scholarly journals Generic coarse-grained model for protein folding and aggregation

2009 ◽  
Vol 130 (23) ◽  
pp. 235106 ◽  
Author(s):  
Tristan Bereau ◽  
Markus Deserno
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model

PathMolD-AB: Spatiotemporal pathways of protein folding using parallel molecular dynamics with a coarse-grained model

2020 ◽  
Vol 87 ◽  
pp. 107301
Author(s):  
Leandro Takeshi Hattori ◽  
Bruna Araujo Pinheiro ◽  
Rafael Bertolini Frigori ◽  
César Manuel Vargas Benítez ◽  
Heitor Silvério Lopes
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Parallel Molecular Dynamics

Coarse-grained model for protein folding based on structural profiles

2011 ◽  
Vol 84 (4) ◽  
Author(s):  
Katrin Wolff ◽  
Michele Vendruscolo ◽  
Markus Porto
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model

Protein folding simulations: From coarse-grained model to all-atom model

IUBMB Life ◽  
2009 ◽  
Vol 61 (6) ◽  
pp. 627-643 ◽  
Author(s):  
Jian Zhang ◽  
Wenfei Li ◽  
Jun Wang ◽  
Meng Qin ◽  
Lei Wu ◽  
...  
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Atom Model ◽  
Folding Simulations

How Concentration and Crowding Impact Protein Stability: Insights From a Coarse-Grained Model

2008 ◽  
Author(s):  
Thomas M. Truskett
Keyword(s):  
Protein Folding ◽  
Protein Stability ◽  
Molecular Species ◽  
Current Understanding ◽  
Coarse Grained ◽  
Heterogeneous Environments ◽  
Native State ◽  
Coarse Grained Model ◽  
High Concentrations ◽  
The Stability

Much of the current understanding of the protein folding problem derives from studies of proteins in dilute solutions. However, in many systems of scientific and engineering interest, proteins must fold in concentrated, heterogeneous environments. Cells are crowded with many molecular species, and chaperones often sequester proteins and promote rapid folding. Proteins are also present in high concentrations in the manufacture, storage, and delivery of biotherapeutics. How does crowding generally affect the stability of the native state? Are all crowding agents created equal? If not, can generic structural or chemical features forecast their effects on protein stability?

scholarly journals Generic Coarse-Grained Model for Protein Folding and Aggregation

2009 ◽  
Vol 96 (3) ◽  
pp. 405a ◽  
Author(s):  
Tristan Bereau ◽  
Markus Deserno
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

2009 ◽  
Vol 131 (7) ◽  
Author(s):  
Vincent K. Shen ◽  
Jason K. Cheung ◽  
Jeffrey R. Errington ◽  
Thomas M. Truskett
Keyword(s):  
Protein Stability ◽  
Coarse Grained ◽  
Protein Solutions ◽  
Native State ◽  
High Concentration ◽  
Coarse Grained Model ◽  
Excluded Volume Effects ◽  
Thermodynamic Phase ◽  
Broad Interest ◽  
Liquid Liquid Phase Separation

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

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