Biomedical subjects

S Kim

Publications and source records attributed to S Kim.

At least 145 records · Page 8Linked to original sources

PubMed2001

Structural study of novel antimicrobial peptides, nigrocins, isolated from Rana nigromaculata.

Novel cationic antimicrobial peptides, named nigrocin 1 and 2, were isolated from the skin of Rana nigromaculata and their amino acid sequences were determined. These peptides manifested a broad spectrum of antimicrobial activity against various microorganisms with different specificity. By primary structural analysis, it was revealed that nigrocin 1 has high sequence homology with brevinin 2 but nigrocin 2 has low sequence homology with any other known antimicrobial peptides. To investigate the structure-activity relationship of nigrocin 2, which has a unique primary structure, circular dichroism (CD) and homonuclear nuclear magnetic resonance spectroscopy (NMR) studies were performed. CD investigation revealed that nigrocin 2 adopts mainly an alpha-helical structure in trifluoroethanol (TFE)/H(2)O solution, sodium dodecyl sulfate (SDS) micelles, and dodecylphosphocholine micelles. The solution structures of nigrocin 2 in TFE/H(2)O (1:1, v/v) solution and in SDS micelles were determined by homonuclear NMR. Nigrocin 2 consists of a typical amphipathic alpha-helix spanning residues 3-18 in both 50% TFE solution and SDS micelles. From the structural comparison of nigrocin 2 with other known antimicrobial peptides, nigrocin 2 could be classified into the family of antimicrobial peptides containing a single linear amphipathic alpha-helix that potentially disrupts membrane integrity, which would result in cell death.

Amino Acid Sequence↗

PubMed2001

Active site residues of cephalosporin acylase are critical not only for enzymatic catalysis but also for post-translational modification.

Cephalosporin acylase (CA) is a recently identified N-terminal hydrolase. It is also a commercially important enzyme in producing 7-aminocephalosporanic acid (7-ACA), a backbone chemical in synthesizing semi-synthetic cephalosporin antibiotics. CA is translated as an inactive single chain precursor, being post-translationally modified into an active enzyme. The post-translational modification takes place in two steps. The first intramolecular autocatalytic proteolysis takes place at one end of the spacer peptide by a nucleophilic Ser or Thr, which in turn becomes a new N-terminal Ser or Thr. The second intermolecular modification cleaves off the other end of the spacer peptide by another CA. Two binary structures in complex with glutaryl-7-ACA (the most favored substrate of CAs) and glutarate (side chain of glutaryl-7-ACA) were determined, and they revealed the detailed interactions of glutaryl-7-ACA with the active site residues (Y. Kim and W. G. J. Hol (2001) Chem. Biol., in press). In this report: 1) we have mutated key active site residues into nonfunctional amino acids, and their roles in catalysis were further analyzed; 2) we performed mutagenesis studies indicating that secondary intermolecular modification is carried out in the same active site where deacylation reaction of CA occurs; and 3) the cleavage site of secondary intermolecular modification by another CA was identified in the spacer peptide using mutational analysis. Finally, a schematic model for intermolecular cleavage of CA is proposed.

Acylation↗

PubMed2001

Peroxisome proliferator-activated receptor gamma ligands inhibit mitogenic induction of p21(Cip1) by modulating the protein kinase Cdelta pathway in vascular smooth muscle cells.

The cyclin-dependent kinase inhibitor p21(Cip1) is up-regulated in response to mitogenic stimulation in various cells. PPARgamma ligands troglitazone (TRO, 10 microm) and rosiglitazone (RSG, 10 microm) attenuated the induction of p21(Cip1) protein by platelet-derived growth factor (PDGF) and insulin without affecting cognate mRNA levels in rat aortic smooth muscle cells (RASMC). The protein kinase Cdelta (PKCdelta) inhibitor rottlerin also blocked the induction of p21(Cip1) protein, whereas the conventional PKC isotype inhibitor Gö 6976 had no effect. Kinetic studies using the protein synthesis inhibitor cycloheximide showed that TRO, RSG, and rottlerin shortened the half-life of p21(Cip1) protein. TRO, RSG, and rottlerin inhibited PDGF-induced expression of p21(Cip1), but they did not affect insulin-induced expression of p21(Cip1). Both ligands inhibited PKCdelta enzymatic activity in PDGF-stimulated RASMC but not in insulin-stimulated cells. Adenovirus-mediated overexpression of PKCdelta rescued the down-regulation of p21(Cip1) expression both by TRO and RSG in PDGF-treated RASMC. These data suggested that the PKCdelta pathway plays a critical role in PDGF-induced expression of p21(Cip1) in RASMC and may be the potential target for PPARgamma ligand effects. Src kinase-dependent tyrosine phosphorylation of PKCdelta was decreased substantially by TRO and RSG. Tyrosine phosphorylation and activation of c-Src in response to PDGF were unaffected by either PPARgamma ligand. Protein-tyrosine-phosphatase inhibitors sodium orthovanadate and dephostatin prevented PPARgamma ligand effects on PKCdelta tyrosine phosphorylation and enzymatic activity. Both inhibitors also reversed PPARgamma ligand effects on p21(Cip1) expression in PDGF-treated RASMC. PPARgamma ligands enhanced protein-tyrosine-phosphatase activity in RASMC, which may be the mechanism for decreased PKCdelta tyrosine phosphorylation and activity. PPARgamma ligands regulate p21(Cip1) at a post-translational level by blocking PKCdelta signaling and accelerating p21(Cip1) turnover.

Acetophenones↗

PubMed2001

A novel nucleophilic substitution of in situ generated 3-tert-butyldimethyl- silyloxyalk-2-enylsulfonium salts with allylindium reagents.

[reaction: see text] In situ generated 3-tert-butyldimethylsilyloxyalk-2-enylsulfonium salts derived from the reaction of alpha,beta-enones with dimethyl sulfide in the presence of TBSOTf undergo a novel nucleophilic substitution with in situ generated allylindium reagents from indium and allyl halides to give silyl enol ethers of delta,epsilon-unsaturated ketones, which correspond to Michael addition products, in good yields.

Journal Article↗

PubMed2001

Multiple isoforms and an unusual cathodic isoform of creatine kinase from channel catfish (Ictalurus punctatus).

In vertebrates, the creatine kinase (CK) family consists of two cytosolic and two mitochondrial isoforms. The two cytosolic isoforms are the muscle type (M-CK) and the brain type (B-CK). Here we report multiple CK isoenzymes in the diploid channel catfish (Ictalurus punctatus) with one unusual cathodic isoform that was previously found only in pathological situations in human. The cathodic CK isoform existed only in the channel catfish stomach, ovary, and spleen, but not in any other species analyzed such as tilapia, smallmouth bass, chicken, or rat. Two genes encode the multiple forms of the channel catfish M-CK cDNAs. M-CK1 has three alleles, M-CK1.1, M-CK1.2, and M-CK1.3, while M-CK2 has just one allele as determined by analysis of 17 cDNA clones and by allele-specific PCR. M-CK1 encodes a protein of 381 amino acids and the M-CK2 cDNA encodes a protein of 380 amino acids. The two cDNAs shared an 86% identity and both have the nine diagnostic boxes for cytosolic CKs and thus are of cytosolic origin. The M-CK1 gene was isolated, sequenced, and characterized and its promoter should be useful for transgenic research for muscle-specific expression.

Amino Acid Sequence↗

PubMed2001

Novel families of three-component reversible redox cycles involving cage deformation via intramolecular redox reaction: tetrathiolate-bridged dinuclear molybda- and tungstacarboranes.

The synthesis and structural analysis of two novel families of three-component reversible redox cycles [(C(2)B(9)H(11))M(mu-SPh)(2)](2)(n)PPN(n) (M = Mo, n = 2-, 2; 1-, 3; 0, 4; and M = W, n = 2-, 6; 1-, 7; 0, 8), where the cleavage and re-formation of the carborane cage C-C bond is observed during the redox reaction, are reported. Electronic saturation of the metal center (18e center) and the lack of bulky substituents on the carborane cage suggest that the deformed carborane cages in 2.PPN(2), 6.PPN(2), and 7.PPN invoke a new kind of deformed cage ("semicloso" framework). The XPS results show that the unprecedented competition for electron density between the metal center and the carborane cage is involved in the cleavage and formation of the carborane C-C bond.

Journal Article↗

PubMed2001

Role of the sequence of the rne-dependent site in 3' processing of M1 RNA, the catalytic component of Escherichia coli RNase P.

The 3' processing of M1 RNA, the catalytic component of Escherichia coli RNase P, occurs by two pathways involving multiple steps. The precursor of M1 RNA has an rne-dependent site downstream of the processing site, whose sequence variation affects the processing efficiency. In this study, we showed that the sequence itself of the rne-dependent site possessed the ability to determine the processing pathways and that it also affected the cleavage specificity with the generation of the processing products at one nucleotide upstream or downstream of the normal cleavage sites.

Base Sequence↗

PubMed2001

Methodology for miniaturized CE and insulation on a silicon substrate.

We have developed a synchronously switched cyclic capillary electrophoresis (CE) separator that is fabricated on a silicon substrate and glass. Au electrodes were also integrated on the chip that could be wire bonded to the printed circuit board (PCB). The advantage of using a cyclic separator is that it has the high resolution and the ability to separate each sample to the designated reservoir from mixed samples. This approach makes it possible to reduce the supplied voltage and the total chip size. Another goal of this work was to introduce the methodology of electroosmotic flow (EOF) on the silicon substrate and to separate DNA samples using a modified double-T injector.

Journal Article↗

PubMed2001

Structural comparison of monomeric variants of the chemokine MIP-1beta having differing ability to bind the receptor CCR5.

MIP-1beta, a member of the chemokine family of proteins, tightly binds the receptor CCR5 as part of its natural function in the immune response, and in doing so also blocks the ability of many strains of HIV to enter the cell. The single most important MIP-1beta residue known to contribute to its interaction with the receptor is Phe13, which when mutated reduces the ability of MIP-1beta to bind to CCR5 by more than 1000-fold. To obtain a structural understanding of the dramatic effect of the absence of Phe13 in MIP-1beta, we used multidimensional heteronuclear NMR to determine the three-dimensional structure of the MIP-1beta F13A variant. We had previously shown that, unlike the wild-type protein which has been shown to be a tight dimer, the F13A mutant is monomeric even at high concentrations [Laurence, J. S., Blanpain, C., Burgner, J. W., Parmentier, M., and LiWang, P. J. (2000) Biochemistry 39, 3401-3409], leading to significant changes in the NMR spectra of F13A and the wild-type protein. We have obtained a total of 940 structural restraints for MIP-1beta F13A, and have calculated a family of structures having a backbone rmsd from the average of 0.55 A (residues 12-67). A structural comparison of the F13A mutant with a fully active monomeric variant, P8A, shows that despite some differences in the (1)H-(15)N HSQC spectra the two are nearly identical in NOE distance restraints and in backbone conformation. A comparison of F13A with the wild-type protein shows largely the same fold, although differences exist in the N-terminal and loop regions for which the loss of the dimer in F13A can mainly account. A dynamics comparison confirms greater flexibility in F13A than in the wild-type protein in regions of dimer contact in the wild-type protein. In an analysis to determine if the large functional effect resulting from the loss of Phe13 is due to the local side chain change or due to more global structural changes, we conclude that local effects predominate. This suggests that a strategy for designing tight binding anti-CCR5 therapeutics should include a Phe-like component.

Amino Acid Substitution↗

PubMed2001

Significance of chymase-dependent angiotensin II-forming pathway in the development of vascular proliferation.

BACKGROUND: Vascular tissues of humans and dogs contain chymase as an angiotensin II-forming enzyme. In this study, we investigated whether chymase-dependent angiotensin II formation plays a crucial role in the development of vascular proliferation in dog grafted veins. METHODS AND RESULTS: The right external jugular vein of dogs was grafted to the ipsilateral carotid artery. As a control group, the right external jugular veins in dogs that had not received grafts were used. In the chymase inhibitor-treated group, the vein was infiltrated with 10 micromol/L Suc-Val-Pro-Phe(P)(OPh)(2) and was grafted to the carotid artery. In the placebo-treated group, ACE activity in the grafted veins was significantly lower than that in the control veins up to 7 days after the operation, whereas chymase activity was increased significantly. After 7 days, the mRNA levels of collagen I, collagen III, and fibronectin, all of which are induced by an increase of angiotensin II action, were significantly increased in the grafted veins, and the intima-media ratio of the grafted veins was also increased. In the chymase inhibitor-treated group, the chymase activity in the grafted veins 7 days after the operation was suppressed to 12.1%. The elevated mRNA levels of fibronectin, collagen I, and collagen III in the grafted veins were significantly suppressed by treatment with the chymase inhibitor, and the intima-media ratio was also decreased significantly. CONCLUSIONS: We demonstrate for the first time that chymase-dependent angiotensin II formation plays an important role in the development of vascular proliferation in the grafted veins.

Angiotensin II↗

PubMed2001

Troglitazone inhibits growth of MCF-7 breast carcinoma cells by targeting G1 cell cycle regulators.

Peroxisome proliferator activated receptor gamma (PPARgamma) is a member of the nuclear receptor superfamily. Ligand activation of PPARgamma has been shown to cause growth arrest in several human tumor cell types, but the underlying molecular mechanism has not been elucidated. We report here that the PPARgamma ligand troglitazone (TRO) inhibited MCF-7 cell proliferation by blocking events critical for G1 --> S progression. Flow cytometry demonstrated that TRO at 20 microM increased the percentage of cells in G1 from 51 to 69% after 24 h. Accumulation of cells in G1 was accompanied by an attenuation of Rb protein phosphorylation associated with decreased CDK4 and CDK2 activities. Inhibition of CDK activity by TRO correlates with decreased protein levels for several G1 regulators of Rb phosphorylation (cyclin D1, and CDKs 2, 4, and 6). Overexpression of cyclin D1 partially rescued MCF-7 cells from TRO-mediated G1 arrest. Targeting of G1 regulatory proteins, particularly cyclin D1, and the resulting induction of G1 arrest by TRO may provide a novel antiproliferative therapy for human breast cancer.

Annexin A5↗

PubMed2001

A novel class of inhibitors for steroid 5alpha-reductase: synthesis and evaluation of umbelliferone derivatives.

A series of umbelliferone derivatives was prepared and their 5alpha-reductase type 1 inhibitory activities were evaluated in cell culture systems. Our studies have identified a new series of potent 5alpha-reductase type 1 inhibitors and provided the basis for further development for the treatment of human endocrine disorders associated with overproduction of DHT by 5alpha-reductase type 1. The preliminary structure-activity relationship was described to elucidate the essential structural requirements.

5-alpha Reductase Inhibitors↗

PubMed2001

Construction and characterization of a bacterial artificial chromosome library from chili pepper.

A library of the bacterial artificial chromosome (BAC) that consisted of a total of 78,336 clones with an average insert size of 80 kb was constructed from Capsicum annuum, 'CM334', which is resistant to Phytophthora capsici and PVY. Based on a haploid genome size of pepper of 2,702 Mbp/C, the BAC library was estimated to contain approximately three genome equivalents and represented at least 90% of the pepper genome. In order to determine the percentage of BAC clones that contained mitochondrial DNAs, the entire library was screened with probes of chili pepper mitochondrial DNAs. The result showed that only twenty-five clones, which is 0.03% of the total BAC clones, were hybridized to mitochondrial gene probes. This indicates that the library is comprised predominantly of the nuclear sequences. The library was also tested for isolating specific clones by screening with a few known genes from the chili pepper, phytoene synthase gene, and two MADS genes--HpMADS1 and HpMADS3. The result showed that the three clones for phytoene synthase and the two clones for each MADS gene were positively hybridized to the specific probes. This indicates that the library is highly reliable and represents a resource for initiating map-based cloning and contig mapping in chili pepper.

Alkyl and Aryl Transferases↗

PubMed2001

Apoptosis signal-regulating kinase 1 controls the proapoptotic function of death-associated protein (Daxx) in the cytoplasm.

Although Daxx (death-associated protein) was first reported to mediate the apoptotic signal from Fas to JNK in the cytoplasm, other data suggested that Daxx is mainly located in the nucleus as a transcriptional regulator. Here, we demonstrated that cellular localization of Daxx could be determined by the relative concentration of a proapoptotic kinase, apoptosis signal-regulating kinase 1 (ASK1) by using immunofluorescence and transcriptional reporter assay. ASK1 sequestered Daxx in the cytoplasm and inhibited the repressive activity of Daxx in transcription. In addition, Daxx was bound to the activated Fas only in the presence of ASK1, accelerating the Fas-mediated apoptosis. These results suggest that Daxx requires ASK1 for its cytoplasmic localization and Fas-mediated signaling. Taken together, we could conclude that ASK1 controls the dual function of Daxx as a transcriptional repressor in the nucleus and as a proapoptotic signal mediator in the cytoplasm.

Adaptor Proteins, Signal Transducing↗

PubMed2001

Complete cross-validation and R-factor calculation of a solid-state NMR derived structure.

Cross-validation of a solid-state NMR-derived membrane polypeptide structure is demonstrated. An initial structure has been achieved directly from solid-state NMR derived orientational restraints based on a variety of anisotropic nuclear spin interactions. Refining the molecular structure involves setting up a penalty function that incorporates all available solid-state NMR experimental data and an energy function. A validation method is required to choose the optimal weighting factor for the total penalty function to balance the contribution from the experimental restraints and the energy function. Complete cross-validation has been used to avoid over-fitting the orientational restraints. Such cross-validation involves partitioning of the experimental data into a test set and a working set followed by checking the free R-value during the refinement process. This approach is similar to the method used in crystallography and solution NMR. Optimizing the weighting factor on the penalty function by cross-validation will increase the quality of the refined structure from solid-state NMR data. The complete cross-validation and R-factor calculation is demonstrated using experimental solid-state NMR data from gramicidin A, a monovalent cation channel in lipid bilayers.

Journal Article↗

PubMed2001

Angiotensin II-responsive element is the insulin-responsive element in the adipocyte fatty acid synthase gene: role of adipocyte determination and differentiation factor 1/sterol-regulatory-element-binding protein 1c.

We have previously shown that angiotensin II (Ang II) increases the expression of the gene encoding adipocyte fatty acid synthase (FAS). Here we investigate the mechanism responsible for increased FAS gene transcription by Ang II. We demonstrate that Ang II increased luciferase activity by 3-fold in 3T3-L1 adipocytes transfected with fusion constructs linking the FAS promoter to the luciferase reporter gene. Interestingly, we mapped the Ang II regulatory sequences to the insulin-responsive region (E box) in the proximal FAS promoter. The E box alone was able to mediate Ang II responsiveness when linked to a heterologous promoter. However, this response was lost when mutations that abolished the binding of the E box to its transcription factors were introduced. Using adenoviral overexpression of a dominant-negative form of adipocyte determination and differentiation factor 1 (ADD1), a transcription factor that binds to the insulin-responsive E box, we demonstrated that ADD1 was required for Ang II regulation of the FAS gene in 3T3-L1 adipocytes. Furthermore, ADD1 expression was also up-regulated by Ang II. With the use of transfections as well as glucose transport assays, we further demonstrated that Ang II stimulation of the FAS gene was dependent on glucose. In conclusion, this is the first report that Ang II regulates adipocyte FAS gene transcription via insulin response sequences in a glucose-dependent manner and that this regulation is mediated at least in part via the ADD1 transcription factor.

3T3 Cells↗

PubMed2001

Down modulation of IL-18 expression by human papillomavirus type 16 E6 oncogene via binding to IL-18.

To understand modulation of a novel immune-related cytokine, interleukin-18, by human papillomavirus type (HPV) 16 oncogenes, HaCaT, normal keratinocyte cell line, and C-33A, HPV-negative cervical cancer cell line, were prepared to establish stable cell lines expressing E6, E6 mutant (E6m), E6E7, or E7 constitutively. Expressions of various HPV oncogene transcripts were identified by RT-PCR. Expression of HPV oncogene E6 was reversely correlated to the expression of interleukin-18, a novel pro-inflammatory cytokine. The expression of E6 in C-33A, independent of E6 splicing, resulted in decreased IL-18 expression and that of IL-18 was also significantly reduced in HaCaT cells expressing E6. The level of p53 was reduced in C-33A cells expressing E6 whereas not altered in HaCaT cells expressing E6, suggesting that E6 downregulated IL-18 expression via an independent pathway of p53 degradation in HaCaT cells which have a mutated p53 form. However, E7 did not affect IL-18 expression significantly in both C-33A and HaCaT cells. Cotransfection experiments showed that E6 oncogene did not inhibit the activities of IL-18 promoter P1 and P2, suggesting that E6 oncogene indirectly inhibited IL-18 expression. Taken together, E6, E6m and E6/E7 inhibited IL-18 expression with some variation, assuming that cells expressing E6 oncogene can evade immune surveillance by downregulating the expression of immune stimulating cytokine gene, IL-18, and inhibiting the cascade of downstream effects that follow activation of the IL-18 receptor.

Binding, Competitive↗

PubMed2001

Both E6 and E7 oncoproteins of human papillomavirus 16 inhibit IL-18-induced IFN-gamma production in human peripheral blood mononuclear and NK cells.

Cervical carcinoma is the predominant cancer among malignancies in women throughout the world, and human papillomavirus (HPV) 16 is the most common agent linked to human cervical carcinoma. The present study was performed to investigate the mechanisms of immune escape in HPV-induced cervical cancer cells. The presence of HPV oncoproteins E6 and E7 in the extracellular fluids of HPV-containing cervical cancer cell lines SiHa and CaSki was demonstrated by ELISA. The effect of HPV 16 oncoproteins E6 and E7 on the production of IFN-gamma by IL-18 was assessed. E6 and E7 proteins reduced IL-18-induced IFN-gamma production in both primary PBMCs and the NK0 cell line. FACS analysis revealed that the viral oncoproteins reduced the binding of IL-18 to its cellular surface receptors on NK0 cells, whereas there was no effect of oncoproteins on IL-1 binding to its surface IL-1 receptors on D10S, a subclone of the murine Th cell D10.G4.1. In vitro pull-down assays also revealed that the viral oncoproteins and IL-18 bound to IL-18R alpha-chain competitively. These results suggest that the extracellular HPV 16 E6 and E7 proteins may inhibit IL-18-induced IFN-gamma production locally in HPV lesions through inhibition of IL-18 binding to its alpha-chain receptor. Down-modulation of IL-18-induced immune responses by HPV oncoproteins may contribute to viral pathogenesis or carcinogenesis.

Adjuvants, Immunologic↗