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

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

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

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

Solution Structure, Dynamics, and Thermodynamics of the Native State Ensemble of the Sem-5 C-Terminal SH3 Domain†

Biochemistry ◽  
2003 ◽  
Vol 42 (19) ◽  
pp. 5582-5591 ◽  
Author(s):  
Josephine C. Ferreon ◽  
David E. Volk ◽  
Bruce A. Luxon ◽  
David G. Gorenstein ◽  
Vincent J. Hilser
Keyword(s):  
Solution Structure ◽  
Sh3 Domain ◽  
Native State ◽  
Structure Dynamics ◽  
State Ensemble

Existence of DNA in yeast microbodies

1978 ◽  
Vol 36 (2) ◽  
pp. 232-233
Author(s):  
Masako Osumi ◽  
Misuzu Nagano ◽  
Hiroko Kazama
Keyword(s):  
Catalase Activity ◽  
Buoyant Density ◽  
Model System ◽  
Contour Length ◽  
Native State ◽  
Normal Alkane ◽  
Remarkable Increase ◽  
Dna Molecule ◽  
Mitochondrial Dnas

We have found that microbodies appeared profusely together with a remarkable increase in catalase activity in normal alkane-grown cells of hydrocarbon-utilizing Candida yeasts, and that the microbodies multiplied by division in these cells. These features of Candida yeasts seem to provide a useful model system for studies on the biogenesis of the microbody. Subsequently, we have succeeded in isolation of Candida microbodies in an apparently native state, as judged biochemically and morphologically. The presence of DNA in the purified microbody fraction thus obtained was proved by the diphenylamine method. DNA molecule of about 15 urn in contour length was released from an isolated microbody. The physicochemical analyses of the microbody DNA revealed that its buoyant density differed from nuclear and mitochondrial DNAs. All these results lead us to the possibility that there is a novel type of DNA in microbodies.

Electron Microscopic Observation of Biological Specimens in Their Native State by Employing Cryogenic Techniques

1972 ◽  
Vol 30 ◽  
pp. 410-411 ◽  
Author(s):  
Tokio Nei ◽  
Haruo Yotsumoto ◽  
Yoichi Hasegawa ◽  
Yuji Nagasawa
Keyword(s):  
Electron Microscopic Observation ◽  
Surface Structures ◽  
Specimen Preparation ◽  
Native State ◽  
Electron Microscopic ◽  
Biological Specimen ◽  
Specimen Holder ◽  
Cold Stage ◽  
Preparation Techniques ◽  
Scanning Electron

In order to observe biological specimens in their native state, that is, still containing their water content, various methods of specimen preparation have been used, the principal two of which are the chamber method and the freeze method.Using its recently developed cold stage for installation in the pre-evacuation chamber of a scanning electron microscope, we have succeeded in directly observing a biological specimen in its frozen state without the need for such conventional specimen preparation techniques as drying and metallic vacuum evaporation. (Echlin, too, has reported on the observation of surface structures using the same freeze method.)In the experiment referred to herein, a small sliced specimen was place in the specimen holder. After it was rapidly frozen by freon cooled with liquid nitrogen, it was inserted into the cold stage of the specimen chamber.

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