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Biomedical subjects

M Zama

Publications and source records attributed to M Zama.

At least 19 recordsLinked to original sources
PubMed2003

Bipedicled skin flaps for reconstruction of the abdominal wall in newborn omphalocele.

Despite technical refinements in surgery and advances in postoperative intensive care, abdominal wall closure in giant omphalocele remains a difficult endeavor. In this respect, bipedicled skin flaps obtained with longitudinal incisions along the margins of the rectus abdominis muscle may represent a good alternative solution to achieve a complete, tension-free midline closure. Incisional areas can subsequently be easily covered with split-thickness thigh grafts. Two neonatal cases were treated with this technique with good results. This has enabled avoidance of palliative coverage as well as complex musculo-cutaneous reconstructions at a later age.

Abdominal Wall↗
PubMed2000

Discontinuous translation and mRNA structure of the coding region.

An analysis of the published data of the electrophoresis of the products of silk fibroin exhibiting discontinuities or pauses in the translational process showed that about 60 times of pauses occur during the translation of the mRNA from silk fibroin. In addition, we estimated that silk fibroin gene as a whole (15 kb) is composed of about 60 alternate, crystalline-noncrystalline, arrays of nucleotide sequence elements each connected by the boundary sequence, on the basis of the nucleotide sequence of the partial cDNA clone of the heavy chain gene of Bombyx mori available in the literature. The coincidence of the total number of pauses with that of the alternate arrays suggests that one translational pausing site exists in each of the unit (alternate array + boundary) nucleotide sequence in the silk fibroin mRNA template.

Animals↗
PubMed1999

Correlation between mRNA structure of the coding region and translational pauses.

Discontinuous translational elongation of polypeptides is observed during spider dragline silk fibroin synthesis (1,2). The repeating segment of one of the two subunit proteins constituting spider major ampullate (dragline) silk of Nephila clavipes, Spidroin 2, consists of alternate alanine-rich and proline-rich regions (3). It was found that the calculated free energy of the secondary structure of Spidroin 2 mRNA per nucleotide for the alanine-rich region is about the same as that for the successive proline-rich region. The small stability changes of local mRNA secondary structures along the mRNA chain suggest that the translational pauses observed for dragline silk fibroin synthesis may not be correlated with Spidroin 2 mRNA structure, in contrast to Spidroin 1 mRNA structure which may explain the translational pauses (4).

Animals↗
PubMed1997

Translational pauses during the synthesis of proteins and mRNA structure.

Translational pauses are observed during a spider fibroin synthesis (1,2). The spider major ampullate (dragline) silk of the spider Nephila clavipes is composed of multiple proteins. The amino acid sequences of the partial cDNA clones for the two major dragline silk fibroin components (Spidroin 1 and 2) exhibit repetitive motifs (3,4). Our detailed inspection of the nucleotide sequences of the repetitive motifs revealed highly selective site-specific codon usage patterns within a motif, suggesting that the secondary structure of the spider fibroin mRNA is optimized by the nucleotide sequence of the fibroin gene. The results, combined with our preceding results on silk fibroin from Bombyx mori (5) suggest that translational pauses of spider silk are interpreted in terms of the mRNA secondary structure.

Amino Acid Sequence↗
PubMed1995

Discontinuous translation and mRNA secondary structure.

It has recently been reported that ribosomes pause at specific sites during translation of the chloroplast photosystem II reaction center protein D1(1). We have obtained the stability map of local secondary structure of the mRNA of psbA gene, encoding for D1, by plotting the free energy of the optimal secondary structure of the local segment of the mRNA against the segment position along a base sequence of the mRNA. It was found that the positions of minima or lower free energy in the map coincide with the positions of the pausing sites during synthesis of D1. The result suggests that synthesis pauses of D1 could-be induced by the mRNA secondary structure.

Hordeum↗
PubMed1992

New case of Bartsocas-Papas syndrome surviving at 20 months.

We report on patient with Bartsocas-Papas syndrome surviving at age 20 months. Similar to 7 previously reported families, this patient is of Mediterranean ancestry, pointing to clustering of the responsible mutant gene in Southern Europe. In 3 of the 11 Bartsocas-Papas syndrome patients described so far, including the present case, the condition has not been neonatally lethal. This suggests that about one-fourth of these patients could survive. This information is important for genetic counseling.

Abnormalities, Multiple↗
PubMed1991

Arginine residues involved in strong histone--DNA interactions to fold DNA into the nucleosome core particle.

The numbers of the arginine residues involved in strong histone-DNA interactions to fold DNA into a nucleosome core particle were determined for each of the four core histones, by kinetic studies of chemical modification of the residues in the nucleosome core particle. It was suggested that the arginines in the globular region of H3 histone make major contributions to the strong binding of the octameric histones to the core DNA.

Animals↗
PubMed1990

Codon usage pattern in alpha 2(I) chain domain of chicken type I collagen and its implications for the secondary structure of the mRNA and the synthesis pauses of the collagen.

A stability map of local secondary structure of the mRNA of the triple-helical alpha 2(I) chain domain of chicken type I collagen was obtained by plotting the free energy of the optimal secondary structure of a local segment in mRNA against the segment position along a base sequence of the mRNA. It was found that the positions of the minima of free energy in the plot coincide with the positions where synthesis pauses of the alpha-chain polypeptides of the corresponding sizes translated from the mRNA have been reported to occur (1). The codon usage pattern of each of the three major amino acids of the alpha-chain domain of the collagen, Gly, Pro and Ala, fluctuates considerably along the base sequence segments of the mRNA and a deviation of the pattern from that of the average of the whole alpha 2(I) chain domain mRNA, particularly for Gly codons, leads to a loss of the stability of the local secondary structure of the mRNA. The results suggest that selection has operated on the codon usage to optimize the secondary structure characteristic of the mRNA of the chicken collagen alpha 2(I) chain domain which leads to a nonuniform polypeptide elongation pattern.

Animals↗
PubMed1990

Codon usage and secondary structure of mRNA.

The specific codon usage pattern of the repetitive unit nucleotide sequence of silk fibroin mRNA suggests that selection has operated on the codon usage to optimize the secondary structure characteristic of the mRNA. The correlation between the stability map of local secondary structure of type I collagen mRNA and the codon usage pattern and the translation rate of the collagen is also implied.

Animals↗
PubMed1988

Specific codon usage pattern and its implications on the secondary structure of silk fibroin mRNA.

We have identified two distinctive regions of the repetitive unit nucleotide sequence of fibroin mRNA of Bombyx mori. The codon usage for the major amino acids, glycine, alanine and serine is distinctly different in these two regions, indicating that it is determined by the fibroin mRNA or gene structure but not by the tRNA population. Comparative computer analyses of nucleotide substitutions in the unit sequence suggest that selection has operated on the codon usage to optimize the secondary structure characteristic of the fibroin mRNA.

Amino Acid Sequence↗
PubMed1988

Interparticle interactions and structural changes of nucleosome core particles in low-salt solution.

The structural behavior of the nucleosome core particles in the range of solvent Na+ concentration from 10.45 to 0.45 mM has been studied by small-angle neutron and synchroton radiation X-ray scattering, sedimentation, atomic absorption spectroscopy, density measurements, and circular dichroism. With decreasing salt concentration, the appearance of a scattering peak that is assignable to interparticle interactions, an intraparticle structural transition, a decrease in the sedimentation velocity of the particle, and a release of bound Na+ ions from the particle are all observed concurrently when the ratio of solvent Na+ ions per particle is below approximately 1000. These observations are interpreted to indicate that a release of bound Na+ ions from the particle brings about structural rearrangements and weakens the electrostatic shielding of the particle, and this introduces long-range repulsive ordering of the particle in low-salt solution. Analyses of the scattering data indicate that the rearrangement within the core particle in low-salt solution is slight, changing the particle's shape slightly from cylindrical to a more spherical form by moving the center of the mass of the DNA somewhat inward with accompanying small decreases in the radii of gyration of both the DNA and the histones.

Animals↗
PubMed1985

Distinction and similarity in the structure of histones H1 and H5 as indicated by 13C nuclear-magnetic-resonance spectroscopy.

The 13C nuclear magnetic resonance studies have been carried out on histones H1 and H5, by focusing our interest on possible formation of specific salt bridges between acidic and basic amino acid residues in the proteins and also on the structural difference between the two proteins. The 13C chemical shift and pKa values of the carboxyl group of glutamic acid residues in the histones coincided with those of free glutamic acid. Based on this result and another experiment using completely modified lysine residues in the histones, no evidence for a specific interaction between acidic and basic residues has been found. It has also been shown that the pH-effects of aliphatic and aromatic resonances are quite different between H1 and H5, suggesting that the globular domain of H5 is more stable than that of H1. The correlation time (1.5 ns) for the alpha-carbons of H5 estimated from 13C nuclear Overhauser enhancement was twice as long as that of H1 (0.9 ns), indicating that the backbone in the N-terminal and C-terminal domains of H5 is less mobile than that of H1.

Arginine↗
PubMed1985

Involvement of the histidine residues in the pH-induced conformational change of histone H5.

Comparative studies on the conformational stability of histones H1 and H5 have been carried out by monitoring the pH-induced conformational transitions of the proteins by CD and 1H NMR spectroscopies. The transition point of H1 agrees with the pKa of the carboxyl groups of the acidic residues. In contrast, the transition of H5 is associated with the ionization of the histidine residues which exist exclusively in H5, as well as the deionization of the acidic residues. These observations, combined with the result of the deuterium exchange rates of the histidine C-2 protons, led us to conclude that His-25 and His-62, which are buried in the globular domain, play an important role in the conformational stability of histone H5.

Animals↗
PubMed1984

Conformation of the HMG17-nucleosome complex.

The nucleosome core binds more than two molecules of HMG17 at low ionic strength (8.9 mM Tris-HCl/8.9 mM boric acid/0.25 mM Na2EDTA, pH 8.3). Circular dichroism of the complexes showed only minor conformational changes of the nucleosome core DNA on binding of HMG17, with no detectable change in the histone secondary structure. The fluorescence of N-(3-pyrene) maleimide bound to -SH groups at Cys-110 of H3 histones in the core particle suggested that the structure of the histone octamer assembly changed little upon binding of HMG17 to the nucleosome. These observations support the idea that even a high level of HMG17 binding, e.g., four HMGs per nucleosome, alone, does not open up the core particle.

Animals↗
PubMed1983

Isolation of deuterated histones from yeast grown on media dissolved in 2H2O.

We have succeeded in growing Saccharomyces cerevisiae (baker's yeast) on media containing 2H2O and isolating the core histones highly deuterated in the non-exchangeable positions. The deuterated histones obtained here are of great value for their possible widespread use for structural studies of chromatin.

Deuterium↗
PubMed1982

Essential role of arginine residues in the folding of deoxyribonucleic acid into nucleosome cores.

The kinetic studies of chemical modifications of the lysine and arginine residues of the nucleosome core particle from chicken erythrocytes with large molar excesses of 2,4,6-trinitrobenzenesulfonic acid and 2,3-butanedione, respectively, were performed over 20 mM-2.0 M NaCl. Each modification reaction was divided into the two, a rapid and an extremely slow, pseudo-first-order processes, and the numbers of the exposed and buried residues of the respective amino acids were determined. At very low ionic strength (20 mM boric buffer) all residues were inaccessible to the reagents. Between 0.3 and 0.6 M NaCl the basic amino acid residues in a nucleosome core particle were classified into the following three groups: (1) 42 arginine and 78 lysine residues in the N-terminal and C-terminal regions of the histones that are exposed to solvent, (2) a small number of arginine residues (approximately less than 14 Arg) that are strongly bound to the DNA phosphates, and (3) 48 arginine and 38 lysine residues buried in the globular region of the histone octamer. The results suggest that a small number of arginine residues play an essential role in the folding of DNA into a nucleosome core particle.

Animals↗