• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2433-2442
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• 2011

The three dimensional quantitative structure activity relationship (3D QSAR) models were developed using Comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and docking studies. The fit of Quinazolinone antifolates inside the active site of modeled bovine dihydrofolate reductase (DHFR) was assessed. Both ligand based (LB) and receptor based (RB) QSAR models were generated, these models showed good internal and external statistical reliability that is evident from the $q^2_{loo}$, $r^2_{ncv}$ and $r^2_{pred}$. The identified key features enabled us to design new Quinazolinone analogues as DHFR inhibitors. This study is a building bridge between docking studies of homology modeled bovine DHFR protein as well as ligand and target based 3D QSAR techniques of CoMFA and CoMSIA approaches.

• Molecules and Cells
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• v.24 no.3
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• pp.437-440
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• 2007

$OGL-20P^T$-358 is a novel 66 amino acid residue protein from the hyperthermophile Thermococcus thioreducens sp. nov., strain $OGL-20P^T$, which was collected from the wall of the hydrothermal black smoker in the Rainbow Vent along the mid-Atlantic ridge. This protein, which has no detectable sequence homology with proteins or domains of known function, has a calculated pI of 4.76 and a molecular mass of 8.2 kDa. We report here the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of $OGL-20P^T$-358. Assignments are 97.5% (316/324) complete. Chemical shift index was used to determine the secondary structure of the protein, which appears to consist of primarily ${\alpha}$-helical regions. This work is the foundation for future studies to determine the three-dimensional solution structure of the protein.

• Korean Journal of Crystallography
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• v.5 no.1
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• pp.20-23
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• 1994

Specific binding to the oric region of E, coli chromsome by IciA protein inhibits initiation of chrorrnsomal replication in vitro by blocking the opening of this region effected by the initiator DnaA protein. The IciA protein has been suggested play a critical role in a key stage of the cell cycle. In order to study the structure-function relationship of IciA protein, we are determining the three-dimensional structure of IciA Votein by X-ray crystallography, As a first step toward its structure detumination E. coli IciA protein has been crystallized using sodium formate as a precipitant.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1120-1126
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• 2013

The syndecan family consists of four transmembrane heparan sulfate proteoglycans present in most cell types and each syndecan shares a common structure containing a heparan sulfate modified extracellular domain, a single transmembrane domain and a C-terminal cytoplasmic domain. To get a better understanding of the mechanism and function of syndecan-4 which is one of the syndecan family, it is crucial to investigate its three-dimensional structure. Unfortunately, it is difficult to prepare the peptide because it is membrane-bound protein that transverses the lipid bilayer of the cell membrane. Here, we optimize the expression, purification, and characterization of transmembrane, cytoplasmic and short extracellular domains of syndecan4 (syndecan-4 eTC). Syndecan-4 eTC was successfully obtained with high purity and yield from the M9 medium. The structural information of syndecan-4 eTC was investigated by MALDI-TOF mass (MS) spectrometry, circular dichroism (CD) spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy. It was confirmed that syndecan-4 eTC had an ${\alpha}$-helical multimeric structure like transmembrane domain of syndecan-4 (syndecan-4 TM) in membrane environments.

• Journal of Microbiology and Biotechnology
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• v.27 no.3
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• pp.644-647
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• 2017

Peptidyl prolyl cis/trans isomerases (PPIases) catalyze the cis/trans isomerization of peptidyl-prolyl peptide bonds preceding prolines. We investigated the protein-protein interaction between a 22 kDa PPIase (VaFKBP22, an FK506-binding protein) and the molecular chaperone DnaK derived from Vibrio anguillarum O1 (VaDnaK) using GST pull-down assays and a bacterial two-hybrid system for in vivo and in vitro studies, respectively. Furthermore, we analyzed the three-dimensional structure of the protein-protein interaction. Based on our results, VaFKBP22 appears to act as a cochaperone of VaDnaK, and contributes to protein folding and stabilization via its peptidyl-prolyl cis/trans isomerization activity.

• Bulletin of the Korean Chemical Society
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• v.27 no.2
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• pp.266-272
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• 2006

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were developed for 67 molecules of 2-amino-benzothiazole-6-anilide derivatives against lymphocyte-specific protein tyrosine kinase (P56 LCK). The molecular field analysis (MFA) and receptor surface analysis (RSA) were employed for QSAR studies and the predictive ability of the model was validated by 15 test set molecules. Structure-based investigations using molecular docking simulation were performed with the crystal structure of P56 LCK. Good correlation between predicted fitness scores versus observed activities was demonstrated. The results suggested that the nature of substitutions at the 2-amino and 6-anilide positions were crucial in enhancing the activity, thereby providing new guidelines for the design of novel P56 LCK inhibitors.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.19 no.12
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• pp.3011-3016
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• 2015

Representing protein three-dimensional structure by concatenating a sequence of protein fragments gives an efficient application in analysis, modeling, search, and prediction of protein structures. This paper investigated the effective combination of distance measures, which can exploit large protein structure database, in order to construct a protein fragment library representing native protein structures accurately. Clustering method was used to construct a protein fragment library. Initial clustering stage used inter alpha-carbon distance having low time complexity, and cluster extension stage used the combination of inter alpha-carbon distance, Binet-Cauchy distance, and root mean square deviation. Protein fragment library was constructed by leveraging large protein structure database using the proposed combination of distance measures. This library gives low root mean square deviation in the experiments representing protein structures with protein fragments.

• Journal of the Korean Magnetic Resonance Society
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• v.2 no.2
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• pp.85-105
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• 1998

Prions cause neurodegenerative diseases in animals and humans. The scrapie prion protein (PrPSc) is the major-possibly only-component of the infectious prion and is generated from the cellular isoform (PrPC) by a conformational change. Limited proteolysis of PrPSc produces an polypeptide comprised primarily of residues 90 to 231, which retains infectivity. The three-dimensional structure of rPrP(90-231), a recombinant protein resembling PrPC with the Syrian hamster (SHa) sequence, was solved using multidimensional NMR. Low-resolution structures of rPrP(90-231), synthetic peptides up to 56 residues, a longer (29-231, full-length) protein with SHa sequence, and a short here further structure refinement of rPrP(90-231) and dynamic features of the protein. Consideration of these features in the context of published data suggests regions of conformational heterogeneity, structural elements involved in the PrPC\longrightarrowPrPSc transformation, and possible structural features related to a species barrier to transmission of prion diseases.

• Genomics & Informatics
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• v.6 no.1
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• pp.50-53
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• 2008

We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC) model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.

• Molecules and Cells
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• v.38 no.2
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• pp.180-186
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• 2015

Escherichia coli AcrAB-TolC is a multidrug efflux pump that expels a wide range of toxic substrates. The dynamic nature of the binding or low affinity between the components has impeded elucidation of how the three components assemble in the functional state. Here, we created fusion proteins composed of AcrB, a transmembrane linker, and two copies of AcrA. The fusion protein exhibited acridine pumping activity, suggesting that the protein reflects the functional structure in vivo. To discern the assembling mode with TolC, the AcrBA fusion protein was incubated with TolC or a chimeric protein containing the TolC aperture tip region. Three-dimensional structures of the complex proteins were determined through transmission electron microscopy. The overall structure exemplifies the adaptor bridging model, wherein the funnel-like AcrA hexamer forms an intermeshing cogwheel interaction with the ${\alpha}$-barrel tip region of TolC, and a direct interaction between AcrB and TolC is not allowed. These observations provide a structural blueprint for understanding multidrug resistance in pathogenic Gram-negative bacteria.