scholarly journals Molecular Recognition between Cadherins Studied by a Coarse-Grained Model Interacting with a Coevolutionary Potential

2020 ◽  
Vol 124 (20) ◽  
pp. 4079-4088
Author(s):  
Sara Terzoli ◽  
Guido Tiana
Keyword(s):  
Molecular Recognition ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Coevolutionary Potential

A MODEL FOR SOLVENT MEDIATED INTERACTIONS BETWEEN MOLECULES AND SURFACES

2009 ◽  
Vol 20 (05) ◽  
pp. 747-759
Author(s):  
JUAN G. DIAZ OCHOA
Keyword(s):  
Game Theory ◽  
Free Energy ◽  
Molecular Recognition ◽  
Adsorption Energy ◽  
Energy Barrier ◽  
Energy Landscape ◽  
Explicit Representation ◽  
Coarse Grained ◽  
Free Energy Barrier ◽  
Coarse Grained Model

This work introduces a novel coarse-grained model representing the dynamics of polar molecules that adsorb on a substrate in the presence of a solvent. The motivation of the model is to avoid the explicit representation of the solvent. Instead, the solvent-mediated interaction is indirectly represented using a fluctuating energy landscape. The dynamics, on which this model is based, are similar to the dynamics in game theory. In particular, the strategy of an agent in a game is similar to the modification of the free energy barrier between the molecule and the substrate induced by other companion molecules. The aim of this method is to show how the interplay between solvents and companion molecules can imply a modification in the adsorption energy of molecules, and how this modification can buffer the adsorption of specific molecules on surfaces. The results, and their implications in the molecular recognition of surfaces, are discussed.

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

THE SIMULATION OF POLYSTYRENE/NANOPARTICLES COMPOSITE MICROSPHERES USING DISSIPATIVE PARTICLE DYNAMICS

2013 ◽  
Vol 12 (02) ◽  
pp. 1250111 ◽  
Author(s):  
HAILONG XU ◽  
QIUYU ZHANG ◽  
HEPENG ZHANG ◽  
BAOLIANG ZHANG ◽  
CHANGJIE YIN
Keyword(s):  
Dissipative Particle Dynamics ◽  
Sodium Dodecyl ◽  
Coarse Graining ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Polystyrene Nanoparticles ◽  
Coarse Grained Model ◽  
Composite Microspheres ◽  
Polystyrene Matrix ◽  
Materials Studio

Dissipative particle dynamics (DPD) was initially used to simulate the polystyrene/nanoparticle composite microspheres (PNCM) in this paper. The coarse graining model of PNCM was established. And the DPD parameterization of the model was represented in detail. The DPD repulsion parameters were calculated from the cohesive energy density which could be calculated by amorphous modules in Materials Studio. The equilibrium configuration of the simulated PNCM shows that the nanoparticles were actually "modified" with oleic acid and the modified nanoparticles were embedded in the bulk of polystyrene. As sodium dodecyl sulfate (SDS) was located in the interface between water and polystyrene, the hydrophilic head of SDS stretched into water while the hydrophobic tailed into polystyrene. All simulated phenomena were consistent with the experimental results in preparation of polystyrene/nanoparticles composite microspheres. The effect of surface modification of nanoparticles on its dispersion in polystyrene matrix was also studied by adjusting the interaction parameters between the OA and NP beads. The final results indicated that the nanoparticles removed from the core of composite microsphere to the surface with increase of a OA-NP . All the simulated results demonstrated that our coarse–grained model was reasonable.

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