Biologic significance of the structure of hydrocarbons. I. Chain structure

1. The biologic experiments with the links of the methane series—n-pentane, n-hexane, n-heptane, n-octane, i-octane, and pentene—gave these qualitative results: (a) The higher the number of CH₂ groups, the longer the chain, the longer the average lifetime of the animal. (b) The ramified chain does not appear to act differently from the saturated straight chain with the same number of C atoms. (c) One double bond within the chain shortens the lifetime to a considerable degree. 2. The quantitative discussion shows that the lifetimes depend exponentially on the molecular weight. 3. Qualitatively the hypothesis is supported that with rising molecular weight the concentration of CH₂ groups within the animal diminishes according to the vapor pressure or the thermodynamic potential. However, lifetime and these physical properties obey different functions. 4. These physical properties are of high biologic importance. But they are not sufficient to explain the biologic effects quantitatively.     

Fine structure of the secretory and non-secretory ameloblasts in the frog. II. Fine structure of the non-secretory ameloblast.

The non-secretory ameloblasts present at the enamel-free surfaces of maxillary teeth in the frog Rana pipiens were examined by electron microscopy at different stages of tooth development. Their main fine structural features seem to reflect a transport function. During early tooth development, the non-secretory ameloblasts adjacent to odontoblasts and predentin exhibit extensive lateral surface specializations and numerous cytoplasmic vesicles. During late tooth development, the non-secretory ameloblasts adjacent to mineralizing dentin show numerous cellular junctions, well-developed intercellular channels with numerous interdigitating processes and labyrinthine configurations at their distal surfaces. An intact basal lamina is present between the non-secretory ameloblasts and the dentin surface until the dentin becomes fully mineralized. At this stage the adjacent cells no longer exhibit surface specializations. It is suggested that the non-secretory ameloblasts may participate in the mineralization of adjacent dentin at the enamel-free surfaces. This surface dentin becomes fully mineralized at a later stage of development than the underlying dentin.     

Fine structure of the secretory and nonsecretory ameloblasts in the frog. I. Fine structure of the secretory ameloblasts.

Amelogenesis in the tooth germs of the frog Rana pipiens was examined by electron microscopy at different stages of tooth development. Cellular changes in secretory ameloblasts during this process showed many basic similarities to those in mammalian amelogenesis. Amelogenesis can be divided into three stages based on histological criteria such as thickness of enamel and the relative position of the tooth germ within the continuous succession of teeth. These stages are early, transitional and late. The fine structure of the enamel-secreting cells reflects the functional role of these ameloblasts as primarily secretory in the early stage, possibly transporting in the late stage and reorganizing between the two functions in the transitional stage. In early amelogenesis the cell exhibits well-developed granular endoplasmic reticulum, Golgi complex, microtubules, dense granules, smooth and coated vesicles, lysosome-like bodies in supranuclear and distal portions of the cell and mitochondria initially concentrated in the basal part of the cell. Numerous autophagic vacuoles are observed concomitant with the loss of some cell organelles at the transitional stage. During late amelogenesis the ameloblasts exhibit numerous vesicles, granules, convoluted cell membranes, junctional complexes and widely distributed mitochondria. Toward the end of amelogenesis, cells become oriented parallel to the enamel surface and the number of organelles is reduced. Amelogenesis in the frog is an extracellular process and mineralization seems to occur simultaneously with matrix formation.     

Three-dimensional structure of acylphosphatase. Refinement and structure analysis.

We report here the complete determination of the solution structure of acylphosphatase, a small enzyme that catalyses the hydrolysis of organic acylphosphates, as determined by distance geometry methods based on nuclear magnetic resonance information. A non-standard strategy for the distance geometry calculations was used and is described here some detail. The five best structures were then refined by restrained energy minimization and molecular dynamics in order to explore the conformational space consistent with the experimental data. We address the question of whether the solution structure of acylphosphatase follows the general principles of protein structure, i.e. those learned from analysing crystal structures. Static and dynamic features are discussed in detail. An uncommon beta-alpha-beta motif, so far found only in procarboxypeptidase B and in an RNA-binding protein, is present in acylphosphatase.     

Refinement of the structure of beta-chitin.

The structure of β-chitin has been refined by rigid-body least-squares methods, based on the intensity data for highly crystalline specimens from the pogonophore Oligobrachia ivanovi. The structure consists of an array of poly-N-acetyl-D -glucosamine chains all having the same sense, which are linked together in sheets by N? H … O?C hydrogen bonding of the amide groups. In addition to the O-3′? H … O-5 intramolecular hydrogen bond, analogous to that in cellulose, the CH₂OH side chain forms an intrasheet hydrogen bond to the carbonyl oxygen on the next chain. This structure shows considerably better agreement between observed and calculated intensities than that possessing an intersheet hydrogen bond, as had been proposed previously. The structure is consistent with the swelling properties of β-chitin and can also be seen to be analogous to that of native cellulose.     

Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structure

We report on a computer experiment in which, using Monte Carlo techniques, we considered a three-turn (30-base-pairs) B-DNA fragment as a solute and a set of 1200 water molecules and 60 sodium counterions (at a temperature of 300 K) as a solvent. From a statistical analysis of the Monte Carlo simulation (applied to the water molecules and counterions in the B-DNA field), we determined that the counterions themselves conform to two helical structures intertwined with the two strands. The strutures of the water molecules solvating both counterion helices and the two B-DNA strands are fully analyzed and described in detail. A model for base-pair recognition based on the above findings is proposed. Aspects of the unwinding mechanism are discussed.     

Solution structure of the luzopeptin-DNA complex.

The luzopeptin-d(C-A-T-G) complex (1 drug/duplex) has been generated in aqueous solution and its structure characterized by a combined application of two-dimensional NMR experiments and molecular dynamics calculations. One equivalent of luzopeptin binds to the self-complementary tetranucleotide duplex with the 2-fold symmetry of the antitumor agent and the DNA oligomer retained on complex formation. We have assigned the exchangeable and nonexchangeable proton resonances of luzopeptin and the d(C-A-T-G) duplex in the complex and identified the intermolecular proton-proton NOEs that define the alignment of the antitumor agent at its binding site in duplex DNA. The analysis was greatly aided by a large number of intermolecular NOEs involving exchangeable protons on both the luzopeptin and the DNA in the complex. The molecular dynamics calculations were guided by 140 intramolecular nucleic acid distance constraints, 74 intramolecular luzopeptin distance constraints, and 96 intermolecular distance constraints between luzopeptin and the nucleic acid protons in the complex. The quinoline rings of luzopeptin bisintercalate at d(C-A).d(T-G) steps in the d(C-A-T-G) duplex and sandwich two Watson-Crick A.T base pairs between the bisintercalation site. The long axis of the quinoline rings are collinear with the long axis of the flanking Watson-Crick C1.G4 and A2.T3 base pairs such that the OCH3-6 group is directed toward the C1-A2 step and the OH-3 group is directed toward the T3-G4 step in the complex. The quinoline chromophore stacks with purines on both strands, with the quinoline A ring stacked on A2 and the quinoline B ring stacked on G4 in the complex. The C1.G4 and A2.T3 base pairs that flank the intercalation sites are parallel to each other with partial overlap of T3 and G4 in the T3-G4 step but no overlap of C1 and A2 in the C1-A2 step in the complex. The cyclic depsipeptide ring of luzopeptin is positioned in the minor groove of the d(C-A-T-G) duplex with the oligopeptide and oligonucleotide chains running antiparallel to each other. The cyclic depsipeptide backbone of luzopeptin exhibits cis peptide bonds at Pyr-Gly and Gly-Sar steps in the luzopeptin-d(C-A-T-G) complex in solution, in contrast to all trans peptide bonds for free luzopeptin in the crystalline state.(ABSTRACT TRUNCATED AT 400 WORDS)     

Concerning the structure of photobilirubin II.

Evidence is presented which supports the postulate that the photobilirubins IIA and IIB are diastereoisomers in which the C-3 vinyl group has cyclized intramolecularly. The evidence comes principally from proton n.m.r. spectroscopy at 400 MHz and from chemical considerations. The cyclic structures require the E-configuration at the C-4 double bond in the precursor; this is the first structural evidence for the Z leads to E isomerization in bilirubin and supports the view that the precursor (photobilirubin IA or IB) is (4E, 15Z)-bilirubin. Brief irradiation of photobilirubin II gives bilirubin, a new compound (photobilirubin III) and unchanged starting material. The various photoisomers are discussed in terms of their inter-relationships and biological fates.     

Subunit structure of the reovirus spike.

Cross-linking reovirus spike protein with the bifunctional reagent dimethyl suberimidate revealed that each spike was composed of a pentameric aggregate of polypeptide lambda 2.     

On the structure of syntenic distance.

This paper examines some of the rich structure of the syntenic distance model of evolutionary distance, introduced by Ferretti et al. (1996). The syntenic distance between two genomes is the minimum number of fissions, fusions, and translocations required to transform one into the other, ignoring gene order within chromosomes. We prove that the previously unanalyzed algorithm given by Ferretti et al. (1996) is a 2-approximation and no better, and that, further, it always outperforms the algorithm presented by DasGupta et al. (1998). We also prove the same results for an improved version of the Ferretti et al. algorithm. We then prove a number of properties which give insight into the structure of optimal move sequences. We give instances in which any move sequence working solely within connected components is nearly twice optimal and prove a general lower bound based on the spread of genes from each chromosome. We then prove a monotonicity property for the syntenic distance, and bound the difficulty of the hardest instance of any size. We discuss the results of implementing these algorithms and testing them on real and simulated synteny data.     

Three-dimensional structure of the yeast ribosome.

The 80S ribosome from Saccharomyces cerevisiae has been reconstructed from cryo electron micrographs to a resolution of 35 A. It is strikingly similar to the 70S ribosome from Escherichia coli, while displaying the characteristic eukaryotic features familiar from reconstructions of ribosomes from higher eukaryotes. Aside from the elaboration of a number of peripherally located features on the two subunits and greater overall size, the largest difference between the yeast and E.coli ribosomes is in a mass increase on one side of the large (60S) subunit. It thus appears more elliptical than the characteristically globular 50S subunit from E.coli. The interior of the 60S subunit reveals a variable diameter tunnel spanning the subunit between the interface canyon and a site on the lower back of the subunit, presumably the exit site through which the nascent polypeptide chain emerges from the ribosome.     

Observations on the structure of bacilysin.

1. Elementary analysis and other properties of a highly purified preparation of bacilysin indicated that a possible molecular formula for the substance is C(12)H(18)N(2)O(5). The results of electrometric titration were consistent with the hypothesis that the substance was a peptide containing one free alpha-amino group and one free carboxyl group. 2. Hydrolysis of bacilysin with 6n-hydrochloric acid at 105 degrees yielded l-alanine and l-tyrosine, but the ultraviolet spectrum of the substance showed that no tyrosine residue was present in the molecule and a nuclear-magnetic-resonance spectrum indicated that olefinic and aromatic protons were absent. The dinitrophenyl (DNP) derivative of bacilysin yielded DNP-alanine on acid hydrolysis. 3. Bacilysin was hydrolysed by leucine aminopeptidase (EC 3.4.1.1) and by Pronase to give alanine and an uncharacterized amino acid. Its infrared spectrum was consistent with the presence of a peptide grouping in the molecule. 4. The optical rotatory dispersion of bacilysin and its reaction with thiosemicarbazide indicated that the substance contained an aldehyde or ketone group. Its behaviour on catalytic reduction and its reaction with sodium thiosulphate and with certain thiols suggested that an epoxide group was present. 5. A possible type of structure for bacilysin is considered in the light of its known properties.