Water-membrane interface and forced transport of moleculesтезисы доклада
Дата последнего поиска статьи во внешних источниках: 28 мая 2015 г.
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Авторы:
Tourleigh Yegor,
Shaitan Konstantin
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Сборник:
Abstracts of the 5th International Conference on Biological Physics
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Тезисы
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Год издания:
2004
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Место издания:
Gothenburg, Sweden
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Первая страница:
61
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Аннотация:
Biological membranes are frequent subject of investigation at molecular modelling. Their structure and functions determine biological processes in many respects. One of the interesting problems affected at study of membranes is a study of their barrier and transport functions. It is known that for hydrophilic substances which are the majority of biological molecules they are a barrier. Thus, in reality passive transport is possible for hydrophobic substances.
In this work two types of membrane were modelled by method of molecular dynamics: one of hydrocarbon (mono-and bilayers of n-tetradecane) and the other of lipid (bilayer of POPC – l-palmitoyl-2-oleyl-sn-glycero-3-phosphatidylcboline). The membranes being investigated were sufficiently hydrated (15 and 44 molecules of water per 1 molecule of tetradecane and POPC, correspondingly). As molecules which interaction with a membrane and possible transport through it were studied were taken single atoms, functional groups of atoms, molecular oxygen, aminoacid residues of variable degree of polarity and hydrophobicity (Ala, Asp, Gly, Phe, Trp, Val), and also carbon nanotube of 13,5 Å in diameter and 35 Å in length ("armchair" type of arrangement of the atoms). The model of water selected for calculation was TIP3P. The calculations were carried out in Amber99© force field. In addition the thermostat on the base of collisional dynamics was used. Periodic conditions were realized in two types of thermodynamic ensembles – NVT and NPT (at isotropic and anisotropic pressure). Barostating was carried out with the help of Berendsen's barostat.
Initially it was supposed to observe spontaneous transport of the more hydrophobic molecules. As it was found, the process at 300 K can be registered during a calculation (which didn't exceed 10 ns) only for oxygen, at that at temperature rise up to 2000 K oxygen permeate into the tetradecane membrane only in NVT-ensemble whereas at the NPT-conditions capable of system volume fluctuations oxygen does not get inside demonstrating thereby decrease of its hydrophobicity (that may be connected with reduction of entropic contribution to the hydrophobic effect). At room temperature the behaviour of the remaining molecules at the interface correlated with their size, polarizability and charge (for comparison experimental aminoacids hydropathy scale and Born law for transfer of spherically symmetrical particles to hydrophobic medium were applied). Not having a possibility to observe spontaneous transport of molecules through a membrane, it is necessary to mark surface-active properties which the molecules showed.
For speedup of transport processes a force (either stationary or alternating) of the magnitude from 0,2 to 10 kcal/mol/Å per atom was applied to the molecules under study. During the calculation again penetration through a membrane was observed only at forces high enough (more than 3 kcal/mol/Å). The relation of penetration speed to the frequency of external field tells about probable existence of a resonance frequency determining the characteristic time of necessary rearrangements of such structured medium as a membrane. Calculated from Stokes-Einstein relation characteristic viscosities and diffusion coefficients of molecules in the medium non-linearly depend on sizes of the latter and applied force that gives cause to suppose different nonequilibrium modes of molecules dynamics at rather big external forces or to consider requirement of greater statistical confidence of these computingly expensive calculations.
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Добавил в систему:
Турлей Егор Владимирович
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Полный текст
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ICBP-2004_Gothenburg.pdf |
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31 января 2013
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