• Proceedings of the PSK Conference
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• 2001.04a
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• pp.90-94
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• 2001

Wondonins A and B, aromatic alkaloids of an unprecedented skeletal class have been isolated form and association of the sponges Poecillastra wondoensis and Jaspis sp. In addition, four novel bromotyrosine-derived metabolites, psammaplins $A_1$ and $A_2$, aplysinellins A and B, have been isolated from the tropical sponge Aplysinella rhax. The structures of these compounds have been determined on the basis of combined chemical and spectral analyses. The new compounds exhibited significant cytotoxicity and antiangiogenic activity as well as inhibitory activities against farnesyl protein transferase and leucine aminopeptidase. In addition to these compounds, several bioactive metabolites have been isolated from sponges of Korean and tropical waters.

• Journal of the Korean Data and Information Science Society
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• v.18 no.2
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• pp.489-506
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• 2007

Gene structure prediction, which is to predict protein coding regions in a given nucleotide sequence, is the most important process in annotating genes and greatly affects gene analysis and genome annotation. As eukaryotic genes have more complicated structures in DNA sequences than those of prokaryotic genes, analysis programs for eukaryotic gene structure prediction have more diverse and more complicated computational models. There are Ab Initio method, Similarity-based method, and Ensemble method for gene prediction method for eukaryotic genes. Each Method use various algorithms. This paper introduce how to predict genes using HMM(Hidden Markov Model) algorithm and present the process of gene prediction with well-known gene prediction programs.

• Genomics & Informatics
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• v.1 no.1
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• pp.1-6
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• 2003

In conclusion, the seemingly fuzzy and disorganized data of biology with thousands of different layers ranging from molecule to the Internet have refused so far to be mapped precisely and predicted successfully by mathematicians, physicists or computer scientists. Genomics and bioinformatics are the fields that process such complex data. The insights on the nature of biological entities as complex interaction networks are opening a door toward a generalization of the representation of biological entities. The main challenge of genomics and bioinformatics now lies in 1) how to data mine the networks of the domains of bioinformatics, namely, the literature, metabolic pathways, and proteome and structures, in terms of interaction; and 2) how to generalize the networks in order to integrate the information into computable genomic data for computers regardless of the levels of layer. Once bioinformatists succeed to find a general principle on the way components interact each other to form any organic interaction network at genomic scale, true simulation and prediction of life in silico will be possible.

• BMB Reports
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• v.41 no.1
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• pp.35-40
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• 2008

The molten globular conformation of V26A ubiquitin (valine to alanine mutation at residue 26) was studied by nuclear magnetic resonance spectroscopy in conjunction with amide hydrogen/deuterium exchange. Most of the amide protons that are involved in the native secondary structures were observed to be protected in the molten globule state with the protection factors from 1.2 to 6.7. These protection factors are about 2 to 6 orders of magnitude smaller than those of the native state. These observations indicate that V26A molten globule has native-like backbone structure with marginal stability. The comparison of amide protection factors of V26A ubiquitin molten globule state with those of initial collapsed state of the wild type ubiquitin suggests that V26A ubiquitin molten globule state is located close to unfolded state in the folding reaction coordinate. It is considered that V26A ubiquitin molten globule is useful model to study early events in protein folding reaction.

• Bulletin of the Korean Chemical Society
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• v.32 no.12
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• pp.4195-4198
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• 2011

Intramolecular ${\pi}-{\pi}$ and ${\sigma}-{\pi}$ interactions are omnipresent for numerous energetic and structural phenomena in nature, and the exact description of these nonbonding interactions plays an important role in the accurate prediction of the three-dimensional structures for numerous interesting molecular systems such as protein folding and polymer shaping. We have selected two prototype molecular systems for benchmarking calculations of intramolecular ${\pi}-{\pi}$ and ${\sigma}-{\pi}$ interactions. Accurately describing conformational energy of such systems requires highly elaborate but very expensive ab initio methods such as coupled cluster singles, doubles, and (triples) (CCSD(T)). Our calculations reveal a double hybrid density functional incorporating dispersion correction (B2PLYP-D) that agrees excellently with the CCSD(T) results, indicating that B2PLYP-D can serve as a practical method of choice.

• Natural Product Sciences
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• v.19 no.3
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• pp.206-214
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• 2013

The crocetin derivatives, crocin (1), gentiobiosyl glucosyl crocetin (3), and mono-gentiobiosyl crocetin (4) were isolated from the fruit of Gardenia jasminoides (Gj) and crocetin (2) from the processed fruit of Gj (PGj) by column chromatography. Their structures were determined on the basis of spectroscopic methods including IR, MS, and NMR (1D and 2D). These compounds were evaluated for their inhibition activity on melanin production in ${\alpha}$-MSH (melanocyte stimulating hormone) activated B16F10 cells. Compounds 1 - 4 reduced melanin content in a dose-dependent manner at concentrations of 20 - 60 uM. They also suppressed tyrosinase protein and m-RNA expressions dose dependently, assayed by western blot analysis, and RT-PCR experiment in B16F10 murine melanoma cells.

• Natural Product Sciences
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• v.19 no.3
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• pp.258-262
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• 2013

Three ergosterol derivatives, ergosta-4,6,8(14),22-tetraen-3-one (1), ergosta-7,24(28)-dien-3-ol (2), and 5,8-epidioxyergosta-6,22-dien-3-ol(3) were isolated from the fruit body of Phellinus pini. Their structures were based on spectroscopic methods including IR, MS, and NMR (1D and 2D). These compounds were evaluated for their activity to decrease melanin production in ${\alpha}$-MSH (melanocyte stimulating hormone) activated B16F10 cells. Compound 1, 2, and 3 reduced melanin content in a dose-dependent manner at concentrations of 5~15 uM. They also suppressed the tyrosinase expression of protein and m-RNA level dose dependently by western blot analysis and RT-PCR experiment in B16F10 murine melanoma cells.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.8
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• pp.3085-3090
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• 2015

The telomeric end structures of the DNA are known to contain tandem repeats of TTAGGG sequence bound with specialised protein complex called the "shelterin complex". It comprises six proteins, namely TRF1, TRF2, TIN2, POT1, TPP1 and RAP1. All of these assemble together to form a complex with double strand and single strand DNA repeats at the telomere. Such an association contributes to telomere stability and its protection from undesirable DNA damage control-specific responses. However, any alteration in the structure and function of any of these proteins may lead to undesirable DNA damage responses and thus cellular senescence and death. In our review, we throw light on how mutations in the proteins belonging to the shelterin complex may lead to various malfunctions and ultimately have a role in tumorigenesis and cancer progression.

• Korean Journal of Pharmacognosy
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• v.39 no.1
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• pp.56-59
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• 2008

Ubiquitin-proteasome proteolytic system plays an important role in selective protein degradation and regulates cellular events including apoptosis. Cancer cells have been shown to be more sensitive to the proapoptotic effects of proteasome inhibition than normal cells. Thus, proteasome inhibitor can be potential anticancer agent. Since the MeOH extracts of psoraleae semen and processed psoraleae semen showed potent proteasome inhibition activity, the fractions of the extracts were evaluated on the activity to screen the proteasome inhibitors. The $CHCl_3$ fr. of the processed psoraleae semen showed the most potent activity, of which chemical investigation led to two coumarins, psoralen and isopsoralen. Their structures were determined by spectroscopic methods such as $^1H-NMR$ and EIMS spectra.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.225-235
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• 2014

6종의 Intermediate filament 중 type IV인 Neurofilaments (NFs)는 신경세포에 존재하는 세포골격세사로 heavy NF(NF-H), medium NF(NF-M), light NF(NF-L) 세가지의 분자 질량 단백질로 구성되어 있다. NF의 side arm은 interfilament spacing과 axonal caliber를 조절하는 중요한 역할을 한다고 생각되어왔다. 또한 이에 대해서 각각의 protein의 역할은 알아내기 위해 isolated NF의 형태와 구조에 대해 많은 연구가 이루어졌는데, NF의 구조적 특성은 NF sidearm의 tail 부분에서 phosphorylation의 정도에 따른 Lys-Ser-Pro(KSP) repeats의 charge distribution을 통해 알 수 있다. 지금까지 NF에 대한 많은 연구가 이루어졌지만 인간에 한해서만 진행되었다. 그렇기 때문에 본 연구에서는 주어진 amino acid sequence와 각 species의 NF-H:NF-M:NF-L의 비율의 정보를 이용하여 The constant-NVT ensemble MC simulation을 통해 인간뿐만이 아닌 다른 species에 대한 NF의 구조적 특성을 알아보고자 한다.