Biomedical subjects

Sunyoung Park

Publications and source records attributed to Sunyoung Park.

3 recordsLinked to original sources

PubMed2006

Chip-based analysis of SUMO (small ubiquitin-like modifier) conjugation to a target protein.

A chip-based analysis of protein interactions and modifications in cell signaling pathways has been of great potential in drug discovery, diagnostics, and cell biology, because it enables rapid and high-throughput biological assays with a small amount of samples. We report a chip-based analysis of sumoylation, the post-translational modification (PTM) process that involves covalent attachment of the small ubiquitin-like modifier (SUMO) protein to a target protein through multiple enzyme reactions in eukaryotic cells. Substrate proteins were spotted onto a glass surface followed by the addition of the reaction mixture for sumoylation, and the SUMO conjugation was readily detected by using fluorescent dye-labeled antibody. Under the optimized condition, on-chip sumoylation of Ran GTPase-activating protein 1 (RanGAP1) domain resulted in highly specific fluorescence intensity compared to that of its mutant (K524A) irrelevant to SUMO conjugation. The on-chip sumoylation was also verified and quantified by using the surface plasmon resonance(SPR) spectroscopy. As the exemplary study for a parallel analysis of sumoylation, fluorescent detection of sumoylation was conducted in a microarray format on a glass slide. The chip-based analysis developed here is expected to be applicable to assay for screening of target proteins from existing protein pools and proteome arrays in a high throughput manner.

GTPase-Activating Proteins↗

PubMed2005

jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences.

jPHYDIT is a Java application designed to furnish a visual and integrated environment for molecular phylogeny. The program can be used to visualize intra-strand base-pairing information in secondary and tertiary structures of ribosomal RNA (rRNA) sequences. A function for the semi-automated alignment was included to facilitate handling of the database containing a large number of multiple-aligned rRNA sequences. Integration of nucleotide sequence editing, pairwise alignment, multiple alignment and phylogenetic treeing functions provide an easy and efficient way of analyzing rRNA sequences for molecular evolution, systematics, epidemiology and ecology.

Algorithms↗

PubMed2003

Mass spectrometric method for the absolute calibration of the intramolecular nitrogen isotope distribution in nitrous oxide.

A mass spectrometric method to determine the absolute intramolecular (position-dependent) nitrogen isotope ratios of nitrous oxide (N2O) has been developed. It is based on the addition of different amounts of doubly labeled 15N2O to an N2O sample of the isotope ratio mass spectrometer reference gas, and subsequent measurement of the relative ion current ratios of species with mass 30, 31, 44, 45, and 46. All relevant quantities are measured by isotope ratio mass spectrometers, which means that the machines' inherent high precision of the order of 10(-5) can be fully exploited. External determination of dilution factors with generally lower precision is avoided. The method itself can be implemented within a day, but a calibration of the oxygen and average nitrogen isotope ratios relative to a primary isotopic reference material of known absolute isotopic composition has to be performed separately. The underlying theoretical framework is explored in depth. The effect of interferences due to 14N15N16O and 15N14N16O in the 15N2O sample and due to 15N2+ formation are fully accounted for in the calculation of the final position-dependent nitrogen isotope ratios. Considering all known statistical uncertainties of measured quantities and absolute isotope ratios of primary isotopic reference materials, we achieve an overall uncertainty of 0.9 per thousand (1 sigma). Using tropospheric N2O as common reference point for intercomparison purposes, we find a substantially higher relative enrichment of 15N at the central nitrogen atom over 15N at the terminal nitrogen atom than measured previously for tropospheric N2O based on a chemical conversion method: 46.3 +/- 1.4 per thousand as opposed to 18.7 +/- 2.2 per thousand. However, our method depends critically on the absolute isotope ratios of the primary isotopic reference materials air-N2 and VSMOW. If they are systematically wrong, our estimates will also necessarily be incorrect.

Journal Article↗