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Y Kim

Publications and source records attributed to Y Kim.

At least 775 records · Page 43Linked to original sources
PubMed1990

Two evolutionarily divergent genes encode a cytoplasmic ribosomal protein of Arabidopsis thaliana.

Two clones of Arabidopsis thaliana possessing high sequence identity to the yeast gene encoding ribosomal (r) protein L3 were isolated by heterologous DNA hybridization. The coding regions of these two clones have approx. 63% amino acid (aa) sequence identity to the yeast L3 r-protein and 85% aa sequence identity to each other. Both genes are expressed in shoots. The presence of two divergent genes in A. thaliana raises the possibility that the gene products participate in the formation of functionally distinct ribosomes.

Alleles↗
PubMed1990

Motional effects on NMR structural data. Comparison of spinach and Escherichia coli acyl carrier proteins.

Proteins in solution need not exist in a single rigid structure but can exist in a dynamic equilibrium among structural forms. The problems that this poses for structure determination using nuclear Overhauser effect data from two-dimensional NMR experiments are discussed and illustrated with data on functionally equivalent proteins from two different species. One of these proteins, acyl carrier protein from Escherichia coli, shows a single set of resonances, easily interpreted on the basis of a single rigid structure. However, the related protein, acyl carrier protein from spinach, shows two sets of resonances, suggesting that two conformers in dynamic equilibrium would be a better structural model.

Acyl Carrier Protein↗
PubMed1990

Proteoglycans synthesized by human glomerular mesangial cells in culture.

Human fetal kidney mesangial cells were cultured for 24 h in the presence of 3H-amino acids and [35S] sulfate and chased for 24 h in nonradioactive medium. Incubation medium and cell layer proteoglycans were purified twice by high performance liquid chromatography-DEAE chromatography followed by gel filtration chromatography. The major medium 35S-macromolecules were chondroitin/dermatan-35SO4 proteoglycans. A small, Sepharose CL-6B Kav 0.14 dermatan-35SO4 proteoglycan was detected in the labeling medium and was released into both the early (time 0-0.5 h) and late (6-24 h) chase media. It contained 38 kDa 4-sulfated 35S-GAGs with a high content of iduronic acid and a 45-kDa protein core. A protein core of similar molecular weight was detected in the culture medium by Western analysis using antibodies to biglycan or proteoglycan-I (Fisher, L. W., Termine, J. D., and Young, M. F. (1989) J. Biol. Chem. 264, 4571-4576). This 35S-proteoglycan was not detected in the cell layer. However, a small dermatan-35SO4 with little or no protein core was present in the intracellular compartment. A large, Sepharose CL-6B excluded chondroitin-35SO4 proteoglycan was released into the culture medium and was detected between 6 and 24 h in chase medium. It eluted near the void volume of both associative and dissociative Sepharose CL-4B columns. It contained 30-kDa 4- and 6-sulfated 35S-GAGs and a 253-kDa protein core. A chondroitin-35SO4 proteoglycan with similar sized 35S-GAGs was detected in both the detergent-soluble and insoluble cell layer compartments. A Sepharose CL-6B Kav 0.11 heparin-35SO4 proteoglycan with a 220-kDa protein core and 38-kDa 35S-GAGs was rapidly released from the cell layer. This proteoglycan was larger than that previously described in isolated rat glomeruli or glomerular basement membranes, but had a core protein similar in size to one previously detected in these tissues. A larger heparan-35SO4 proteoglycan with larger 35S-GAGs was present in the detergent-insoluble cell layer compartment. The proteoglycans released by glomerular mesangial cells in culture resembled those synthesized by aortic smooth muscle cells in culture or extracted from aorta, supporting the notion that these cells are of vascular origin.

Blotting, Western↗
PubMed1990

Molecular cloning, transcriptional characterization, and sequencing of cDNA encoding the H-protein of the mitochondrial glycine decarboxylase complex in peas.

The glycine decarboxylase multienzyme complex is located in the mitochondrial matrix and catalyzes a key reaction of the photorespiratory C-2 cycle of C3 plants. The cDNA encoding the smallest subunit, the 13,900-dalton H-protein, of the glycine decarboxylase complex from pea (Pisum sativum) leaves was cloned, identified, characterized, and sequenced. The 678-nucleotide sequence contained a 495-nucleotide open reading frame capable of encoding the 165-amino-acid H-protein precursor. The N terminus of this protein contains a 34-amino-acid sequence which does not appear in the mature protein. This presequence resembles the amphiphilic helices observed with mitochondrial leader sequences in yeast. The 131-amino-acid mature protein from peas shares substantial homology with the enzyme isolated from chicken liver. The abundance of the H-protein mRNA was about 5-fold greater in light-grown pea seedlings compared to dark-grown seedlings. The amount of H-protein transcript increased within 4 h after the plants were transferred to white light and continued to increase up to 24 h. The time course for the accumulation of the H-protein mRNA was similar to that for the mRNA of the small subunit of ribulose-1,5-bisphosphate carboxylase.

Amino Acid Oxidoreductases↗
PubMed1990

Refinement of the NMR structures for acyl carrier protein with scalar coupling data.

Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHN alpha coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance constraints were used to calculate the 3-D structure of ACP. A three-step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics approach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two-state averaging model for the protein was used, did molecular energies drop significantly.

Acyl Carrier Protein↗
PubMed1990

Partial characterization of proteoglycans synthesized by human glomerular epithelial cells in culture.

Confluent adult and fetal human glomerular epithelial cells were incubated for 24 h in the presence of [3H]-amino acids and [35S]sulfate. Two heparan-35SO4 proteoglycans were released into the culture medium. These 35S-labeled proteoglycans eluted as a single peak from anion exchange chromatographic columns, but were separable by gel filtration on Sepharose CL-6B columns. The larger heparan-35SO4 proteoglycan eluted with the column void volume and at a Kav of 0.26 from Sepharose CL-4B columns. The most abundant medium heparan-35SO4 proteoglycan was a high buoyant density proteoglycan similar in hydrodynamic size (Sepharose CL-6B Kav 0.23) to those previously described in glomerular basement membranes and isolated glomeruli. Heparan-35SO4 chains from both proteoglycans were 36 kDa. A smaller proportion of Sepharose CL-6B excluded dermatan-35SO4 proteoglycan was also synthesized by these cells. The predominant protein cores of both medium heparan-35SO4 proteoglycans were approximately 230 and 180 kDa. A hybrid chondroitin/dermatan-heparan-35SO4 proteoglycan with an 80-kDa protein core copurified with the smaller medium heparan-35SO4 proteoglycan. This 35S-labeled proteoglycan appeared as a diffuse, chondroitinase ABC sensitive 155-kDa fluorographic band in sodium dodecyl sulfate-polyacrylamide gels after the Sepharose CL-6B Kav 0.23 35S-labeled proteoglycan fraction was digested with heparitinase. The heparitinase generated heparan sulfate proteoglycan protein cores and the 155-kDa hybrid proteoglycan fragment had molecular weights similar to those previously identified in rat glomerular basement membrane and glomeruli using antibodies against a basement membrane tumor proteoglycan precursor (Klein et al. J. Cell Biol. 106, 963-970, 1988). Thus, human glomerular epithelial cells in culture are capable of synthesizing, processing, and releasing heparan sulfate proteoglycans which are similar to those synthesized in vivo and found in the glomerular basement membrane. These proteoglycans may belong to a family of related basement membrane proteoglycans.

Adult↗
PubMed1990

Renal injury of diet-induced hypercholesterolemia in rats.

Abnormalities in lipid metabolism frequently accompany renal disease and may be important in the pathogenesis of progressive renal injury. In the present study, the effects of a high cholesterol diet on renal histology, cortical lipids, and glomerular hemodynamic function were examined in normal rats with and without reduced renal mass. Cholesterol feeding for 19 weeks increased serum cholesterol from 66 +/- 10 mg/dl to 256 +/- 93 mg/dl in two-kidney rats, and from 73 +/- 15 mg/dl to 407 +/- 274 mg/dl in nephrectomy rats (P less than 0.01). Both sham-operated and unilateral nephrectomy rats fed a high cholesterol diet had a greater amount of glomerulosclerosis and tubulointerstitial damage than rats fed standard chow. Cortical cholesteryl esters were increased by the cholesterol diet, and correlated with the amount of glomerulosclerosis (r = 0.90, P less than 0.01) and tubulointerstitial injury (r = 0.64, P less than 0.05). Cholesterol feeding and nephrectomy both caused alterations in tissue essential fatty acids, and a panel of specific monoclonal antibodies indicated that renal injury and cortical lipid alterations were associated with an increase in glomerular macrophages. Finally, micropuncture experiments carried out in a separate group of rats fed high cholesterol for 8 to 10 weeks demonstrated increases in glomerular capillary pressure. These results suggest that additional investigations may ultimately determine how cholesterol deposition, altered fatty acid metabolism, macrophages, and increased glomerular pressure might combine to cause chronic progressive renal injury.

Animals↗
PubMed1990

Characterization of c-Ki-ras and N-ras oncogenes in aflatoxin B1-induced rat liver tumors.

c-Ki-ras and N-ras oncogenes have been characterized in aflatoxin B1-induced hepatocellular carcinomas. Detection of different protooncogene and oncogene sequences and estimation of their frequency distribution were accomplished by polymerase chain reaction, cloning, and plaque screening methods. Two c-Ki-ras oncogene sequences were identified in DNA from liver tumors that contained nucleotide changes absent in DNA from livers of untreated control rats. Sequence changes involving G.C to T.A or G.C to A.T nucleotide substitutions in codon 12 were scored in three of eight tumor-bearing animals. Distributions of c-Ki-ras sequences in tumors and normal liver DNA indicated that the observed nucleotide changes were consistent with those expected to result from direct mutagenesis of the germ-line protooncogene by aflatoxin B1. N-ras oncogene sequences were identified in DNA from two of eight tumors. Three N-ras gene regions were identified, one of which was shown to be associated with an oncogene containing a putative activating amino acid residing at codon 13. All three N-ras sequences, including the region detected in N-ras oncogenes, were present at similar frequencies in DNA samples from control livers as well as liver tumors. The presence of a potential germ-line oncogene may be related to the sensitivity of the Fischer rat strain to liver carcinogenesis by aflatoxin B1 and other chemical carcinogens.

Aflatoxin B1↗