DNA.

scholarly journals Simplicial closure and higher-order link prediction

2018 ◽  
Vol 115 (48) ◽  
pp. E11221-E11230 ◽  
Author(s):  
Austin R. Benson ◽  
Rediet Abebe ◽  
Michael T. Schaub ◽  
Ali Jadbabaie ◽  
Jon Kleinberg
Keyword(s):  
Link Prediction ◽  
Higher Order ◽  
Edge Density ◽  
Limited Attention ◽  
Order Structure ◽  
Pairwise Interactions ◽  
Positive Indicators ◽  
New Interactions ◽  
Organizational Principles ◽  
Order Structures

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once—for example, communication within a group rather than person to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental difference from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

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.

scholarly journals On Higher Order Structures in Thermodynamics

Entropy ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. 1147
Author(s):  
Valentin Lychagin ◽  
Mikhail Roop
Keyword(s):  
Fourth Order ◽  
Theory Of Measurement ◽  
Higher Order ◽  
Order Structure ◽  
Random Vectors ◽  
Cubic Form ◽  
Extremal Measures ◽  
Lagrangian Manifolds ◽  
Classical Thermodynamics ◽  
Order Structures

We present the development of the approach to thermodynamics based on measurement. First of all, we recall that considering classical thermodynamics as a theory of measurement of extensive variables one gets the description of thermodynamic states as Legendrian or Lagrangian manifolds representing the average of measurable quantities and extremal measures. Secondly, the variance of random vectors induces the Riemannian structures on the corresponding manifolds. Computing higher order central moments, one drives to the corresponding higher order structures, namely the cubic and the fourth order forms. The cubic form is responsible for the skewness of the extremal distribution. The condition for it to be zero gives us so-called symmetric processes. The positivity of the fourth order structure gives us an additional requirement to thermodynamic state.

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.

scholarly journals Septin Phosphorylation and Coiled-Coil Domains Function in Cell and Septin Ring Morphology in the Filamentous Fungus Ashbya gossypii

2012 ◽  
Vol 12 (2) ◽  
pp. 182-193 ◽  
Author(s):  
Rebecca A. Meseroll ◽  
Patricia Occhipinti ◽  
Amy S. Gladfelter
Keyword(s):  
Filamentous Fungus ◽  
Cell Function ◽  
Coiled Coil ◽  
Higher Order ◽  
Ring Formation ◽  
Order Structure ◽  
Ashbya Gossypii ◽  
Septin Ring ◽  
Order Structures

ABSTRACT Septins are a class of GTP-binding proteins conserved throughout many eukaryotes. Individual septin subunits associate with one another and assemble into heteromeric complexes that form filaments and higher-order structures in vivo . The mechanisms underlying the assembly and maintenance of higher-order structures in cells remain poorly understood. Septins in several organisms have been shown to be phosphorylated, although precisely how septin phosphorylation may be contributing to the formation of high-order septin structures is unknown. Four of the five septins expressed in the filamentous fungus, Ashbya gossypii , are phosphorylated, and we demonstrate here the diverse roles of these phosphorylation sites in septin ring formation and septin dynamics, as well as cell morphology and viability. Intriguingly, the alteration of specific sites in Cdc3p and Cdc11p leads to a complete loss of higher-order septin structures, implicating septin phosphorylation as a regulator of septin structure formation. Introducing phosphomimetic point mutations to specific sites in Cdc12p and Shs1p causes cell lethality, highlighting the importance of normal septin modification in overall cell function and health. In addition to discovering roles for phosphorylation, we also present diverse functions for conserved septin domains in the formation of septin higher-order structure. We previously showed the requirement for the Shs1p coiled-coil domain in limiting septin ring size and reveal here that, in contrast to Shs1p, the coiled-coil domains of Cdc11p and Cdc12p are required for septin ring formation. Our results as a whole reveal novel roles for septin phosphorylation and coiled-coil domains in regulating septin structure and function.

Microsized Structures Fabricated with Nanoparticles as Building Blocks

1998 ◽  
Vol 536 ◽  
Author(s):  
Yongchi Tian ◽  
A. D. Dinsmore ◽  
S. B. Qadri ◽  
B. R. Ratna
Keyword(s):  
Radial Growth ◽  
Building Blocks ◽  
Higher Order ◽  
Surfactant Templating ◽  
Order Structures

AbstractHere we report a nanoparticulate route to Y2O3 nanofibers (~50 nm in diameter and a few micrometers in length) and for the radial growth of ZnS spheres (200-800 nm diameter). Well-defined higher order structures are developed upon thermostatically aging the dispersions of monomeric nanocrystals. The shapes of the “macromolecules„ are correlated to primary monomeric nanocrystallites, the growing time and temperature, and surfactant templating agents. It is anticipated that this approach should inspire fabrication of nanoparticulate structures by using primary nanoparticles as monomers.

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