scholarly journals Equilibration of complexes of DNA and H-NS proteins on charged surfaces: A coarse-grained model point of view

2014 ◽  
Vol 141 (11) ◽  
pp. 115102 ◽  
Author(s):  
Marc Joyeux
Keyword(s):  
Point Of View ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Charged Surfaces ◽  
Model Point

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.

Rheology of hydrocarbon gels

1950 ◽  
Vol 200 (1061) ◽  
pp. 183-188 ◽  
Keyword(s):  
Mechanical Properties ◽  
Experimental Measurement ◽  
Theoretical Basis ◽  
Continuous Media ◽  
Point Of View ◽  
Coarse Grained ◽  
Testing Instrument ◽  
Fine Grained ◽  
Mineral Oils ◽  
Space And Time

Hydrocarbon gels contain a number of materials, such as rubber, greases, saponified mineral oils, etc., of great interest for various engineering purposes. Specific requirements in mechanical properties have been met by producing gels in appropriately chosen patterns of constituent components of visible, colloidal, molecular and atomic sizes, ranging from coarse-grained aggregates, represented by sponges, foams, emulsions, etc.; to fine-grained and apparently homogeneous ones, represented by optically clear compounds. The engineer who has to deal with the whole range of such materials will adopt a macroscopic point of view, based on an apparent continuity of all the material structures and of the distributions in space and time of the displacements and forces occurring under mechanical actions. It has been possible to determine these distributions in the framework of a comprehensive scheme in which the fundamental principles of the mechanics of continuous media provide the theoretical basis, and a testing instrument of new design, termed Rheogoniometer, the means of experimental measurement (Weissenberg 1931, 1934, 1946, 1947, 1948).

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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