Crystal Structure of a Type-II Cohesin Module from the Bacteroides cellulosolvens Cellulosome Reveals Novel and Distinctive Secondary Structural Elements

2005 ◽  
Vol 348 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Ilit Noach ◽  
Felix Frolow ◽  
Hilla Jakoby ◽  
Sonia Rosenheck ◽  
LindaJ.W. Shimon ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Type Ii ◽  
Structural Elements ◽  
Secondary Structural Elements

Secondary Structure of Decorin-Derived Peptides in Solution

MRS Advances ◽  
2016 ◽  
Vol 1 (27) ◽  
pp. 1965-1970
Author(s):  
Axel T. Neffe ◽  
Stefania Federico ◽  
Andreas Lendlein
Keyword(s):  
Crystal Structure ◽  
Outer Surface ◽  
Cd Spectroscopy ◽  
Helical Conformation ◽  
Structural Elements ◽  
Original Sequence ◽  
X Ray ◽  
Inner Surface ◽  
Β Sheet ◽  
Secondary Structural Elements

ABSTRACTDecorin is a small leucine-rich repeat proteoglycan supporting collagen fibril formation by controlling the rate of collagen fibrillogenesis and fibril dimensions. Peptides derived from the inner surface of decorin have been shown to bind to collagen, while peptides derived from the outer surface do not display such binding affinity. As typical secondary structural elements such as β-sheets and α-helical regions were found in the decorin X-ray crystal structure, here it was investigated by Circular Dichroism (CD) spectroscopy in solution, whether the same structural elements can be found in the derived peptides. Here it is shown that the peptide derived from decorin’s outer surface has the propensity to adopt helical conformation, as it was found in the crystal structure. The results were more pronounced in 80 vol% TFE solution, which led to an increase in the number as well as the length of helices. In contrast, peptides derived from the inner surface had a higher tendency to adopt β-sheet conformation, also in TFE, which corresponds to the conformation of the original sequence in the crystal structure of decorin. This suggests that the peptides derived from decorin adopt the structures present in the native protein.

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.

Crystal structure of magnesium chromium vanadate Mg2CrV3O11, a member of the A2BV3O11 vanadate family

2007 ◽  
Vol 22 (3) ◽  
pp. 246-252 ◽  
Author(s):  
A. Worsztynowicz ◽  
S. M. Kaczmarek ◽  
W. Paszkowicz ◽  
R. Minikayev
Keyword(s):  
Crystal Structure ◽  
Rietveld Method ◽  
Ion Pairs ◽  
Exchange Constant ◽  
Type I ◽  
Type Ii ◽  
Paramagnetic Resonance ◽  
Interatomic Distances ◽  
Electron Paramagnetic ◽  
Full Occupancy

The crystal structure of recently discovered chromium (III) dimagnesium trivanadate (V) Mg2CrV3O11 was refined using the Rietveld method. The crystal system of Mg2CrV3O11 is triclinic with space group P1− (Mg1.7Zn0.3GaV3O11 type) and lattice parameters a=6.4057(1) Å, b=6.8111(1) Å, c=10.0640(2) Å, α=97.523(1)°, β=103.351(1)°, γ=101.750(1)°, and Z=2. The characteristic feature of compounds in the A2BV3O11 (A=Mg, Zn and B=Ga, Fe, Cr) family is a strong tendency to share the octahedral M(1) and M(2) sites by both divalent A and trivalent B atoms, and the bipyramidal M(3) sites occupied by divalent A ions. In the present refinement, the only constraint assuming full occupancy of the M(1), M(2), and M(3) sites leads to the following Cr/(Cr+Mg) ratios: 0.70(2) at M(1), 0.24(2) at M(2), and 0.03(2) at M(3). These occupancies are discussed and compared to those of isotypic compounds. The values of interatomic distances are found to be comparable with those reported by R. D. Shannon in 1976. Electron paramagnetic resonance has been also analyzed. Two absorption lines with g≈2.0 (type I) and g≈1.98 (type II) have been recorded in the EPR spectra, and attributed to V4+ ions and Cr3+–Cr3+ ion pairs, respectively. The exchange constant J between Cr3+ ions has been calculated.

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.

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

Structure of mitogen-activated protein kinase kinase 1 in the DFG-out conformation

2021 ◽  
Vol 77 (12) ◽  
Author(s):  
Setsu Nakae ◽  
Maho Kitamura ◽  
Daisuke Fujiwara ◽  
Masaaki Sawa ◽  
Tsuyoshi Shirai ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Kinase ◽  
Binding Mode ◽  
Mitogen Activated Protein Kinase ◽  
Structural Elements ◽  
Atp Binding Site ◽  
Starting Point ◽  
Mitogen Activated Protein ◽  
Activation Segment ◽  
Protein Kinase Kinase

Eukaryotic protein kinases contain an Asp-Phe-Gly (DFG) motif, the conformation of which is involved in controlling the catalytic activity, at the N-terminus of the activation segment. The motif can be switched between active-state (DFG-in) and inactive-state (DFG-out) conformations: however, the mechanism of conformational change is poorly understood, partly because there are few reports of the DFG-out conformation. Here, a novel crystal structure of nonphosphorylated human mitogen-activated protein kinase kinase 1 (MEK1; amino acids 38–381) complexed with ATP-γS is reported in which MEK1 adopts the DFG-out conformation. The crystal structure revealed that the structural elements (the αC helix and HRD motif) surrounding the active site are involved in the formation/stabilization of the DFG-out conformation. The ATP-γS molecule was bound to the canonical ATP-binding site in a different binding mode that has never been found in previously determined crystal structures of MEK1. This novel ATP-γS binding mode provides a starting point for the design of high-affinity inhibitors of nonphosphorylated inactive MEK1 that adopts the DFG-out conformation.

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.

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