scholarly journals Simulating protein unfolding under pressure with a coarse-grained model

2012 ◽  
Vol 137 (18) ◽  
pp. 185102 ◽  
Author(s):  
Ramiro Perezzan ◽  
Antonio Rey
Keyword(s):  
Protein Unfolding ◽  
Coarse Grained ◽  
Coarse Grained Model

scholarly journals Protein Unfolding and Aggregation near a Hydrophobic Interface

Polymers ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 156
Author(s):  
David March ◽  
Valentino Bianco ◽  
Giancarlo Franzese
Keyword(s):  
Neurodegenerative Diseases ◽  
Protein Concentration ◽  
Protein Unfolding ◽  
Hydrophobic Surface ◽  
The Other ◽  
Coarse Grained ◽  
Aqueous Environment ◽  
Coarse Grained Model ◽  
Hydrophobic Interface

The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we study how the presence of a hydrophobic surface affects this course of events. To this goal, we use a coarse-grained model of proteins and study by simulations their folding and aggregation near an ideal hydrophobic surface in an aqueous environment by changing parameters such as temperature and hydrophobic strength, related, e.g., to ions concentration. We show that the hydrophobic surface, as well as the other parameters, affect both the protein unfolding and aggregation. We discuss the interpretation of these results and define future lines for further analysis, with their possible implications in neurodegenerative diseases.

scholarly journals Optimal proteome allocation and the temperature dependence of microbial growth laws

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Francis Mairet ◽  
Jean-Luc Gouzé ◽  
Hidde de Jong
Keyword(s):  
Growth Rate ◽  
Stress Responses ◽  
Protein Unfolding ◽  
Microbial Growth ◽  
Coarse Grained ◽  
Effect Of Temperature ◽  
Temperature Sensitive ◽  
Coarse Grained Model ◽  
Proteomic Data ◽  
Growth Laws

AbstractAlthough the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial growth, including the processes of temperature-sensitive protein unfolding and chaperone-assisted (re)folding. We determine the proteome sector allocation that maximizes balanced growth rate as a function of nutrient limitation and temperature. Calibrated with quantitative proteomic data for Escherichia coli, the model allows us to clarify general principles of temperature-dependent proteome allocation and formulate generalized growth laws. The same activation energy for metabolic enzymes and ribosomes leads to an Arrhenius increase in growth rate at constant proteome composition over a large range of temperatures, whereas at extreme temperatures resources are diverted away from growth to chaperone-mediated stress responses. Our approach points at risks and possible remedies for the use of ribosome content to characterize complex ecosystems with temperature variation.

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.

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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