scholarly journals Computational Modelling of the Interaction of Gold Nanoparticle with Lung Surfactant Monolayer

MRS Advances ◽  
2019 ◽  
Vol 4 (20) ◽  
pp. 1177-1185 ◽  
Author(s):  
Sheikh I. Hossain ◽  
Neha S. Gandhi ◽  
Zak E. Hughes ◽  
Suvash C. Saha
Keyword(s):  
Respiratory Diseases ◽  
Lung Surfactant ◽  
Computational Modelling ◽  
Fine Tuning ◽  
Coarse Grained ◽  
Normal Lung ◽  
Open Questions ◽  
Compression And Expansion ◽  
Modelling Studies ◽  
Dynamics Simulations

ABSTRACTLung surfactant (LS), a thin layer of phospholipids and proteins inside the alveolus of the lung is the first biological barrier to inhaled nanoparticles (NPs). LS stabilizes and protects the alveolus during its continuous compression and expansion by fine-tuning the surface tension at the air-water interface. Previous modelling studies have reported the biophysical function of LS monolayer and its role, but many open questions regarding the consequences and interactions of airborne nano-sized particles with LS monolayer remain. In spite of gold nanoparticles (AuNPs) having a paramount role in biomedical applications, the understanding of the interactions between bare AuNPs (as pollutants) and LS monolayer components still unresolved. Continuous inhalation of NPs increases the possibility of lung ageing, reducing the normal lung functioning and promoting lung malfunction, and may induce serious lung diseases such as asthma, lung cancer, acute respiratory distress syndrome, and more. Different medical studies have shown that AuNPs can disrupt the routine lung functions of gold miners and promote respiratory diseases. In this work, coarse-grained molecular dynamics simulations are performed to gain an understanding of the interactions between bare AuNPs and LS monolayer components at the nanoscale. Different surface tensions of the monolayer are used to mimic the biological process of breathing (inhalation and exhalation). It is found that the NP affects the structure and packing of the lipids by disordering lipid tails. Overall, the analysed results suggest that bare AuNPs impede the normal biophysical function of the lung, a finding that has beneficial consequences to the potential development of treatments of various respiratory diseases.

scholarly journals Catalysis: transition-state molecular recognition?

2010 ◽  
Vol 6 ◽  
pp. 1026-1034 ◽  
Author(s):  
Ian H Williams
Keyword(s):  
Free Energy ◽  
Molecular Recognition ◽  
Transition State ◽  
Computational Modelling ◽  
Catalytic Antibodies ◽  
Single Atom ◽  
Boat Conformation ◽  
Methyl Transferase ◽  
Modelling Studies ◽  
Dynamics Simulations

The key to understanding the fundamental processes of catalysis is the transition state (TS): indeed, catalysis is a transition-state molecular recognition event. Practical objectives, such as the design of TS analogues as potential drugs, or the design of synthetic catalysts (including catalytic antibodies), require prior knowledge of the TS structure to be mimicked. Examples, both old and new, of computational modelling studies are discussed, which illustrate this fundamental concept. It is shown that reactant binding is intrinsically inhibitory, and that attempts to design catalysts that focus simply upon attractive interactions in a binding site may fail. Free-energy changes along the reaction coordinate for SN2 methyl transfer catalysed by the enzyme catechol-O-methyl transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically.

scholarly journals Revisiting Plant Heterosis—From Field Scale to Molecules

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1688
Author(s):  
Attiq ur Rehman ◽  
Trang Dang ◽  
Shanzay Qamar ◽  
Amina Ilyas ◽  
Reemana Fatema ◽  
...  
Keyword(s):  
Agricultural Production ◽  
Field Experiments ◽  
Computational Modelling ◽  
Hybrid Vigor ◽  
Superior Performance ◽  
Genetic Studies ◽  
Open Questions ◽  
F1 Progeny ◽  
Underlying Basis ◽  
Modelling Studies

Heterosis refers to the increase in biomass, stature, fertility, and other characters that impart superior performance to the F1 progeny over genetically diverged parents. The manifestation of heterosis brought an economic revolution to the agricultural production and seed sector in the last few decades. Initially, the idea was exploited in cross-pollinated plants, but eventually acquired serious attention in self-pollinated crops as well. Regardless of harvesting the benefits of heterosis, a century-long discussion is continued to understand the underlying basis of this phenomenon. The massive increase in knowledge of various fields of science such as genetics, epigenetics, genomics, proteomics, and metabolomics persistently provide new insights to understand the reasons for the expression of hybrid vigor. In this review, we have gathered information ranging from classical genetic studies, field experiments to various high-throughput omics and computational modelling studies in order to understand the underlying basis of heterosis. The modern-day science has worked significantly to pull off our understanding of heterosis yet leaving open questions that requires further research and experimentation. Answering these questions would possibly equip today’s plant breeders with efficient tools and accurate choices to breed crops for a sustainable future.

scholarly journals Shape matters—the interaction of gold nanoparticles with model lung surfactant monolayers

2021 ◽  
Vol 18 (183) ◽  
Author(s):  
Sheikh I. Hossain ◽  
Zhen Luo ◽  
Evelyne Deplazes ◽  
Suvash C. Saha
Keyword(s):  
Gold Nanoparticles ◽  
Air Pollutants ◽  
Biomedical Applications ◽  
Lung Surfactant ◽  
Coarse Grained ◽  
Surfactant Monolayers ◽  
Structure And Dynamics ◽  
Inhaled Particles ◽  
Dynamics Simulations ◽  
Future Work

The lung surfactant monolayer (LSM) forms the main biological barrier for any inhaled particles to enter our bloodstream, including gold nanoparticles (AuNPs) present as air pollutants and under investigation for use in biomedical applications. Understanding the interaction of AuNPs with lung surfactant can assist in understanding how AuNPs enter our lungs. In this study, we use coarse-grained molecular dynamics simulations to investigate the effect of four different shape D AuNPs (spherical, box, icosahedron and rod) on the structure and dynamics of a model LSM, with a particular focus on differences resulting from the shape of the AuNP. Monolayer-AuNP systems were simulated in two different states: the compressed state and the expanded state, representing inhalation and exhalation conditions, respectively. Our results indicate that the compressed state is more affected by the presence of the AuNPs than the expanded state. Our results show that in the compressed state, the AuNPs prevent the monolayer from reaching the close to zero surface tension required for normal exhalation. In the compressed state, all four nanoparticles (NPs) reduce the lipid order parameters and cause a thinning of the monolayer where the particles drag surfactant molecules into the water phase. Comparing the different properties shows no trend concerning which shape has the biggest effect on the monolayer, as shape-dependent effects vary among the different properties. Insights from this study might assist future work of how AuNP shapes affect the LSM during inhalation or exhalation conditions.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

scholarly journals Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

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