• Membrane Journal
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• v.7 no.1
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• pp.15-21
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• 1997

Carbon molecular sieve (CMS) membranes were synthesized by the pyrolysis of polymeric precursors. The CMS materials had oxygen-nitrogen selectivities much higher than those observed for the polymeric precursors. Typically molecular sieving materials have diffusion selectivities much higher than polymeric materials. This has been identified as a result of higher entropic selectivity of the molecular sieving materials. A study of the development of molecular sieving properties as the polymeric precursor is pyrolyzed into a CMS material will offer us an insight into polymeric molecular structures needed for enhanced entropic selectivity membrane materials.

• Bulletin of the Korean Chemical Society
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• v.34 no.9
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• pp.2680-2684
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• 2013

Protein kinases (PKs) are an important source of drug targets, especially in oncology. With 500 or more kinases in the human genome and only few kinase inhibitors approved, kinase inhibitor discovery is becoming more and more valuable. Because the discovery of kinase inhibitors with an increased selectivity is an important therapeutic concept, many researchers have been trying to address this issue with various methodologies. Although many attempts to predict the activity and selectivity of kinase inhibitors have been made, the issue of selectivity has not yet been resolved. Here, we studied kinase selectivity by generating predictive models and analyzing their descriptors by using kinase-profiling data. The 5-fold cross-validation accuracies for the 51 models were between 72.4% and 93.7% and the ROC values for all the 51 models were over 0.7. The phylogenetic tree based on the descriptor distance is quite different from that generated on the basis of sequence alignment.

• Bulletin of the Korean Chemical Society
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• v.34 no.7
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• pp.2187-2190
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• 2013

• Membrane Journal
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• v.28 no.6
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• pp.388-394
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• 2018

Carbon nanotube (CNT) based membranes are promising candidates for separation membranes by showing high water transport rate and ion rejection rate according to their radii. The ion selectivity is an important factor to discover the full potential of CNT membranes, and it is affected by the functionalization of CNTs. With multivalent/size ion mixtures, the ion selectivity is affected by not only ion-functional groups interaction but also ion-ion interactions and ion size exclusion in a complex manner. In this study, molecular dynamics simulations are performed to study the ion selectivity of functionalized carbon nanotubes when multivalent/size ions are contained. The permeation energy barriers are calculated by plotting potential of mean force profiles, and various factors, such as CNT size and partial charges, affecting ion selectivity are investigated. The results presented here will be useful for designing CNT membranes for ion separation, biomimetic ion channels, etc.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.911-916
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• 2012

Ion selectivity in a simple cyclic peptide nanotube, composed of four cyclo[-(D-Ala-Glu-D-Ala-Gln)$_2-$] units, is investigated by calculating the PMF profiles of $Na^+$, $K^+$, and $Cl^-$ ions permeating through the peptide nanotube in water. The final PMF profiles of the ions obtained from the umbrella sampling (US) method show an excellent agreement with those from the thermodynamic integration (TI) method. The PMF profiles of $Na^+$ and $K^+$ display free energy wells while the PMF curve of $Cl^-$ features free energy barriers, indicating the selectivity of the cyclic peptide nanotube to cations. Decomposition of the total mean force into the contribution from each component in the system is also accomplished by using the TI method. The mean force decomposition profiles of $Na^+$ and $K^+$ demonstrate that the dehydration free energy barriers by water molecules near the channel entrance and inside the channel are completely compensated for by attractive electrostatic interactions between the cations and carbonyl oxygens in the nanotube. In the case of $Cl^-$, the dehydration free energy barriers are not eliminated by an interaction between the anion and the peptide nanotube, leading to the high free energy barriers in the PMF profile. Calculations of the coordination numbers of the ions with oxygen atoms pertaining to either water molecules or carbonyl groups in the peptide nanotube reveal that the stabilization of the cations in the midplane regions of the nanotube arises from the favorable interaction of the cations with the negatively charged carbonyl oxygens.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.48 no.1
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• pp.71-75
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• 2015

Nicotinic acetylcholine receptors (nAChRs) are essential for neurotransmission and important therapeutic targets of diseases related to neurotransmission. A recent experimental study identified three residues (Lys185, Asp187, and Ile188) of the ${\alpha}6$ nAChR subunit as determinants of ${\alpha}$-conotoxin BuIA selectivity, yet how these residues confer toxin selectivity remains unclear. In this study, we performed all-atom molecular dynamics simulations with two toxin-bound ${\alpha}4{\beta}2$ nAChR systems: the wild-type ${\alpha}4{\beta}2$ and one in which we replaced the three ${\alpha}4$ subunit residues with three ${\alpha}6$ subunit residues identified in an experimental study (Tyr185Lys, Thr187Asp, and Arg188Ile). After mutation, Asp199 lost the salt bridge formed with Arg188 in the wild type located around loop C. Then, the loop C conformation changed and became more flexible than that of the wild type. We also detected reduced space between the toxin and the binding site in the mutant simulation, resulting in increased binding affinity to the toxin. Therefore, we propose a new Asp199 mutation that breaks the salt bridge and may produce similar selectivity to that of the Arg188 mutation.

• Korean Membrane Journal
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• v.5 no.1
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• pp.43-53
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• 2003

The selectivity of a gas in the carbon molecular sieve membrane (CMSM) can be expressed as the ratio of the product of the diffusivity and the solubility of two different gases. The diffusivity is also expressed as the product of the entropy and the total energy (kinetic and potential energy) in the nano-sized pore of the membrane. The present study calculates the entropic-energy and selectivity of penetrant gases such as H$_2$, O$_2$, N$_2$, and CO$_2$ from the gas-in-a box theory to physically analyze the diffusivity of penetrant gas in slit-shaped pore of CMSM focusing on the restriction of gas motion based on the size difference between penetrant gas pairs. The contribution of each energy term is converted to entropic term separately. By the conjugated calculation for each entropic-energy, the entropic effects on diffusivity-selectivity for gas pairs such as H$_2$/N$_2$, CO$_2$/N$_2$, and O$_2$/N$_2$ were analyzed within active pore of CMSM. In the activated diffusion domain, the calculated value of entropic-selectivity lies between 9.25 and 111.6 for H$_2$/N$_2$, between 3.36 and 6.0 for CO$_2$/N$_2$, and between 1.25 and 16.94 for O$_2$/N$_2$, respectively. The size decrement of active pore in CMSM had the direct effect on the reduction of translational entropic-energy and the contribution of vibrational entropic-energy for N$_2$, O$_2$, and H$_2$ was almost negligible. However, the vibrational entropic term of CO$_2$ might extravagantly affect on the entropic-selectivity.

• Animal cells and systems
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• v.11 no.2
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• pp.93-98
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• 2007

Gonadotropin-releasing hormone (GnRH), synthesized in the hypothalamus, plays a pivotal role in the regulation of vertebrate reproduction. Since molecular isoforms of GnRH and their receptors (GnRHR) have been isolated in a broad range of vertebrate species, GnRH and GnRHR provide an excellent model for understanding the molecular co-evolution of a peptide ligand-receptor pair. Vertebrate species possess multiple forms of GnRH, which have been created through evolutionary mechanisms such as gene/chromosome duplication, gene deletion and modification. Similar to GnRHs, GnRH receptors (GnRHR) have also been diversified evolutionarily. Comparative ligand-receptor interaction studies for non-mammalian and mammalian GnRHRs combined with mutational mapping studies of GnRHRs have aided the identification of domains or motifs responsible for ligand binding and receptor activation. Here we discuss the molecular basis of GnRH-GnRHR co-evolution, particularly the structure-function relationship regarding ligand selectivity and signal transduction of mammalian and non-mammalian GnRHRs.

• Proceedings of the Korean Biophysical Society Conference
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• 2001.06a
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• pp.36-36
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• 2001

Small conductance $Ca^{2＋}$-activated $K^{+}$ channels (or S $K_{Ca}$ channels) are a group of $K^{＋}$-selective ion channels activated by sub-micromolar concentrations of intracellular $Ca^{2＋}$ independent of membrane voltage. We expressed a cloned S $K_{Ca}$ channel, rSK2, in Xenopus oocytes and investigated the monovalent cation selectivity of the channels. We have used site-directed mutagenesis and macro-channel recordings to identify amino acid residues influencing the ion selectivity.(omitted)d)

• Bulletin of the Korean Chemical Society
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• v.34 no.3
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• pp.963-966
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• 2013