Cavity-ligand binding in a simple two-dimensional water model
By means of Monte Carlo computer simulations in the isothermal-isobaric ensemble, we investigated the interaction of a hydrophobic ligand with the hydrophobic surfaces of various curvatures (planar, convex and concave). A simple two-dimensional model of water, hydrophobic ligand and surface was used...
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| Дата: | 2016 |
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| Автори: | , , |
| Формат: | Стаття |
| Мова: | English |
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Інститут фізики конденсованих систем НАН України
2016
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| Назва видання: | Condensed Matter Physics |
| Онлайн доступ: | http://dspace.nbuv.gov.ua/handle/123456789/155776 |
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| Назва журналу: | Digital Library of Periodicals of National Academy of Sciences of Ukraine |
| Цитувати: | Cavity-ligand binding in a simple two-dimensional water model / G. Mazovec, M. Lukšič, B. Hribar-Lee // Condensed Matter Physics. — 2016. — Т. 19, № 1. — С. 13004: 1–6 . — Бібліогр.: 20 назв. — англ. |
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irk-123456789-1557762019-06-18T01:29:23Z Cavity-ligand binding in a simple two-dimensional water model Mazovec, G. Lukšič, M. Hribar-Lee, B. By means of Monte Carlo computer simulations in the isothermal-isobaric ensemble, we investigated the interaction of a hydrophobic ligand with the hydrophobic surfaces of various curvatures (planar, convex and concave). A simple two-dimensional model of water, hydrophobic ligand and surface was used. Hydration/dehidration phenomena concerning water molecules confined close to the molecular surface were investigated. A notable dewetting of the hydrophobic surfaces was observed together with the reorientation of the water molecules close to the surface. The hydrogen bonding network was formed to accommodate cavities next to the surfaces as well as beyond the first hydration shell. The effects were most strongly pronounced in the case of concave surfaces having large curvature. This simplified model can be further used to evaluate the thermodynamic fingerprint of the docking of hydrophobic ligands. Використовуючи комп’ютерне моделювання в iзотермiчно-iзобаричному ансамблi, дослiджено взаємодiю гiдрофобного лiганда з гiдрофобними поверхнями рiзної кривизни (плоскi, випуклi та вгнутi). Використано просту двовимiрну модель води, гiдрофобний лiганд та гiдрофобну поверхню. Дослiджено явища гiдратацiї/дегiдратацiї молекул води близьких до молекулярної поверхнi. Спостерiгалось суттєве незмочування гiдрофобних поверхонь поряд з переорiєнтацiєю молекул води поблизу поверхнi. Спостережено формування мережi водневих зв’язкiв так що порожнини розташовуються бiля поверхнi, а також поза межами першої гiдратної оболонки. Згаданi ефекти найбiльш вираженi у випадку ввiгнутих поверхонь з великою кривизною. Цю спрощену модель можна використовувати щоб оцiнити термодинамiчнi аспекти докування гiдрофобних лiгандiв. 2016 Article Cavity-ligand binding in a simple two-dimensional water model / G. Mazovec, M. Lukšič, B. Hribar-Lee // Condensed Matter Physics. — 2016. — Т. 19, № 1. — С. 13004: 1–6 . — Бібліогр.: 20 назв. — англ. 1607-324X DOI:10.5488/CMP.19.13004 arXiv:1603.02163 PACS: 02.70.Uu, 05.10.Ln, 61.20.Gy, 61.20.Ja, 61.30.Hn http://dspace.nbuv.gov.ua/handle/123456789/155776 en Condensed Matter Physics Інститут фізики конденсованих систем НАН України |
| institution |
Digital Library of Periodicals of National Academy of Sciences of Ukraine |
| collection |
DSpace DC |
| language |
English |
| description |
By means of Monte Carlo computer simulations in the isothermal-isobaric ensemble, we investigated the interaction of a hydrophobic ligand with the hydrophobic surfaces of various curvatures (planar, convex and concave). A simple two-dimensional model of water, hydrophobic ligand and surface was used. Hydration/dehidration phenomena concerning water molecules confined close to the molecular surface were investigated. A notable dewetting of the hydrophobic surfaces was observed together with the reorientation of the water molecules close to the surface. The hydrogen bonding network was formed to accommodate cavities next to the surfaces as well as beyond the first hydration shell. The effects were most strongly pronounced in the case of concave surfaces having large curvature. This simplified model can be further used to evaluate the thermodynamic fingerprint of the docking of hydrophobic ligands. |
| format |
Article |
| author |
Mazovec, G. Lukšič, M. Hribar-Lee, B. |
| spellingShingle |
Mazovec, G. Lukšič, M. Hribar-Lee, B. Cavity-ligand binding in a simple two-dimensional water model Condensed Matter Physics |
| author_facet |
Mazovec, G. Lukšič, M. Hribar-Lee, B. |
| author_sort |
Mazovec, G. |
| title |
Cavity-ligand binding in a simple two-dimensional water model |
| title_short |
Cavity-ligand binding in a simple two-dimensional water model |
| title_full |
Cavity-ligand binding in a simple two-dimensional water model |
| title_fullStr |
Cavity-ligand binding in a simple two-dimensional water model |
| title_full_unstemmed |
Cavity-ligand binding in a simple two-dimensional water model |
| title_sort |
cavity-ligand binding in a simple two-dimensional water model |
| publisher |
Інститут фізики конденсованих систем НАН України |
| publishDate |
2016 |
| url |
http://dspace.nbuv.gov.ua/handle/123456789/155776 |
| citation_txt |
Cavity-ligand binding in a simple two-dimensional water model / G. Mazovec, M. Lukšič, B. Hribar-Lee // Condensed Matter Physics. — 2016. — Т. 19, № 1. — С. 13004: 1–6
. — Бібліогр.: 20 назв. — англ. |
| series |
Condensed Matter Physics |
| work_keys_str_mv |
AT mazovecg cavityligandbindinginasimpletwodimensionalwatermodel AT luksicm cavityligandbindinginasimpletwodimensionalwatermodel AT hribarleeb cavityligandbindinginasimpletwodimensionalwatermodel |
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2023-05-20T17:47:39Z |
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2023-05-20T17:47:39Z |
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1796154099989741568 |