scholarly journals Selecting Folded Proteins from a Library of Secondary Structural Elements

2008 ◽  
Vol 130 (1) ◽  
pp. 176-185 ◽  
Author(s):  
James J. Graziano ◽  
Wenshe Liu ◽  
Roshan Perera ◽  
Bernhard H. Geierstanger ◽  
Scott A. Lesley ◽  
...  
Keyword(s):  
Structural Elements ◽  
Folded Proteins ◽  
Secondary Structural Elements

scholarly journals Parametric Analysis of the Shear Lag Effect in Tube Structural Systems of Tall Buildings

2020 ◽  
Vol 11 (1) ◽  
pp. 278
Author(s):  
Ivan Hafner ◽  
Anđelko Vlašić ◽  
Tomislav Kišiček ◽  
Tvrtko Renić
Keyword(s):  
Parametric Analysis ◽  
Numerical Models ◽  
Tall Buildings ◽  
Structural Systems ◽  
Structural Elements ◽  
Structural System ◽  
Shear Lag ◽  
Shear Lag Effect ◽  
Lag Effect ◽  
Secondary Structural Elements

Horizontal loads such as earthquake and wind are considered dominant loads for the design of tall buildings. One of the most efficient structural systems in this regard is the tube structural system. Even though such systems have a high resistance when it comes to horizontal loads, the shear lag effect that is characterized by an incomplete and uneven activation of vertical elements may cause a series of problems such as the deformation of internal panels and secondary structural elements, which cumulatively grow with the height of the building. In this paper, the shear lag effect in a typical tube structure will be observed and analyzed on a series of different numerical models. A parametric analysis will be conducted with a great number of variations in the structural elements and building layout, for the purpose of giving recommendations for an optimal design of a tube structural system.

In Silico Genetic Robustness Analysis of Secondary Structural Elements in the miRNA Gene

2008 ◽  
Vol 67 (5) ◽  
pp. 560-569 ◽  
Author(s):  
Wenjie Shu ◽  
Ming Ni ◽  
Xiaochen Bo ◽  
Zhiqiang Zheng ◽  
Shengqi Wang
Keyword(s):  
In Silico ◽  
Mirna Gene ◽  
Robustness Analysis ◽  
Structural Elements ◽  
Genetic Robustness ◽  
Secondary Structural Elements

In silico identification and characterization of sensory motifs in the transcriptional regulators of the ArsR-SmtB family

Metallomics ◽  
2018 ◽  
Vol 10 (10) ◽  
pp. 1476-1500 ◽  
Author(s):  
Rima Roy ◽  
Saikat Samanta ◽  
Surajit Patra ◽  
Nav Kumar Mahato ◽  
Rudra P. Saha
Keyword(s):  
In Silico ◽  
Transcriptional Regulators ◽  
Transcriptional Repressors ◽  
Structural Elements ◽  
In Silico Identification ◽  
Metal Efflux ◽  
Identification And Characterization ◽  
Secondary Structural Elements ◽  
Efflux Proteins

The ArsR-SmtB family of transcriptional repressors regulates the transcription of metal-efflux proteins by binding specific metals at a variety of secondary structural elements, called motifs, on the surface of the proteins.

Targeting G-quadruplexes in the rhinovirus genome by Pyridostatin inhibits uncoating 3 and highlights a critical role for sodium ions.

2021 ◽  
Author(s):  
Antonio Real-Hohn ◽  
Martin Groznica ◽  
Georg Kontaxis ◽  
Rong Zhu ◽  
Otávio Chaves ◽  
...  
Keyword(s):  
Common Cold ◽  
Critical Role ◽  
Sodium Ions ◽  
Structural Elements ◽  
Temperature Dependent ◽  
Physiological Conditions ◽  
Metastable Structures ◽  
G Quadruplex ◽  
The Common ◽  
Secondary Structural Elements

Abstract The ~ 2.4 µm long rhinovirus ss(+)RNA genome consists of roughly 7,200 nucleotides. It is tightly folded to fit into the ~ 22 nm diameter void in the protein capsid. In addition to previously predicted secondary structural elements in the RNA, using the QGRS mapper, we revealed the presence of multiple quadruplex forming G-rich sequences (QGRS) in the RV-A, B, and C clades, with four of them being exquisitely conserved. The biophysical analyses of ribooligonucleotides corresponding to selected QGRS demonstrate G-quadruplex (GQ) formation in each instance and resulted in discovering another example of an unconventional, two-layer zero-nucleotide loop RNA GQ stable at physiological conditions. By exploiting the temperature-dependent viral breathing to allow diffusion of small compounds into the virion, we demonstrate that the GQ-binding compounds PhenDC3 and pyridostatin (PDS) uniquely interfere with viral uncoating. Remarkably, this inhibition was entirely prevented in the presence of K+ but not Na+, despite the higher GQ stabilising effect of K+. Based on virus thermostability studies combined with ultrastructural imaging of isolated viral RNA, we propose a mechanism where Na+ keeps the encapsidated genome loose, allowing its penetration by PDS to promote the transition of QGRS sequestered in alternative metastable structures into GQs. The resulting conformational change then materialises in a severely compromised RNA release from the proteinaceous shell. Targeting extracellularly circulating RVs with GQ-stabilisers might thus become a novel way of combating the common cold.

scholarly journals NMR resonance assignment and dynamics of profilin from Heimdallarchaeota

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Syed Razaul Haq ◽  
Sabeen Survery ◽  
Fredrik Hurtig ◽  
Ann-Christin Lindås ◽  
Celestine N. Chi
Keyword(s):  
Structural Analysis ◽  
Structural Properties ◽  
Resonance Assignment ◽  
Eukaryotic Cell ◽  
Nmr Resonance Assignment ◽  
Metagenomic Data ◽  
Divergent Evolution ◽  
Structural Elements ◽  
Scientific Question ◽  
Secondary Structural Elements

Abstract The origin of the eukaryotic cell is an unsettled scientific question. The Asgard superphylum has emerged as a compelling target for studying eukaryogenesis due to the previously unseen diversity of eukaryotic signature proteins. However, our knowledge about these proteins is still relegated to metagenomic data and very little is known about their structural properties. Additionally, it is still unclear if these proteins are functionally homologous to their eukaryotic counterparts. Here, we expressed, purified and structurally characterized profilin from Heimdallarchaeota in the Asgard superphylum. The structural analysis shows that while this profilin possesses similar secondary structural elements as eukaryotic profilin, it contains additional secondary structural elements that could be critical for its function and an indication of divergent evolution.

Packing of Secondary Structural Elements in Proteins

1993 ◽  
Vol 233 (3) ◽  
pp. 464-479 ◽  
Author(s):  
B.V.B. Reddy ◽  
Tom L. Blundell
Keyword(s):  
Structural Elements ◽  
Secondary Structural Elements

scholarly journals The Interactions Of Secondary Structural Elements In The Achitecture Of Membrane Proteins

2009 ◽  
Vol 96 (3) ◽  
pp. 339a
Author(s):  
Jean-Pierre Duneau ◽  
Jaime Arce ◽  
James N. Sturgis
Keyword(s):  
Membrane Proteins ◽  
Structural Elements ◽  
Secondary Structural Elements

Importance of mRNA Secondary Structural Elements for the Expression of Influenza Virus Genes

2009 ◽  
Vol 13 (5) ◽  
pp. 421-430 ◽  
Author(s):  
Petr O. Ilyinskii ◽  
Thorsten Schmidt ◽  
Dmitry Lukashev ◽  
Anatoli B. Meriin ◽  
Galini Thoidis ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Structural Elements ◽  
Secondary Structural Elements
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