Effective interaction between small unilamellar vesicles as probed by coarse-grained molecular dynamics simulations

2014 ◽  
Vol 86 (2) ◽  
pp. 215-222 ◽  
Author(s):  
Wataru Shinoda ◽  
Michael L. Klein
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Effective Interaction ◽  
Md Simulations ◽  
Coarse Grained ◽  
Repulsive Interaction ◽  
Spontaneous Curvature ◽  
Unilamellar Vesicles ◽  
Small Unilamellar Vesicles ◽  
Dynamics Simulations

Abstract A series of molecular dynamics (MD) simulations has been undertaken to investigate the effective interaction between vesicles including PC (phosphatidylcholine) and PE (phosphatidylethanolamine) lipids using the Shinoda–DeVane–Klein coarse-grained force field. No signatures of fusion were detected during MD simulations employing two apposed unilamellar vesicles, each composed of 1512 lipid molecules. Association free energy of the two stable vesicles depends on the lipid composition. The two PC vesicles exhibit a purely repulsive interaction with each other, whereas two PE vesicles show a free energy gain at the contact. A mixed PC/PE (1:1) vesicle shows a higher flexibility having a lower energy barrier on the deformation, which is caused by lipid sorting within each leaflet of the membranes. With a preformed channel or stalk between proximal membranes, PE molecules contribute to stabilize the stalk. The results suggest that the lipid components forming the membrane with a negative spontaneous curvature contribute to stabilize the stalk between two vesicles in contact.

Vesicle deformation and division induced by flip-flop of lipid molecules

Soft Matter ◽  
2021 ◽  
Author(s):  
Naohito Urakami ◽  
Yuka Sakuma ◽  
Toshikaze Chiba ◽  
Masayuki Imai
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Component ◽  
Coarse Grained ◽  
Spontaneous Curvature ◽  
Unilamellar Vesicles ◽  
Flip Flop ◽  
Small Unilamellar Vesicles ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

We investigated the deformation of small unilamellar vesicles (SUVs) induced by flip-flops of lipids using coarse-grained molecular dynamics simulations. In case of single-component SUVs composed of zero spontaneous curvature lipids...

Cholesterol solubility limit in lipid membranes probed by small angle neutron scattering and MD simulations

Soft Matter ◽  
2014 ◽  
Vol 10 (46) ◽  
pp. 9313-9317 ◽  
Author(s):  
Sumit Garg ◽  
Francisco Castro-Roman ◽  
Lionel Porcar ◽  
Paul Butler ◽  
Pedro Jesus Bautista ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Small Angle ◽  
Lipid Membranes ◽  
Small Angle Neutron Scattering ◽  
Md Simulations ◽  
Solubility Limit ◽  
Coarse Grained ◽  
Small Unilamellar Vesicles ◽  
Cholesterol Solubility

The solubility limits of cholesterol in small unilamellar vesicles made of POPS and POPC were probed using Small Angle Neutron Scattering (SANS) and coarse grained (CG) molecular dynamics (MD) simulations.

scholarly journals Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

2016 ◽  
Vol 472 (2186) ◽  
pp. 20150556 ◽  
Author(s):  
Radek Erban
Keyword(s):  
Molecular Dynamics ◽  
Differential Equations ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Brownian Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Computational Domain ◽  
Coarse Grained Model ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations of ions (K + , Na + , Ca 2+ and Cl − ) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

scholarly journals Coarse-grained molecular dynamics simulations of nanoplastics interacting with a hydrophobic environment in aqueous solution

RSC Advances ◽  
2021 ◽  
Vol 11 (44) ◽  
pp. 27734-27744
Author(s):  
Lorenz F. Dettmann ◽  
Oliver Kühn ◽  
Ashour A. Ahmed
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Water Treatment ◽  
Md Simulations ◽  
Coarse Grained ◽  
Treatment Technologies ◽  
Dynamics Simulations ◽  
Binding Mechanisms ◽  
Soil And Water

The binding mechanisms of nanoplastics (NPs) to carbon nanotubes as hydrophobic environmental systems have been explored by coarse-grained MD simulations. The results could be closely connected to fate of NPs in soil and water treatment technologies.

scholarly journals Protein-Protein Interactions: Insight from Molecular Dynamics Simulations and Nanoparticle Tracking Analysis

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5696
Author(s):  
Wei Lim Chong ◽  
Koollawat Chupradit ◽  
Sek Peng Chin ◽  
Mai Mai Khoo ◽  
Sook Mei Khor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Protein Binding ◽  
Protein Interactions ◽  
Binding Free Energy ◽  
Single Point ◽  
Md Simulations ◽  
Nanoparticle Tracking Analysis ◽  
Buffer Solution ◽  
Dynamics Simulations

Protein-protein interaction plays an essential role in almost all cellular processes and biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle tracking analysis (NTA) assay offered a simple, rapid, and direct approach in monitoring the protein-protein binding process and predicting the binding affinity. Our case study of designed ankyrin repeats proteins (DARPins)—AnkGAG1D4 and the single point mutated AnkGAG1D4-Y56A for HIV-1 capsid protein (CA) were investigated. As reported, AnkGAG1D4 bound with CA for inhibitory activity; however, it lost its inhibitory strength when tyrosine at residue 56 AnkGAG1D4, the most key residue was replaced by alanine (AnkGAG1D4-Y56A). Through NTA, the binding of DARPins and CA was measured by monitoring the increment of the hydrodynamic radius of the AnkGAG1D4-gold conjugated nanoparticles (AnkGAG1D4-GNP) and AnkGAG1D4-Y56A-GNP upon interaction with CA in buffer solution. The size of the AnkGAG1D4-GNP increased when it interacted with CA but not AnkGAG1D4-Y56A-GNP. In addition, a much higher binding free energy (∆GB) of AnkGAG1D4-Y56A (−31 kcal/mol) obtained from MD further suggested affinity for CA completely reduced compared to AnkGAG1D4 (−60 kcal/mol). The possible mechanism of the protein-protein binding was explored in detail by decomposing the binding free energy for crucial residues identification and hydrogen bond analysis.

scholarly journals Multiscale Modeling of Structure, Transport and Reactivity in Alkaline Fuel Cell Membranes: Combined Coarse-Grained, Atomistic and Reactive Molecular Dynamics Simulations

Polymers ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 1289 ◽  
Author(s):  
Dengpan Dong ◽  
Weiwei Zhang ◽  
Adam Barnett ◽  
Jibao Lu ◽  
Adri van Duin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Anion Exchange Membranes ◽  
Reactive Molecular Dynamics ◽  
Advantages And Disadvantages ◽  
Ionic Groups ◽  
Dynamics Simulations ◽  
Equilibrium Morphology ◽  
Hydrated Anion

In this study, molecular dynamics (MD) simulations of hydrated anion-exchange membranes (AEMs), comprised of poly(p-phenylene oxide) (PPO) polymers functionalized with quaternary ammonium cationic groups, were conducted using multiscale coupling between three different models: a high-resolution coarse-grained (CG) model; Atomistic Polarizable Potential for Liquids, Electrolytes and Polymers (APPLE&P); and ReaxFF. The advantages and disadvantages of each model are summarized and compared. The proposed multiscale coupling utilizes the strength of each model and allows sampling of a broad spectrum of properties, which is not possible to sample using any of the single modeling techniques. Within the proposed combined approach, the equilibrium morphology of hydrated AEM was prepared using the CG model. Then, the morphology was mapped to the APPLE&P model from equilibrated CG configuration of the AEM. Simulations using atomistic non-reactive force field allowed sampling of local hydration structure of ionic groups, vehicular transport mechanism of anion and water, and structure equilibration of water channels in the membrane. Subsequently, atomistic AEM configuration was mapped to ReaxFF reactive model to investigate the Grotthuss mechanism in the hydroxide transport, as well as the AEM chemical stability and degradation mechanisms. The proposed multiscale and multiphysics modeling approach provides valuable input for the materials-by-design of novel polymeric structures for AEMs.

scholarly journals Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations

2019 ◽  
Vol 47 (13) ◽  
pp. 6618-6631 ◽  
Author(s):  
Jianzhong Chen ◽  
Xingyu Wang ◽  
Laixue Pang ◽  
John Z H Zhang ◽  
Tong Zhu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Drug Targets ◽  
Md Simulations ◽  
Free Energy Perturbation ◽  
Potential Drug ◽  
Free Energy Decomposition ◽  
Energy Perturbation ◽  
Dynamics Simulations ◽  
Potential Drug Targets

Abstract Riboswitches can regulate gene expression by direct and specific interactions with ligands and have recently attracted interest as potential drug targets for antibacterial. In this work, molecular dynamics (MD) simulations, free energy perturbation (FEP) and molecular mechanics generalized Born surface area (MM-GBSA) methods were integrated to probe the effect of mutations on the binding of ligands to guanine riboswitch (GR). The results not only show that binding free energies predicted by FEP and MM-GBSA obtain an excellent correlation, but also indicate that mutations involved in the current study can strengthen the binding affinity of ligands GR. Residue-based free energy decomposition was applied to compute ligand-nucleotide interactions and the results suggest that mutations highly affect interactions of ligands with key nucleotides U22, U51 and C74. Dynamics analyses based on MD trajectories indicate that mutations not only regulate the structural flexibility but also change the internal motion modes of GR, especially for the structures J12, J23 and J31, which implies that the aptamer domain activity of GR is extremely plastic and thus readily tunable by nucleotide mutations. This study is expected to provide useful molecular basis and dynamics information for the understanding of the function of GR and possibility as potential drug targets for antibacterial.

Revisiting stress–strain behavior and mechanical reinforcement of polymer nanocomposites from molecular dynamics simulations

2020 ◽  
Vol 22 (29) ◽  
pp. 16760-16771 ◽  
Author(s):  
Jianxiang Shen ◽  
Xiangsong Lin ◽  
Jun Liu ◽  
Xue Li
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Nanocomposites ◽  
Md Simulations ◽  
Coarse Grained ◽  
Stress Strain ◽  
Mechanical Reinforcement ◽  
Strain Behavior ◽  
Nanoparticle Interactions ◽  
Dynamics Simulations

Through coarse-grained MD simulations, the effects of nanoparticle properties, polymer–nanoparticle interactions, chain crosslinks and temperature on the stress–strain behavior and mechanical reinforcement of PNCs are comprehensively investigated.

MOLECULAR DYNAMICS SIMULATIONS OF HELIX BUNDLE PROTEINS USING UNRES FORCE FIELD AND ALL-ATOM FORCE FIELD

2012 ◽  
Vol 11 (06) ◽  
pp. 1201-1215 ◽  
Author(s):  
KAIFU GAO ◽  
MINGHUI YANG
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Protein A ◽  
Md Simulations ◽  
Time Frame ◽  
Coarse Grained ◽  
Staphylococcal Protein A ◽  
Villin Headpiece ◽  
Helix Bundle ◽  
Dynamics Simulations

We have investigated the folding of two helix-bundle proteins, 36-residue Villin headpiece and 56-residue E-domain of Staphylococcal protein A, by combining molecular dynamics (MD) simulations with Coarse-Grained United-Residue (UNRES) Force Field and all-atom force field. Starting from extended structures, each of the proteins was folded to a stable structure within a short time frame using the UNRES model. However, the secondary structures of helices were not well formed. Further refinement using MD simulations with the all-atom force field was able to fold the protein structure into the native-like state with the smallest main-chain root-mean-square deviation of around 3 Å. Detailed analysis of the folding trajectories was presented and the performance of GPU-based MD simulations was also discussed.

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