• Title/Summary/Keyword: affinity interaction

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A Knowledge based Interaction idea Categorizer for Electronic Meeting Systems

  • Kim, Jae-Kyeong;Lee, Jae-Kwang
    • Journal of Intelligence and Information Systems
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    • v.6 no.2
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    • pp.63-76
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    • 2000
  • Research on group decisions and electroinc meeting systems have been increasing rapidly according to the widespread of Internet technology. Although various issues have been raised in empirical research, we will try to solve an issue on idea categorizing in the group decision making process of elecronic meeting systems. Idea categorizing used at existing group decision support systems was performed in a top-down procedure and mostly participants\` by manual work. This resulted in tacking as long in idea categorizing as it does for idea generating, clustering an idea in multiple categories, and identifying almost similar redundant categories. However such methods have critical limitation in the electronic meeting systems, we suggest an intelligent idea categorizing methodology which is a bottom-up approach. This method consists of steps to present idea using keywords, identifying keywords\` affinity, computing similarity among ideas, and clustering ideas. This methodology allows participants to interact iteratively for clear manifestation of ambiguous ideas. We also developed a prototype system, IIC (intelligent idea categorizer) and evaluated its performance using the comparision experimetn with other systems. IIC is not a general purposed system, but it produces a good result in a given specific domain.

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Trigger Factor Interacts with DnaA Protein to Stimulate its Interaction with DnaA Box

  • Lee, Yong-Sun;Lee, June;Kim, Hak-Kyun;Kang, Sukhyun;Han, Joo-Seok;Kim, Jae-Bum;Hwang, Deog-Su
    • Animal cells and systems
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    • v.7 no.1
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    • pp.81-87
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    • 2003
  • While screening proteins that interact with DnaA protein, the initiator protein for Escherichia coil chromosomal DNA replication, we found a 52-kD sized protein which bound to DnaA protein in a salt-dependent manner. This protein was identified as trigger factor, a ribosome-associated peptidyl-prolyl- cisltrans isomerase with chaperone activity. Trigger factor was overproduced and purified to near homogeneity, and its effect on the function of DnaA protein was examined, Enhanced binding of DnaA protein to DnaA box with no apparent supershift in the gel-shift experiments suggested that trigger factor, by virtue of its chaperone activity, exerts a change on DnaA protein thus increasing its binding affinity for DnaA box.

Anti-inflammatory Activity of Sambucus Plant Bioactive Compounds against TNF-α and TRAIL as Solution to Overcome Inflammation Associated Diseases: The Insight from Bioinformatics Study

  • Putra, Wira Eka;Salma, Wa Ode;Rifa'i, Muhaimin
    • Natural Product Sciences
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    • v.25 no.3
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    • pp.215-221
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    • 2019
  • Inflammation is the crucial biological process of immune system which acts as body's defense and protective response against the injuries or infection. However, the systemic inflammation devotes the adverse effects such as multiple inflammation associated diseases. One of the best ways to treat this entity is by blocking the tumor necrosis factor alpha ($TNF-{\alpha}$) and TNF-related apoptosis-inducing ligand (TRAIL) to avoid the proinflammation cytokines production. Thus, this study aims to evaluate the potency of Sambucus bioactive compounds as anti-inflammation through in silico approach. In order to assess that, molecular docking was performed to evaluate the interaction properties between the $TNF-{\alpha}$ or TRAIL with the ligands. The 2D structure of ligands were retrieved online via PubChem and the 3D protein modeling was done by using SWISS Model. The prediction results of the study showed that caffeic acid (-6.4 kcal/mol) and homovanillic acid (-6.6 kcal/mol) have the greatest binding affinity against the $TNF-{\alpha}$ and TRAIL respectively. This evidence suggests that caffeic acid and homovanillic acid may potent as anti-inflammatory agent against the inflammation associated diseases. Finally, this study needs further examination and evaluation to validate the potency of Sambucus bioactive compounds.

Backbone assignment of HMGB1 A-box and molecular interaction with Hoxc9DBD studied by paramagnetic probe

  • Choi, Ji Woong;Park, Sung Jean
    • Journal of the Korean Magnetic Resonance Society
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    • v.25 no.2
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    • pp.17-23
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    • 2021
  • High mobility group protein B1 (HMGB1) is a highly conserved, non-histone, chromatin associated nuclear protein encoded by HMGB1 gene. HMGB1 proteins may be general co-factors in Hox-mediated transcriptional activation that facilitate the access of Hox proteins to specific DNA targets. It is unclear that the exact binding interface of Hoxc9DBD and HMGB1. To identify the interface and binding affinity of Hoxc9DBD and HMGB1 A-box, the paramagnetic probe, MTSL was used in NMR titration experiment. It is attached to the N-terminal end of HMGB1 A-box by reaction with thiol groups. The backbone assignment of HMGB1 A-box was achieved with 3D NMR techinques. The 15N-labeled HMGB1 A-box was titrated with MTSL-labeled Hoxc9DBD respectively. Based on the chemical shift changes we can identify the interacting residues and further map out the binding sites on the protein structure. The NMR titration result showed that the binding interface of HMGB1 A-box is around loop-1 between helix-1 and helix-2. In addition, the additional contacts were found in N- and C-terminus. The N-terminal arm region of Hoxc9DBD is the major binding region and the loop between helix1 and helix2 is the minor binding region.

Structure Characterization and Antihypertensive Effect of an Antioxidant Peptide Purified from Alcalase Hydrolysate of Velvet Antler

  • Seung Tae Im;Seung-Hong Lee
    • Food Science of Animal Resources
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    • v.43 no.1
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    • pp.184-194
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    • 2023
  • Recently, interest in food-derived bioactive peptides as promising ingredients for the prevention and improvement of hypertension is increasing. The purpose of this study was to determine the structure and antihypertensive effect of an antioxidant peptide purified from velvet antler in a previous study and evaluate its potential as a various bioactive peptide. Molecular weight (MW) and amino acid sequences of the purified peptide were determined by quadrupole time-of-flight electrospray ionization mass spectroscopy. The angiotensin I-converting enzyme (ACE) inhibition activity of the purified peptide was assessed by enzyme reaction methods and in silico molecular docking analysis to determine the interaction between the purified peptide and ACE. Also, antihypertensive effect of the purified peptide in spontaneously hypertensive rats (SHRs) was investigated. The purified antioxidant peptide was identified to be a pentapeptide Asp-Asn-Arg-Tyr-Tyr with a MW of 730.31 Da. This pentapeptide showed potent inhibition activity against ACE (IC50 value, 3.72 μM). Molecular docking studies revealed a good and stable binding affinity between purified peptide and ACE and indicated that the purified peptide could interact with HOH2570, ARG522, ARG124, GLU143, HIS387, TRP357, and GLU403 residues of ACE. Furthermore, oral administration of the pentapeptide significantly reduced blood pressure in SHRs. The pentapeptide derived from enzymatic hydrolysate of velvet antler is an excellent ACE inhibitor. It might be effectively applied as an animal-based functional food ingredient.

Sorption Characteristics of Tetracycline in Water on Microplastics (수중 테트라사이클린의 미세플라스틱에 대한 흡착 특성)

  • Yu Jin Seo;Ruri Lee;Eun Hea Jho
    • Korean Journal of Environmental Agriculture
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    • v.41 no.4
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    • pp.276-281
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    • 2022
  • BACKGROUND: Plastics that are used in our daily lives largely end up in the environment. In agricultural environments, plastic wastes and microplastics can be found due to the uses and improper management of plastic products (e.g., vinyl greenhouses and mulching vinyl). Microplastics can also interact with contaminants in the agricultural environment. Therefore, this study was set to investigate the sorption characteristics of tetracycline, one of widely used antibiotics, on microplastics. METHODS AND RESULTS: The sorption tests were carried out with the tetracycline solutions (0-30 mg L-1) and microplastic films prepared from low density polyethylene (LDPE) and polyvinyl chloride (PVC). The residual tetracycline concentrations were analyzed and fitted to the Freundlich and Langmuir isotherm models. The tetracycline sorption patterns on LDPE and PVC films were described better with the Freundlich isotherm model than the Langmuir isotherm model. The isotherm model parameters suggested that the maximum sorption amount of tetracyline was greater for PVC, while the sorption affinity was greater for LDPE. CONCLUSION(S): Different types of microplastics can have different sorption characteristics of tetracycline. Therefore, there is a need for continuous research on the interaction of various types and shapes of microplastics and contaminants in the environment.

Induced Circular Dichroism Spectra and Chromatography by Interaction of Some Racemic Cobalt (III) Complexes and d-Tartrate$^2$- in Aqueous Solution (d-주석산이온과 라세미코발트(III) 착물과의 상호작용에 따른 유발원편광이색성 Spectra와 크로마토그래피)

  • Chang Eon Oh;Dae Ho Kang;Gab Choul Shin
    • Journal of the Korean Chemical Society
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    • v.25 no.5
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    • pp.306-310
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    • 1981
  • Induced circular dichroism spectra of racemic cobalt(III) complexes for $[Co(en)_3]^{3+},\;[Co(tn_)3]^{3+},\;cis-[Co(NH_3)(en)_2]^{3+},\;[Co({\beta}-ala)(en)2_]^{2+},\;[Co(gly)(en)_2]^{2+}\;and\;[Co(acac)(en)_2]^{2+}$ were measured when they were dissolved in aqueous d-tartrate2- solution at room temperature. Only a single negative CD spectrum was observed for all the complexes above in visible region(400∼500nm). It was interpreted that these CD bands were attributed to the difference in interaction between ${\Lambda}$-and ${\Delta}$-enantiomers with d-tartrate$^{2-}$. Namely, when d-tartrate$^{2-}$ was added to ${\Lambda}$-enantiomer and ${\Delta}$-enantiomer, it caused ${\Lambda}$-enantiomer to change greatly and ${\Delta}$-enantiomer to change only slightly; combined the results proved induced circular dichroism. The enantiomer for which the eluent has a stronger affinity should be eluted faster in ion-exchange column chromatography. It is possible to predict the elution order of chromatography from the sign of the induced CD if stronger interaction of chiral anion with the complex leads to greater change in the natural CD spectrum of the complex. The elution order was in complete agreement with the prediction from the sign of the induced CD spectrum for all the measured complexes.

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Molecular Dynamics Simulation Study for Ionic Strength Dependence of RNA-host factor Interaction in Staphylococcus aureus Hfq

  • Lazar, Prettina;Lee, Yun-O;Kim, Song-Mi;Chandrasekaran, Meganathan;Lee, Keun-Woo
    • Bulletin of the Korean Chemical Society
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    • v.31 no.6
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    • pp.1519-1526
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    • 2010
  • The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.

Manganese and Iron Interaction: a Mechanism of Manganese-Induced Parkinsonism

  • Zheng, Wei
    • Proceedings of the Korea Environmental Mutagen Society Conference
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    • 2003.10a
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    • pp.34-63
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    • 2003
  • Occupational and environmental exposure to manganese continue to represent a realistic public health problem in both developed and developing countries. Increased utility of MMT as a replacement for lead in gasoline creates a new source of environmental exposure to manganese. It is, therefore, imperative that further attention be directed at molecular neurotoxicology of manganese. A Need for a more complete understanding of manganese functions both in health and disease, and for a better defined role of manganese in iron metabolism is well substantiated. The in-depth studies in this area should provide novel information on the potential public health risk associated with manganese exposure. It will also explore novel mechanism(s) of manganese-induced neurotoxicity from the angle of Mn-Fe interaction at both systemic and cellular levels. More importantly, the result of these studies will offer clues to the etiology of IPD and its associated abnormal iron and energy metabolism. To achieve these goals, however, a number of outstanding questions remain to be resolved. First, one must understand what species of manganese in the biological matrices plays critical role in the induction of neurotoxicity, Mn(II) or Mn(III)? In our own studies with aconitase, Cpx-I, and Cpx-II, manganese was added to the buffers as the divalent salt, i.e., $MnCl_2$. While it is quite reasonable to suggest that the effect on aconitase and/or Cpx-I activites was associated with the divalent species of manganese, the experimental design does not preclude the possibility that a manganese species of higher oxidation state, such as Mn(III), is required for the induction of these effects. The ionic radius of Mn(III) is 65 ppm, which is similar to the ionic size to Fe(III) (65 ppm at the high spin state) in aconitase (Nieboer and Fletcher, 1996; Sneed et al., 1953). Thus it is plausible that the higher oxidation state of manganese optimally fits into the geometric space of aconitase, serving as the active species in this enzymatic reaction. In the current literature, most of the studies on manganese toxicity have used Mn(II) as $MnCl_2$ rather than Mn(III). The obvious advantage of Mn(II) is its good water solubility, which allows effortless preparation in either in vivo or in vitro investigation, whereas almost all of the Mn(III) salt products on the comparison between two valent manganese species nearly infeasible. Thus a more intimate collaboration with physiochemists to develop a better way to study Mn(III) species in biological matrices is pressingly needed. Second, In spite of the special affinity of manganese for mitochondria and its similar chemical properties to iron, there is a sound reason to postulate that manganese may act as an iron surrogate in certain iron-requiring enzymes. It is, therefore, imperative to design the physiochemical studies to determine whether manganese can indeed exchange with iron in proteins, and to understand how manganese interacts with tertiary structure of proteins. The studies on binding properties (such as affinity constant, dissociation parameter, etc.) of manganese and iron to key enzymes associated with iron and energy regulation would add additional information to our knowledge of Mn-Fe neurotoxicity. Third, manganese exposure, either in vivo or in vitro, promotes cellular overload of iron. It is still unclear, however, how exactly manganese interacts with cellular iron regulatory processes and what is the mechanism underlying this cellular iron overload. As discussed above, the binding of IRP-I to TfR mRNA leads to the expression of TfR, thereby increasing cellular iron uptake. The sequence encoding TfR mRNA, in particular IRE fragments, has been well-documented in literature. It is therefore possible to use molecular technique to elaborate whether manganese cytotoxicity influences the mRNA expression of iron regulatory proteins and how manganese exposure alters the binding activity of IPRs to TfR mRNA. Finally, the current manganese investigation has largely focused on the issues ranging from disposition/toxicity study to the characterization of clinical symptoms. Much less has been done regarding the risk assessment of environmenta/occupational exposure. One of the unsolved, pressing puzzles is the lack of reliable biomarker(s) for manganese-induced neurologic lesions in long-term, low-level exposure situation. Lack of such a diagnostic means renders it impossible to assess the human health risk and long-term social impact associated with potentially elevated manganese in environment. The biochemical interaction between manganese and iron, particularly the ensuing subtle changes of certain relevant proteins, provides the opportunity to identify and develop such a specific biomarker for manganese-induced neuronal damage. By learning the molecular mechanism of cytotoxicity, one will be able to find a better way for prediction and treatment of manganese-initiated neurodegenerative diseases.

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A Study on the Possibility of Family Particpation Education through the "Educational Culture Festival" at the Educational Museum (교육박물관에서의 "교육문화 페스티벌" 개최를 통해 본 가족 참여 교육 가능성 고찰)

  • Eom, Hye-Yoon
    • The Journal of the Korea Contents Association
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    • v.18 no.5
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    • pp.545-553
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    • 2018
  • As the share of leisure culture increases these days, expectations are rising for the high quality of culture while increasing interest in leisure and tourism. The percentage of the population going on weekend trips to broaden the horizons of elementary, middle and high school students has continued to rise in proportion to the expectations for cultural enjoyment. We expect that visitors' weekend family activities will include relaxing, playing and educational purposes. Recent educational programs have moved from the past where only children were allowed to be onsite, to a shared style in which parents can engage in educational activities, potentially leading to the implicit involvement of family ties and family elasticity. The effects of education are not expressed by the period that ends in a single moment of experience, but by the continuity of training and experience. The same holds true for family affinity, communication and empathy. Providing opportunities for family experience and education is a national responsibility for broken family and restoring solidarity with the growing number of single-person households. Furthermore, it is a duty of museums and galleries today, and it is necessary to come up with methods to enhance family solidarity and family affinity. In particular, it is imperative to develop and provide educational programs for educational purposes at the Education Museum, and to develop " education for family " at the social level. This paper aims to analyze the results of all family participating education programs provided by family education programs at the Education Museum through family surveys and interviews, and to enhance the activation of family types education programs more actively.