• Journal of Microbiology and Biotechnology
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• v.15 no.6
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• pp.1392-1396
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• 2005

Proteolytic digestion and CD measurement of wild-type and mutant cyclic AMP receptor proteins (CRPs) were performed either in the presence or absence of cyclic nucleotide. Results indicated that transition of a structural change to the hinge region by the binding of cAMP to the anti site was required for the binding of cAMP to the syn site near the hinge region and, although the occupancy of cAMP in the anti site increased the protein stability, CRP adopted more a stable conformation by the binding of cAMP to the syn site.

• Journal of Integrative Natural Science
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• v.4 no.3
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• pp.222-226
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• 2011

Cyclic AMP receptor protein(CRP) is involved in the activation of many genes corresponding to catabolite enzymes in Escherichia coli. In this study, mutant CRP(S128A) was used to elucidate the effect of Ser 128 on the cAMP-induced structural change. Based on the protease digestion and thermal analysis, serine 128 in CRP affects the cAMP binding capability and then structural change of CRP protein. In addition, CD spectra in near UV region revealed that S128A CRP retained the sensitive conformation to thermal effect relative to that of wild-type CRP, in spite of identical Tm values in the absence of cAMP.

• BMB Reports
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• v.45 no.12
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• pp.693-699
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• 2012

Together with protein tyrosine kinases (PTKs), protein tyrosine phosphatases (PTPs) serve as hallmarks in cellular signal transduction by controlling the reversible phosphorylation of their substrates. The human genome is estimated to encode more than 100 PTPs, which can be divided into eleven sub-groups according to their structural and functional characteristics. All the crystal structures of catalytic domains of sub-groups have been elucidated, enabling us to understand their precise catalytic mechanism and to compare their structures across all sub-groups. In this review, I describe the structure and mechanism of catalytic domains of PTPs in the structural context.

• Journal of the Korean Magnetic Resonance Society
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• v.28 no.3
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• pp.10-14
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• 2024

Caveolin3, mainly expressed in muscle tissue types, is a structural scaffolding protein of caveolae which are microdomains of plasma membrane. To elucidate the relationship between structure and function, several studies on the structure of caveolins using NMR have been reported. Because the ionic strength can affect the electrostatic-driven association of proteins with ligand and protein structure, the effect of salt in the structural studies has to be considered. In this work, we observed that the chemical shifts of Cav3 in the LPPG detergent change depending on salt concentration. The R2 values also show salt concentration-dependent changes. Specifically, in the N-terminal region where conformational changes and various interactions occur, the R2 values decrease. Interestingly, the R2 values of residues expected to be located in the LPPG detergent are also influenced by the salt concentration. This work suggests that the concentration of NaCl can affect interpretation of NMR data from membrane proteins.

• Proceedings of the Korean Magnetic Resonance Society Conference
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• 2002.08a
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• pp.76-76
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• 2002

• BMB Reports
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• v.34 no.1
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• pp.73-79
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• 2001

Transcriptional activation domains are known to be inherently "unstructured" with no tertiary structure. A recent NMR study, however, has shown that the transactivation domain in human p53 is populated with an amphipathic helix and two nascent turns. This suggests that the presence of such local secondary structures within the overall "unstructured" structural framework is a general feature of acidic transactivation domains. These pre-existing local structures in p53, formed selectively by positional conserved hydrophobic residues that are known to be critical for transcriptional activity, thus appear to constitute the specific structural motifs that regulate recognition of the p53 transactivation domain by target proteins. Here, we report the results of a NMR structural comparison between the native human p53 transactivation domain and an inactive mutant (22L,23W$\rightarrow$22R,23S). Results show that the mutant has an identical overall structural topology as the native protein, to the extent that the amphipathic helix formed by the residues 18T 26L within the native p53 transactivating domain is preserved in the double mutant. Therefore, the lack of transcriptional activity in the double mutant should be ascribed to the disruption of the essential hydrophobic contacts between the p53 transactivation domain and target proteins due to the (22L,23W$\rightarrow$22R,23S) mutation.

• Journal of Life Science
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• v.14 no.5
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• pp.752-760
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• 2004

The function of the [4Fe-4S] cluster containing iron (Fe-) protein in nitrogenase catalysis is to serve as the nucleotide-dependent electron donor to the MoFe protein which contains the sites for substrate binding and reduction. The ability of the Fe protein to function in this manner is dependent on its ability to adopt the appropriate conformation for productive interaction with the MoFe protein and on its ability to change redox potentials to provide the driving force required for electron transfer. The MgADP-bound (or off) conformational state of the nitrogenase Fe protein structure described reveals mechanisms for long-range communication from the nucleotide-binding sites to control affinity of association with the MoFe protein component. Two pathways, termed switches I and II, appear to be integral to this nucleotide signal transduction mechanism. In addition, the structure of the MgADP bound Fe protein provides the basis for the changes in the biophysical properties of the [4Fe-4S] observed when Fe protein binds nucleotides. The structures of the nitrogenase Fe protein with defined amino acid substitutions in the nucleotide dependent signal transduction pathways of the Switch I and Switch II have been determined by X-ray diffraction methods. These two pathways have been also implicated by site directed mutagenesis studies, structural analysis and analogies to other proteins that utilize similar nucleotide dependent signal transduction pathways. We have examined the validity of the assignment of these pathways in linking the signals generated by MgATP binding and hydrolysis to macromolecular complex formation and intermolecular electron transfer. The results provide a structural basis for the observed biophysical and biochemical properties of the Fe protein variants and interactions within the nitrogenase Fe protein-MoFe protein complex.

• Journal of Life Science
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• v.11 no.1
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• pp.43-47
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• 2001

A mutant tryptophan synthase $\alpha$-subunit, where Pro28 was replaced with Leu, tends to be expressed in recombinant E. coli. CD and fluorescence spectra of this protein indicate some changes in secondary and tertiary structure. Wild type protein was more or less affected by {TEX}$Ca^{2+}${/TEX} ion in regards of the fluorescent properties of its native, unfolded and intermediate forms, but the mutant protein was not at all. The dramatic structural changes may be related to the aggregation of this mutant protein.

• Journal of IKEEE
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• v.13 no.3
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• pp.18-23
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• 2009

FEATURE is a computational method to recognize functional and structural sites for automatic protein function prediction. By profiling physicochemical properties around residues, FEATURE can characterize and predict functional and structural sites in 3D protein structures in a high-throughput manner. Despite its effectiveness, it has been challenging to apply FEATURE to novel protein data due to limited customization support. To address this problem, we thoroughly analyze the internal modules of FEATURE and propose a methodology to customize FEATURE so that it can be used for new protein data for automatic functional annotations.

• Journal of Life Science
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• v.9 no.5
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• pp.497-503
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• 1999

Change on the structural carbohydrate(several fiberous components) was determined by vegetables(crown daisy and butterbur)-cultivated in Ulsan, Kyungnam, Korea-as its stage of maturity developed. Samples were separated into leaf and stem, which were dried at 7$0^{\circ}C$ for 24hr, and ground to pass a 1mm screen. They were subjected to moisture, crude protein, crude fat and several dietary fiber-DF(dietary fiber, include unavaible components), NDF(neutral detergent fiber), ADF(acid detergent fiber), lignin, hemicellulose, cellulose and protein corrected NDF(c-NDF), IDF(indigestible fiber, include lignin, hemicellulose and cellulose). In general, structural carbohytrate(several dietary fiber) of vegetable was affected by the growth stage. In case of crown daisy and butterbur, dietary fiber in leaf was higher than DF in stem.