Faculty Opinions recommendation of Cooperative unfolding of residual structure in heat denatured proteins by urea and guanidinium chloride.

Author(s):  
Lisa J Lapidus
PLoS ONE ◽  
2015 ◽  
Vol 10 (6) ◽  
pp. e0128740 ◽  
Author(s):  
Ritu Singh ◽  
Md. Imtaiyaz Hassan ◽  
Asimul Islam ◽  
Faizan Ahmad

1967 ◽  
Vol 242 (19) ◽  
pp. 4486-4489 ◽  
Author(s):  
Kirk C. Aune ◽  
Ahmad Salahuddin ◽  
Mario H. Zarlengo ◽  
Charles Tanford

1973 ◽  
Vol 51 (5) ◽  
pp. 581-585 ◽  
Author(s):  
M. Kugimiya ◽  
C. C. Bigelow

The denaturation of hen egg-white lysozyme has been studied under a variety of denaturing conditions by difference spectroscopy, polarimetry, and viscometry. It has been found that the lysozyme molecule can take up four different denatured conformations, depending on the denaturant used. Urea and guanidinium chloride produce the most completely denatured state, IV, and, listed in the order of increasing residual structure, lithium chloride gives state III, temperature state II, and lithium perchlorate state I. Differences in the spectra at 300 nm have been a valuable aid in relating the different denatured states to each other.


1996 ◽  
Vol 1 (5) ◽  
pp. R95-R106 ◽  
Author(s):  
Lorna J. Smith ◽  
Klaus M. Fiebig ◽  
Harald Schwalbe ◽  
Christopher M. Dobson

2018 ◽  
Author(s):  
M. S. Chandak ◽  
T. Nakamura ◽  
M. Yagi-Utsumi ◽  
T. Yamaguchi ◽  
K. Kato ◽  
...  

AbstractThe characterization of residual structures persistent in unfolded proteins in concentrated denaturant solution is currently an important issue in studies of protein folding, because the residual structure present, if any, in the unfolded state may form a folding initiation site and guide the subsequent folding reactions. Here, we thus studied the hydrogen/deuterium (H/D)-exchange behavior of unfolded ubiquitin in 6.0 M guanidinium chloride at pH 2.6 and 20°C. We employed a dimethylsulfoxide (DMSO)-quenched H/D-exchange NMR technique with the use of spin desalting columns, which allowed us to make a quick medium exchange from 6.0 M guanidinium chloride to a quenching DMSO solution. The technique is particularly effective for studies of the H/D-exchange kinetics of unfolded proteins in concentrated denaturant. By the backbone resonance assignment of the hetero-nuclear single quantum coherence spectrum of 15N-labeled ubiquitin in the DMSO solution, we successfully investigated the H/D-exchange kinetics of 27 identified peptide amide groups in the ubiquitin sequence. Although most of these amide groups were not protected, the four amide groups of Ile3, Val5, Ile13 and Leu73 were weakly but significantly protected with a protection factor of 2.5–3.0, indicating that there were residual structures in unfolded ubiquitin and that these amide groups were 60–67% hydrogen-bonded by the residual structures. We show that the first native β-hairpin, composed of residues 2–16 in the native ubiquitin structure, is partially structured even in 6.0 M guanidinium chloride and that the amide group of Leu73 is protected by a nonnative hydrogen-bonding interaction. From comparison with the previous folding studies of ubiquitin, it is concluded that the residual native β-hairpin in unfolded ubiquitin forms a folding initiation site and guides the subsequent folding reactions of the protein.


2005 ◽  
Vol 387 (2) ◽  
pp. 479-488 ◽  
Author(s):  
Beatriz MAESTRO ◽  
Jesús M. SANZ

Choline-binding modules are present in some virulence factors and many other proteins of Streptococcus pneumoniae (Pneumococcus). The most extensively studied choline-binding module is C-LytA, the C-terminal moiety of the pneumococcal cell-wall amidase LytA. The three-dimensional structure of C-LytA is built up from six loop-hairpin structures forming a left-handed β-solenoid with four choline-binding sites. The affinity of C-LytA for choline and other structural analogues allows its use as an efficient fusion tag for single-step purification of hybrid proteins. In the present study, we characterize the folding and stability of C-LytA by chemical and thermal equilibrium denaturation experiments. Unfolding experiments using guanidinium chloride at pH 7.0 and 20 °C suggest the existence of two partly folded states (I1 and I2) in the following model: N (native)→I1⇆I2. The N→I1 transition is non-co-operative and irreversible, and is significant even in the absence of a denaturant. In contrast, the I1⇆I2 transition is co-operative and reversible, with an associated freeenergy change (ΔG0) of 30.9±0.8 kJ·mol−1. The residual structure in the I2 state is unusually stable even in 7.4 M guanidinium chloride. Binding of choline stabilizes the structure of the native state, induces its dimerization and prevents the accumulation of the I1 species ([N]2⇆[I2]2, ΔG0=50.1±0.8 kJ·mol−1). Fluorescence and CD measurements, gel-filtration chromatography and limited proteolysis suggest that I1 differs from N in the local unfolding of the N-terminal β-hairpins, and that I2 has a residual structure in the C-terminal region. Thermal denaturation of C-LytA suggests the accumulation of at least the I1 species. These results might pave the way for an effective improvement of its biotechnological applications by protein engineering.


Author(s):  
A. B. Edwards

During a petrological examination of samples of bauxite from Boolarra, in south Gippsland, Victoria, it was noted that some specimens of the bauxite, which is largely derived from Tertiary olivine-basalt, contained numerous grains of yellow-brown to amber-yellow leucoxene. The leucoxene is clearly pseudo-morphous after ilmenite, residual particles of ilmenite being enclosed in many of the leucoxene grains. Most of the leucoxene grains are opaque, but occasional grains are translucent to transparent, though isotropic. Some of them show parallel markings suggestive of cleavage, but probably a residual structure from the replaced ilmenite. In view of the highly aluminous nature of the enclosing rock, there seemed some possibility that this mineral might be the little-known aluminium titanate, xanthitane. It was thought, therefore, that if a pure sample of the mineral could be prepared, a chemical analysis would establish its identity.


2021 ◽  
Vol 11 (12) ◽  
pp. 5656
Author(s):  
Yufan Zeng ◽  
Jiashan Tang

Graph neural networks (GNNs) have been very successful at solving fraud detection tasks. The GNN-based detection algorithms learn node embeddings by aggregating neighboring information. Recently, CAmouflage-REsistant GNN (CARE-GNN) is proposed, and this algorithm achieves state-of-the-art results on fraud detection tasks by dealing with relation camouflages and feature camouflages. However, stacking multiple layers in a traditional way defined by hop leads to a rapid performance drop. As the single-layer CARE-GNN cannot extract more information to fix the potential mistakes, the performance heavily relies on the only one layer. In order to avoid the case of single-layer learning, in this paper, we consider a multi-layer architecture which can form a complementary relationship with residual structure. We propose an improved algorithm named Residual Layered CARE-GNN (RLC-GNN). The new algorithm learns layer by layer progressively and corrects mistakes continuously. We choose three metrics—recall, AUC, and F1-score—to evaluate proposed algorithm. Numerical experiments are conducted. We obtain up to 5.66%, 7.72%, and 9.09% improvements in recall, AUC, and F1-score, respectively, on Yelp dataset. Moreover, we also obtain up to 3.66%, 4.27%, and 3.25% improvements in the same three metrics on the Amazon dataset.


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