Precise estimation of transfer free energies for ionic species between similar media

2018 ◽  
Vol 20 (42) ◽  
pp. 27003-27010
Author(s):  
Carmen Esposito ◽  
Andreas Vitalis
Keyword(s):  
Molecular Dynamics ◽  
Ionic Species ◽  
Umbrella Sampling ◽  
Two Dimensional ◽  
Free Energies ◽  
Precise Estimation ◽  
Transfer Properties

Two-dimensional umbrella sampling is combined with molecular dynamics to calculate correction-free estimates of transfer properties for individual ions.

scholarly journals Membrane Insertion of MoS2 Nanosheets: Fresh vs. Aged

2021 ◽  
Vol 9 ◽  
Author(s):  
Rui Ye ◽  
Wei Song ◽  
Xinwen Ou ◽  
Zonglin Gu ◽  
Dong Zhang
Keyword(s):  
Molecular Dynamics ◽  
Lipid Membranes ◽  
Biomedical Applications ◽  
Ambient Air ◽  
Umbrella Sampling ◽  
Membrane Insertion ◽  
Two Dimensional ◽  
Mos2 Nanosheets ◽  
Bilayer Membranes ◽  
Dynamics Simulations

Fresh two-dimensional molybdenum disulfide (MoS2) absorbs the hydrocarbon contaminations in the ambient air and makes surface aging. To understand how the surface aging influences the interactions between MoS2 and biomolecules is important in the biomedical applications. Here, employing all-atom molecular dynamics simulations, we investigated the interactions of the fresh and aged MoS2 nanosheets with the lipid membranes of different components. Our results demonstrate that both the fresh and aged MoS2 nanosheets can spontaneously insert into the bilayer membranes. However, the fresh MoS2 nanosheet displays significantly stronger interaction and then has a larger penetration depth than the aged counterpart, regardless of the lipid components. The calculations of potential mean forces through the umbrella sampling further confirm that the insertion of fresh MoS2 into the lipid membranes is more energetically favorable. Moreover, we found that the fresh MoS2 nanosheet can cause a larger damage to the integrity of lipid membranes than the aged one. This work provides insightful understandings of the surface-aging-dependent interactions of the MoS2 nanosheets with biomembranes, which could facilitate the design of novel MoS2-based nanodevices with advanced surface properties.

scholarly journals Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1051
Author(s):  
Edgardo Becerra ◽  
Giovanny Aguilera-Durán ◽  
Laura Berumen ◽  
Antonio Romo-Mancillas ◽  
Guadalupe García-Alcocer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Binding Energy ◽  
Binding Site ◽  
Binding Sites ◽  
Adenosine Monophosphate ◽  
Competitive Inhibitor ◽  
Umbrella Sampling ◽  
Coarse Grained ◽  
Nucleotide Polymorphisms

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.

scholarly journals Doxorubicin Encapsulation in Carbon Nanotubes Having Haeckelite or Stone–Wales Defects as Drug Carriers: A Molecular Dynamics Approach

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1586
Author(s):  
Leonor Contreras ◽  
Ignacio Villarroel ◽  
Camila Torres ◽  
Roberto Rozas
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Drug Delivery Systems ◽  
Nitrogen Doping ◽  
Drug Carriers ◽  
Acidic Ph ◽  
Free Energies ◽  
Interaction Forces ◽  
Chiral Nanotubes ◽  
Binding Free Energies

Doxorubicin (DOX), a recognized anticancer drug, forms stable associations with carbon nanotubes (CNTs). CNTs when properly functionalized have the ability to anchor directly in cancerous tumors where the release of the drug occurs thanks to the tumor slightly acidic pH. Herein, we study the armchair and zigzag CNTs with Stone–Wales (SW) defects to rank their ability to encapsulate DOX by determining the DOX-CNT binding free energies using the MM/PBSA and MM/GBSA methods implemented in AMBER16. We investigate also the chiral CNTs with haeckelite defects. Each haeckelite defect consists of a pair of square and octagonal rings. The armchair and zigzag CNT with SW defects and chiral nanotubes with haeckelite defects predict DOX-CNT interactions that depend on the length of the nanotube, the number of present defects and nitrogen doping. Chiral nanotubes having two haeckelite defects reveal a clear dependence on the nitrogen content with DOX-CNT interaction forces decreasing in the order 0N > 4N > 8N. These results contribute to a further understanding of drug-nanotube interactions and to the design of new drug delivery systems based on CNTs.

Molecular dynamics study of two dimensional and adsorbed microclusters

1980 ◽  
Vol 72 (8) ◽  
pp. 4562-4568 ◽  
Author(s):  
Mariana Weissmann ◽  
Norah V. Cohan
Keyword(s):  
Molecular Dynamics ◽  
Two Dimensional

Molecular Dynamics Simulations of Shock-Defect Interactions in Two-Dimensional Nonreactive Crystals

1992 ◽  
Vol 296 ◽  
Author(s):  
Robert S. Sinkovits ◽  
Lee Phillips ◽  
Elaine S. Oran ◽  
Jay P. Boris
Keyword(s):  
Molecular Dynamics ◽  
Hexagonal Lattice ◽  
Square Lattice ◽  
Two Dimensional ◽  
Connection Machine ◽  
Defect Sites ◽  
Principal Axes ◽  
Shock Motion ◽  
Defect Interactions ◽  
Dynamics Simulations

AbstractThe interactions of shocks with defects in two-dimensional square and hexagonal lattices of particles interacting through Lennard-Jones potentials are studied using molecular dynamics. In perfect lattices at zero temperature, shocks directed along one of the principal axes propagate through the crystal causing no permanent disruption. Vacancies, interstitials, and to a lesser degree, massive defects are all effective at converting directed shock motion into thermalized two-dimensional motion. Measures of lattice disruption quantitatively describe the effects of the different defects. The square lattice is unstable at nonzero temperatures, as shown by its tendency upon impact to reorganize into the lower-energy hexagonal state. This transition also occurs in the disordered region associated with the shock-defect interaction. The hexagonal lattice can be made arbitrarily stable even for shock-vacancy interactions through appropriate choice of potential parameters. In reactive crystals, these defect sites may be responsible for the onset of detonation. All calculations are performed using a program optimized for the massively parallel Connection Machine.

Conformation of deltorphin-II in membrane environment studied by two-dimensional NMR spectroscopy and molecular dynamics calculations

1993 ◽  
Vol 212 (1) ◽  
pp. 185-191 ◽  
Author(s):  
Yasunori OHNO ◽  
Motozumi SEGAWA ◽  
Hirofumi OHISHI ◽  
Mitsunobu DOI ◽  
Kunihiro KITAMURA ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Nmr Spectroscopy ◽  
Two Dimensional ◽  
Molecular Dynamics Calculations ◽  
Deltorphin Ii
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