scholarly journals Higher-order Structure of Yeast tRNATyr and Its Chimeric Mutants in Aqueous Solution As Studied by Hydroxyl Radical "Footprinting".

1993 ◽  
Vol 5 (4) ◽  
pp. 85-90
Author(s):  
Ichirou MOTOKI ◽  
Takashi YOKOGAWA ◽  
Tsunemi HASEGAWA ◽  
Kimitsuna WATANABE ◽  
Kazuya NISHIKAWA
Keyword(s):  
Aqueous Solution ◽  
Hydroxyl Radical ◽  
Higher Order ◽  
Order Structure ◽  
Hydroxyl Radical Footprinting

Higher-Order Structure Formation in Adsorbed Monolayers at Aqueous Solution Surfaces Studied by Brewster Angle Microscopy

Langmuir ◽  
2000 ◽  
Vol 16 (7) ◽  
pp. 3345-3348 ◽  
Author(s):  
Md. Mufazzal Hossain ◽  
Masaaki Yoshida ◽  
Teiji Kato
Keyword(s):  
Aqueous Solution ◽  
Structure Formation ◽  
Higher Order ◽  
Brewster Angle ◽  
Order Structure ◽  
Brewster Angle Microscopy

Macrocycles of Higher Ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

Macrocycles of Higher ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

2019 ◽  
Vol 26 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Natalie K. Garcia ◽  
Galahad Deperalta ◽  
Aaron T. Wecksler
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Solvent Accessibility ◽  
Higher Order ◽  
Structure Characterization ◽  
Order Structure ◽  
Protein Footprinting ◽  
Wide Range

Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. Conclusion: Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

Heterogeneous Fenton Catalytic Removal of Organic Pollutant in Aqueous Solution by using Coal Gangue as a Catalyst

2019 ◽  
Vol 12 (4) ◽  
pp. 312-325
Author(s):  
Jiwei Zhang ◽  
Jingjing Xu ◽  
Shuaixia Liu ◽  
Baoxiang Gu ◽  
Feng Chen ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Peroxide ◽  
Hydroxyl Radical ◽  
Removal Rate ◽  
Organic Pollutant ◽  
Coal Gangue ◽  
Ion Leakage ◽  
Heterogeneous Fenton ◽  
Solution Ph ◽  
X Ray

Background: Coal gangue was used as a catalyst in heterogeneous Fenton process for the degradation of azo dye and phenol. The influencing factors, such as solution pH gangue concentration and hydrogen peroxide dosage were investigated, and the reaction mechanism between coal gangue and hydrogen peroxide was also discussed. Methods: Experimental results showed that coal gangue has the ability to activate hydrogen peroxide to degrade environmental pollutants in aqueous solution. Under optimal conditions, after 60 minutes of treatment, more than 90.57% of reactive red dye was removed, and the removal efficiency of Chemical Oxygen Demand (COD) up to 72.83%. Results: Both hydroxyl radical and superoxide radical anion participated in the degradation of organic pollutant but hydroxyl radical predominated. Stability tests for coal gangue were also carried out via the continuous degradation experiment and ion leakage analysis. After five times continuous degradation, dye removal rate decreased slightly and the leached Fe was still at very low level (2.24-3.02 mg L-1). The results of Scanning Electron Microscope (SEM), energy dispersive X-Ray Spectrometer (EDS) and X-Ray Powder Diffraction (XRD) indicated that coal gangue catalyst is stable after five times continuous reuse. Conclusion: The progress in this research suggested that coal gangue is a potential nature catalyst for the efficient degradation of organic pollutant in water and wastewater via the Fenton reaction.

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