Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model

2013 ◽  
Vol 82 (3) ◽  
pp. 505-516 ◽  
Author(s):  
Abhijeet Kapoor ◽  
Alex Travesset
Keyword(s):  
Coarse Grained ◽  
Native State ◽  
Large Proteins ◽  
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.

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 Molecular Dynamics Study of Ganglioside GM3/DPPC Membrane by Using Coarse-Grained Model

2016 ◽  
Vol 110 (3) ◽  
pp. 323a
Author(s):  
Kento Inoue ◽  
Eiji Ymamoto ◽  
Daisuke Takaiwa ◽  
Kenji Yasuoka ◽  
Masuhiro Mikami
Keyword(s):  
Molecular Dynamics ◽  
Coarse Grained ◽  
Ganglioside Gm3 ◽  
Coarse Grained Model
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