Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics.
It is known that crowded molecular environment affects the structure, thermodynamics, and dynamics of macromolecules. Most of the previous works on molecular crowding have majorly focused on the behavior of the macromolecule with less emphasis on the behavior of the crowder and water molecules. In t...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC6235303?pdf=render |
| _version_ | 1819241176378638336 |
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| author | Atul Kumar Jaiswal Rakesh Srivastava Preeti Pandey Pradipta Bandyopadhyay |
| author_facet | Atul Kumar Jaiswal Rakesh Srivastava Preeti Pandey Pradipta Bandyopadhyay |
| author_sort | Atul Kumar Jaiswal |
| collection | DOAJ |
| description | It is known that crowded molecular environment affects the structure, thermodynamics, and dynamics of macromolecules. Most of the previous works on molecular crowding have majorly focused on the behavior of the macromolecule with less emphasis on the behavior of the crowder and water molecules. In the current study, we have precisely focused on the behavior of the crowder, (ethylene glycol (EG)), salt ions, and water in the presence of a DNA with the increase of the EG concentration. We have probed the behavior of water and crowder using molecular dynamics (MD) simulation and by calculating localized thermodynamic properties. Our results show an interesting competition between EG and water molecules to make hydrogen bonds (H-bond) with DNA. Although the total number of H-bonds involving DNA with both EG and water remains essentially same irrespective of the increase in EG concentration, there is a proportional change in the H-bonding pattern between water-water, EG-EG, and EG-water near DNA and in bulk. At low concentrations of EG, the displacement of water molecules near DNA is relatively easy. However, the displacement of water becomes more difficult as the concentration of EG increases. The density of Na+ (Cl-) near DNA increases (decreases) as the concentration of EG is increased. The density of Cl- near Na+ increases with the increase in EG concentration. It was also found that the average free energy per water in the first solvation shell increases with the increase in EG concentration. Putting all these together, a microscopic picture of EG, water, salt interaction in the presence of DNA, as a function of EG concentration, has emerged. |
| first_indexed | 2024-12-23T14:19:45Z |
| format | Article |
| id | doaj.art-f265e16a9cab418db44ba358d6df3654 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T14:19:45Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-f265e16a9cab418db44ba358d6df36542022-12-21T17:43:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-011311e020635910.1371/journal.pone.0206359Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics.Atul Kumar JaiswalRakesh SrivastavaPreeti PandeyPradipta BandyopadhyayIt is known that crowded molecular environment affects the structure, thermodynamics, and dynamics of macromolecules. Most of the previous works on molecular crowding have majorly focused on the behavior of the macromolecule with less emphasis on the behavior of the crowder and water molecules. In the current study, we have precisely focused on the behavior of the crowder, (ethylene glycol (EG)), salt ions, and water in the presence of a DNA with the increase of the EG concentration. We have probed the behavior of water and crowder using molecular dynamics (MD) simulation and by calculating localized thermodynamic properties. Our results show an interesting competition between EG and water molecules to make hydrogen bonds (H-bond) with DNA. Although the total number of H-bonds involving DNA with both EG and water remains essentially same irrespective of the increase in EG concentration, there is a proportional change in the H-bonding pattern between water-water, EG-EG, and EG-water near DNA and in bulk. At low concentrations of EG, the displacement of water molecules near DNA is relatively easy. However, the displacement of water becomes more difficult as the concentration of EG increases. The density of Na+ (Cl-) near DNA increases (decreases) as the concentration of EG is increased. The density of Cl- near Na+ increases with the increase in EG concentration. It was also found that the average free energy per water in the first solvation shell increases with the increase in EG concentration. Putting all these together, a microscopic picture of EG, water, salt interaction in the presence of DNA, as a function of EG concentration, has emerged.http://europepmc.org/articles/PMC6235303?pdf=render |
| spellingShingle | Atul Kumar Jaiswal Rakesh Srivastava Preeti Pandey Pradipta Bandyopadhyay Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics. PLoS ONE |
| title | Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics. |
| title_full | Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics. |
| title_fullStr | Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics. |
| title_full_unstemmed | Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics. |
| title_short | Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics. |
| title_sort | microscopic picture of water ethylene glycol interaction near a model dna by computer simulation concentration dependence structure and localized thermodynamics |
| url | http://europepmc.org/articles/PMC6235303?pdf=render |
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