• 한국정밀공학회지
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• 제19권1호
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• pp.33-42
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• 2002

• KSBB Journal
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• 제16권2호
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• pp.107-114
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• 2001

The dynamic evolution process has resulted in the myriad shapes, functions, and systems evident in every living organism. For centuries, people have been harnessing the power of evolution to produce new varieties of plants and animals, such as producing tomatoes from berries and Chihuahuas from wolves. Now scientists are using it to produce better molecules, ranging from drugs to industrial chemicals, and doing it in days or weeks rather than eons. The ingenious process, which creates genetic diversity and selects those with desired features in the laboratory, is called directed evolution or test tube evolution. In this paper, concepts of directed molecular evolution and some examples will be discussed.

• BMB Reports
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• 제52권1호
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• pp.3-4
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• 2019

Cellular senescence is defined as a state of stable cell cycle exit in response to various stimuli, which include both cytotoxic stress and physiological cues. In addition to the core non-proliferative aspect, senescence is associated with diverse functionalities, which contribute to the role of senescence in a wide range of pathological and physiological processes. Such functionality is often mediated by the capability of senescent cells to communicate with their surroundings. Emerging evidence suggests that senescence is not a single entity, but a dynamic and heterogeneous collective phenotype. Understanding the diverse nature of senescence should provide insights into the complexity of tissue homeostasis and its disruption, such as in aging and tumorigenesis.

• BMB Reports
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• 제52권3호
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• pp.175-180
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• 2019

Telomeres are nucleoprotein complexes at the physical ends of linear eukaryotic chromosomes. They protect the chromosome ends from various external attacks to avoid the loss of genetic information. Telomeres are maintained by cellular activities associated with telomerase and telomere-binding proteins. In addition, epigenetic regulators have pivotal roles in controlling the chromatin state at telomeres and subtelomeric regions, contributing to the maintenance of chromosomal homeostasis in yeast, animals, and plants. Here, we review the recent findings on chromatin modifications possibly associated with the dynamic states of telomeres in Arabidopsis thaliana.

• 한국광물학회지
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• 제32권3호
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• pp.151-162
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• 2019

토도로카이트(todorokite)는 $3{\times}3$ 망간 팔면체로 이루어진 상대적으로 큰 나노공극(nanopore)을 가지는 터널구조의 산화망간광물로 나노공극에 다양한 양이온 함유가 가능하기 때문에 금속이온 거동에 큰 역할을 할 수 있다. 주로 결정도가 낮고 다른 산화망간광물들과 함께 집합체로 발견되어 나노 공극 내부 양이온의 배위(coordination)구조는 실험만으로 여전히 규명하기 매우 어렵다. 이번 논문에서는 고전분자동력학(classical molecular dynamics, MD) 시뮬레이션을 이용하여 토도로카이트 터널에 함유된 $Mg^{2+}$ 이온의 배위구조에 대한 연구결과를 처음으로 소개한다. 기존 실험에서는 토도로카이트 내부에 함유된 $Mg^{2+}$가 공극의 중앙에 우세하게 자리한다고 알려져 있다. MD 시뮬레이션 결과, $Mg^{2+}$ 이온의 약 60 %가 나노공극의 중앙에 위치하지만, 약 40 %의 $Mg^{2+}$는 광물의 표면에 해당하는 공극의 코너에 위치하였다. 공극 중앙의 $Mg^{2+}$는 수용액에서처럼 물 분자와 6배위수를 보였다. 공극 코너의 $Mg^{2+}$ 역시 6배위수를 보였는데, 물 분자 이외에도 망간 팔면체 표면 산소와 배위를 보였다. $Mg^{2+}$ 이온의 동적 거동을 파악하기 위해 계산한 평균 제곱 변위(mean squared displacement) 결과에서는, 수용액 벌크(bulk) 상태에서 갖는 물 분자와 양이온의 동적 성질이 토도로카이트 1D 나노공극에서는 유지되지 못하고 잃어버리는 것을 확인할 수 있었다.

• 대한약침학회지
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• 제27권1호
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• pp.1-13
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• 2024

Background: Diabetic nephropathy (DN) is one of the major complications of chronic hyperglycaemia affecting normal kidney functioning. The ayurvedic medicine curcumin (CUR) is pharmaceutically accepted for its vast biological effects. Objectives: The Curcuma-derived diferuloylmethane compound CUR, loaded on Poly (lactide-co-glycolic) acid (PLGA) nanoparticles was utilized to combat DN-induced renal apoptosis by selectively targeting and modulating Bcl2. Methods: Upon in silico molecular docking and screening study CUR was selected as the core phytocompound for nanoparticle formulation. PLGA-nano-encapsulated-curcumin (NCUR) were synthesized following standard solvent displacement method. The NCUR were characterized for shape, size and other physico-chemical properties by Atomic Force Microscopy (AFM), Dynamic Light Scattering (DLS) and Fourier-Transform Infrared (FTIR) Spectroscopy studies. For in vivo validation of nephro-protective effects, Mus musculus were pre-treated with CUR at a dose of 50 mg/kg b.w. and NCUR at a dose of 25 mg/kg b.w. (dose 1), 12.5 mg/kg b.w (dose 2) followed by alloxan administration (100 mg/kg b.w) and serum glucose levels, histopathology and immunofluorescence study were conducted. Results: The in silico study revealed a strong affinity of CUR towards Bcl2 (dock score -10.94 Kcal/mol). The synthesized NCUR were of even shape, devoid of cracks and holes with mean size of ~80 nm having -7.53 mV zeta potential. Dose 1 efficiently improved serum glucose levels, tissue-specific expression of Bcl2 and reduced glomerular space and glomerular sclerosis in comparison to hyperglycaemic group. Conclusion: This study essentially validates the potential of NCUR to inhibit DN by reducing blood glucose level and mitigating glomerular apoptosis by selectively promoting Bcl2 protein expression in kidney tissue.

• 한국지능시스템학회논문지
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• 제25권6호
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• pp.529-535
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• 2015

지금까지 생체 네트워크 분석 연구는 정적(static)인 개념으로만 다루어졌다. 그러나 실제 생명현상이 발생하는 세포 내에서는 세포의 상태 및 외부 환경에 따라 일부 단백질과 그 상호작용만이 선택적으로 활성화된다. 따라서 생체 네트워크의 구조가 시간의 흐름에 따라 변화하는 동적(dynamic)인 개념이 적용되어야 하며, 이런 개념은 질병의 진행 추이를 분석하는데 효율적이다. 본 논문에서는 동적인 네트워크 방법을 알츠하이머 질병에 적용하여 질병이 진행되는 단계에 따라 변화하는 단백질 상호작용 네트워크의 구조적, 기능적 특징에 대하여 분석하고자 한다. 우선, 유전자 발현데이터를 기반으로 각 질병의 진행 상태에 따른 부분 네트워크(정상, 초기, 중기, 말기)를 구축하였다. 이를 기반으로, 네트워크의 구조적 특성 분석을 수행하였다. 또한 기능적 특성 분석을 위해 유전자 군집(module)을 탐색하고, 군집별 유전자 기능(Gene Ontology) 분석을 수행했다. 그 결과, 네트워크의 특성들은 각 질병의 단계와 잘 대응되며, 동적 네트워크 분석법이 중요한 생물학적 이벤트를 설명하는데 이용될 수 있음을 보였다. 결론적으로 제안된 연구 방법을 통하여 그동안 알려지지 않았던 질병유발에 관련된 주요 네트워크 변화를 관측할 수 있고, 질병에 관여하는 복잡한 분자 수준의 발생 기작과 진행 과정을 이해하는데 중요한 정보를 획득할 수 있다.

• Molecules and Cells
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• 제26권1호
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• pp.41-47
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• 2008

Mitogen-activated protein kinase (MAPK) signaling is a crucial component of eukaryotic cells; it plays an important role in responses to extracelluar stimuli and in the regulation of various cellular activities. The signaling cascade is evolutionarily conserved in the eukaryotic kingdom from yeast to human. In response to a variety of extracellular signals, MAPK activity is known to be regulated via phosphorylation of a conserved $T{\times}Y$ motif at the activation loop in which both threonine and tyrosine residues are phosphorylated by the upstream kinase. However, the mechanism by which both residues are phosphorylated continues to remain elusive. In the budding yeast, Saccharomyces cerevisiae, Fus3 MAPK is involved in the mating signaling pathway. In order to elucidate the functional mechanism of MAPK activation, we quantitatively profiled phosphorylation of the $T{\times}Y$ motif in Fus3 using mass spectrometry (MS). We used synthetic heavy stable isotope-labeled phosphopeptides and nonphosphopeptides corresponding to the proteolytic $T{\times}Y$ motif of Fus3 and accompanying data-dependent tandem MS to quantitatively monitor dynamic changes in the phosphorylation events of MAPK. Phosphospecific immunoblotting and the MS data suggested that the tyrosine residue is dynamically phosphorylated upon stimulation and that this leads to dual phosphorylation. In contrast, the magnitude of threonine phosphorylation did not change significantly. However, the absence of a threonine residue leads to hyperphosphorylation of the tyrosine residue in the unstimulated condition, suggesting that the threonine residue contributes to the control of signaling noise.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2013년도 제44회 동계 정기학술대회 초록집
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• pp.186-186
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• 2013

Nitrogen doped Ge-Sb-Te (N-GST) thin films for phase change random access memory (PRAM) applications were investigated by synchrotron-radiation-based x-ray photoelectron spectroscopy and absorption spectroscopy. Nitrogen doping in GST resulted in more favorable N atoms' bonding with Ge atoms rather than with Sb and Te atoms [1,2], which explains the higher phase change transition temperature than that of undoped Ge-Sb-Te thin film. Surprisingly, it was noticed that N atoms also existed in the form of molecular nitrogen, $N_2$, which is detrimental to the stability of the GST performance [3]. N-doped GST experimental features were also supported by ab-initio molecular dynamic calculations [2]. References [1] M.-C. Jung, Y. M. Lee, H.-D. Kim, M. G. Kim, and H. J. Shin, K. H. Kim, S. A. Song, H. S. Jeong, C. H. Ko, and M. Han, "Ge nitride formation in N-doped amorphous Ge2Sb2Te5", Appl. Phys. Lett. 91, 083514 (2007). [2] Zhimei Sun, Jian Zhou, Hyun-Joon Shin, Andreas Blomqvist, and Rajeev Ahuja, "Stable nitride complex and molecular nitrogen in N doped amorphous Ge2Sb2Te5", Appl. Phys. Lett. 93, 241908 (2008). [3] Kihong Kim, Ju-Chul Park, Jae-Gwan Chung, and Se Ahn Song, Min-Cherl Jung, Young Mi Lee, Hyun-Joon Shin, Bongjin Kuh, Yongho Ha, Jin-Seo Noh, "Observation of molecular nitrogen in N-doped Ge2Sb2Te5", Appl. Phys. Lett. 89, 243520 (2006).

• 한국자기공명학회논문지
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• 제8권2호
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• pp.77-85
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• 2004

$^1$H-detected $^{15}$N NMR was employed to investigated the effect of mutation (Y14F) on the dynamic properties of catalytic residues in ${\Delta}^5$-3- ketosteroid isomerase (KSI) from Conamonas testosteroni. In particular, the backbone dynamics of the catalytic residues have been studied in free enzyme and its complex with a steroid ligand, 19-nortestosterone hemisuccinate, by $^{15}$N relaxation measurements. The relaxation data were analyzed using the model-free formalism to extract the model-free parameters (S$^2$, ${\tau}_e$, and R$_{ex}$). The results show that the mutation causes a significant decrease in the order parameter (S$^2$) for the catalytic residues of free Y14F KSI, presumably due to breakdown of the hydrogen bond network by mutation. In addition, the order parameters of Phe-14 and Asp-99 increased slightly upon ligand binding, indicating a slight restriction of the high-frequency (pico- to nanosecond) internal motions of the residues in the complexed Y14F KSI, while the order parameter of Tyr-55 decreased significantly upon ligand binding.