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Biomedical subjects

T Yamane

Publications and source records attributed to T Yamane.

At least 577 records · Page 32Linked to original sources
PubMed1976

Direct experimental evidence for kinetic proofreading in amino acylation of tRNAIle.

Kinetic proofreading is a reaction scheme with a structure more complicated than that of Michaelis kinetics, which leads to a proofreading for errors in the recognition of a correct substrate by an enzyme. We have measured the stoichiometry between ATP hydrolysis and tRNAIle charging, using the enzyme isoleucyl-tRNA synthetase [L-isoleucine:tRNAIle ligase (AMP-forming), EC 6.1.1.5] and the amino acids isoleucine (correct) and valine (incorrect). The enzymatic deacylation of charged tRNA, which would normally prevent meaningful stoichiometry studies, was eliminated by the use of transfer factor Tu-GTP, (which binds strongly to charged tRNA) in the reaction mixture. For isoleucine, 1.5 ATP molecules are hydrolyzed per tRNA charged, but for valine, 270. These stoichiometry ratios are fundamental to kinetic proofreading, for the energy coupling is essential and proofreading is obtained only by departing from 1:1 stoichiometry between energy coupling and product formation. Within the known reaction pathway, these ratios demonstrate that kinetic proofreading induces a reduction in errors by a factor of 1/180. An overall error rate of about 10(-4) for tRNA charging is obtained by a kinetic proofreading using a fundamental discrimination level of about 10(-2), and is compatible with the low in vivo error rate of protein synthesis.

Adenosine Triphosphate↗
PubMed1975

The crystal structure of bonito (katsuo) ferrocytochrome c at 2.3 A resolution. II. Structure and function.

The structure analysis of bonito heart ferrocytochrome c was carried out at 2.3 A resolution by X-ray diffraction, and a Kendrew-type skeletal model was built up. This molecule has an overall egg shape, 35 A in height, 30 A in width and 23 A in thickness; the 5th ligand of the heme iron atom is the N-epsilon atom of the His-18 imidazole ring and the 6th is the Met-80 sulfur atom. Distinct alpha-helix regions are found between the N-terminus and reside 11, between 60 and 69, and between 90 and the C-terminus. The most distinct difference between the conformation of the present molecule and that of the horse oxidized molecule is the location of the Phe-82 phenyl ring. In the present reduced molecule, the phyenyl ring is in closer contact with the iron atom and gives influences on the character of the iron atom. Inside the molecule, at the lower part of the heme pocket, there is an extended hydrogen bond network including the propionic acid residues of the heme group. Both Phe-82 and the hydrogen bond network may play a key role in the function of this molecule.

Amino Acid Sequence↗
PubMed1975

High resolution 31P nuclear magnetic resonance studies of intact yeast cells.

High resolution 31P nuclear magnetic resonance (NMR) spectra at 145.7 MHZ are presented for intact yeast cells. Several peaks are resolved and assigned. They include the middle phosphate peaks from long chain or cyclic polyphosphates. Our results are consistent with the suggestion that these polyphosphates act as a phosphate store in the cell. We have also been able to measure cytoplasmic pH using the orthophosphate peak inside the cell, as compared with outside the cell. The results show that yeast cells maintain their cytoplasmic pH around 6.3. This value is considerably higher than the acidic extracellular pH at which they normally live. These preliminary results indicate that 31P NMR at 145.7 MHZ can be a rapid, informative, and non-invasive method for probing biochemical events within living cells.

Hydrogen-Ion Concentration↗
PubMed1975

Erythropoietic protoporphyria and lead intoxication: the molecular basis for difference in cutaneous photosensitivity. II. Different binding of erythrocyte protoporphyrin to hemoglobin.

Acidic solvents extract the same porphyrin-protoporphyrin-from the erythrocytes of patients with either erythropoietic protoporphyria or lead intoxication. However, extractable protoporphyrin disappears rapidly, both in vivo and in vitro, from erythrocytes in erythropoietic protoporphyria but slowly, if at all, in lead intoxication. Consistent with these observations, fluorescence spectroscopy revealed that the intracellular state of the erythrocyte protoporphyrin is different in the two diseases. Spectrofluorometric measurements coupled with fractionations and biochemical syntheses showed that in erythropoietic protoporphyria the protoporphyrin is bound as the free base to hemoglobin molecules at sites other than the heme binding sites. In lead intoxication the fluorescent porphyrin is also bound to hemoglobin but is present as zinc protoporphyrin. The data suggest that the zinc protoporphyrin is bound at heme binding sites. Acidic extraction solvents remove the chelated zinc, but zinc protoporphyrin may be extracted intact from erythrocytes with acetone, ethanol, or the detergent Ammonyx-LO.

Anemia, Hypochromic↗
PubMed1973

Cholesterol hydroperoxide formation in red cell membranes and photohemolysis in erythropoietic protoporphyria.

3beta-Hydroxy-5alpha-hydroperoxy-Delta(6)-cholestene is produced in protoporphyrin-containing red blood cell ghosts irradiated with approximately 400-nanometer light in the presence of oxygen. Incorporation of this cholesterol photooxidation product into normal red blood cells leads to increased osmotic fragility and eventual hemolysis. These results may be relevant to photohemolysis associated with erythropoietic protoporphyria.

Carbon Isotopes↗