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Ko, Sunggeon,Jun, Sung-Hoon,Bae, Hansol,Byun, Jung-Sue,Han, Woong,Park, Heeyoung,Yang, Seong Wook,Park, Sam-Yong,Jeon, Young Ho,Cheong, Chaejoon,Kim, Woo Taek,Lee, Weontae,Cho, Hyun-Soo Oxford University Press 2008 Nucleic acids research Vol.36 No.8
<P>Telomeres are protein–DNA elements that are located at the ends of linear eukaryotic chromosomes. In concert with various telomere-binding proteins, they play an essential role in genome stability. We determined the structure of the DNA-binding domain of NgTRF1, a double-stranded telomere-binding protein of tobacco, using multidimensional NMR spectroscopy and X-ray crystallography. The DNA-binding domain of NgTRF1 contained the Myb-like domain and C-terminal Myb-extension that is characteristic of plant double-stranded telomere-binding proteins. It encompassed amino acids 561–681 (NgTRF1<SUP>561–681</SUP>), and was composed of 4 α-helices. We also determined the structure of NgTRF1<SUP>561–681</SUP> bound to plant telomeric DNA. We identified several amino acid residues that interacted directly with DNA, and confirmed their role in the binding of NgTRF1 to telomere using site-directed mutagenesis. Based on a structural comparison of the DNA-binding domains of NgTRF1 and human TRF1 (hTRF1), NgTRF1 has both common and unique DNA-binding properties. Interaction of Myb-like domain with telomeric sequences is almost identical in NgTRF1<SUP>561–681</SUP> with the DNA-binding domain of hTRF1. The interaction of Arg-638 with the telomeric DNA, which is unique in NgTRF1<SUP>561–681</SUP>, may provide the structural explanation for the specificity of NgTRF1 to the plant telomere sequences, (TTTAGGG)<SUB>n</SUB>.</P>
Sunggeon Ko,Youngmin Lee,Jong-Bok Yoon,이원태 대한화학회 2009 Bulletin of the Korean Chemical Society Vol.30 No.5
RNA polymerase II C-terminal domain phosphatase 1 containing ubiquitin like domain (UBLCP1) has been identified as a regulatory molecule of RNA polymerase II. UBLCP1 consists of ubiquitin like domain (UBL) and phosphatase domain homologous with UDP and CTD phosphatase. UBLCP1 was cloned into the E.coli expression vectors, pET32a and pGEX 4T-1 with TEV protease cleavage site and purified using both affinity and gel-filtration chromatography. Domains of UBLCP1 protein were successfully purified as 7 mg/500 mL (UBLCP1, 36.78 KDa), 32 mg/500 mL (UBL, 9 KDa) and 8 mg/500 mL (phosphatase domain, 25 KDa) yielded in LB medium, respectively. Isotope-labeled samples including triple-labeled (2H/15N/13C) UBLCP1 were also prepared for hetero-nuclear NMR experiments. 15N-1H 2D-HSQC spectra of UBLCP1 suggest that both UBL and phosphatase domain are properly folded and structurally independent each other. These data will promise us further structural investigation of UBLCP1 by NMR spectroscopy and/or X-ray crystallography.
Prediction of parathyroid hormone signalling potency using SVMs
Yoo, Ahrim,Ko, Sunggeon,Lim, Sung-Kil,Lee, Weontae,Yang, Dae Ryook Springer-Verlag 2009 Molecules and cells Vol.27 No.5
<P>Parathyroid hormone is the most important endocrine regulator of calcium concentration. Its N-terminal fragment (1-34) has sufficient activity for biological function. Recently, site-directed mutagenesis studies demonstrated that substitutions at several positions within shorter analogues (1-14) can enhance the bioactivity to greater than that of PTH (1-34). However, designing the optimal sequence combination is not simple due to complex combinatorial problems. In this study, support vector machines were introduced to predict the biological activity of modified PTH (1-14) analogues using mono-substituted experimental data and to analyze the key physicochemical properties at each position that correlated with bioactivity. This systematic approach can reduce the time and effort needed to obtain desirable molecules by bench experiments and provide useful information in the design of simpler activating molecules.</P>
Purification and NMR studies on Phosphatase domain of UBLCP1
이원태,신항철,Sunjin Moon,Sunggeon Ko,Hyosun Oh 한국자기공명학회 2009 Journal of the Korean Magnetic Resonance Society Vol.13 No.2
UBLCP1 is composed of Ubiquitin Like domain and RNA Polymerase Ⅱ PhosphataseⅠdomain. Phosphatase domain (25.9KDa) has been cloned into the E.coli using pET32a vector with TEV protease cleavage site and successfully purified as a monomer using affinity chromatography and histidine tag was cleaved with TEV protease for structural studies. Our results indicated that the Phosphatase domain showed well-defined folded structure based on data from one-dimensional and two-dimensional NMR spectroscopy. Data form circular dichroism also suggested that Phosphatase domain consisted of both α-helix and β-sheet. This information will be used for detailed structural study of UBLCP1.
Youngmin Lee,Kyo-Eun Ahn,Sunggeon Ko,이원태 대한화학회 2009 Bulletin of the Korean Chemical Society Vol.30 No.5
Human protein tyrosine kinase-6 (PTK6) is a member of the non-receptor protein tyrosine kinase family and it is found in two-thirds of all breast tumors. Very recently, we proposed that the SH3 domain of PTK6 interacts with the linker region (Linker) between the SH2 and kinase domains, proving that the interaction between SH3 domain and Linker plays an important role in auto-inhibition mechanism. Residues from 1 to 191 corresponding region of SH3-SH2-Linker (SH32L) of PTK6 was cloned into the pET32a expression vector with Tobbaco etch virus (TEV) protease enzyme site by sequence homology and 3D structural model. The purified PTK6-SH32L was determined as a monomer conformation in solution. The amide proton resonances in the 15N-1H 2D-HSQC spectrum suggest that PTK6-SH32L possesses disordered structural region of the flexible/unstructured linker region. In addition, the backbone amide proton chemical shifts of the SH3 domain in the PTK6-SH32L differ from that of the independent domain, indicating that intra-molecular interaction between SH3 and Linker in the PTK6-SH32L is present.