Chaejoon Cheong

Structural characterization of β-D-(1 → 3, 1 → 6)-linked glucans using NMR spectroscopy

Abstract Nondestructive structural analysis of a series of β- d -(1→3, 1→6)-linked glucans (laminaran, curdlan, yeast glucan, scleroglucan, etc.) was performed using two-dimensional NMR spectroscopy. The relative ratios of H-1 at different AGUs provided the information about DP n and DB. The α-, and β-anomeric protons on reducing terminals were assigned at 5.02∼5.03 ppm ( J 3.6∼3.7 Hz), and 4.42∼4.43 ppm ( J 7.6∼7.9 Hz), respectively, whereas the H-1 protons of internal AGUs and β-(1→6)-branched AGUs appeared at 4.56∼4.59 ppm ( J 7.6∼7.8 Hz), and 4.26∼4.28 ppm ( J 7.6∼10.6 Hz), respectively, in a mixed solvent of 6:1 Me 2 SO- d 6 –D 2 O at 80xa0°C. In the solvent, the OH peaks were eliminated from the spectra allowing the H-1 protons to appear clearly. In addition, the nonreducing terminal H-1 and H-1 at the AGU next to reducing terminal could be assigned at 4.45∼4.46 ppm ( J 7.8∼7.9 Hz), and 4.51∼4.53 ppm ( J 7.8 Hz), respectively. The DP n of the laminaran was 33 (polydispersity 1.12) and the DB was 0.07. The number of glucosyl units in the side chain of laminaran is more than one. The DP n and DB of the water-insoluble yeast glucan were 228 and 0.003, respectively. However the DP n of water soluble yeast glucan phosphate and curdlan was changed upon the number of freeze-drying processes and the content of water in the mixed solvent, respectively. And the DB of those were calculated as 0.02 and 0, respectively. The DB of scleroglucan was precisely calculated as 0.33, compared with the previously reported data. The H-1s at different AGUs of the various β- d -(1→3, 1→6)-linked glucans having different DB can be exactly assigned by their chemical shifts in the mixed solvent system. This NMR analysis can be effectively used to determine the DP and DB of polysaccharides in a simple and non-destructive manner.

An Activatable Prodrug for the Treatment of Metastatic Tumors

Metastatic cancers have historically been difficult to treat. However, metastatic tumors have been found to have high levels of reactive oxygen species such as hydrogen peroxide (H2O2), supporting the hypothesis that a prodrug could be activated by intracellular H2O2 and lead to a potential antimetastatic therapy. In this study, prodrug 7 was designed to be activated by H2O2-mediated boronate oxidation, resulting in activation of the fluorophore for detection and release of the therapeutic agent, SN-38. Drug release from prodrug 7 was investigated by monitoring fluorescence after addition of H2O2 to the cancer cells. Prodrug 7 activated by H2O2, selectively inhibited tumor cell growth. Furthermore, intratracheally administered prodrug 7 showed effective antitumor activity in a mouse model of metastatic lung disease. Thus, this H2O2-responsive prodrug has therapeutic potential as a novel treatment for metastatic cancer via cellular imaging with fluorescence as well as selective release of the anticancer drug, SN-38.

Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram-negative bacterial outer membrane

The outer membrane protein A (OmpA) plays important roles in anchoring of the outer membrane to the bacterial cell wall. The C‐terminal periplasmic domain of OmpA (OmpA‐like domain) associates with the peptidoglycan (PGN) layer noncovalently. However, there is a paucity of information on the structural aspects of the mechanism of PGN recognition by OmpA‐like domains. To elucidate this molecular recognition process, we solved the high‐resolution crystal structure of an OmpA‐like domain from Acinetobacter baumannii bound to diaminopimelate (DAP), a unique bacterial amino acid from the PGN. The structure clearly illustrates that two absolutely conserved Asp271 and Arg286 residues are the key to the binding to DAP of PGN. Identification of DAP as the central anchoring site of PGN to OmpA is further supported by isothermal titration calorimetry and a pulldown assay with PGN. An NMR‐based computational model for complexation between the PGN and OmpA emerged, and this model is validated by determining the crystal structure in complex with a synthetic PGN fragment. These structural data provide a detailed glimpse of how the anchoring of OmpA to the cell wall of gram‐negative bacteria takes place in a DAP‐dependent manner.—Park, J. S., Lee, W. C., Yeo, K. J., Ryu, K.‐S., Kumarasiri, M., Hesek, D., Lee, M., Mobashery, S., Song, J. H., Lim, S. I., Lee, J. C., Cheong, C., Jeon, Y. H., Kim, H.‐Y. Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram‐negative bacterial outer membrane. FASEB J. 26, 219–228 (2012). www.fasebj.org

Solution structure of an antimicrobial peptide buforin II

The structure of 21‐residue antimicrobial peptide buforin II has been determined by using NMR spectroscopy and restrained molecular dynamics. Buforin II adopts a flexible random structure in H2O. In trifluoroethanol (TFE)/H2O (1 : 1, v/v) mixture, however, buforin II assumes a regular α‐helix between residues Val12 and Arg20 and a distorted helical structure between residues Gly7 and Pro11. The model structure obtained shows an amphipathic character in the region from Arg5 to the C‐terminus, Lys21. Like other known cationic antimicrobial peptides, the amphipathic structure might be the key factor for antimicrobial activity of buforin II.

Identification of structurally diverse alkaloids in Corydalis species by liquid chromatography/electrospray ionization tandem mass spectrometry

RATIONALEnAlkaloids with significant therapeutic effects are the main active constituents of Corydalis (C.) species. There are several kinds of alkaloids in C. species associated with diverse alkaloid metabolism in plants, but they are rarely identified. This study aimed to identify diverse alkaloids in C. species by liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS).nnnMETHODSnSeveral types of alkaloids were extracted from C. species using ultrasonication with 70% CH(3)OH, and the extract was partitioned at pH 2 and 12. Separation of alkaloids was achieved by C18 high-performance liquid chromatography (HPLC), and MS/MS analysis was conducted by electrospray ionization triple-quadrupole mass spectrometry. For further confirmation, LC/Fourier transform ion cyclotron resonance (FTICR)-MS was used to obtain accurate mass data and gas chromatography (GC)/MS combined with trimethylsilyl derivatization was applied for identification of the minor alkaloids.nnnRESULTSnThirty-three alkaloids among three different C. species were successfully separated and identified by LC/ESI-MS/MS and LC/FTICR-MS. Structural assignment of individual alkaloids was performed according to MS/MS spectral patterns. For further confirmation, accurate mass data of alkaloids by LC/FTICR-MS were obtained within 5 ppm and the GC/MS data for the trimethylsilyl alkaloids were also obtained. Among 33 alkaloids identified from this study, 13 alkaloids were reported for the first time in the investigated C. species.nnnCONCLUSIONSnThe LC/ESI-MS/MS technique was effective in obtaining structural information and yielded diagnostic ions for diverse alkaloids. Based on the identified 33 alkaloids, marker compounds were suggested for the three C. species with different geographic origins. This study may also be useful for elucidating unknown alkaloids in herbal medicines.

Proteomic and bioinformatic analysis of membrane proteome in type 2 diabetic mouse liver

Type 2 diabetes mellitus (T2DM) is the most prevalent and serious metabolic disease affecting people worldwide. T2DM results from insulin resistance of the liver, muscle, and adipose tissue. In this study, we used proteomic and bioinformatic methodologies to identify novel hepatic membrane proteins that are related to the development of hepatic insulin resistance, steatosis, and T2DM. Using FT‐ICR MS, we identified 95 significantly differentially expressed proteins in the membrane fraction of normal and T2DM db/db mouse liver. These proteins are primarily involved in energy metabolism pathways, molecular transport, and cellular signaling, and many of them have not previously been reported in diabetic studies. Bioinformatic analysis revealed that 16 proteins may be related to the regulation of insulin signaling in the liver. In addition, six proteins are associated with energy stress‐induced, nine proteins with inflammatory stress‐induced, and 14 proteins with endoplasmic reticulum stress‐induced hepatic insulin resistance. Moreover, we identified 19 proteins that may regulate hepatic insulin resistance in a c‐Jun amino‐terminal kinase‐dependent manner. In addition, three proteins, 14–3‐3 protein beta (YWHAB), Slc2a4 (GLUT4), and Dlg4 (PSD‐95), are discovered by comprehensive bioinformatic analysis, which have correlations with several proteins identified by proteomics approach. The newly identified proteins in T2DM should provide additional insight into the development and pathophysiology of hepatic steatosis and insulin resistance, and they may serve as useful diagnostic markers and/or therapeutic targets for these diseases.

60th residues of ubiquitin and Nedd8 are located out of E2-binding surfaces, but are important for K48 ubiquitin-linkage

MINT‐7263328: NEDD8 (uniprotkb:Q15843) and Ubiquitin (uniprotkb:P62988) physically interact (MI:0914) by enzymatic studies (MI:0415)

Differential Ubiquitin Binding by the Acidic Loops of Ube2g1 and Ube2r1 Enzymes Distinguishes Their Lys-48-ubiquitylation Activities

Background: The acidic loops of E2 enzymes are important for their Lys-48-ubiquitylation activity. Results: The presence of Tyr residues modulates the ubiquitin binding property of the acidic loop. Conclusion: A proper interaction of the acidic loop with the attached donor ubiquitin is important for Lys-48-ubiquitylation activity. Significance: One of molecular bases to study the mechanism of Lys-48-ubiquitylation is provided. The ubiquitin E2 enzymes, Ube2g1 and Ube2r1, are able to synthesize Lys-48-linked polyubiquitins without an E3 ligase but how that is accomplished has been unclear. Although both E2s contain essential acidic loops, only Ube2r1 requires an additional C-terminal extension (184–196) for efficient Lys-48-ubiquitylation activity. The presence of Tyr-102 and Tyr-104 in the Ube2g1 acidic loop enhanced both ubiquitin binding and Lys-48-ubiquitylation and distinguished Ube2g1 from the otherwise similar truncated Ube2r11–183 (Ube2r1C). Replacement of Gln-105–Ser-106–Gly-107 in the acidic loop of Ube2r1C (Ube2r1CYGY) by the corresponding residues from Ube2g1 (Tyr-102–Gly-103–Tyr-104) increased Lys-48-ubiquitylation activity and ubiquitin binding. Two E2∼UB thioester mimics (oxyester and disulfide) were prepared to characterize the ubiquitin binding activity of the acidic loop. The oxyester but not the disulfide derivative was found to be a functional equivalent of the E2∼UB thioester. The ubiquitin moiety of the Ube2r1CC93S-[15N]UBK48R oxyester displayed two-state conformational exchange, whereas the Ube2r1CC93S/YGY-[15N]UBK48R oxyester showed predominantly one state. Together with NMR studies that compared UBK48R oxyesters of the wild-type and the acidic loop mutant (Y102G/Y104G) forms of Ube2g1, in vitro ubiquitylation assays with various mutation forms of the E2s revealed how the intramolecular interaction between the acidic loop and the attached donor ubiquitin regulates Lys-48-ubiquitylation activity.

Purification, crystallization and preliminary X-ray crystallographic analysis of diaminopimelate epimerase from Acinetobacter baumannii

The meso isomer of diaminopimelate (meso-DAP) is a biosynthetic precursor of L-lysine in bacteria and plants, and is a key component of the peptidoglycan layer in the cell walls of Gram-negative and some Gram-positive bacteria. Diaminopimelate epimerase (DapF) is a pyridoxal-5-phosphate-independent racemase which catalyses the interconversion of (6S,2S)-2,6-diaminopimelic acid (LL-DAP) and meso-DAP. In this study, DapF from Acinetobacter baumannii was overexpressed in Escherichia coli strain SoluBL21, purified and crystallized using a vapour-diffusion method. A native crystal diffracted to a resolution of 1.9u2005Å and belonged to space group P3(1) or P3(2), with unit-cell parameters axa0=xa0bxa0=xa074.91, c = 113.35u2005Å, α = β = 90, γ = 120°. There were two molecules in the asymmetric unit.

Cation Recognition by Picolyl-Armed Calix[4]crown-5-azacrown-5s

A series of N-pivot calix[4]crown-5-azacrown-5 ethers substituted by 2-picolyl, 3-picolyl and benzyl groups respectively were synthesized. The nitrogen atom of the 2-picolyl group is found to participate in the silver ion complexation through three dimensional encapsulation.