Inhibition of DNA-dependent Protein Kinase by Blocking Interaction between Ku Complex and Catalytic Subunit of DNA-dependent Protein Kinase

Kim, Chung-Hui,Cuong, Dang-Van,Kim, Jong-Su,Kim, Na-Ri,Kim, Eui-Yong,Han, Jin The Korean Society of Pharmacology 2003 The Korean Journal of Physiology & Pharmacology Vol.7 No.1

Recent studies indicated that cancer cells become resistant to ionizing radiation (IR) and chemotherapy drugs by enhanced DNA repair of the lesions. Therefore, it is expected to increase the killing of cancer cells and reduce drug resistance by inhibiting DNA repair pathways that tumor cells rely on to escape chemotherapy. There are a number of key human DNA repair pathways which depend on multimeric polypeptide activities. For example, Ku heterodimer regulatory DNA binding subunits (Ku70/Ku80) on binding to double strand DNA breaks (DSBs) are able to interact with 470-kDa DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and are essential for DNA-dependent protein kinase (DNA-PK) activity. It has been known that DNA-PK is an important factor for DNA repair and also is a sensor-transmitting damage signal to downstream targets, leading to cell cycles arrest. Our ultimate goal is to develop a treatment of breast tumors by targeting proteins involved in damage-signaling pathway and/or DNA repair. This would greatly facilitate tumor cell cytotoxic activity and programmed cell death through DNA damaging drug treatment. Therefore, we designed a domain of Ku80 mutants that binds to Ku70 but not DNA end binding activity and used the peptide in co-therapy strategy to see whether the targeted inhibition of DNA-PK activity sensitized breast cancer cells to irradiation or chemotherapy drug. We observed that the synthesized peptide (HNI-38) prevented DNA-PKcs from binding to Ku70/Ku80, thus resulting in inactivation of DNA-PK activity. Consequently, the peptide treated cells exhibited poor to no DNA repair, and became highly sensitive to IR or chemotherapy drugs, and the growth of breast cancer cells was inhibited. Additionally, the results obtained in the present study also support the physiological role of resistance of cancer cells to IR or chemotherapy.

Optical Properties of GaFeO₃

Kim, Tae Jung,Park, Han Gyeol,Long Le, Van,Kim, Hwa Seob,Yoo, Chang Hyun,Uk Kim, Hyoung,Kim, Young Dong,Park, Chang Bae,Shin, Kwangwoo,Kim, Kee Hoon American Scientific Publishers 2018 Science of advanced materials Vol.10 No.2

<P>The complex dielectric function epsilon and critical-point (CP) structures of orthorhombic GaFeO3 are reported at temperatures from 39 to 350 K and photon energies from 0.74 to 6.42 eV. Data were obtained by rotating-compensator spectroscopic ellipsometry on the (010) direction of single-crystalline GaFeO3. A multilayer version of the B-splines method was used to extract the optical properties of GaFeO3, and CP energies were accurately determined by analyzing numerically calculated second-energy-derivatives of the data. At low temperature the CP structures are clearly enhanced and their energies are blue-shifted. Temperature dependencies were obtained by fitting the data to a phenomenological expression that contains a Bose-Einstein statistical factor and a temperature coefficient.</P>

Scalable Solvothermal Synthesis of Superparamagnetic Fe₃O₄ Nanoclusters for Bioseparation and Theragnostic Probes

Kim, Jeonghyo,Tran, Van Tan,Oh, Sangjin,Kim, Chang-Seok,Hong, Jong Chul,Kim, SungIl,Joo, Young-Seon,Mun, Saem,Kim, Myoung-Ho,Jung, Jae-Wan,Lee, Jiyoung,Kang, Yong Seok,Koo, Ja-Won,Lee, Jaebeom American Chemical Society 2018 ACS APPLIED MATERIALS & INTERFACES Vol.10 No.49

<P>Magnetic nanoparticles have had a significant impact on a wide range of advanced applications in the academic and industrial fields. In particular, in nanomedicine, the nanoparticles require specific properties, including hydrophilic behavior, uniform and tunable dimensions, and good magnetic properties, which are still challenging to achieve by industrial-scale synthesis. Here, we report a gram-scale synthesis of hydrophilic magnetic nanoclusters based on a one-pot solvothermal system. Using this approach, we achieved the nanoclusters with controlled size composed of magnetite nanocrystals in close-packed superstructures that exhibited hydrophilicity, superparamagnetism, high magnetization, and colloidal stability. The proposed solvothermal method is found to be highly suitable for synthesizing industrial quantities (gram-per-batch level) of magnetic spheres with unchanged structural and magnetic properties. Furthermore, coating the magnetic spheres with an additional silica layer provided further stability and specific functionalities favorable for biological applications. Using in vitro and in vivo studies, we successfully demonstrated both positive and negative separation and the use of the magnetic nanoclusters as a theragnostic nanoprobe. This scalable synthetic procedure is expected to be highly suitable for widespread use in biomedical, energy storage, photonics, and catalysis fields, among others.</P> [FIG OMISSION]</BR>

Deamination Effects in Formalin-Fixed, Paraffin-Embedded Tissue Samples in the Era of Precision Medicine

Kim, S.,Park, C.,Ji, Y.,Kim, D.G.,Bae, H.,van Vrancken, M.,Kim, D.H.,Kim, K.M. American Society for Investigative Pathology and t 2017 The Journal of molecular diagnostics Vol.19 No.1

<P>Deamination of nucleotides causes C:G>T:A changes in formalin-fixed, paraffin-embedded (FFPE) tissue samples and produces false positives during next-generation sequencing (NGS). Uracil DNA glycosylase (UDG) helps eliminate this issue, but the effect of UDG in different tissue preparation conditions has not been rigorously studied. To investigate whether UDG can reduce false-positive single-nucleotide variant (SNV) calls, we used tumor and normal tissues from gastric adenocarcinoma patients prepared using different fixation times and pH conditions. FFPE tumor blocks >10 years were also evaluated for the comparison. We performed semiconductor-based NGS to evaluate nucleotide changes and used UDG to test deamination-related effects. Sequencing quality parameters mildly worsened with prolonged fixation time, acidic pH, and delayed fixation. SNV calls and C:G>T:A changes increased after >48 hours of fixation. In both recently prepared and old FFPE tissue blocks, UDG treatment reduced deamination-induced nucleotide changes. In the recently prepared samples, both high-quality SNVs and mean target coverage were remarkably increased on treatment with UDG. However, the quality of NGS results from old-age samples varied irrespective of UDG treatment. In conclusion, based on our findings, we believe that when performing NGS on recently embedded blocks, it is important to consider that certain poorly fixed samples may be at the risk of being deaminated, which can be corrected with UDG treatment.</P>

Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein

Kim, Tae Wu,Yang, Cheolhee,Kim, Youngmin,Kim, Jong Goo,Kim, Jeongho,Jung, Yang Ouk,Jun, Sunhong,Lee, Sang Jin,Park, Sungjun,Kosheleva, Irina,Henning, Robert,van Thor, Jasper J.,Ihee, Hyotcherl The Royal Society of Chemistry 2016 Physical chemistry chemical physics Vol.18 No.13

<P>Real-time probing of structural transitions of a photoactive protein is challenging owing to the lack of a universal time-resolved technique that can probe the changes in both global conformation and light-absorbing chromophores of the protein. In this work, we combine time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) spectroscopy to investigate how the global conformational changes involved in the photoinduced signal transduction of photoactive yellow protein (PYP) is temporally and spatially related to the local structural change around the light-absorbing chromophore. In particular, we examine the role of internal proton transfer in developing a signaling state of PYP by employing its E46Q mutant (E46Q-PYP), where the internal proton transfer is inhibited by the replacement of a proton donor. The comparison of TRXSS and TA spectroscopy data directly reveals that the global conformational change of the protein, which is probed by TRXSS, is temporally delayed by tens of microseconds from the local structural change of the chromophore, which is probed by TA spectroscopy. The molecular shape of the signaling state reconstructed from the TRXSS curves directly visualizes the three-dimensional conformations of protein intermediates and reveals that the smaller structural change in E46Q-PYP than in wild-type PYP suggested by previous studies is manifested in terms of much smaller protrusion, confirming that the signaling state of E46Q-PYP is only partially developed compared with that of wildtype PYP. This finding provides direct evidence of how the environmental change in the vicinity of the chromophore alters the conformational change of the entire protein matrix.</P>

Four novel RUNX2 mutations including a splice donor site result in the cleidocranial dysplasia phenotype

Kim, Hyo-Jin,Nam, Soon-Hyeun,Kim, Hyun-Jung,Park, Hyo-Sang,Ryoo, Hyun-Mo,Kim, Shin-Yoon,Cho, Tae-Joon,Kim, Seung-Gon,Bae, Suk-Chul,Kim, In-San,Stein, Janet L.,van Wijnen, Andre J.,Stein, Gary S.,Lian, Liss 2006 Journal of Cellular Physiology Vol.207 No.1

<P>Cleidocranial dysplasia (CCD) is an autosomal dominant disorder caused by haploinsufficiency of the RUNX2 gene. In this study, we analyzed by direct sequencing RUNX2 mutations from eleven CCD patients. Four of seven mutations were novel: two nonsense mutations resulted in a translational stop at codon 50 (Q50X) and 112 (E112X); a missense mutation converted arginine to glycine at codon 131 (R131G); and an exon 1 splice donor site mutation (donor splice site GT/AT, IVS1 + 1G > A) at exon 1–intron junction resulted in the deletion of QA stretch contained in exon 1 of RUNX2. We focused on the functional analysis of the IVS1 + 1G > A mutation. A full-length cDNA of this mutation was cloned (RUNX2Δe1) and expressed in Chinese hamster ovary (CHO) and HeLa cells. Functional analysis of RUNX2Δe1 was performed with respect to protein stability, nuclear localization, DNA binding, and transactivation activity of a downstream RUNX2 target gene. Protein stability of RUNX2Δe1 is similar to wild-type RUNX2 as determined by Western blot analysis. Subcellular localization of RUNX2Δe1, assessed by in situ immunofluorescent staining, was observed with partial retention in both the nucleus and cytoplasm. This finding is in contrast to RUNX2 wild-type, which is detected exclusively in the nucleus. DNA binding activity was also compromised by the RUNX2Δe1 in gel shift assay. Finally, RUNX2Δe1 blocked transactivation of the osteocalcin gene determined by transient transfection assay. Our findings demonstrate for the first time that the CCD phenotype can be caused by a splice site mutation, which results in the deletion of N-terminus amino acids containing the QA stretch in RUNX2 that contains a previously unidentified second nuclear localization signal (NLS). We postulate that the QA sequence unique to RUNX2 contributes to a competent structure of RUNX2 that is required for nuclear localization, DNA binding, and transactivation function. J. Cell. Physiol. 207: 114–122, 2006. © 2005 Wiley-Liss, Inc.</P>

Van Don-An International Sea Port of Vietnam

Nguyen Van Kim 국립목포대학교 도서문화연구원 2009 島嶼文化 Vol.0 No.33

A key engine for the growth of the culture industry can be found at the development of specialized strategic products. For Korea’s southwestern coastal area, where Mokpo takes a central position, the possibility of such products may be found from culture-related islands and their marine resources. Among the many candidates, the theme of ocean heroes may be the most powerful asset to increase its cultural competitiveness via its potential for global recognition. In this thesis, I have tried to find new possibilities for the area’s specialized strategic industry by focusing on the Ocean’s Worldwide Heroes Park, an amusement park planned from such a viewpoint. Planned according to the necessity to promote public awareness of the value of ocean, the Ocean’s Worldwide Heroes Park aims to raise a “global workforce” through the discovery of the latent maritime assets in Korea and achieve commercial success as a theme park. What is noteworthy regarding the plan is that the world’s ocean heroes are divided into three categories: (a) the heroes who pioneered the world oceans, (b) the heroes who guarded the oceans during the wars, and (c) the heroes in history and folk tales. Also, the park is divided into six zones each of which offers an opportunity to experience an encounter with ocean heroes of the world. As for the exhibitions and productions, content and stories are regarded as more important than other elements, and ‘imagineering’ more essential than engineering. Considering that the development of content is a crucial factor for the success of the park, I concluded that even the first step of planning should progress side by side with the effort to develop visual content and characters. The development of content focused on the world’s ocean heroes and the local culture of the Korea’s southwestern region could lead to the birth of creative and globally competitive cultural products.

Characterization of a complete genome of a circular single-stranded DNA virus from porcine stools in Korea

Kim, A Reum,Chung, Hee Chun,Kim, Hye Kwon,Kim, Eun Ok,Nguyen, Van Giap,Choi, Min Gyung,Yang, Hye Jung,Kim, Jung Ah,Park, Bong Kyun Springer-Verlag 2014 Virus genes Vol.48 No.1

Optical Characterization of the PtSi/Si by Using Spectroscopic Ellipsometry

Van Long Le,Tae Jung Kim,Han Gyeol Park,Hwa Seob Kim,Chang Hyun Yoo,Hyoung Uk Kim,김영동,Junsoo Kim,Sol Yee Im,Wonchul Choi,Seung Eon Moon,Eunsoo Nam 한국물리학회 2016 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.69 No.3

We report an optical characterization of PtSi films for thermoelectric device applications which was done by using nondestructive spectroscopic ellipsometry (SE). A Pt monolayer and a Pt-Si multilayer which consisted of three pairs of Pt and Si layers were deposited on p-doped-silicon substrates by using sputtering method; then, rapid annealing process was done to form PtSi films through intermixing of Pt and Si atoms at the interface. Pseudodielectric function data < " > = < "1 > + i < "2 > for the PtSi/Si samples were obtained from 1.12 to 6.52 eV by using spectroscopic ellipsometry. Employing the Tauc-Lorentz and the Drude models, determined the dielectric function (") of the PtSi films. We found that the composition ratio of Pt:Si was nearly 1:1 for the PtSi monolayer and we observed transitions between occupied and unoccupied states in the Pt 5d states. We also observed the formation of PtSi layers in the Pt-Si multilayer sample. The SE results were confirmed by the transmission electron microscopy and energy dispersive X-ray spectroscopy.

Protein Structural Dynamicsof Photoactive YellowProtein in Solution Revealed by Pump–Probe X-ray Solution Scattering

Kim, Tae Wu,Lee, Jae Hyuk,Choi, Jungkweon,Kim, Kyung Hwan,van Wilderen, Luuk J.,Guerin, Laurent,Kim, Youngmin,Jung, Yang Ouk,Yang, Cheolhee,Kim, Jeongho,Wulff, Michael,van Thor, Jasper J.,Ihee, Hyotch American Chemical Society 2012 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.134 No.6

<P>Photoreceptor proteins play crucial roles in receiving light stimuli that give rise to the responses required for biological function. However, structural characterization of conformational transition of the photoreceptors has been elusive in their native aqueous environment, even for a prototype photoreceptor, photoactive yellow protein (PYP). We employ pump probe X-ray solution scattering to probe the structural changes that occur during the photocycle of PYP in a wide time range from 3.16 mu s to 300 ms. By the analysis of both kinetics and structures of the intermediates, the structural progression of the protein in the solution phase is vividly visualized. We identify four structurally distinct intermediates and their associated five time constants and reconstructed the molecular shapes of the four intermediates from time-independent, species-associated difference scattering curves. The constructed structures of the intermediates show the large conformational changes such as the protrusion of N-terminus, which is restricted in the crystalline phase due to the crystal contact and thus could not be clearly observed by X-ray crystallography. The protrusion of the N-terminus and the protein volume gradually increase with the progress of the photocycle and becomes maximal in the final intermediate, which is proposed to be the signaling state. The data not only reveal that a common kinetic mechanism is applicable to both the crystalline and the solution phases, but also provide direct evidence for how the sample environment influences structural dynamics and the reaction rates of the PYP photocycle.</P>