Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain

2011 ◽  
Vol 80 (3) ◽  
pp. 858-870 ◽  
Author(s):  
Arash Zarrine-Afsar ◽  
Zhuqing Zhang ◽  
Katrina L. Schweiker ◽  
George I. Makhatadze ◽  
Alan R. Davidson ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Sh3 Domain ◽  
Native State

The Native State Conformational Ensemble of the SH3 Domain from α-Spectrin†

Biochemistry ◽  
1999 ◽  
Vol 38 (28) ◽  
pp. 8899-8906 ◽  
Author(s):  
Mourad Sadqi ◽  
Salvador Casares ◽  
María A. Abril ◽  
Obdulio López-Mayorga ◽  
Francisco Conejero-Lara ◽  
...  
Keyword(s):  
Sh3 Domain ◽  
Conformational Ensemble ◽  
Native State

Self-Similarity of Protein Folding Flows

2012 ◽  
Vol 7 (4) ◽  
pp. 136-141
Author(s):  
I. Kalgin ◽  
Sergey Chekmarev
Keyword(s):  
Protein Folding ◽  
Sh3 Domain ◽  
Atomic Level ◽  
The Self ◽  
Coarse Grained ◽  
Folding Kinetics ◽  
Native State ◽  
Self Similarity ◽  
Folding Dynamics ◽  
Fractal Character

The problem of how a protein folds into its functional (native) state is one of the central problems of molecular biology, which attracts the attention of researchers from biology, physics and chemistry for many years. Of particular interest are general properties of the folding process, because the mechanisms of folding of different proteins can be essentially different. Previously, in the study of folding of fyn SH3 domain, we found that despite all the diversity and complexity of individual folding trajectories, the folding flows possess a well pronounced property of self-similarity, with a fractal character of the flow distributions. In the present paper, we study this phenomenon for another protein – beta3s, which is essentially different from the SH3 domain in its structure and folding kinetics. Also, in contrast to the fyn SH3 domain, for which a coarse-grained representation was used, we perform simulations on the atomic level of resolution. We show that the self-similarity and fractality of folding flows are observed is this case too, which suggests that these properties are characteristic of the protein folding dynamics

scholarly journals A single mutation in an SH3 domain increases amyloid aggregation by accelerating nucleation, but not by destabilizing thermodynamically the native state

FEBS Letters ◽  
2009 ◽  
Vol 583 (4) ◽  
pp. 801-806 ◽  
Author(s):  
Lorena Varela ◽  
Bertrand Morel ◽  
Ana I. Azuaga ◽  
Francisco Conejero-Lara
Keyword(s):  
Sh3 Domain ◽  
Single Mutation ◽  
Amyloid Aggregation ◽  
Native State

scholarly journals Atomic view of cosolute-induced protein denaturation probed by NMR solvent paramagnetic relaxation enhancement

2021 ◽  
Vol 118 (34) ◽  
pp. e2112021118
Author(s):  
Yusuke Okuno ◽  
Janghyun Yoo ◽  
Charles D. Schwieters ◽  
Robert B. Best ◽  
Hoi Sung Chung ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Electrostatic Interactions ◽  
Dynamic Equilibrium ◽  
Protein Denaturation ◽  
Group Versus ◽  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement ◽  
Native State ◽  
Unfolded State ◽  
Loop Regions

The cosolvent effect arises from the interaction of cosolute molecules with a protein and alters the equilibrium between native and unfolded states. Denaturants shift the equilibrium toward the latter, while osmolytes stabilize the former. The molecular mechanism whereby cosolutes perturb protein stability is still the subject of considerable debate. Probing the molecular details of the cosolvent effect is experimentally challenging as the interactions are very weak and transient, rendering them invisible to most conventional biophysical techniques. Here, we probe cosolute–protein interactions by means of NMR solvent paramagnetic relaxation enhancement together with a formalism we recently developed to quantitatively describe, at atomic resolution, the energetics and dynamics of cosolute–protein interactions in terms of a concentration normalized equilibrium average of the interspin distance, 〈r−6〉norm, and an effective correlation time, τc. The system studied is the metastable drkN SH3 domain, which exists in dynamic equilibrium between native and unfolded states, thereby permitting us to probe the interactions of cosolutes with both states simultaneously under the same conditions. Two paramagnetic cosolute denaturants were investigated, one neutral and the other negatively charged, differing in the presence of a carboxyamide group versus a carboxylate. Our results demonstrate that attractive cosolute–protein backbone interactions occur largely in the unfolded state and some loop regions in the native state, electrostatic interactions reduce the 〈r−6〉norm values, and temperature predominantly impacts interactions with the unfolded state. Thus, destabilization of the native state in this instance arises predominantly as a consequence of interactions of the cosolutes with the unfolded state.

Four-State Folding of a SH3 Domain: Salt-Induced Modulation of the Stabilities of the Intermediates and Native State

Biochemistry ◽  
2012 ◽  
Vol 51 (23) ◽  
pp. 4723-4734 ◽  
Author(s):  
Amrita Dasgupta ◽  
Jayant B. Udgaonkar
Keyword(s):  
Sh3 Domain ◽  
Native State
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