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RISS 인기검색어
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- 저자 : Hyonseok Song (검색결과 5 건)
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Song, Yeonho,Lee, Ji Hye,Hwang, Hoon,Schatz, George C.,Hwang, Hyonseok American Chemical Society 2016 The Journal of physical chemistry B Vol.120 No.46
<P>Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na+ and K+ are calculated to elucidate the translocation of ions through a 0.10 cyclic peptide nanotube, composed of 8 x cyclo[-(D-LeuTrp)(4)-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and in lipid bilayers, and that the selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to a decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. The PMF and diffusivity profiles for Na+ and K+ reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system, while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na+ and K+ ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition, this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly.</P>
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Seo, Yongil,Song, Yeonho,Schatz, George C.,Hwang, Hyonseok American Chemical Society 2018 The Journal of physical chemistry B Vol.122 No.34
<P>The transport behavior of glucose through a cyclic peptide nanotube (CPN), composed of 8 × cyclo[-(Trp-<SMALL>D</SMALL>-Leu)<SUB>4</SUB>-Gln-<SMALL>D</SMALL>-Leu-] rings embedded in DMPC lipid bilayers was examined using all-atom molecular dynamics (AAMD) simulations. Two conformational isomers of β-<SMALL>D</SMALL>-glucose, equatorial (<SUP>4</SUP>C<SUB>1</SUB>) and axial (<SUP>1</SUP>C<SUB>4</SUB>) chair conformers, were used to examine conformational effects on the hydrogen bond network, energetics, and diffusivity of glucose transport through the CPN. Calculations of the number of hydrogen bonds of the two glucose conformers with water molecules and with the CPN illustrate that the total number of hydrogen bonds of the conformers decreases inside the channel compared to bulk water due to the confinement characteristics of the interior of the CPNs although new hydrogen bonds between the hydroxyl and hydroxymethyl hydrogens of glucose and the carbonyl oxygens in the CPN backbone are formed. Despite the decrease of the number of hydrogen bonds inside the CPN, intramolecular hydrogen bonds of <SUP>1</SUP>C<SUB>4</SUB> are maintained during permeation of <SUP>1</SUP>C<SUB>4</SUB> through the CPN. The retention of intramolecular hydrogen bonds and the spherical shape of <SUP>1</SUP>C<SUB>4</SUB> give rise to considerably weaker orientational preferences and higher diffusion coefficients for <SUP>1</SUP>C<SUB>4</SUB> than those of <SUP>4</SUP>C<SUB>1</SUB> inside and outside the CPN. Due to larger dipole moments induced by the alignment of hydroxyl and hydroxymethyl groups, <SUP>1</SUP>C<SUB>4</SUB> has more favorable interactions with the CPN backbone at the channel entrances and inside the channel than <SUP>4</SUP>C<SUB>1</SUB>. In the middle of the CPN channel, entropic gains originating from higher orientational and translational degrees of freedom of <SUP>1</SUP>C<SUB>4</SUB> than those of <SUP>4</SUP>C<SUB>1</SUB> also contribute to lower free energy wells for <SUP>1</SUP>C<SUB>4</SUB> inside the CPN. This work reveals that the conformational variation and intramolecular hydrogen bond formation of β-<SMALL>D</SMALL>-glucose can have important effects on the energetics and dynamics of glucose transport through CPNs, providing insight into the translocation mechanism of <SMALL>D</SMALL>-glucose into the cell through glucose transporters (GLUTs) and the dynamics of glucose confined in silica nanochannels. It is also demonstrated that CPNs can indeed facilitate the permeation of small hydrophilic molecules such as glucose and can be utilized as a novel carrier system for hydrophilic drug compounds into the cell.</P> [FIG OMISSION]</BR>
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Choi Inhyeok,Kim Namho,Song Yeonho,Schatz George C.,Hwang Hyonseok 대한화학회 2022 Bulletin of the Korean Chemical Society Vol.43 No.3
An extended version of the original kinetic lattice grand canonical Monte Carlo simulation method combined with mean field theory (KLGCMC/MF) (J. Chem. Phys. 2007, 127, 024706) is presented for the study of transport of multicomponent ion mixtures through a model nanopore. Comparison of the extended KLGCMC/MF (eKLGCMC/MF) simulation results with Poisson–Nernst– Planck (PNP) calculations is also made to confirm the validity of the extended simulation approach. Unlike the original version of KLGCMC/MF simulation method that treats only a binary ionic solution with one cation and one anion species, this extended version can deal with a system that includes ternary ion mixtures. A diffusion probability algorithm is also added to the extended version of the simulation method to describe the inhomogeneous diffusivity of ions that is often observed in the ion permeation through nanopores. Both Legendre and Chebyshev polynomials of the second kind were tested as a basis set for the basis set expansion (BSE) method with which to calculate the reaction field energy in the eKLGCMC/MF simulation. It turned out that the Legendre polynomials perform better than the Chebyshev polynomials, and as a result, the Legendre polynomials were implemented in the current version of eKLGCMC/MF simulation algorithm. The presented eKLGCMC/MF simulation method with new features finds its potential applications in nanopore systems where the correlation between ion species with the same sign of charges plays a key role such as oscillating ion currents or anomalous mole fraction effects.
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