Structure and sequence elements of the CR4/5 domain of medaka telomerase RNA important for telomerase function

Kim, Nak-Kyoon,Zhang, Qi,Feigon, Juli Oxford University Press 2014 Nucleic acids research Vol.42 No.5

<P>Telomerase is a unique reverse transcriptase that maintains the 3′ ends of eukaryotic chromosomes by adding tandem telomeric repeats. The RNA subunit (TR) of vertebrate telomerase provides a template for reverse transcription, contained within the conserved template/pseudoknot domain, and a conserved regions 4 and 5 (CR4/5) domain, all essential for catalytic activity. We report the nuclear magnetic resonance (NMR) solution structure of the full-length CR4/5 domain from the teleost fish medaka (<I>Oryzias latipes</I>). Three helices emanate from a structured internal loop, forming a Y-shaped structure, where helix P6 stacks on P5 and helix P6.1 points away from P6. The relative orientations of the three helices are Mg<SUP>2+</SUP> dependent and dynamic. Although the three-way junction is structured and has unexpected base pairs, telomerase activity assays with nucleotide substitutions and deletions in CR4/5 indicate that none of these are essential for activity. The results suggest that the junction is likely to change conformation in complex with telomerase reverse transcriptase and that it provides a flexible scaffold that allows P6 and P6.1 to correctly fold and interact with telomerase reverse transcriptase.</P>

Biophysical characterization of Ca²⁺-binding of S100A5 and Ca²⁺-induced interaction with RAGE

Kim, Iktae,Lee, Ko On,Yun, Young-Joo,Jeong, Jea Yeon,Kim, Eun-Hee,Cheong, Haekap,Ryu, Kyoung-Seok,Kim, Nak-Kyoon,Suh, Jeong-Yong Elsevier 2017 Biochemical and biophysical research communication Vol. No.

<P><B>Abstract</B></P> <P>S100A5 is a calcium-binding protein of S100 family, which represents a major ligand to the receptor for advanced glycation end product (RAGE), a pattern recognition receptor engaged in diverse pathological processes. Here we have characterized calcium binding of S100A5 and the complex formation between S100A5 and RAGE using calorimetry and NMR spectroscopy. S100A5 binds to calcium ions in a sequential manner with the equilibrium dissociation constants (<I>K</I> <SUB>D</SUB>) of 1.3 μM and 3.5 μM, which corresponds to the calcium-binding at the C-terminal and N-terminal EF-hands. Upon calcium binding, S100A5 interacts with the V domain of RAGE (RAGE-v) to form a heterotrimer (<I>K</I> <SUB>D</SUB> ∼5.9 μM) that is distinct among the S100 family proteins. Chemical shift perturbation data from NMR titration experiments indicates that S100A5 employs the periphery of the dimer interface to interact with RAGE-v. Distinct binding mode and stoichiometry of RAGE against different S100 family proteins could be important to modulate diverse RAGE signaling.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Thermodynamic of sequential Ca<SUP>2+</SUP>-binding to S100A5 is determined quantitatively. </LI> <LI> S100A5 binds to RAGE-v to form a distinct dynamic heterotrimer with <I>K</I> <SUB>D</SUB> ∼5.9 μM. </LI> <LI> RAGE-v binds to the rim of the S100A5 dimer interface via hydrophobic interaction. </LI> <LI> Different binding modes of S100 proteins to RAGE may modulate RAGE signaling. </LI> </UL> </P>

NMR methods for structural analysis of RNA: a Review

Kim, Nak-Kyoon,Nam, Yun-Sik,Lee, Kang-Bong Korean Magnetic Resonance Society 2014 Journal of the Korean Magnetic Resonance Society Vol.18 No.1

In last three decades, RNA molecules have been revealed to play the central roles in many cellular processes. Structural understanding of RNA molecules is essential to interpret their functions, and many biophysical techniques have been adopted for this purpose. NMR spectroscopy is a powerful tool to study structures and dynamics of RNA molecules, and it has been further applied to study tertiary interactions between RNA molecules, RNA-protein, and RNA-small molecules. This short article accounts for the general methods for NMR sample preparations, and also partially covers the resonance assignments of structured RNA molecules.

Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis

Kim, Hee-Eun,Kim, Wanhui,Lee, Ae-Ree,Jin, Suhyun,Jun, A.Rim,Kim, Nak-Kyoon,Lee, Joon-Hwa,Ahn, Ji Hoon Academic Press 2017 Biochemical and biophysical research communication Vol. No.

<P><B>Abstract</B></P> <P>Internal and environmental cues, including ambient temperature changes, regulate the timing of flowering in plants. Arabidopsis miR156 represses flowering and plays an important role in the regulation of temperature-responsive flowering. However, the molecular basis of miR156 processing at lower temperatures remains largely unknown. Here, we performed nuclear magnetic resonance studies to investigate the base-pair opening dynamics of model RNAs at 16 °C and investigated the <I>in vivo</I> effects of the mutant RNAs on temperature-responsive flowering. The A9C and A10CG mutations in the B5 bulge of the lower stem of pri-miR156a stabilized the C15∙G98 and U16∙A97 base-pairs at the cleavage site of pri-miR156a at 16 °C. Consistent with this, production of mature miR156 was severely affected in plants overexpressing the A9C and A10CG constructs and these plants exhibited almost no delay in flowering at 16 °C. The A10G and A9AC mutations did not strongly affect C15∙G98 and U16∙A97 base-pairs at 16 °C, and plants overexpressing A10G and A9AC mutants of miR156 produced more mature miR156 than plants overexpressing the A9C and A10CG mutants and showed a strong delay in flowering at 16 °C. Interestingly, the A9AC mutation had distinct effects on the opening dynamics of the C15∙G98 and U16∙A97 base-pairs between 16 °C and 23 °C, and plants expressing the A9AC mutant miR156 showed only a moderate delay in flowering at 16 °C. Based on these results, we propose that fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A mutation in pri-miR156a B5 affected base-pairing stability at the cleavage site. </LI> <LI> Mutations in the B5 bulge increased base-pair stabilities and decreased miR156. </LI> <LI> The A9AC mutation affected opening dynamics between 16 and 23 °C. </LI> <LI> Cleavage site base-pair stabilities reflected miR156 levels and flowering time. </LI> </UL> </P>

복합 폐비닐 재활용 기술에 대한 연구

안낙균 ( Nak-kyoon Ahn ),김승환 ( Seung Hwan Kim ),김정환 ( Jung Hwan Kim ),박필환 ( Pil Hwan Park ),윤진호 ( Jin-ho Yoon ) 한국폐기물자원순환학회(구 한국폐기물학회) 2019 한국폐기물자원순환학회 추계학술발표논문집 Vol.2019 No.-

우리 생활에 가장 일반적으로 쓰이는 자원인 비닐과 플라스틱은 우수한 편리성으로 일회용 음료용기, 필름, 섬유 등에서의 높은 활용도에 따라 넓은 분야에서 많이 사용되어 지고 있는 것에 비해 폐비닐, 폐플라스틱 재활용율은 약 25%이며, 이 외에는 소각이나 매립 등의 방법으로 처리되고 있다. 폐비닐, 폐플라스틱이 소각과 매립의 형태로 처리됨에 따른 환경오염 유발 및 활용 가능한 자원의 최종 폐기에 의한 경제적 손실이 나타남에 따라 국내에서도 효율적인 폐비닐 및 플라스틱 재활용기술 개발이 요구되고 있다. 일반적으로 폐비닐을 재활용하는 방법으로는 일반적으로 물질회수, 연료화, 유화환원 등이 알려져 있지만 다양한 종류와 이물질 및 불순물 혼입되어 선별과정을 거치게 되는데 이 과정에서 재활용에 대한 경제성 및 생산효율이 낮아지게 된다. 따라서 본 논문에서는 토사, 유리, 금속, 음식물, 목재 등의 다양한 불순물 및 이물질이 혼입된 생활계 복합 폐비닐을 효율적으로 선별, 분리하는 기술을 개발하여 복합재생원료로 재활용하는 방법에 대하여 연구하였다.

폐비닐 재활용을 위한 불순물 제거 및 재생원료 제조 공정 연구

안낙균 ( Nak-kyoon Ahn ),윤진호 ( Jin-ho Yoon ),김정환 ( Jung-hwan Kim ),김승환 ( Seung-hwan Kim ) 한국폐기물자원순환학회 2023 한국폐기물자원순환학회 춘계학술발표논문집 Vol.2023 No.-

대용폐색방식 시행방법 개선에 관한 연구 (A Study on the Improvement for the Implement Way of a Substitute Block System)

송낙균(Nak-Kyoon Song),김해곤(Hae-Gon Kim),김호순(Ho-Soon Kim),주창훈(Chang-Hun Joo),김대식(Dae-Sik Kim) 한국철도학회 2011 한국철도학회 학술발표대회논문집 Vol.2011 No.5

Presently, The Regular Block System(Automatic, Interlocking block system) is usually used during the operation of block section. However, In case that the regular block system fails because of the failure of the fixed signals and block equipment or in case of the unexpected emergent situation which should drive on the single-track due to the accidents in the double-track section or the repair work of the one-track, the Substitute Block System to make use of the driving permission license(mapping ticket, mapping paper) is used. In case of the operation of the opposite line and the temporary one-track, the safety gets worse and the SBS may cause the fatal accidents such as a head-on & a rear-end collision. Also, the unmanned railroad stations has recently increased owing to the effective operation of the stations, for it is difficult to execute the SBS in their absence. As a result, the increase of the operation time made the train delayed. Being on the rise of these problems, in this study, we analyzed the problems and difficulties of the SBS on the single line which is lacking stability and safety and on the sections combined between maned and unmaned railroad stations. And we proposed the method to improve the existing drive permission license used for 50 years into the brand-new one with state-of-the art technology and scientific way. In the era of the 21th century, Carrying out the new SBS equipped with stability and safety, we will contribute to the effective operation of trains and the satisfaction of our customers in the future.

기존선 대용폐색방식 개선에 관한 연구

송낙균(Nak-Kyoon Song),김해곤(Hae-Gon Kim),김호순(Ho-Soon Kim),김대식(Dae-Sik Kim),주창훈(Chang-Hun Joo) 한국철도학회 2011 한국철도학회 학술발표대회논문집 Vol.2011 No.10

Presently The Regular Block System(Automatic Interlocking block system) is usually used during the operation of block section. However In case that the regular block system fails because of the failure of the fixed signals and block equipment or in case of the unexpected emergency which should drive on the single line due to the accidents in the double line section or the repair work of the single line the Substitute Block System to use the driving permission license(mapping ticket and paper) is used. In case of the operation of the opposite line and the temporary one line the safety gets worse and the SBS may cause the fatal accidents such as a head-on & a rear-end collision. Also the unmanned railroad stations has recently increased owing to the effective operation of the stations for it is difficult to execute the SBS in their absence. As a result the increase of the operation time made the train delayed. Being on the rise of these problems in this study we analyzed the problems and difficulties of the SBS on one line which is lacking stability and safety and on the sections combined between maned and unmaned railroad stations. And we proposed the suitable method in KORAIL referring to the examples of European & Japan railways lately According to the passing of the high tech time If the new SBS equipped with stability and safety is executed it will contribute to the effective operation of trains and the satisfaction of KORAIL customers in the future.

Analysis of Tertiary Interactions between SART3 and U6 Small Nuclear RNA Using Modified Nanocapillaries

Lee, Choongman,Park, Joon Kyu,Youn, Yeoan,Kim, Joo Hyoung,Lee, Kyo-Seok,Kim, Nak-kyoon,Kim, Eunji,Kim, Eunice Eunkyeong,Yoo, Kyung-Hwa American Chemical Society 2017 ANALYTICAL CHEMISTRY - Vol.89 No.4

<P>We employed modified glass nanocapillaries to investigate interactions between the RNA-binding protein, known as cell carcinoma antigen recognized by T cells-3 (SART3), and the noncoding spliceosome component, U6 small nuclear RNA (snRNA), at the single-molecule level. We functionalized the nanocapillaries with U6 snRNA fragments, which were hybridized to DNA molecules and then covalently attached to the nanocapillary surface. When transported through the modified nanocapillaries, two different SART3-derived constructs, HAT-RRM1-RRM2 and RRM1-RRM2, exhibited resistive ionic current pulses with different dwell times, which represented their different binding affinities to tethered U6 snRNAs. The dissociation constants (K-D), estimated from the bias voltage dependence of translocation events, were approximately 1.9 mu M and 201 mu M for HAT-RRM1-RRM2 and RRM1-RRM2, respectively. These values were comparable to corresponding values obtained with isothermal titration calorimetry, demonstrating that the modified glass nanocapillaries are applicable to analyses of protein ligand interactions at the single-molecule level.</P>

Structural Characterization of pre-miRNA 155

Kim, Won-Je,Shin, JiYeon,Bang, Kyeongmi,Song, Hyun Kyu,Kim, Nak-Kyoon Korean Magnetic Resonance Society 2016 Journal of the Korean Magnetic Resonance Society Vol.20 No.2

MiRNA-155, upregulated in various cancers, is one of the miRNAs that suppress apoptosis of human cancer. Thus, inhibition of the maturation of miRNA-155 could be an effective way to induce apoptotic cancer cell death. The apical stem-loop of the pre-miRNA-155 has been known as a Dicer biding site for RNA cleavage. Here, to understand the molecular basis of the tertiary interaction between pre-miRNA-155 with Dicer, we characterize the structure of the apical stem-loop of pre-miRNA-155 using NMR spectroscopy. The RNA has a stem-bulge-stem-loop-stem structure, which is consist of G-C Watson-Crick and G-U Wobble base pairs. The assignments of imino- protons were further confirmed by 2D $^{15}N-^1H$ HSQC NMR spectrum. The NMR parameters obtained in this study can be further used to investigate the tertiary interaction between pre-miRNA-155 and other biomolecules such as protein, nucleic acids, or small chemicals which might be used to control the apoptosis of cancer.