• Title/Summary/Keyword: Chemistry domain

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Structure Determination of Syndecan-4 Transmembrane Domain using PISA Wheel Pattern and Molecular Dynamics simulation

  • Choi, Sung-Sub;Jeong, Ji-Ho;Kim, Ji-Sun;Kim, Yongae
    • Journal of the Korean Magnetic Resonance Society
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    • v.18 no.2
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    • pp.58-62
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    • 2014
  • Human transmembrane proteins (hTMPs) are closely related to transport, channel formation, signaling, cell to cell interaction, so they are the crucial target of modern medicinal drugs. In order to study the structure and function of these hTMPs, it is important to prepare reasonable amounts of proteins. However, their preparation is seriously difficult and time-consuming due to insufficient yields and low solubility of hTMPs. We tried to produce large amounts of Syndecan-4 transmembrane domain (Syd4-TM) that is related to the healing wounds and tumor for a long time. In this study, we performed the structure determination of Syd4-TM combining the Polarity Index at Slanted Angle (PISA) wheel pattern analysis based on $^{15}N-^1H$ 2D SAMPI-4 solid-state NMR of expressed Syd4-TM and Molecular Dynamics (MD) simulation using Discovery Studio 3.1.

Optimization of the experimental conditions for structural studies of the second transmembrane domain from human wild-type & mutant melanocortin-4 receptor

  • Gang, Ga-Ae;Choi, Sung-Sub;Park, Tae-Joon;Kim, Yong-Ae
    • Journal of the Korean Magnetic Resonance Society
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    • v.14 no.2
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    • pp.88-104
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    • 2010
  • Human melanocortin-4 receptor (hMC4R) has a critical role in part of energy homeostasis, and their heterozygous mutations related in genetic cause of severe human obesity. In order to study the structure and function of these membrane proteins, it is important to prepare the samples. However, the preparation of transmembrane peptide is seriously difficult and time-consuming. Overexpression and purification of membrane proteins was reported to be difficult due to their innate insoluble and toxic properties. Among the many difficulties, the most important is the difficulty in obtaining sufficient quantities of purified protein. Recently, we succeed to produce large amounts of the second transmembrane domain from the wild-type hMC4R (wt-TM2) and D90N mutant hMC4R (m-TM2) and proposed the structural difference of them in membrane-like environments. In this paper, we demonstrate the optimization procedures to express and purify wt-TM2 or m-TM2 peptides, and solution NMR studies in different detergents to get high-resolution spectra were also described.

NMR Study on the Preferential Binding of the Zα Domain of Human ADAR1 to CG-repeat DNA Duplex

  • Lee, Ae-Ree;Choi, Seo-Ree;Seo, Yeo-Jin;Lee, Joon-Hwa
    • Journal of the Korean Magnetic Resonance Society
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    • v.21 no.3
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    • pp.90-95
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    • 2017
  • The Z-DNA domain of human ADAR1 ($Z{\alpha}_{ADAR1}$) produces B-Z junction DNA through preferential binding to the CG-repeat segment and destabilizing the neighboring AT-rich region. However, this study could not answer the question of how many base-pairs in AT-rich region are destabilized by binding of $Z{\alpha}_{ADAR1}$. Thus, we have performed NMR experiments of $Z{\alpha}_{ADAR1}$ to the longer DNA duplex containing an 8-base-paired (8-bp) CG-repeat segment and a 12-bp AT-rich region. This study revealed that $Z{\alpha}_{ADAR1}$ preferentially binds to the CG-repeat segment rather than AT-rich region in a long DNA and then destabilizes at least 6 base-pairs in the neighboring AT-rich region for efficient B-Z transition of the CG-repeat segment.

Structural Effects of the GXXXG Motif on the Oligomer Formation of Transmembrane Domain of Syndecan-4

  • Song, Jooyoung;Kim, Ji-Sun;Choi, Sung-Sub;Kim, Yongae
    • Bulletin of the Korean Chemical Society
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    • v.34 no.12
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    • pp.3577-3585
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    • 2013
  • Syndecan-4 (heparan sulfate proteoglycan), biologically important in cell-to-cell interactions and tumor suppression, was studied through mutation of the GXXXG motif of its transmembrane domain (Syd4-TM), a motif which governs dimerization. The expression and purification of the mutant (mSyd4-TM) were optimized here to assess the function of the GXXXG motif in the dimerization of Syd4-TM. mSyd4-TM was obtained in M9 minimal media and its oligomerization was identified by SDS PAGE, Circular Dichroism (CD) spectroscopy, mass spectrometry and NMR spectroscopy. The mutant, unlike Syd4-TM, did not form dimers and was observed as monomers. The GXXXG motif of Syd-4TM was shown to be an important structural determinant of its dimerization.

Mutational Analysis of the Effector Domain of Brassica Sar1 Protein

  • Kim, Min-Gab;Lee, Jung-Ro;Lim, Hye-Song;Shin, Mi-Rim;Cheon, Min-Gyeong;Lee, Deok-Ho;Kim, Woe-Yeon;Lee, Sang-Yeol
    • Journal of Applied Biological Chemistry
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    • v.50 no.3
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    • pp.109-114
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    • 2007
  • Sar1p is a ras-related GTP-binding protein that functions in intracellular protein transport between the endoplasmic reticulum (ER) and the Golgi complex. The effector domain of Ras family proteins is highly conserved and this domain is functionally interchangeable in plant, yeast and mammalian Sar1. Using a recombinant Brassica sar1 protein (Bsar1p) harboring point mutations in its effector domain, we here investigated the ability of Sar1p to bind and hydrolyze GTP and to interact with the two sar1-specific regulators, GTPase activating protein (GAP) and guanine exchange factor (GEF). The T51A and T55A mutations impaired Bsar1p intrinsic GTP-binding and GDP-dissociation activity. In contrast, mutations in the switch domain of Bsar1 did not affect its intrinsic GTPase activity. Moreover, the P50A, P54A, and S56A mutations affected the interaction between Bsar1p and GAP. P54A mutant protein did not interact with two regulating proteins, GEF and GAP, even though the mutation didn't affect the intrinsic GTP-binding, nucleotide exchange or GTPase activity of Bsar1p.

The Role of DNA Binding Domain in hHSF1 through Redox State (산화환원에 따른 hHSF1의 DNA binding domain의 역할)

  • Kim, Sol;Hwang, Yun-Jeong;Kim, Hee-Eun;Lu, Ming;Kim, An-D-Re;Moon, Ji-Young;Kang, Ho-Sung;Park, Jang-Su
    • Journal of Life Science
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    • v.16 no.6
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    • pp.1052-1059
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    • 2006
  • The heat shock response is induced by environmental stress, pathophysiological state and non-stress conditions and wide spread from bacteria to human. Although translations of most proteins are stopped under a heat shock response, heat shock proteins (HSPs) are produced to protect cell from stress. When heat shock response is induced, conformation of HSF1 was changed from monomer to trimer and HSF1 specifically binds to DNA, which was called a heat shock element(HSE) within the promoter of the heat shock genes. Human HSF1(hHSFl) contains five cysteine(Cys) residues. A thiol group(R-SH) of Cys is a strong nucleophile, the most readily oxidized and nitrosylated in amino acid chain. This consideration suggests that Cys residues may regulate the change of conformation and the activity of hHSF1 through a redox-dependent thiol/disulfide exchange reaction. We want to construct role of five Cys residues of hHSF by redox reagents. According to two studies, Cys residues are related to trimer formation of hHSF1. In this study, we want to demonstrate the correlation between structural change and DNA-binding activity of HSF1 through forming disulfide bond and trimerization. In this results, we could deduce that DNA binding activity of DNA binding domain wasn't affected by redox for always expose outside to easily bind to DNA. DNA binding activity of wild-type HSF's DNA binding domain was affected by conformational change, as conformational structure change (trimerization) caused DNA binding domain.

Crystal Structure of p97-N/D1 Hexamer Complexed with FAF1 UBX Domain

  • Wonchull Kang
    • Journal of the Korean Chemical Society
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    • v.67 no.5
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    • pp.348-352
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    • 2023
  • p97, a universally conserved AAA+ ATPase, holds a central position in the ubiquitin-proteasome system, orchestrating myriad cellular activities with significant therapeutic implications. This protein primarily interacts with a diverse set of adaptor proteins through its N-terminal domain (NTD), which is structurally located at the periphery of the D1 hexamer ring. While there have been numerous structural elucidations of p97 complexed with adaptor proteins, the stoichiometry has remained elusive. In this work, we present the crystal structure of the p97-N/D1 hexamer bound to the FAF1-UBX domain at a resolution of 3.1 Å. Our findings reveal a 6:6 stoichiometry between the p97 hexamer and FAF1-UBX domain, deepening our understanding from preceding structural studies related to p97-NTD and UBX domain-containing proteins. These insights lay the groundwork for potential therapeutic interventions addressing cancer and neurodegenerative diseases.

NMR Signal Assignments of Human Adenylate Kinase 1 (hAK1) and its R138A Mutant (hAK1R138A)

  • Kim, Gilhoon;Chang, Hwanbong;Won, Hoshik
    • Journal of the Korean Magnetic Resonance Society
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    • v.20 no.2
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    • pp.56-60
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    • 2016
  • Adenylate kinase (AK) enzyme which acts as the catalyst of reversible high energy phosphorylation reaction between ATP and AMP which associate with energetic metabolism and nucleic acid synthesis and signal transmission. This enzyme has three distinct domains: Core, AMP binding domain (AMPbd) and Lid domain (LID). The primary role of AMPbd and LID is associated with conformational changes due to flexibility of two domains. Three dimensional structure of human AK1 has not been confirmed and various mutation experiments have been done to determine the active sites. In this study, AK1R138A which is changed arginine[138] of LID domain with alanine[138] was made and conducted with NMR experiments, backbone dynamics analysis and mo-lecular docking dynamic simulation to find the cause of structural change and substrate binding site. Synthetic human muscle type adenylate kinase 1 (hAK1) and its mutant (AK1R138A) were re-combinded with E. coli and expressed in M9 cell. Expressed proteins were purified and finally gained at 0.520 mM hAK1 and 0.252 mM AK1R138A. Multinuclear multidimensional NMR experiments including HNCA, HN(CO)CA, were conducted for amino acid sequence analysis and signal assignments of $^1H-^{15}N$ HSQC spectrum. Our chemical shift perturbation data is shown LID domain residues and around alanine[138] and per-turbation value(0.22ppm) of valine[179] is consid-ered as inter-communication effect with LID domain and the structural change between hAK1 and AK1R138A.