Biomedical subjects

Kwang-Seuk Ko

Publications and source records attributed to Kwang-Seuk Ko.

6 recordsLinked to original sources

PubMed2005

Fluorous-based carbohydrate microarrays.

The success of microarrays, such as DNA chips, for biosample screening with minimal sample usage has led to a variety of technologies for assays on glass slides. Unfortunately, for small molecules, such as carbohydrates, these methods usually rely on covalent bond formation, which requires unique functional handles and multiple chemical steps. A new simpler concept in microarray formation is based on noncovalent fluorous-based interactions. A fluorous tail is designed not only to aid in saccharide purification but also to allow direct formation of carbohydrate microarrays on fluorous-derivatized glass slides for biological screening with lectins, such as concanavalin A. The noncovalent interactions in the fluorous-based array are even strong enough to withstand the detergents used in assays with the Erythrina crystagalli lectin. Additionally, the utility of benzyl carbonate protecting groups on fucose building blocks for the formation of alpha-linkages is demonstrated.

Carbohydrate Conformation↗

PubMed2005

Platinum(II) complex as an artificial peptidase: selective cleavage of peptides and a protein by cis-[Pt(en)(H2O)2]2+ ion under ultraviolet and microwave irradiation.

Two synthetic peptides were completely cleaved by the cis-[Pt(en)(H2O)2]2+ (en is ethylenediamine) complex at pH 2.5 under thermal heating at 60 degrees C in a selective way: only the amide bonds involving the carboxylic group of the methionine residue, i.e., the Met-Z bonds (where the residue Z has a noncoordinating side chain), were hydrolyzed. Under irradiation at 300 nm, the rate constants for these cleavage reactions were approximately doubled, but side reactions occurred. Under microwave irradiation, the rate constants were increased 2-3 times at 60 degrees C and ca. 7 times at 100 degrees C, and no side reactions were detected. Microwave irradiation similarly accelerated the complete and selective cleavage of Met-Z bonds in cytochrome c at 60 degrees C in comparison with this cleavage under thermal heating, again without detected side reactions. The microwave-assisted cleavage of peptides and proteins by the platinum(II) reagent holds promise in proteomics and other biotechnological applications.

Cations, Divalent↗

PubMed2005

Strategies for the chemoenzymatic synthesis of deoxysugar nucleotides: substrate binding versus catalysis.

Sugar nucleotidyltransferases, also known as sugar pyrophosphorylases, catalyze the formation of a phosphate linkage to produce sugars activated for use by Leloir pathway glycosyltransferases and are subjects of protein engineering for chemoenzymatic synthesis strategies. Herein we present evidence that differences in substrate binding affinity do not primarily account for substantial contrasts in deoxysugar nucleotide product yields with this class of enzymes. Prokaryotic and eukaryotic glucose-1-phosphate uridylyltransferases (EC 2.7.7.9) can exercise kinetic discrimination in choosing carbohydrates of comparable binding affinity for catalytic turnover. These findings have implications for the in vivo and in vitro function and use of these enzymes.

Binding Sites↗

PubMed2004

Surprising bacterial nucleotidyltransferase selectivity in the conversion of carbaglucose-1-phosphate.

The drive to understand the molecular determinants of carbohydrate binding as well as the search for more chemically and biochemically stable sugar derivatives and carbohydrate-based therapeutics has led to the synthesis of a variety of analogues that replace the glycosidic oxygen with sulfur or carbon. In contrast, the effect of substitution of the ring oxygen on the conformations and enzymatic tolerance of sugars has been largely neglected, in part because of the difficulty in obtaining these analogues. Herein we report the first synthesis of the carbocyclic version of the most common naturally occurring sugar-1-phosphate, glucose-1-phosphate, and its evaluation with bacterial and eukaryotic sugar nucleotidyltransferases. In contrast to results with the eukaryotic enzyme, the carbaglucose-1-phosphate serves as a substrate for the bacterial enzyme to provide the carbocyclic uridinediphosphoglucose. This result demonstrates the first chemoenzymatic strategy to this class of glycosyltransferase inhibitors and stable activated sugar mimics for cocrystallization with glycosyltransferases and their glycosyl acceptors. This difference in turnover between enzymes also suggests the possibility of using sugar nucleotidyltransferases in vivo to convert prodrug forms of glycosyltransferase inhibitors. In addition, we report several microwave-assisted reactions, including a five minute Ferrier rearrangement with palladium, that accelerate the synthesis of carbocyclic sugars for further studies.

Bacteria↗

PubMed2004

Discovery of the chemical function of glycosidases: design, synthesis, and evaluation of mass-differentiated carbohydrate libraries.

[reaction: see text] Discovery of the catalytic chemical function of the many putative glycosidases coded in genomes currently relies on individual testing of possible substrates, usually as their p-nitrophenol conjugate. Herein, we present an alternative chemical proteomics approach using a synthetic mass-differentiated heat-stable substrate library with mass spectrometry readout. Library components do not serve as reaction inhibitors and both primary and secondary enzyme substrates can be delineated.

Carbohydrates↗

PubMed2003

Synthesis of isobutyl-C-galactoside (IBCG) as an isopropylthiogalactoside (IPTG) substitute for increased induction of protein expression.

[reaction: see text] Addition of isopropyl-beta-d-thiogalactopyranoside (IPTG) to bacterial cultures is often used to induce expression of plasmid-based genes for the production of recombinant proteins under control of the lac promoter, but a simple method to circumvent the inherent instability of this compound has not been addressed experimentally. Herein we report the first synthesis of isobutyl-C-galactoside (IBCG), the C-glycoside analogue of IPTG, and show that IBCG is superior to IPTG in inducing protein expression over long induction times.

DNA↗