• BMB Reports
• /
• v.28 no.3
• /
• pp.204-209
• /
• 1995

The pH dependence of kinetic parameters in the amination direction of the aspartase from Hafnia alvei has been determined. The V/K for fumarate is bell shaped with pK values of 6.4 and 8.7. The maximum velocity for fumarate is also bell shaped with pK values of 7.2 and 9.1. The pH dependence of 1/K, for potassium (competitive inhibitor of ammonia) decreases at low pH with pK 7.6. Together with data [Yoon and Cook (1994) Korean J. Biochem. 27, 1-5] on the deamination direction of the aspartase, these results are consistent with two enzyme groups which are necessary for catalysis. An enzymatic group that must be deprotonated has been identified. Another enzyme group must be protonated for substrate binding. Both the general base and general acid group are in a protonation state opposite that in which they started when aspartate was bound. A proton is abstracted from C-3 of the monoanionic form of L-aspartate by an enzyme general base with, a pK of 6.3~6.6 in the absence and presence of $Mg^{2+}$ Ammonia is then expelled with the assistance of a general acid group giving $NH_{4+}$ as the product.

• BMB Reports
• /
• v.43 no.11
• /
• pp.766-771
• /
• 2010

The biological evaluation of a new synthesized Pt(II)-complex, 2,2'-bipyridin Butylglycinato Pt(II) nitrate, an anti-tumor component, was studied at different temperatures by fluorescence and far UV circular dichroism (CD) spectroscopic methods. Human serum albumin (HSA) and human tumor cell line K562 were as targets. The Pt(II)-complex has a strong ability to quench the intrinsic fluorescence of HSA. Binding and thermodynamic parameters of the interaction were calculated by fluorescence quenching method. Far-UV-CD results showed that Pt(II)-complex induced increasing in content of $\alpha$ helical structure of the protein and stabilized it. The 50% cytotoxic concentration ($Cc_{50}$) of complex was determined using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay at different incubation times. Also, fluorescence staining with DAPI (4,6-diamidino-2-phenylindole) revealed some typical nuclear changes, which are characteristic of apoptosis. Above results suggest that Pt (II) complex is a promising anti-proliferative agent and should execute its biological effects by inducing apoptosis.

• Genomics & Informatics
• /
• v.21 no.2
• /
• pp.21.1-21.14
• /
• 2023

Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as "Uncharacterized." Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.

• The Journal of Korean Association of Computer Education
• /
• v.6 no.3
• /
• pp.9-18
• /
• 2003

In this paper, I present a programming idiom for extending message protocols incrementally in C++, where effectiveness of message transmission is regarded as static binding. Our techniques analyze message protocols with a message handler that examines message types, parameters, and effectiveness dynamically. The result of this analysis is not only to cope with incremental extension of message protocols effectively but also to simulate all essential elements of the object-oriented programming. This result also makes it possible to write high level of procedure like message transmission to object groups.

• BMB Reports
• /
• v.29 no.3
• /
• pp.210-214
• /
• 1996

The pH dependence of the kinetic parameters of mutant O-acetylserine sulfhydrylase (OASS) from Salmonella typhimurium LT-2 has been determined in order to obtain information on the chemical mechanism. The initial velocity pattern obtained by varying the concentrations of OAS at several fixed concentrations of TNB, shows an intersection on the left of the ordinate at pH 7.0, indicating that the kinetic mechanism is a sequential mechanism in which substrate inhibition by OAS is observed while the wild type enzyme showed a ping pong mechanism. The values of $V/E_t$, $V/K_{OAS}E_{t}$ and $V/K_{TNB}E_{t}$ decreased by about 68%, 14% and 16% as compared with the wild type enzyme. The $V/K_{OAS}E_{t}$ is a pK of 6.5 on the acid side of the pH profile, and the $V/K_{TNB}$ is pH independent. As compared with the wild type enzyme, the pKs in the V/K profiles are shifted, reflecting that binding of the cofactor in free E:OAS is less asymmetric.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2005.09a
• /
• pp.147-150
• /
• 2005

Proper PCR primer design determines the success or failure of Polymerase Chain Reaction (PCR) reactions. In this project, we develop GENE-PRIMER, a genomes specific PCR primer design program that is amenable to a genome-wide scale. To achieve this, we incorporated various parameters with biological significance into our program, namely, primer length, melting temperature of primers Tm, guanine/cytosine (GC) content of primer, homopolymeric runs in primer and self-hybridization tendency of primer. In addition, BLAST algorithm is utilized for the purpose of primer specificity check. In summary, selected primers adhered to both physico-chemical criteria and also display specificity to intended binding site in the genome.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
• /
• v.14 no.10
• /
• pp.835-844
• /
• 2001

In this paper, we report the successful growth of crystalline carbon nitride films in Si(100) by a laser-electric discharge method. The laser ablation of the target leads to vapor plume plasma expending into the ambient nitrogen arc discharge area. X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy(AES) were used to identify the binding structure and the content of the nitrogen species in the deposited films. The surface morphology of the films with a deposition time of 2 hours is studied using a scanning electron microscopy (SEM). In order to determine the structural crystalline parameters, X-ray diffraction (XRD) was used to analysis the grown films.

• Molecules and Cells
• /
• v.25 no.2
• /
• pp.279-288
• /
• 2008

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.

• Textile Coloration and Finishing
• /
• v.14 no.2
• /
• pp.85-85
• /
• 2002

The interaction between berberine and tannin in aqueous solution was investigated spectrophotometerically. The dyeing mechanism of silk fabrics (control and tannin treated silk fabrics) with berberine was based on thermodynamic parameters obtained from equilibrium adsorption experiments. In adsorption spectra of aqueous solution of berberine and tannin mixture two isosbestic points (328nm, 357nm) were found and the mole fraction of reaction of components was 1:1. Initial dyeing rates were increased and the diffusion of dye was more effective by tannin treatment. Without regard to tannin treatment the adsorption isotherm of berberine was the langmuir type except high temperature, 80℃. By tannin treatment the saturation dye uptake was increased, the increase of dye uptake appeared to be a result of entropy change rather than enthalpy change. All these results can be interpreted by the hydrophobic interaction between berberine and silk treated with tannin and it is reasonable to conclude that not only the ionic force, but also the hydrophobic interaction contributes to the binding of berberine and tannin treated silk treated with tannin.

• Textile Coloration and Finishing
• /
• v.14 no.2
• /
• pp.9-17
• /
• 2002

The interaction between berberine and tannin in aqueous solution was investigated spectrophotometerically. The dyeing mechanism of silk fabrics (control and tannin treated silk fabrics) with berberine was based on thermodynamic parameters obtained from equilibrium adsorption experiments. In adsorption spectra of aqueous solution of berberine and tannin mixture two isosbestic points (328nm, 357nm) were found and the mole fraction of reaction of components was 1:1. Initial dyeing rates were increased and the diffusion of dye was more effective by tannin treatment. Without regard to tannin treatment the adsorption isotherm of berberine was the langmuir type except high temperature, $80^\circ{C}$. By tannin treatment the saturation dye uptake was increased, the increase of dye uptake appeared to be a result of entropy change rather than enthalpy change. All these results can be interpreted by the hydrophobic interaction between berberine and silk treated with tannin and it is reasonable to conclude that not only the ionic force, but also the hydrophobic interaction contributes to the binding of berberine and tannin treated silk treated with tannin.