Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model
We study a rectifying mutant of the OmpF porin ion channel using both all-atom and reduced models. The mutant was created by Miedema et al. [Nano Lett., 2007, 7, 2886] on the basis of the NP semiconductor diode, in which an NP junction is formed. The mutant contains a pore region with positive amino...
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| Дата: | 2016 |
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| 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/123456789/155786 |
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| Назва журналу: | Digital Library of Periodicals of National Academy of Sciences of Ukraine |
| Цитувати: | Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model / Z. Ható, D. Boda, D. Gillespie, J. Vrabec, G. Rutkai, T. Kristóf // Condensed Matter Physics. — 2016. — Т. 19, № 1. — С. 13802: 1–16 . — Бібліогр.: 85 назв. — англ. |
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irk-123456789-1557862019-06-18T01:27:33Z Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model Ható, Z. Boda, D. Gillespie, D. Vrabec, J. Rutkai, G. Kristóf, T. We study a rectifying mutant of the OmpF porin ion channel using both all-atom and reduced models. The mutant was created by Miedema et al. [Nano Lett., 2007, 7, 2886] on the basis of the NP semiconductor diode, in which an NP junction is formed. The mutant contains a pore region with positive amino acids on the left-hand side and negative amino acids on the right-hand side. Experiments show that this mutant rectifies. Although we do not know the structure of this mutant, we can build an all-atom model for it on the basis of the structure of the wild type channel. Interestingly, molecular dynamics simulations for this all-atom model do not produce rectification. A reduced model that contains only the important degrees of freedom (the positive and negative amino acids and free ions in an implicit solvent), on the other hand, exhibits rectification. Our calculations for the reduced model (using the Nernst-Planck equation coupled to Local Equilibrium Monte Carlo simulations) reveal a rectification mechanism that is different from that seen for semiconductor diodes. The basic reason is that the ions are different in nature from electrons and holes (they do not recombine). We provide explanations for the failure of the all-atom model including the effect of all the other atoms in the system as a noise that inhibits the response of ions (that would be necessary for rectification) to the polarizing external field. Ми вивчаємо випростовуючий мутант iонного каналу OmpF порiну, використовуючи повну атомiстичну i спрощену моделi. Даний мутант був створений Мiедемою та iн. [Nano Lett., 2007, 7, 2886] на основi напiвпровiдникового дiода, в якому сформувався N-P-перехiд. Мутант мiстить пористу зону з позитивно зарядженими амiнокислотами злiва вiд бiксторону та негативно зарядженi амiнокислоти справа. Дослiди показали, що цей мутант має випростовуючi властивостi. Хоча структура цього мутанта невiдома, можна побудувати його повнiстю атомарну модель. Моделювання молекулярної динамiки для цiєї атомарної моделi не забезпечує ефекту випростовування. Водночас, спрощена модель, яка мiстить лише важливi ступенi вiльностi (додатнi та вiд’ємнi амiнокислоти i вiльнi iони у неявному розчиннику), забезпечує випростовування. Дослiдження, виконанi для спрощеної моделi (з використанням рiвняння Нернста-Планка у поєднаннi з моделюванням Монте Карло iз локальною рiвновагою), показали механiзм випростовування, який суттєво вiдрiзняється вiд напiвпровiдникових дiодiв. Головна причина полягає в тому, що iони за своєю природою вiдрiзняються вiд електронiв та дiрок (iони не рекомбiнуються). Ми пояснюємо неспроможнiсть повної атомарної моделi, включно з ефектом решти атомiв як шуму, який блокує вiдгук iонiв на зовнiшнє поляризуюче поле необхiдний для появи ефекту випростовування. 2016 Article Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model / Z. Ható, D. Boda, D. Gillespie, J. Vrabec, G. Rutkai, T. Kristóf // Condensed Matter Physics. — 2016. — Т. 19, № 1. — С. 13802: 1–16 . — Бібліогр.: 85 назв. — англ. 1607-324X DOI:10.5488/CMP.19.13802 arXiv:1603.02440 PACS: 87.16.Vy, 87.10.Tf, 05.10.Ln, 82.45.Gj, 61.20.Ja http://dspace.nbuv.gov.ua/handle/123456789/155786 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 |
We study a rectifying mutant of the OmpF porin ion channel using both all-atom and reduced models. The mutant was created by Miedema et al. [Nano Lett., 2007, 7, 2886] on the basis of the NP semiconductor diode, in which an NP junction is formed. The mutant contains a pore region with positive amino acids on the left-hand side and negative amino acids on the right-hand side. Experiments show that this mutant rectifies. Although we do not know the structure of this mutant, we can build an all-atom model for it on the basis of the structure of the wild type channel. Interestingly, molecular dynamics simulations for this all-atom model do not produce rectification. A reduced model that contains only the important degrees of freedom (the positive and negative amino acids and free ions in an implicit solvent), on the other hand, exhibits rectification. Our calculations for the reduced model (using the Nernst-Planck equation coupled to Local Equilibrium Monte Carlo simulations) reveal a rectification mechanism that is different from that seen for semiconductor diodes. The basic reason is that the ions are different in nature from electrons and holes (they do not recombine). We provide explanations for the failure of the all-atom model including the effect of all the other atoms in the system as a noise that inhibits the response of ions (that would be necessary for rectification) to the polarizing external field. |
| format |
Article |
| author |
Ható, Z. Boda, D. Gillespie, D. Vrabec, J. Rutkai, G. Kristóf, T. |
| spellingShingle |
Ható, Z. Boda, D. Gillespie, D. Vrabec, J. Rutkai, G. Kristóf, T. Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model Condensed Matter Physics |
| author_facet |
Ható, Z. Boda, D. Gillespie, D. Vrabec, J. Rutkai, G. Kristóf, T. |
| author_sort |
Ható, Z. |
| title |
Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model |
| title_short |
Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model |
| title_full |
Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model |
| title_fullStr |
Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model |
| title_full_unstemmed |
Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model |
| title_sort |
simulation study of a rectifying bipolar ion channel: detailed model versus reduced model |
| publisher |
Інститут фізики конденсованих систем НАН України |
| publishDate |
2016 |
| url |
http://dspace.nbuv.gov.ua/handle/123456789/155786 |
| citation_txt |
Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model / Z. Ható, D. Boda, D. Gillespie, J. Vrabec, G. Rutkai, T. Kristóf // Condensed Matter Physics. — 2016. — Т. 19, № 1. — С. 13802: 1–16
. — Бібліогр.: 85 назв. — англ. |
| series |
Condensed Matter Physics |
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2023-05-20T17:48:04Z |
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