Simple Cryoprotectant-Free Method to Advance Pulsed Dipolar ESR Spectroscopy for Capturing Protein Conformational Ensembles

2022 ◽  
Author(s):  
Te-Yu Kao ◽  
Chien-Lun Hung ◽  
Yu-Jing Lan ◽  
Su Wei Lee ◽  
Yun-Wei Chiang
Keyword(s):  
Esr Spectroscopy ◽  
Conformational Ensembles

Electrochemical behaviour and ESR spectra of nitro substituted mono- and dibenzoylmethylenebenzthiazolines and selenazolines

1979 ◽  
Vol 44 (5) ◽  
pp. 1540-1551 ◽  
Author(s):  
Jaro Komenda ◽  
Jiří Huzlík
Keyword(s):  
Electron Transfer ◽  
Esr Spectroscopy ◽  
Electrochemical Behaviour ◽  
Spectroscopic Studies ◽  
Esr Spectra ◽  
Slow Electron

Compounds of the type of 2-(4'-nitrobenzoyl)methylene-3-ethylbenzothiazoline (I) and 2-bis-(p-nitrobenzoyl)methylene-3-ethylbenzothiazoline (II) were studied polarographically and by ESR spectroscopy to obtain informations about their electrochemical and follow-up reactions and their conformation. Whereas with compounds of the type I the conjugation in their molecules is preserved, with type II the coplanarity of the molecules is disturbed, which is manifested in the values of the splitting constants of the ESR spectra and a slow electron transfer between both nitrophenyl substituents. These conclusions are supported by NMR spectroscopic studies.

Association of radical anion with alkali cations. IV. ESR study of the 4-nitrobenzophenone radical anion

1980 ◽  
Vol 45 (2) ◽  
pp. 369-375 ◽  
Author(s):  
Stanislav Miertuš ◽  
Ondrej Kyseľ
Keyword(s):  
Hyperfine Splitting ◽  
Radical Anion ◽  
Esr Spectroscopy ◽  
Supporting Electrolyte ◽  
Esr Spectra ◽  
Proton Donor ◽  
Alkali Cations

The 4-nitrobenzophenone radical anion prepared by electrolysis was studied by ESR spectroscopy. On the basis of the interpretation of ESR spectra, the conformation of this system was estimated. The effect of the concentration of supporting electrolyte and of the presence of a proton-donor agent (C2H5OH) was examined. It is assumed that changes in hyperfine splitting constants are caused by association.

Stability of radical anions derived from substituted 5-nitrofurans investigated by ESR spectroscopy

1985 ◽  
Vol 50 (7) ◽  
pp. 1594-1601 ◽  
Author(s):  
Jiří Klíma ◽  
Larisa Baumane ◽  
Janis Stradinš ◽  
Jiří Volke ◽  
Romualds Gavars
Keyword(s):  
Radical Anion ◽  
High Stability ◽  
Esr Spectroscopy ◽  
Reaction Path ◽  
Order Reaction ◽  
Second Order ◽  
Radical Anions ◽  
Second Order Reaction ◽  
Unpaired Electron Density ◽  
The Stability

It has been found that the decay in dimethylformamide and dimethylformamide-water mixtures of radical anions in five of the investigated 5-nitrofurans is governed by a second-order reaction. Only the decay of the radical anion generated from 5-nitro-2-furfural III may be described by an equation including parallel first- and second-order reactions; this behaviour is evidently caused by the relatively high stability of the corresponding dianion, this being an intermediate in the reaction path. The presence of a larger conjugated system in the substituent in position 2 results in a decrease of the unpaired electron density in the nitro group and, consequently, an increase in the stability of the corresponding radical anions.

The effect of cation concentration on the nitrogen splitting constant of nitroxide free radicals

1990 ◽  
Vol 55 (10) ◽  
pp. 2377-2380
Author(s):  
Hamza A. Hussain
Keyword(s):  
Hydrogen Peroxide ◽  
Hydrogen Bonding ◽  
Free Radicals ◽  
Esr Spectroscopy ◽  
The Other ◽  
Tetraethylammonium Bromide ◽  
Splitting Constant ◽  
The One ◽  
Positively Charged ◽  
Two Equilibria

Nitroxide free radicals prepared from diethylamine, piperidine and pyrrolidine by oxidation with hydrogen peroxide were studied by ESR spectroscopy. The changes in the 14N splitting constant (aN) caused by the addition of KBr or tetraethylammonium bromide were measured in dependence on the concentration of the ions. For diethylamine nitroxide and piperidine nitroxide, the results are discussed in terms of two equilibria: the one, involving the anion, is associated with a gain or loss of hydrogen bonds to the nitroxide oxygen atom, the other is associated with the formation of solvent shared units involving the cation, which results in changes in the hydrogen bonding strenght. The large increase in the aN value in the case of pyrrolidine nitroxide is explained in terms of an interaction from one side of the positively charged N atom; the increase in aN in the case of diethylamine and piperidine nitroxides is explained in terms of interactions with both sides of the positively charged N atom.

Conformational ensembles

Science ◽  
2021 ◽  
Vol 372 (6538) ◽  
pp. 142.2-142
Author(s):  
Valda Vinson
Keyword(s):  
Conformational Ensembles

scholarly journals Exploring Curated Conformational Ensembles of Intrinsically Disordered Proteins in the Protein Ensemble Database

2021 ◽  
Vol 1 (7) ◽  
Author(s):  
Federica Quaglia ◽  
Tamas Lazar ◽  
András Hatos ◽  
Peter Tompa ◽  
Damiano Piovesan ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Conformational Ensembles ◽  
Intrinsically Disordered

scholarly journals A graph-based algorithm for detecting rigid domains in protein structures

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Truong Khanh Linh Dang ◽  
Thach Nguyen ◽  
Michael Habeck ◽  
Mehmet Gültas ◽  
Stephan Waack
Keyword(s):  
Structural Changes ◽  
Viterbi Algorithm ◽  
Structural Information ◽  
Line Graph ◽  
Clustering Algorithms ◽  
Protein Structures ◽  
Alternative Methods ◽  
Structural Transitions ◽  
Tuning Parameters ◽  
Conformational Ensembles

Abstract Background Conformational transitions are implicated in the biological function of many proteins. Structural changes in proteins can be described approximately as the relative movement of rigid domains against each other. Despite previous efforts, there is a need to develop new domain segmentation algorithms that are capable of analysing the entire structure database efficiently and do not require the choice of protein-dependent tuning parameters such as the number of rigid domains. Results We develop a graph-based method for detecting rigid domains in proteins. Structural information from multiple conformational states is represented by a graph whose nodes correspond to amino acids. Graph clustering algorithms allow us to reduce the graph and run the Viterbi algorithm on the associated line graph to obtain a segmentation of the input structures into rigid domains. In contrast to many alternative methods, our approach does not require knowledge about the number of rigid domains. Moreover, we identified default values for the algorithmic parameters that are suitable for a large number of conformational ensembles. We test our algorithm on examples from the DynDom database and illustrate our method on various challenging systems whose structural transitions have been studied extensively. Conclusions The results strongly suggest that our graph-based algorithm forms a novel framework to characterize structural transitions in proteins via detecting their rigid domains. The web server is available at http://azifi.tz.agrar.uni-goettingen.de/webservice/.

scholarly journals Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs

2021 ◽  
Vol 22 (3) ◽  
pp. 1364
Author(s):  
V. V. Krishnan ◽  
Timothy Bentley ◽  
Alina Xiong ◽  
Kalyani Maitra
Keyword(s):  
Principal Component ◽  
Md Simulations ◽  
Conformational Space ◽  
Random Coil ◽  
Radius Of Gyration ◽  
Small Peptides ◽  
Conformational Ensembles ◽  
Solution State ◽  
Peptide Motifs ◽  
Explicit Solvent

Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, AEVXEVG with X = L, F, A, or G, comprehensive NMR, and MD simulations were performed. The rationale for selecting the particular model peptides is based on the high variability in the occurrence of tri-peptide E*L between the transmembrane β-barrel (TMB) than in globular proteins. The ensemble of conformations sampled by E*L was compared between the three sets of ensembles derived from NMR spectroscopy, MD simulations with explicit solvent, and the random coil conformations. In addition to the estimation of global determinants such as the radius of gyration of a large sample of structures, the ensembles were analyzed using principal component analysis (PCA). In general, the results suggest that the -EVL- peptide indeed adopts a conformational preference that is distinctly different not only from a random distribution but also from other peptides studied here. The relatively straightforward approach presented herein could help understand the conformational preferences of small peptides in the solution state.

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