• EDISON SW 활용 경진대회 논문집
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• 제3회(2014년)
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• pp.63-74
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• 2014

Predicting protein loop structures is an important modeling problem since protein loops are often involved in diverse biological functions by participating in enzyme active sites, ligand binding sites, etc. However, loop structure prediction is difficult even when structures of homologous proteins are known due to large sequence and structure variability among loops of homologous proteins. Therefore, an ab initio approach is necessary to solve loop modeling problems. One of the difficulties in the development of ab initio loop modeling method is to derive an accurate scoring function that closely approximates the true free energy function. In particular, entropy as well as energy contribution have to be considered adequately for loops because loops tend to be flexible compared to other parts of protein. In this study, the contribution of conformational entropy is considered in scoring loop conformations by employing "colony energy" which was previously proposed to estimate the free energy for an ensemble of conformations. Loop conformations were generated by using two EDISON_Chem programs GalaxyFill and GalaxySC, and colony energy was designed for this sampling by tuning relevant parameters. On a test set of 40 loops, the accuracy of predicted loop structure improved on average by scoring with the colony energy compared to scoring by energy alone. In addition, high correlation between colony energy and deviation from the native structure suggested that more extensive sampling can further improve the prediction accuracy. In another test on 6 ligand-binding loops that show conformational changes by ligand binding, both ligand-free and ligand-bound states could be identified by using colony energy when no information on the ligand-bound conformation is used.

• 대한화학회지
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• 제47권2호
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• pp.109-114
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• 2003

trans-$[CrX_2([15]aneN_4)]ClO_4 ([15]aneN_4=1,4,8,12-tetraazacyclopentadecane; X=F, Cl)$의 전자흡수 스펙트럼을 리간드장 이론으로 해석하였다. AOMX 프로그램을 사용하여 관측한 스핀허용 전이와 계산값을 최적화시켰다. 결정한 CFT 파라미터를 AOM, NSH 및 여러 가지 다른 파라미터와 관련시켜 구하고, 이를 화학적 견지에서 논의하였다. 리간드장 해석으로부터 이들 착물에서는 F 리간드가 강한${\sigma}-$ 및 ${\pi}-$주개인 반면에 Cl 원자는 Cr(III) 이온에 약한 ${\sigma}-$ 및 ${\pi}-$주개 성질이 있음을 확인할 수 있었다.

• Bulletin of the Korean Chemical Society
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• 제26권6호
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• pp.892-898
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• 2005

A long, bis(monodentate), linking Schiff-base ligand L (py-CH=N-$C_6H_4$-N=CH-py) was prepared from 1,4-phenylenediamine and 3-pyridinecarboxaldehyde by the Schiff-base condensation. Ligand L has two terminal pyridyl groups capable of coordinating to metals through their nitrogen atoms. In contrast, the same reaction between 1,2-phenylenediamine and 3-pyridinecarboxaldehyde produced a mixture of imidazol isomers (2-pyridin-3-yl-1H-benzoimidazole), which are connected to one another by the N-H…N hydrogen bonding to form a tetramer. From Zn($NO_3)_2{\cdot}6H_2O$ and ligand L under various conditions, one discrete molecule, trans- [Zn($H_2O)_4L_2]{\cdot}(NO_3)_2{\cdot}(MeOH)_2$, and two 1-D zinc polymers, [Zn$(NO_3)(H_2O)_2(L)]{\cdot}(NO_3){\cdot}(H_2O)_2$ and [Zn(L) (OBC)($H_2O$)], were prepared. In ligand L, the N$\ldots$N separation between the terminal pyridyl groups is 13.994 $\AA$, with their nitrogen atoms at the meta positions (3,3’) in a trans manner. The corresponding N$\ldots$N separations in its compounds range from 13.853 to 14.754 $\AA$.

• Journal of Ginseng Research
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• 제32권2호
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• pp.99-106
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• 2008

A ligand - whether an endogenous hormone, neurotransmitter, exogenous toxin or synthetic drug - binds to plasma membrane proteins (e.g., ion channels, receptors or other functional proteins) to exert its physiological or pharmacological effects. Ligands can also have functional groups, showing stereospecificity for interaction sites on their counterpart plasma membrane proteins. Previous reports have shown that the ginsenoside Rg$_3$, a bioactive ginsenoside, meets these criteria in that: 1) an aliphatic side chain of $Rg_3$ plays a role as a functional group, 2) Rg$_3$ regulates voltage- and ligand-gated ion channels in a stereospecific manner with respect to carbon-20, and 3) $Rg_3$ regulates subsets of ligand-gated and voltage-gated ion channels through specific interactions with identified amino acid residues inside the channel pore, in the outer pore entryway, or in toxin binding sites. Rg$_3$, therefore, could be a candidate for a novel ginseng-derived glycosidic ligand regulating ion channels and receptors. This review will examine how Rg$_3$ regulates voltage-gated and ligand-gated ion channels through interactions with its target proteins in the plasma membrane. Hopefully, this review will advance understanding of ginseng pharmacology at the cellular and molecular levels.

• Animal cells and systems
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• 제1권1호
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• pp.157-164
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• 1997

Ly-6E.1 antigen was proposed as a regulatory molecule of T lymphocyte activation, a hematopoietic stem cell marker, a memory cell marker, and an adhesion molecule. Though there were several reports suggesting the presence of Ly-6 ligand, the characterization of the ligand was not yet performed, As an attempt to screen the expression of Ly-6E.1 ligand, we prepared a probe for detecting Ly-6E.1 ligand by producing a fusion protein between Ly-6E.1 and $hlgC_{r1}$, A mammalian cell expression vector with Ly-6E.$1/hlgC_{r1}$ chimeric cDNA was transfected in SP2/0-Ag14 myeloma cells, and stable transfectants were selected. The fusion protein was produced as a dimer and maintained the epitopes for monoclonal antibodies specific for Ly-6E.1 and for anti-human lgG antibody. The purified fusion protein through Gammabind G column was used for FACS analyses for the expression of Ly-6E.1 ligand. The fusion protein interacted with several cell lines originating from B cells, T cells, or monocytes. The fusion Protein also strongly stained bone marrow, lymph node, and spleen cells, but thymic cells weakly, if any. The staining was more obvious in C57BL/6 $(Ly-6^b)$ than Balb/c $(Ly-6^a)$ mice. These results suggest that the interaction of Ly-6E.1 with Ly-6E.1 ligand may function both in the stem cell environment and in the activation of mature lymphocytes. The fusion protein may be a valuable tool in characterization of biochemical properties of the Ly-6E.1 ligand and, further, in isolating its cDNA.

• Bulletin of the Korean Chemical Society
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• 제31권9호
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• pp.2668-2671
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• 2010

• Bulletin of the Korean Chemical Society
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• 제35권1호
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• pp.269-272
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• 2014

• 대한화학회지
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• 제52권4호
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• pp.445-449
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• 2008

• Bulletin of the Korean Chemical Society
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• 제35권2호
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• pp.647-650
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• 2014

• Bulletin of the Korean Chemical Society
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• 제30권5호
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• pp.1204-1206
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• 2009