scholarly journals Molecular Mechanism of Protein Folding in the Cell

Cell ◽  
2011 ◽  
Vol 146 (6) ◽  
pp. 851-854 ◽  
Author(s):  
James E. Rothman ◽  
Randy Schekman
Keyword(s):  
Protein Folding ◽  
Molecular Mechanism

A new way to recognize downhill folding based on generalized path length

2020 ◽  
Vol 19 (04) ◽  
pp. 2040005 ◽  
Author(s):  
Xuewei Jiang ◽  
Zhengwu Wu ◽  
Zhenyuan Fan ◽  
Junhua Yin ◽  
Lu Zheng
Keyword(s):  
Protein Folding ◽  
Molecular Mechanism ◽  
Path Length ◽  
Energy Profile ◽  
Scientific Problem ◽  
Downhill Folding ◽  
Barrier Energy ◽  
Insight Into

The protein folding is an important scientific problem and many methods were designed to elucidate the protein folding and obtain insight into the molecular mechanism. A novel means is presented to identify the downhill pathways of protein folding in this paper. This method is based on barrier energy profile projected onto the generalized path length (GPL) with Breadth-first searching (BFS) algorithm. We show the effectiveness of this approach by constructing the barrier energy profile of trpzip2 and comparing with other methods.

Effects of heme binding on myoglobin folding: Coarse grained molecular simulations

2015 ◽  
Vol 14 (08) ◽  
pp. 1550059
Author(s):  
Erbin He ◽  
Weitong Ren ◽  
Jun Wang ◽  
Wenfei Li ◽  
Wei Wang
Keyword(s):  
Protein Folding ◽  
Molecular Mechanism ◽  
Energy Landscape ◽  
Coarse Grained ◽  
Heme Binding ◽  
Energy Landscape Theory ◽  
Cofactor Binding ◽  
Induced Folding ◽  
The Stability ◽  
Dynamics Simulations

Many proteins contain cofactors, such as heme, ATP and metal ions. Binding of cofactors is not only essential for their biological functions, but also can reshape the intrinsic energy landscape of protein molecules and modulate the folding and stability. However, the molecular mechanism of cofactor coupled protein folding is not well understood. In this work, we study the cofactor coupled folding of myoglobin, which is a typical cofactor (heme) containing protein, by performing molecular dynamics simulations with a structure-based protein model developed based on the energy landscape theory. We showed that the heme binding increases the stability of the myoglobin. More importantly, the heme binding tends to increase the protein folding cooperativity, and switch the folding process from a “three-state” mechanism to a “two-state” mechanism. We also showed that the folding pathways of the myoglobin can be modulated by the heme binding. By performing comparative simulations, we revealed that the above effects of heme binding are resulted from the heme induced folding of F-helix, which is otherwise unstructured at apo state, and the heme mediated contacting interactions around the heme binding site. The simulation results are consistent with available experimental data, and provide insights into the molecular mechanism of the effects of cofactor binding on the protein folding and stability.

scholarly journals Self-organization, entropy and allostery

2018 ◽  
Vol 46 (3) ◽  
pp. 587-597 ◽  
Author(s):  
Alexandr P. Kornev
Keyword(s):  
Protein Folding ◽  
Molecular Recognition ◽  
Molecular Mechanism ◽  
Broad Spectrum ◽  
Regulatory Mechanism ◽  
Signal Transmission ◽  
Self Organization ◽  
Common Root ◽  
The Cross ◽  
Polypeptide Chains

Allostery is a fundamental regulatory mechanism in biology. Although generally accepted that it is a dynamics-driven process, the exact molecular mechanism of allosteric signal transmission is hotly debated. We argue that allostery is as a part of a bigger picture that also includes fractal-like properties of protein interior, hierarchical protein folding and entropy-driven molecular recognition. Although so far all these phenomena were studied separately, they stem from the same common root: self-organization of polypeptide chains and, thus, has to be studied collectively. This merge will allow the cross-referencing of a broad spectrum of multi-disciplinary data facilitating progress in all these fields.

Additional evidence for AQP1 vesicle trafficking as a molecular mechanism for ductal bile secretion

2001 ◽  
Vol 120 (5) ◽  
pp. A91-A91
Author(s):  
P TIETZ ◽  
P SPLINTER ◽  
M MCNIVEN ◽  
R HUEBERT ◽  
N LARUSSO
Keyword(s):  
Molecular Mechanism ◽  
Vesicle Trafficking ◽  
Bile Secretion

Hypoxia/Reoxygenation on human myometrial and decidual cells: A molecular mechanism involved in preterra labor

1998 ◽  
Vol 5 (1) ◽  
pp. 187A-187A
Author(s):  
J CARVAJAL ◽  
S KATO ◽  
J SAEZ ◽  
F LEIGHTON ◽  
G VALENZUELA ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Decidual Cells ◽  
Hypoxia Reoxygenation

Molecular Mechanism of Apoptosis Induction by Resveratrol, a Natural Cancer Chemopreventive Agent

2008 ◽  
Vol 78 (1) ◽  
pp. 3-8 ◽  
Author(s):  
Fan ◽  
Jiang ◽  
Zhang ◽  
Bai
Keyword(s):  
Cancer Treatment ◽  
Molecular Mechanism ◽  
Apoptosis Induction ◽  
Protective Agents ◽  
Chemopreventive Agent ◽  
Naturally Occurring ◽  
Apoptosis Pathways ◽  
Present Understanding

In efforts to identify naturally occurring compounds that act as protective agents, resveratrol, a phytoalexin existing in wine, has attracted much interest because of its diverse pharmacological characteristics. Considering that apoptosis induction is the most potent defense approach for cancer treatment, we have tried to summarize our present understanding of apoptosis induction by resveratrol based on the two major apoptosis pathways.

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