Cold Shock Domain of the Human Y-Box Protein YB-1. Backbone Dynamics and Equilibrium between the Native State and a Partially Unfolded State†

Biochemistry ◽  
2004 ◽  
Vol 43 (31) ◽  
pp. 10237-10246 ◽  
Author(s):  
Cathelijne P. A. M. Kloks ◽  
Marco Tessari ◽  
Geerten W. Vuister ◽  
Cornelis W. Hilbers
Keyword(s):  
Cold Shock ◽  
Backbone Dynamics ◽  
Native State ◽  
Unfolded State ◽  
Cold Shock Domain ◽  
Partially Unfolded

Salt as a catalyst in the mitochondria: returning cytochrome c to its native state after it misfolds on the surface of cardiolipin containing membranes

2014 ◽  
Vol 50 (28) ◽  
pp. 3674-3676 ◽  
Author(s):  
Leah A. Pandiscia ◽  
Reinhard Schweitzer-Stenner
Keyword(s):  
Cytochrome C ◽  
Native State ◽  
Unfolded State ◽  
Partially Unfolded

After binding to TOCL/DOPC(20%/80%) liposomes ferricytochrome c remains mostly in its partially unfolded state under folding conditions. The addition of 100 mM NaCl switches it back to the native state.

scholarly journals Reversible deactivation of β-lactamase by quinacillin. Extent of the conformational change in the isolated transitory complex

1986 ◽  
Vol 237 (3) ◽  
pp. 723-730 ◽  
Author(s):  
K C Persaud ◽  
R H Pain ◽  
R Virden
Keyword(s):  
Relative Viscosity ◽  
Fold Increase ◽  
Order Rate Constant ◽  
Side Chain ◽  
Native State ◽  
Significant Difference ◽  
Unfolded State ◽  
Normal Enzyme ◽  
Partially Unfolded ◽  
Asymmetric Environment

Conditions have been established where the deactivation of the beta-lactamase from Staphylococcus aureus PC1 by the penicillin substrate, quinacillin, is close to complete but fully reversible. The temperature-dependence of the rate of re-activation indicated a half-life of about 170 min for the deactivated state at 0 degrees C. Measurement of the relative viscosity of mixtures of enzyme and quinacillin at 8.4 degrees C ruled out any significant difference in shape or solvation between the deactivated and the normal enzyme. C.d. measurements of the deactivated protein, separated from excess quinacillin, showed that the quinacillin side-chain chromophore was bound in an asymmetric environment. The ellipticity associated with the bound quinacillin chromophore decreased with the same first-order rate constant as that for reappearance of enzyme activity. These findings support the accumulation of a deactivated state that contains bound quinacillin or a derivative. Quinacillin caused a 3-fold increase in the rate of 3H exchange-out (at a rate that was low compared with that for the substantially unfolded or expanded protein). However, there was rapid exchange-out of about 50 3H atoms on addition of 1 M-urea to the deactivated enzyme, whereas the same concentration had no effect on the exchange-out of 3H from native enzyme. The interpretation that quinacillin increases the susceptibility of the native state to unfolding in the presence of urea is supported by the demonstration that SO4(2)- ions decreased the rate and extent of deactivation but had no effect on the rate of re-activation, as predicted from the observation that SO4(2)- ions, in competition with urea, stabilize the native state relative to the partially unfolded state H [Mitchinson & Pain (1985) J. Mol. Biol. 184, 331-342].

scholarly journals Spectroscopic Studies on Unfolding Processes of Apo-Neuroglobin Induced by Guanidine Hydrochloride and Urea

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Cui Zhang ◽  
Chaohui Gao ◽  
Jianshuai Mu ◽  
Zhanglei Qiu ◽  
Lianzhi Li
Keyword(s):  
Structural Transition ◽  
Guanidine Hydrochloride ◽  
Fluorescence Emission ◽  
Emission Spectra ◽  
Spectroscopic Studies ◽  
Native State ◽  
Fluorescence Emission Spectra ◽  
Unfolded State ◽  
Partially Unfolded ◽  
Far Ultraviolet

Neuroglobin (Ngb), a recently discovered globin, is predominantly expressed in the brain, retina, and other nerve tissues of vertebrates. The unfolding processes of apo-neuroglobin (apoNgb) induced by guanidine hydrochloride (GdnHCl) and urea were investigated by spectroscopic methods. In the unfolding processes, apoNgb's tertiary structural transition was monitored by the changes of intrinsic fluorescence emission spectra, and its secondary structural transition was measured by the changes of far-ultraviolet circular dichroism (CD) spectra. In addition, 8-anilino-1-naphthalenesulfonic acid (ANS), a hydrophobic cluster binding dye, was also used to monitor the unfolding process of apoNgb and to explore its intermediates. Results showed that GdnHCl-induced unfolding of apoNgb was via a three-state pathway, that is, Native state(N)→ Intermediate state(I)→ Unfolded state(U), during which the intermediate was inferred by an increase in fluorescence intensity and the change of CD value. Gibbs free energy changes are 10.2 kJ·mol−1for the first unfolding transition and 14.0 kJ·mol−1for the second transition. However, urea-induced unfolding of apoNgb only underwent a two-state transition: Native state(N)→ Partially unfolded state(P). The result showed that GdnHCl can efficiently affect the conformational states of apoNgb compared with those of urea. The work will benefit to have an understanding of the unfolding mechanism of apoNgb induced by GdnHCl and urea.

scholarly journals Microsecond sub-domain motions and the folding and misfolding of the mouse prion protein

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Rama Reddy Goluguri ◽  
Sreemantee Sen ◽  
Jayant Udgaonkar
Keyword(s):  
Prion Protein ◽  
Conformational Dynamics ◽  
Correlation Spectroscopy ◽  
Native State ◽  
Fluorescence Correlation ◽  
Stochastic Fluctuations ◽  
Unfolded State ◽  
State Ensemble ◽  
Partially Unfolded ◽  
Domain Motions

Protein aggregation appears to originate from partially unfolded conformations that are sampled through stochastic fluctuations of the native protein. It has been a challenge to characterize these fluctuations, under native like conditions. Here, the conformational dynamics of the full-length (23-231) mouse prion protein were studied under native conditions, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS). The slowest fluctuations could be associated with the folding of the unfolded state to an intermediate state, by the use of microsecond mixing experiments. The two faster fluctuations observed by PET-FCS, could be attributed to fluctuations within the native state ensemble. The addition of salt, which is known to initiate the aggregation of the protein, resulted in an enhancement in the time scale of fluctuations in the core of the protein. The results indicate the importance of native state dynamics in initiating the aggregation of proteins.

Improved Stability of a Protein Vaccine Through Elimination of a Partially Unfolded State

2004 ◽  
Author(s):  
Colleen A. McHugh ◽  
Ralph F. Tammariello ◽  
Charles B. Millard ◽  
John H. Carra
Keyword(s):  
Protein Vaccine ◽  
Unfolded State ◽  
Improved Stability ◽  
Partially Unfolded

scholarly journals Lin28, a major translation reprogramming factor, gains access to YB-1-packaged mRNA through its cold-shock domain

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Anastasiia Samsonova ◽  
Krystel El Hage ◽  
Bénédicte Desforges ◽  
Vandana Joshi ◽  
Marie-Jeanne Clément ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Cold Shock ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Binding Protein ◽  
Large Set ◽  
Core Component ◽  
The Core ◽  
Cold Shock Domain ◽  
Global Translation

AbstractThe RNA-binding protein Lin28 (Lin28a) is an important pluripotency factor that reprograms translation and promotes cancer progression. Although Lin28 blocks let-7 microRNA maturation, Lin28 also binds to a large set of cytoplasmic mRNAs directly. However, how Lin28 regulates the processing of many mRNAs to reprogram global translation remains unknown. We show here, using a structural and cellular approach, a mixing of Lin28 with YB-1 (YBX1) in the presence of mRNA owing to their cold-shock domain, a conserved β-barrel structure that binds to ssRNA cooperatively. In contrast, the other RNA binding-proteins without cold-shock domains tested, HuR, G3BP-1, FUS and LARP-6, did not mix with YB-1. Given that YB-1 is the core component of dormant mRNPs, a model in which Lin28 gains access to mRNPs through its co-association with YB-1 to mRNA may provide a means for Lin28 to reprogram translation. We anticipate that the translational plasticity provided by mRNPs may contribute to Lin28 functions in development and adaptation of cancer cells to an adverse environment.

scholarly journals A novel growth-inducible gene that encodes a protein with a conserved cold-shock domain

1994 ◽  
Vol 22 (11) ◽  
pp. 2036-2041 ◽  
Author(s):  
Kikukatsu Ito ◽  
Ken-ichi Tsutsumi ◽  
Takejiro Kuzumaki ◽  
Paul F. Gomez ◽  
Kaoru Otsu ◽  
...  
Keyword(s):  
Cold Shock ◽  
Cold Shock Domain ◽  
Inducible Gene
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