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

• Journal of Microbiology and Biotechnology
• /
• 제14권3호
• /
• pp.450-455
• /
• 2004

A reducing glucose-carrying polymer, called poly [3-O-(4'-vinylbenzyl)-D-glucose］(PVG), was interacted with HepG2 cells including a type-l glucose transporter (GLUT-1) on the cell membrane. The cooperative interaction between a number of GLUT-1s and a number of reducing 3-O-methyl-D-glucose moieties on the PVG polymer chain was found to be responsible for the increase in the interaction with HepG2 cells. The affinity between the cells and the PVG was studied using RITC-labeled glycopolymers. The specific interaction between the GLUT-1 on HepG2 cells and the PVG polymer carrying reducing glucose moieties was suppressed by the inhibitors, phloretin, phloridzin, and cytochalasin B. Direct observation by confocal laser microscopy with the use of RITC-labeled PVG and pretreatment of HepG2 cells with the inhibitors demonstrated that the cells interacted with the soluble form of the PVG polymer via GLUT-1, while fluorescence labeling of the cell surface was prevented after pretreatment with the inhibitors of GLUT-1.

• Asian Pacific Journal of Cancer Prevention
• /
• 제16권16호
• /
• pp.7089-7095
• /
• 2015

Clinical evidence shows that dual inhibition of kinases as well angiogenesis provides ideal therapeutic option in the treatment of medullary thyroid carcinoma (MTC) than inhibiting either of these with the events separately. Although treatment with dual inhibitors has shown good clinical responses in patients with MTC, it has been associated with serious side effects. Some inhibitors are active agents for both angiogenesis or kinase activity. Owing to narrow therapeutic window of established inhibitors, the present study aims to identify high affinity dual inhibitors targeting RET and VEGFR2 respectively for kinase and angiogenesis activity. Established inhibitors like Vandetanib, Cabozantinib, Motesanib, PP121, RAF265 and Sunitinib served as query parent compounds for identification of structurally similar compounds by Tanimoto-based similarity searching with a threshold of 95% against the PubChem database. All the parent inhibitors and respective similar compounds were docked against RET and VEGFR2 in order to retrieve high affinity compounds with these two proteins. AGN-PC-0CUK9P PubCID: 59320403 a compound related to PPI21 showed almost equal affinity for RET and VEGFR2 and unlike other screened compounds with no apparent bias for either of the receptors. Further, AGNPC- 0CUK9P demonstrated appreciable interaction with both RET and VEGFR2 and superior kinase activity in addition to showed optimal ADMET properties and pharmacophore features. From our in silico investigation we suggest AGN-PC-0CUK9P as a superior dual inhibitor targeting RET and VEGFR2 with high efficacy which should be proposed for pharmacodynamic and pharmacokinetic studies for improved treatment of MTC.

• Journal of Microbiology and Biotechnology
• /
• 제12권2호
• /
• pp.196-203
• /
• 2002

A novel process for urokinase purification was studied using p-aminobenzamidine as the ligand and sepharose 4B as the matrix. The adsorption, washing, and elution conditions were optimized by an unusual method. An adsorption buffer containing 2.5 M NaCl and $1\%$ Tween 80 facilitated the adsorption of urokinase on the affinity media and prevented contaminants from binding to the p-aminobenzamidine affinity gel. It was found that $5\%$ Tween 80 removed most of the contaminants from the affinity column. A 0.2 M glycine elution buffer containing 0.5 M NaCl (pH 3.0) was found to have a strong elution ability with a high recovery and purity of urokinase. A crude urokinase material of231 IU/mg protein from human urine was purified to 124,300 IU/mg protein with a purification factor of 538 and yield of $86.7\%$. As a result, a high purity urokinase was obtained with only a single affinity chromatography step. The purification process was successfully scaled-up to a 2-1 chromatography column. The resulting urokinase eluate could be directly lyophilized, thereby complying with Chinese pharmacopoeia (1995 version) standards.

• Asian Pacific Journal of Cancer Prevention
• /
• 제16권9호
• /
• pp.3759-3765
• /
• 2015

Background: Approaches in disruption of MDM2-p53 interactions have now emerged as an important therapeutic strategy in resurrecting wild type p53 functional status. The present study highlights virtual screening strategies in identification of high affinity small molecule non-peptidic inhibitors. Nutlin3A and RG7112 belonging to compound class of Cis-imidazoline, MI219 of Spiro-oxindole class and Benzodiazepine derived TDP 665759 served as query small molecules for similarity search with a threshold of 95%. The query molecules and the similar molecules corresponding to each query were docked at the transactivation binding cleft of MDM2 protein. Aided by MolDock algorithm, high affinity compound against MDM2 was retrieved. Patch Dock supervised Protein-Protein interactions were established between MDM2 and ligand (query and similar) bound and free states of p53. Compounds with PubCid 68870345, 77819398, 71132874, and 11952782 respectively structurally similar to Nutlin3A, RG7112, Mi219 and TDP 665759 demonstrated higher affinity to MDM2 in comparison to their parent compounds. Evident from the protein-protein interaction studies, all the similar compounds except for 77819398 (similar to RG 7112) showed appreciable inhibitory potential. Of particular relevance, compound 68870345 akin to Nutlin 3A had highest inhibitory potential that respectively showed 1.3, 1.2, 1.16 and 1.26 folds higher inhibitory potential than Nutilin 3A, MI 219, RG 7112 and TDP 1665759. Compound 68870345 was further mapped for structure based pharamacophoric features. In the study, we report Cis-imidazoline derivative compound; Pubcid: 68870345 to have highest inhibitory potential in blocking MDM2-p53 interactions hitherto discovered.

• KSBB Journal
• /
• 제18권4호
• /
• pp.306-311
• /
• 2003

융합단백질의 절단을 위해 EK를 고정화하여 액상 절단반응과 같은 80％의 절단수율을 얻을 수 있었다. 그리고 니켈 친화칼럼을 이용하여 간단한 정제공정을 구축하였다. 공유결합한 EK의 경우 니켈친화 결합한 EK보다 높은 재접힘 수율을 나타내었고 풀림과 재접힘을 이용하여 효소의 초기 활성을 회복함에 따라서 반복사용을 통한 경제적인 절단공정을 구축할 수 있게 되었다. 그러나 고정화 과정에서 효소의 활성이 감소하는 문제점과 고정화 수율을 높이기 위한 연구가 필요하다.

• Journal of Veterinary Science
• /
• 제23권3호
• /
• pp.50.1-50.12
• /
• 2022

Background: There is an urgent need to find reliable and rapid bovine tuberculosis (bTB) diagnostics in response to the rising prevalence of bTB worldwide. Toll-like receptor 2 (TLR2) recognizes components of bTB and initiates antigen-presenting cells to mediate humoral immunity. Evaluating the affinity of antigens with TLR2 can form the basis of a new method for the diagnosis of bTB based on humoral immunity. Objectives: To develop a reliable and rapid strategy to improve diagnostic tools for bTB. Methods: In this study, we expressed and purified the sixteen bTB-specific recombinant proteins in Escherichia coli. The two antigenic proteins, MPT70 and MPT83, which were most valuable for serological diagnosis of bTB were screened. Molecular docking technology was used to analyze the affinity of MPT70, MPT83, dominant epitope peptide of MPT70 (M1), and dominant epitope peptide MPT83 (M2) with TLR2, combined with the detection results of enzyme-linked immunosorbent assay to evaluate the molecular docking effect. Results: The results showed that interaction surface Cα-atom root mean square deviation of proteins (M1, M2, MPT70, MPT83)-TLR2 protein are less than 2.5 A, showing a high affinity. It is verified by clinical serum samples that MPT70, MPT83, MPT70-MPT83 showed good diagnostic potential for the detection of anti-bTB IgG and M1, M2 can replace the whole protein as the detection antigen. Conclusions: Molecular docking to evaluate the affinity of bTB protein and TLR2 combined with ELISA provides new insights for the diagnosis of bTB.

• Journal of Pharmaceutical Investigation
• /
• 제23권3호
• /
• pp.119-125
• /
• 1993

The protein binding of salicylate analogs has been investigated by equilibrium dialysis. A series of binding experiments were performed in order to elucidate the effects of physicochemical properties of salicylate analogs on the binding with bovine serum albumin. Attempts to correlate affinity constants with capacity factor, steric factor and Hammett ${\sigma}$ values suggested hydrophobic forces to be involved in the binding of salicylate analogs. Steric factor contributes to binding process partly, whereas electronic interaction appears to be insignificant.

• Journal of Pharmaceutical Investigation
• /
• 제18권3호
• /
• pp.133-137
• /
• 1988

In vitro studies were performed on the interaction of indomethacin with cholestyramine, a hypocholesterolemic substance. Cholestyramine showed a marked affinity for indomethacin among tested acidic drugs and the intensity of adsorption was dependent on pH, temperature and sodium chloride. Moreover, the combination of indomethacin with some acidic drugs that formed complexes with cholestyramine, considerably inhibited the adsorption of indomethacin on the resin.

• 한국생물물리학회:학술대회논문집
• /
• 한국생물물리학회 1999년도 학술발표회 진행표 및 논문초록
• /
• pp.44-44
• /
• 1999

Yeast cytochrome c peroxidase (CcP) was cloned and overexpressed in E. coli, and purified by a Ni$^{2＋}$-affinity column. HoloCcP was obtained by reconstituting apoCcP with Mn$^{3+}$-protoporphyrin IX (MnPP). Electron paramagnetic resonance (EPR) spectra of spin-labeled holoCcP showed a slightly more immobilized signal than spin-labeled apoCcP.(omitted)