scholarly journals Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

2015 ◽  
Vol 11 ◽  
pp. 2459-2473 ◽  
Author(s):  
Giuseppina Raffaini ◽  
Antonino Mazzaglia ◽  
Fabio Ganazzoli
Keyword(s):  
Molecular Dynamics ◽  
Building Blocks ◽  
Dispersion Interactions ◽  
Nucleation Stage ◽  
Aggregation Behaviour ◽  
Apolar Solvent ◽  
Initial Nucleation ◽  
Molecular Dynamics Methods ◽  
Pharmaceutical Properties ◽  
Dynamics Simulations

Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a “bottom up” approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties.

scholarly journals Simulated Breathing: Application of Molecular Dynamics Simulations to Pulmonary Lung Surfactant

Symmetry ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1259
Author(s):  
Maksymilian Dziura ◽  
Basel Mansour ◽  
Mitchell DiPasquale ◽  
P. Charukeshi Chandrasekera ◽  
James W. Gauld ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Pulmonary Surfactant ◽  
Lung Surfactant ◽  
Protein Composition ◽  
Md Simulations ◽  
Building Blocks ◽  
Future Research ◽  
Total Composition ◽  
Protein Components ◽  
Dynamics Simulations

In this review, we delve into the topic of the pulmonary surfactant (PS) system, which is present in the respiratory system. The total composition of the PS has been presented and explored, from the types of cells involved in its synthesis and secretion, down to the specific building blocks used, such as the various lipid and protein components. The lipid and protein composition varies across species and between individuals, but ultimately produces a PS monolayer with the same role. As such, the composition has been investigated for the ways in which it imposes function and confers peculiar biophysical characteristics to the system as a whole. Moreover, a couple of theories/models that are associated with the functions of PS have been addressed. Finally, molecular dynamic (MD) simulations of pulmonary surfactant have been emphasized to not only showcase various group’s findings, but also to demonstrate the validity and importance that MD simulations can have in future research exploring the PS monolayer system.

scholarly journals Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations

2018 ◽  
Vol 115 (45) ◽  
pp. 11519-11524 ◽  
Author(s):  
Caitlin M. Quinn ◽  
Mingzhang Wang ◽  
Matthew P. Fritz ◽  
Brent Runge ◽  
Jinwoo Ahn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Building Blocks ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Capsid Assembly ◽  
Dynamic Regulation ◽  
Angle Spinning ◽  
Dynamics Simulations ◽  
Hiv 1

The host factor protein TRIM5α plays an important role in restricting the host range of HIV-1, interfering with the integrity of the HIV-1 capsid. TRIM5 triggers an antiviral innate immune response by functioning as a capsid pattern recognition receptor, although the precise mechanism by which the restriction is imposed is not completely understood. Here we used an integrated magic-angle spinning nuclear magnetic resonance and molecular dynamics simulations approach to characterize, at atomic resolution, the dynamics of the capsid’s hexameric and pentameric building blocks, and the interactions with TRIM5α in the assembled capsid. Our data indicate that assemblies in the presence of the pentameric subunits are more rigid on the microsecond to millisecond timescales than tubes containing only hexamers. This feature may be of key importance for controlling the capsid’s morphology and stability. In addition, we found that TRIM5α binding to capsid induces global rigidification and perturbs key intermolecular interfaces essential for higher-order capsid assembly, with structural and dynamic changes occurring throughout the entire CA polypeptide chain in the assembly, rather than being limited to a specific protein-protein interface. Taken together, our results suggest that TRIM5α uses several mechanisms to destabilize the capsid lattice, ultimately inducing its disassembly. Our findings add to a growing body of work indicating that dynamic allostery plays a pivotal role in capsid assembly and HIV-1 infectivity.

scholarly journals Coarse-Grained Molecular Dynamics Simulations of Nanoplastics Interacting with a Hydrophobic Environment in Aqueous Solution

2021 ◽  
Author(s):  
Lorenz Dettmann ◽  
Oliver Kühn ◽  
Ashour A. Ahmed
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Functional Groups ◽  
Critical Role ◽  
Terrestrial Ecosystems ◽  
Building Blocks ◽  
Coarse Grained ◽  
Hydrophobic Polymers ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

<div><div><div><p>Nanoplastics (NPs) are emerging threats for marine and terrestrial ecosystems, but little is known about their fate in the environment at the molecular scale. In this work, coarse-grained molecular dynamics simulations were performed to investigate nature and strength of the interaction between NPs and hydrophobic environments. Specifically, NPs were simulated with different hydrophobic and hydrophilic polymers while carbon nanotubes (CNTs) were used to mimic surface and confinement effects of hydrophobic building blocks occurring in a soil environment. The hydrophobicity of CNTs was modified by introducing different hydrophobic and hydrophilic functional groups at their inner surfaces. The results show that hydrophobic polymers have a strong affinity to adsorb at the outer surface and to be captured inside the CNT. The accumulation within the CNT is even increased in presence of hydrophobic functional groups. This contribution is a first step towards a mechanistic understanding of a variety of processes connected to interaction of nanoscale material with environmental systems. Regarding the fate of NPs in soil, the results point to the critical role of the hydrophobicity of NPs and soil organic matter (SOM) as well as of the chemical nature of functionalized SOM cavities/voids in controlling the accumulation of NPs in soil. Moreover, the results can be related to water treatment technologies as it is shown that the hydrophobicity of CNTs and functionalization of their surfaces may play a crucial role in enhancing the adsorption capacity of CNTs with respect to organic compounds and thus their removal efficiency from wastewater.</p><p><br></p></div></div></div>

scholarly journals A Molecular Dynamics Study of a Photodynamic Sensitizer for Cancer Cells: Inclusion Complexes of γ-Cyclodextrins with C70

2019 ◽  
Vol 20 (19) ◽  
pp. 4831 ◽  
Author(s):  
Giuseppina Raffaini ◽  
Fabio Ganazzoli
Keyword(s):  
Molecular Dynamics ◽  
Cancer Therapy ◽  
Cancer Cells ◽  
Inclusion Complexes ◽  
Direct Injection ◽  
Theoretical Work ◽  
Stable Complex ◽  
Apolar Solvent ◽  
Molecular Dynamics Methods ◽  
The Stability

Photodynamic therapy is an emerging treatment of tumor diseases. The complexes with γ-cyclodextrins (γ-CD) and fullerenes or their derivatives can be used as photosensitizers by direct injection into cancer cells. Using molecular mechanics and molecular dynamics methods, the stability and the geometry of the 2:1 complexes [(γ-CD)2/C70] are investigated analyzing the differences with the analogous C60 complexes, studied in a previous theoretical work and experimentally found to be much less efficient in cancer therapy. The inclusion complex of γ-CD and C70 has a 2:1 stoichiometry, the same as C60, but is significantly less stable and displays an unlike arrangement. In vacuo, mimicking an apolar solvent, the complex is compact, whereas in water the two γ-CDs encapsulate C70 forming a relatively stable complex by interacting through their primary rims, however exposing part of C70 to the solvent. Other higher-energy complexes with the γ-CDs facing different rims can form in water, but in all cases part of the hydrophobic C70 surface remains exposed to water. The stability and arrangement of these peculiar amphiphilic inclusion complexes having non-covalent interactions in water can be an important key for cancer therapy to enhance both the solubilization and the fullerene insertion into liposomes or cell membranes.

scholarly journals Thermodynamics of the self-assembly of non-ionic chromonic molecules using atomistic simulations. The case of TP6EO2M in aqueous solution

Soft Matter ◽  
2015 ◽  
Vol 11 (4) ◽  
pp. 680-691 ◽  
Author(s):  
Anna Akinshina ◽  
Martin Walker ◽  
Mark R. Wilson ◽  
Gordon J. T. Tiddy ◽  
Andrew J. Masters ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Liquid Crystal ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Atomistic Simulations ◽  
Aggregation Behaviour ◽  
Dynamics Simulations

Molecular dynamics simulations of non-ionic triphenylene-based chromonic liquid crystal molecules demonstrate self-assembly of the molecules into stacks and “quasi-isodesmic” aggregation behaviour.

scholarly journals Conformational changes in amyloid-beta (12–28) alloforms studied using action-FRET, IMS and molecular dynamics simulations

2015 ◽  
Vol 6 (8) ◽  
pp. 5040-5047 ◽  
Author(s):  
Steven Daly ◽  
Alexander Kulesza ◽  
Frederic Poussigue ◽  
Anne-Laure Simon ◽  
Chang Min Choi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Amyloid Beta ◽  
Conformational Changes ◽  
Aggregation Behaviour ◽  
Dynamics Simulations

The gas phase conformations of two amyloid beta mutants are studied by multiple techniques to elucidate the origin of the different aggregation behaviour.

scholarly journals Coarse-Grained Molecular Dynamics Simulations of Nanoplastics Interacting with a Hydrophobic Environment in Aqueous Solution

2021 ◽  
Author(s):  
Lorenz Dettmann ◽  
Oliver Kühn ◽  
Ashour A. Ahmed
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Functional Groups ◽  
Critical Role ◽  
Terrestrial Ecosystems ◽  
Building Blocks ◽  
Coarse Grained ◽  
Hydrophobic Polymers ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

<div><div><div><p>Nanoplastics (NPs) are emerging threats for marine and terrestrial ecosystems, but little is known about their fate in the environment at the molecular scale. In this work, coarse-grained molecular dynamics simulations were performed to investigate nature and strength of the interaction between NPs and hydrophobic environments. Specifically, NPs were simulated with different hydrophobic and hydrophilic polymers while carbon nanotubes (CNTs) were used to mimic surface and confinement effects of hydrophobic building blocks occurring in a soil environment. The hydrophobicity of CNTs was modified by introducing different hydrophobic and hydrophilic functional groups at their inner surfaces. The results show that hydrophobic polymers have a strong affinity to adsorb at the outer surface and to be captured inside the CNT. The accumulation within the CNT is even increased in presence of hydrophobic functional groups. This contribution is a first step towards a mechanistic understanding of a variety of processes connected to interaction of nanoscale material with environmental systems. Regarding the fate of NPs in soil, the results point to the critical role of the hydrophobicity of NPs and soil organic matter (SOM) as well as of the chemical nature of functionalized SOM cavities/voids in controlling the accumulation of NPs in soil. Moreover, the results can be related to water treatment technologies as it is shown that the hydrophobicity of CNTs and functionalization of their surfaces may play a crucial role in enhancing the adsorption capacity of CNTs with respect to organic compounds and thus their removal efficiency from wastewater.</p><p><br></p></div></div></div>

scholarly journals How a Hemicarcerand Incarcerates Guests at Room Temperature Decoded with Modular Simulations

2020 ◽  
Author(s):  
Katherine G. McFerrin ◽  
Yuan-Ping Pang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Model Building ◽  
Three Dimensional ◽  
Building Blocks ◽  
Water Soluble ◽  
Modular Approach ◽  
Molecular Complexation ◽  
Three Dimensional Models ◽  
Dynamics Simulations

AbstractHemicarcerands are host molecules created to study constrictive binding with guest molecules for insights into the rules of molecular complexation. However, the molecular dynamics simulations that facilitate such studies have been limited because three-dimensional models of hemicarcerands are tedious to build and their atomic charges are complicated to derive. There have been no molecular dynamics simulations of the reported water-soluble hemicarcerand (Octacid4) that explain how it uniquely encapsulates its guests at 298 K and keeps them encapsulated at 298 K in NMR experiments. Herein we report a modular approach to hemicarcerand simulations that simplifies the model building and charge derivation in a manner reminiscent of the approach to protein simulations with truncated amino acids as building blocks. We also report that apo Octacid4 in water adopts two clusters of conformations, one of which has an equatorial portal open thus allowing guests to enter the cavity of Octacid4, in microsecond molecular dynamics simulations performed using the modular approach at 298 K. Under the same simulation conditions, the guest-bound Octacid4 adopts one cluster of conformations with all equatorial portals closed thus keeping the guests incarcerated. These results explain the unique constrictive binding of Octacid4 and suggest that the guest-induced host conformational change that impedes decomplexation is a previously unrecognized conformational characteristic that promotes strong molecular complexation.

Following the Crystal Growth of Anthradithiophenes through Atomistic Molecular Dynamics Simulations and Graph Characterization

2022 ◽  
Author(s):  
Sean M. Ryno ◽  
Ramin Noruzi ◽  
Chamikara Karunasena ◽  
Balaji Sesha Sarath Pokuri ◽  
Shi Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Crystal Growth ◽  
Molecular Dynamics Simulations ◽  
Organic Semiconductors ◽  
Building Blocks ◽  
Nucleation And Growth ◽  
Distinctive Features ◽  
Molecular Building Blocks ◽  
Dynamics Simulations

While organic semiconductors (OSC) offer distinctive features for several electronic and optical technologies, questions remain as to how the chemistries of the molecular building blocks impact material nucleation and growth...

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