• 한국자기공명학회논문지
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• 제15권1호
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• pp.80-89
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• 2011

3D structures of STAM1 UIM-ubiquitin complex were presented to predict and analyze the interaction between UIM and ubiquitin. To generate the protein-peptide complex structure, the RosettaDock method was used with and without NMR restraints. High resolution complex structure was acquired successfully and evaluated electrostatic interaction in the protein-peptide binding with several charged residues at the binding site. From docking results, the Rosettadock method could be useful to acquire essential information of protein-protein or protein-peptide interaction with minimal biological evidences.

• Journal of Microbiology and Biotechnology
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• 제12권2호
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• pp.286-291
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• 2002

Histone deacetylase I (HDAC1) works as one of the components in a nucleosome remodeling (NuRD) complex that consists of several proteins, including metastasis-associated protein 1 (MTA1). Since the protein-protein interaction of HDAC1 and MTA1 would appear to be important for both the integrity and functionality of the HDAC1 complex, the interruption of the HDAC1 and MTA1 interaction may be an efficient way to regulate the biological function of the HDAC1 complex. Based on this idea, a yeast two-hybrid system was constructed with HDAC1 and MTA1 expressing vectors in the DNA binding and activation domains, respectively. To verify the efficiency of the assay system, 3,500 microbial metabolite libraries were tested using the paper disc method, and KB0699 was found to inhibit the HDAC1 and MTA1 interaction without any toxicity to the wild-type yeast. Furthermore, KB0699 blocked the interaction of HDAC1 and MTA1 in an in vitro GST pull down assay and induced morphological changes in B16/BL6 melanoma cells, indicating the interruption of the HDAC1 complex function. Accordingly, these results demonstrated that the yeast assay strain developed in this study could be a valuable tool for the isolation of a HDAC1 complex disruptor.

• 대한수의학회지
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• 제40권1호
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• pp.63-71
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• 2000

An immunogenic, high molecular weight lipopolysaccharide (LPS)-protein complex isolated from a potassium thioncyanate extract of a Pasteurella multocida (P multocida ; strain P-2383, capsular type A and somatic type 3) was characterized. Chemical analysis of the complex by gas chromatography on a capillary column demonstrated that this complex contained most of the chemical constituents characteristic of LPS extracted by the phenol-water methed from the whole bacterium. However, there was proportionately more carbohydrate than fatty acid in the complex in contrast to LPS in which fatty acid seemed to be in excess. When toxicity of the complex was evaluated in 10-day-old chicken embryos, the complex was less toxic ($LD_{50}=12.72{\mu}g$) than the purified LPS ($LD_{50}=0.44{\mu}g$). The $LD_{50}$, of the LPS moiety extracted from the complex was $5.24{\mu}g$. Composition of the complex was analyzed by SDS-PAGE with silver staining and Western immunoblotting. The complex did not migrate through the polyacrylamide gel unless dissociated with SDS. The complex dissociated with SDS contained at least 32 different protein and polysaccharide components: 18 components reacted with an antiserum against the complex. There was no significant compositional variation between the complexes from different strains, but quantitative differences in individual components were noted. When cross-protectivity of the complex was evaluated in mice, this complex provided substantial protection not only against the homologous bacteriun but also against different P multocida strains of the same serotype. LPS-protein complexes isolated by the same method from other strains also induced protection against an challenge with P-2383.

• 한국자기공명학회논문지
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• 제18권1호
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• pp.1-4
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• 2014

It is generally understood that protein-protein interactions proceed via transient encounter complexes that rapidly evolve into the functional stereospecific complex. Direct detection and characterization of the encounter complexes, however, been difficult due to their low population and short lifetimes. Recent application of NMR paramagnetic relaxation enhancement first visualized the structures of the encounter complex ensemble, and allowed the characterization of their physicochemical properties. Further, rational protein mutations that perturbed the encounter complex formation provided a clue to the target search pathway during protein-protein association. Understanding the structure and dynamics of encounter complexes will provide useful information on the mechanism of protein association.

• Journal of Photoscience
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• 제9권2호
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• pp.275-277
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• 2002

We have recently found that a detergent-resistant raft like membrane (DRM) can be prepared from bovine rod outer segment membranes as a low-density buoyant fraction in sucrose density gradient ultracentrifugation. G protein (transducin) and its effector enzyme (phosphodiesterase: PDE) drastically change their affinities to DRM in the process of phototransduction. We report here that the recruitment of transducin and/or $^2$PDE to DRM has close relationship with their states in signal transduction. Active T$\alpha$/PDE-complex has a high affinity to DRM, whereas inactive transducin, or inactive PDE are excluded from DRM. Active T$\alpha$/PDE-complex seems to bind to a GTPase activating protein (GRS9) in multi- protein complexes localized on DRM. Physiological significance of the multi-protein complex on the raft-like membrane in vertebrate phototransduction would be discussed.

• Journal of Plant Biology
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• 제26권2호
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• pp.91-99
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• 1983

The formation of chlorophyll-protein complexes (CP-complexes) during the greening of rape cotyledons (Brassica napus cv. Yongdang) was investigated by the SDS-polyacrylamide gel electrophoresis. The total chlorophyll content and Chl a/b ratio were also determined. In addition, the effects of dark treatment on the CP-complex patterns during greening have been examined with respect to their photosynthetic electron transport activity. Greening has brought about the increasein total chlorophyll content and the decrease in Chl a/b ratio, but there have been no changes in Chl a/b ratio after 24 hrs of greening. The light-harvesting chlorophyll a/b-protein complex (LHCP-complex0 was predominant during the initial greening period. Thereafter, the amout of chlorophyll a-protein complex (CP I-complex) was gradually increased. Twenty-four-hr dark treatment immediately after illumination for 6 hrs and 12 hrs resulted in the increase of the Chl a/b ration and the CP I complex, otherwise the decrease of the LHCP-complex. The LHCP/CP I ratio was gradually decreased with further greening, and appeared no change after 48 hrs illumination. The investigation of the photosynthetic electron transport activity indicated that photosystem (PS) II activity (H2Olongrightarrowp-PD*＋FeCy**) did not change, but the activity of PS I was increased suddenly due to the dark treatment. The data suggests that the increase of CP I-complex may result in that of P-700, that is, the increase of PS I activity.

• Bulletin of the Korean Chemical Society
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• 제32권spc8호
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• pp.3051-3056
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• 2011

We calculate the free energy surfaces for two small proteins and a protein-RNA complex system by using a lattice model approach. In particular, we employ the Munoz-Eaton model, which is a native-structure based statistical mechanical model for studying protein folding problem. The model can provide very useful insights into the folding mechanisms by allowing one to calculate the free energy surfaces efficiently. We first calculate the free energy surfaces of ubiquitin and BBL, using both approximate and recently developed exact solutions of the model. Ubiquitin exhibits a typical two-state folding behavior, while BBL downhill folding in our study. We then extend the method to study of a protein-RNA complex. In particular, we focus on PAZ-siRNA complex. In order to elucidate the interplay between folding and binding kinetics for this system we perform comparative studies of PAZ only, PAZ-siRNA complex and two mutated complexes. We find that folding and binding are strongly coupled with each other and the bound PAZ is more stable than the unbound PAZ. Our results also suggest that the binding sites of the siRNA may serve act as a nucleus in the folding process.

• 한국환경과학회지
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• 제1권2호
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• pp.69-80
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• 1992

Effects of light on leaf senescence of Phseolus vulgaris were investigated by measuring the disassembly of chlorophyll-protein complexes in detached leaves which had been kept in the dark or under light. The loss of chlorophyll accompanied by degradation of chlorophyll- protein complexes. PSI (photosystem I) complex containing LHCI (light harvesting complex of PSI) apoproteins was rapidly decreased after the early stage of dark-induced senescence. RC(reaction center)-Cores was slightly increased until 4 d and slowly decreased thereafter. As disassembly of LHCII trimer progressed after the late stage of senescence, there was a steady increase in the relative amount of SC(small complex)-2 containing LHCII monomer. On the other hand, white and red light adaptation caused the structural stability of chlorophyll-protein complexes during dark-induced senescence. Particularly, red light was more effective in the retardation of LHCII breakdown than white light, whereas white light was slightly effect in protecting the disassembly of PSI complex compared to red light. These results suggest, therefore, that light may be a regulatory factor for stability of chlorophyll-protein complexes in the senescent leaves.

• 기술사
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• 제31권3호
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• pp.60-64
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• 1998

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.313-318
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• 2005

Estimating the reliability of protein-protein interaction data sets obtained by high-throughput technologies such as yeast two-hybrid assays and mass spectrometry is of great importance. We develop a maximum likelihood estimation method that uses both protein localization and gene expression data to estimate the reliability of protein interaction data sets. By integrating protein localization data and gene expression data, we can obtain more accurate estimates of the reliability of various interaction data sets. We apply the method to protein physical interaction data sets and protein complex data sets. The reliability of the yeast two-hybrid interactions by Ito et al. (2001) is 27%, and that by Uetz et at.(2000) is 68%. The reliability of the protein complex data sets using tandem affinity purification-mass spec-trometry (TAP) by Gavin et at. (2002) is 45%, and that using high-throughput mass spectrometric protein complex identification (HMS-PCI) by Ho et al. (2002) is 20%. The method is general and can be applied to analyze any protein interaction data sets.