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Kim, Jun-Hwan,Lee, Kang-Keun,Sun, Younguk,Seo, Gang-Jin,Cho, Sung Suk,Kwon, Suk Hyung,Kwon, Suk-Tae Springer 2013 Extremophiles Vol.17 No.3
<P>The nucleotide cofactor specificity of the DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus (Hbu) was studied to investigate the evolutionary relationship of DNA ligases. The Hbu DNA ligase gene was expressed under control of the T7lac promoter of pTARG in Escherichia coli BL21-CodonPlus(DE3)-RIL. The expressed enzyme was purified using the IMPACT-CN system (intein-mediated purification with an affinity chitin-binding tag) and cation-ion (Arg-tag) chromatography. The optimal temperature for Hbu DNA ligase activity was 75 C, and the optimal pH was 8.0 in Tris-HCl. The activity was highly dependent on MgCl2 or MnCl2 with maximal activity above 5 mM MgCl2 and 2 mM MnCl2. Notably, Hbu DNA ligase can use ADP and GTP in addition to ATP. The broad nucleotide cofactor specificity of Hbu DNA ligase might exemplify an undifferentiated ancestral stage in the evolution of DNA ligases. This study provides new evidence for possible evolutionary relationships among DNA ligases.</P>
Research on the development of standard reference data for image-based growth data in crops
Dongsoo Jung,Nyunhee Kim,Eunsook An,Minji Kim,Jeongho Baek,Younguk Kim,Sang-Ho Kang,Hwang Weon Jeong,Jaeil Lyu,Jaeyoung Kim,Hyenso Ji,Hyoja Oh,Seoyeon Lee,Mi Hyun Cho,Ji Sun Song,Yeongtae Kim,Kyung-Hw 한국육종학회 2024 한국육종학회 학술발표회지 Vol.2024 No.6
Computational Drug Discovery Approach Based on Nuclear Factor-κB Pathway Dynamics
남기엽,노경태,Won Seok Oh,Chul Kim,Miyoung Song,Jong Young Joung,,Jaeseong Park,Sin Moon Gang,YoungUk Cho,Sunyoung Kim 대한화학회 2011 Bulletin of the Korean Chemical Society Vol.32 No.12
The NF-κB system of transcription factors plays a crucial role in inflammatory diseases, making it an important drug target. We combined quantitative structure activity relationships for predicting the activity of new compounds and quantitative dynamic models for the NF-κB network with intracellular concentration models. GFA-MLR QSAR analysis was employed to determine the optimal QSAR equation. To validate the predictability of the IKKβ QSAR model for an external set of inhibitors, a set of ordinary differential equations and mass action kinetics were used for modeling the NF-κB dynamic system. The reaction parameters were obtained from previously reported research. In the IKKb QSAR model, good cross-validated q^2 (0.782) and conventional r^2 (0.808) values demonstrated the correlation between the descriptors and each of their activities and reliably predicted the IKKβ activities. Using a developed simulation model of the NF-κB signaling pathway, we demonstrated differences in IκB mRNA expression between normal and different inhibitory states. When the inhibition efficiency increased, inhibitor 1 (PS-1145) led to long-term oscillations. The combined computational modeling and NF-κB dynamic simulations can be used to understand the inhibition mechanisms and thereby result in the design of mechanism-based inhibitors.