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 Higher order structure of proteins and allosterism.

Kobunshi ◽  
1986 ◽  
Vol 35 (10) ◽  
pp. 942-945
Author(s):  
Hiroshi Kihara
Keyword(s):  
Higher Order ◽  
Order Structure ◽  
Structure Of Proteins

Application of Bayesian Network in Learning Gene Network

2007 ◽  
pp. 319-341
Author(s):  
Tie-Fei Liu ◽  
Wing-Kin Sung ◽  
Ankush Mittal
Keyword(s):  
Mathematical Models ◽  
Bayesian Network ◽  
Gene Networks ◽  
Gene Network ◽  
Higher Order ◽  
Learning Performance ◽  
Biological Factors ◽  
Stochastic Events ◽  
Order Structures

Exact determination of a gene network is required to discover the higher-order structures of an organism and to interpret its behavior. Currently, learning gene network is one of the central themes of the post genome era. A lot of mathematical models are applied to learn gene networks. Among them, Bayesian network has shown its advantages over other methods because of its abilities to handle stochastic events, control noise, and handle dataset with a few replicates. In this chapter, we will introduce how Bayesian network has been applied to learn gene networks and how we integrated the important biological factors into the framework of Bayesian network to improve the learning performance.

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.

Higher order structure of proteins solubilized in AOT reverse micelles

2004 ◽  
Vol 38 (3-4) ◽  
pp. 179-185 ◽  
Author(s):  
Kazumitsu Naoe ◽  
Kazuki Noda ◽  
Mikio Kawagoe ◽  
Masanao Imai
Keyword(s):  
Reverse Micelles ◽  
Higher Order ◽  
Order Structure ◽  
Aot Reverse Micelles ◽  
Structure Of Proteins

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.

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