Conservation of the Folding Mechanism between Designed Primordial (βα)8-Barrel Proteins and Their Modern Descendant

2012 ◽  
Vol 134 (30) ◽  
pp. 12786-12791 ◽  
Author(s):  
Linn Carstensen ◽  
Josef M. Sperl ◽  
Marco Bocola ◽  
Felix List ◽  
Franz X. Schmid ◽  
...  
Keyword(s):  
Folding Mechanism

From Levinthal’s Paradox to the Effects of Cell Environmental Perturbation on Protein Folding

2020 ◽  
Vol 26 (42) ◽  
pp. 7537-7554 ◽  
Author(s):  
Juan Zeng ◽  
Zunnan Huang
Keyword(s):  
Protein Folding ◽  
Posttranslational Modifications ◽  
Three Dimensional ◽  
Rational Drug Design ◽  
Basic Knowledge ◽  
Sequence Evolution ◽  
3D Structures ◽  
Folding Mechanism ◽  
Cellular Environment ◽  
Environment Temperature

Background: The rapidly increasing number of known protein sequences calls for more efficient methods to predict the Three-Dimensional (3D) structures of proteins, thus providing basic knowledge for rational drug design. Understanding the folding mechanism of proteins is valuable for predicting their 3D structures and for designing proteins with new functions and medicinal applications. Levinthal’s paradox is that although the astronomical number of conformations possible even for proteins as small as 100 residues cannot be fully sampled, proteins in nature normally fold into the native state within timescales ranging from microseconds to hours. These conflicting results reveal that there are factors in organisms that can assist in protein folding. Methods: In this paper, we selected a crowded cell-like environment and temperature, and the top three Posttranslational Modifications (PTMs) as examples to show that Levinthal’s paradox does not reflect the folding mechanism of proteins. We then revealed the effects of these factors on protein folding. Results: The results summarized in this review indicate that a crowded cell-like environment, temperature, and the top three PTMs reshape the Free Energy Landscapes (FELs) of proteins, thereby regulating the folding process. The balance between entropy and enthalpy is the key to understanding the effect of the crowded cell-like environment and PTMs on protein folding. In addition, the stability/flexibility of proteins is regulated by temperature. Conclusion: This paper concludes that the cellular environment could directly intervene in protein folding. The long-term interactions of the cellular environment and sequence evolution may enable proteins to fold efficiently. Therefore, to correctly understand the folding mechanism of proteins, the effect of the cellular environment on protein folding should be considered.

The Role of Ligand Binding in the Kinetic Folding Mechanism of Human p21H-rasProtein†

Biochemistry ◽  
1998 ◽  
Vol 37 (42) ◽  
pp. 14891-14899 ◽  
Author(s):  
Jing Zhang ◽  
C. Robert Matthews
Keyword(s):  
Ligand Binding ◽  
Folding Mechanism ◽  
Kinetic Folding

The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding-binding process during target recognition

2018 ◽  
Vol 87 (4) ◽  
pp. 265-275
Author(s):  
Junwen Xiong ◽  
Meng Gao ◽  
Jingjing Zhou ◽  
Sen Liu ◽  
Zhengding Su ◽  
...  
Keyword(s):  
Target Recognition ◽  
Binding Process ◽  
Unfolded Protein ◽  
Folding Mechanism

scholarly journals A structural model of the Fábrica Nova region, Santa Rita syncline, Quadrilátero Ferrífero: flanking folds as a folding mechanism

2015 ◽  
Vol 68 (2) ◽  
pp. 153-162 ◽  
Author(s):  
Daniel Quinaud Rossi ◽  
Issamu Endo
Keyword(s):  
Structural Model ◽  
Axial Direction ◽  
Ore Deposits ◽  
Tectonic Deformation ◽  
Folding Mechanism ◽  
Structural Framework ◽  
Deformation Phase ◽  
Proposed Model ◽  
Quadrilátero Ferrífero ◽  
Iron Ore Deposits

AbstractThis study focuses on the eastern flank of the Santa Rita syncline (Dorr 1969), with specific emphasis on the region known as Fábrica Nova. Important iron ore deposits are located on the flanks of this structure, such as Timbopeba, Alegria, São Luiz, Tamanduá, Almas and Fábrica Nova. The Santa Rita syncline is a fold with N-S axial direction and of subregional scale, with roots in the adjacent basement of the Santa Bárbara Complex and sectioned by the Água Quente thrust fault. The hypothesis of this study is that the structural framework of the region resulted from the superposition of at least three deformation phases on the Ouro Preto nappe. The Fábrica Nova mine, located in the central portion of the study area, is embedded in a synformal structure with a 100/20 trending axis named Fábrica Nova synform. The proposed model to explain the particular structural geometry of this region is based on the flanking folding mechanism (Passchier 2001). This mechanism may have been developed by E-W crustal shortening during the F4 tectonic deformation phase.

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