Fine structure of DNA melting curves.

Theoretical calculations predict that the differential melting curves for random polynucleotide sequences having lengths up to several tens of thousands of base pairs have a clear-cut fine structure. This structure appears in the form of multiple narrow peaks 0.3–0.4°C wide on the bell shaped main curve. The differential melting curves have different shapes for different specific sequences. The theory also predicts the disappearance of the fine structure when the length of the sequence increases and when circular, covalently closed DNA is considered instead of the open structure. The predictions of the theory were confirmed by the measurements of differential melting curves for open and covalently closed circular forms of DNA for PM2 phage (N = 10⁴ base pairs) and also for other phage DNA's of different length: T7 (N = 3.8 × 10⁴); S_D (N = 9.2 × 10⁴); T2 (N = 17 × 10⁴). It was shown that the effect of fine structure results mainly from the cooperative melting out of DNA regions 300–500 base pairs long.     

The structure of neuromelanin as studied by chemical degradative methods

The biosynthesis, structure and function of neuromelanin (NM), the dark brown melanin-like pigment present in the substantia nigra (SN), are not well characterized, in spite of the possible involvement of NM in the etiology and pathogenesis of Parkinson's disease. NM was isolated from the SN of five non-Parkinsonian human brains. NM and synthetic melanins, employed as models, were characterized by chemical analysis. Alkaline hydrogen peroxide (H2O2) oxidation of NM generated four degradation products, pyrrole-2,3-dicarboxylic acid (PDCA), pyrrole-2,3,5-tricarboxylic acid (PTCA), thiazole-4,5-dicarboxylic acid (TDCA) and thiazole-2,3,5-tricarboxylic acid (TTCA), whose ratios, especially the TTCA to PDCA ratio, indicate that NM is derived mostly from dopamine (DA) with 25% incorporation of cysteine (Cys) in the form of a benzothiazine structure. Hydriodic acid (HI) reductive hydrolysis of NM yielded 4-amino-3-hydroxyphenylethylamine (4-AHPEA) as a marker of cysteinyldopamine (CysDA)-derived units. The 4-AHPEA to PDCA ratio indicates a 21% incorporation of CysDA-derived units into NM. These degradative experiments also suggest that DOPA is not incorporated into NM to a significant extent (approximately 6% the level of DA). It is concluded that the TTCA to PDCA ratio is a useful indicator of CysDA-derived units in NM, and NM consists mainly of DA-melanin with some contribution from CysDA-melanin. The involvement of DA and CysDA as building blocks of NM demonstrates the detoxifying role of NM synthesis, since it prevents the intraneuronal accumulation of DA and CysDA, which would cause toxic effects.     

Properties of cupric ions in benzylamine oxidase from pig plasma as studied by magnetic-resonance and kinetic methods.

Benzylamine oxidase from pig plasma has been studied by a variety of chemical and physical techniques. 1. Analytical ultracentrifugation, gel electrophoresis and isoelectric-focusing studies suggest that the enzyme is composed of two subunits with closely similar primary structures. 2. E.s.r. and n.m.r. measurements show that the enzyme contains two well-separated (greater than 0.6 nm) Cu2+ ions at chemically distinct sites. Each Cu2+ ion is coordinated by two water molecules, one 'axial' and the other 'equatorial'. Both water molecules undergo fast exchange (10(5)--10(8) s-1) with solvent and are deprotonated in the pH range 8--9, but only the equatorial water molecule is displaced by the inhibitors N3- and CN-. 3. Kinetic and e.s.r. measurements show that azide and cyanide compete against O2 binding and also make the two Cu2+ sites identical. It is concluded that Cu2+ must participate in the re-oxidation of reduced enzyme by molecular O2.     

Interaction of ethidium bromide with DNA as studied by kinetic spectrophotometry.

The interaction of ethidium bromide (EB) with DNA has been investigated using the pulse radiolysis technique. In particular, the absolute rate constant for the reaction of hydrated electrons, generated by single pulses of high-energy electrons, with EB is shown to drop dramatically in the presence of DNA. This drop in diffusion-limited reactivity results from the interaction of EB with DNA, effectively immobilising it, thus lowering the reaction cross-section or probability. Analysis of the resulting kinetic spectrophotometric data shows that they are consistent with a reversible interaction of EB with DNA as described by the law of mass action. The Scatchard-type plots obtained are linear, and give quantitative information on the extent and degree of association, comparable with that obtained by more conventional methods. The potential of the pulse radiolysis technique for studying different types of interactions between small molecules and various biopolymers has been demonstrated.     

Histological structure of human nail as studied by synchrotron X-ray microdiffraction.

Three layers (characterized by different orientations of the keratin molecules) from the outer to the inner side of human nail were observed by synchrotron X-ray microdiffraction. These layers are associated with the histological dorsal, intermediate and ventral plates. The hair-like type alpha-keratin filaments (81 A in diameter), are only present in the intermediate layer (accounting for approximately 2/3 of the nail width) and are perfectly oriented perpendicular to the growth axis, in the nail plane. Keratin filaments of stratum corneum (epidermis) type, found in the dorsal and ventral cells, are oriented in two privileged directions; parallel and perpendicular to the growth axis. This "sandwich" structure in the corneocytes and the strong intercellular junctions, gives the nail high mechanical rigidity and hardness, both in the curvature direction and in the growth direction. Lipid bilayers (49 A thick) parallel to the nail surface fill certain ampullar dilations of the dorsal plate and intercellular spaces in the ventral plate. Using X-ray micro-diffraction, we show that onychomycosis disrupts the keratin structure, probably during the synthesis phase.     

The structure of sitting-atop complexes of metalloporphyrins studied by theoretical methods

The metallation of tetrapyrroles is believed to proceed via a sitting-atop (SAT) complex, in which some of the pyrrole nitrogen atoms are still protonated and the metal ion resides above the ring plane. No crystal structure of such a complex has been presented, but NMR and extended X-ray absorption fine structure (EXAFS) data has been reported for Cu(2+) in acetonitrile. We have used density functional calculations to obtain reasonable models for SAT complexes of porphyrins with Mg(2+), Fe(2+), and Cu(2+). The results show that there are many possible SAT complexes with 1-5 solvent molecules, one or two metal ions, and cis or trans protonation of the porphyrin ring. Many of these have similar energies and their relative stabilities vary with the metal ion. A complex with two cis pyrrolenine nitrogens atoms and 2-4 solvent molecules coordinated to Cu(2+) fits the NMR and EXAFS data best. However, we cannot fully exclude the possibility that what is observed is rather a mixture of a doubly protonated porphyrin and the copper porphyrin. Mg(2+) has a lower affinity for porphyrin and stronger affinity for water, so a complex with five water molecules and only one bond to porphyrin seems to be most stable. For Fe(2+), a cis structure with two first-sphere water molecules and four interactions to the porphyrin seems to be most likely.     

Structure and structure formation of viroids

The structure of viroids and the mechanism of structure formation were investigated by different methods. Results from gel analysis, partial degradation pattern, electron microscopy, dye binding, hydrodynamic studies, and temperature-jump kinetics were interpreted in a common structural and mechanistic scheme. Gel analysis, electron microscopy and kinetic investigations show that viroids may assume the native as well as metastable conformations under the same conditions. The native conformation is obtained by complete renaturation, i.e. slow cooling throughout the transition range (e.g. 52 to 48 ° C for potato spindle tuber viroid (PST viroid) in 0.01 m-sodium cacodylate, pH 6.8). In contrast, metastable conformations were trapped if viroids were redissolved in the cold from their ethanol precipitate or if they were denatured and cooled quickly.The native secondary structure of the recently sequenced PST viroid (Gross et al., 1978) was optimized for the free energy of base-pairing. The scheme agrees with that proposed by Gross et al. (1978), which was derived from chemical arguments. The extended structure does not undergo tertiary structure folding under a wide range of conditions, as was concluded from electron microscopy, sedimentation measurements and binding studies of ethidium bromide and a new dye specific for A · U pairs (2-(4′-aminophenyl)-5-(4′-methylpiperazin-1″yl)-benzirnidazol).Intermediate structures during viroid denaturation were analysed on theoretical and experimental grounds. The experimental data, in combination with the model calculations, show that all of the native base-pairs of viroids are dissociated in one highly co-operative main transition, and that during the same process very stable hairpins are formed that are not present in the native structure. The formation of stable hairpins induces a new type of long range cooperativity, which is responsible in part for the high co-operativity observed experimentally. This interpretation is in good agreement with kinetic results presented elsewhere (Henco et al., 1979).In order to understand the uniqueness of viroids, the structure and the conformational transitions of circular RNA molecules of the same base composition as PST viroids but with 359 nucleotides arranged randomly, were studied theoretically. Common viroid features, such as the number of base-pairs, the high co-operativity and the formation of very stable hairpins, are found to be improbable in such random sequences. It is concluded that various viroid species, although differing in nucleotide sequence, follow common principles of structure and structure formation.     

Interfacial structure and lipase action. Characterization of taurodeoxycholate-didecanoylglycerol monolayers by physical and kinetic methods.

Surface pressure-area isotherms for 1,3-didecanoyl-glycerol (dicaprin) were determined as a function of the concentration of taurodeoxycholate in the subphase. Analysis of these curves indicates that, from 0.05 to 0.80 mM bile salt, surface structure is dependent only on the surface concentration of the diglyceride. The limiting areas for dicaprin in the presence and absence of bile salt were about 38 A2/molecule. Subjecting the monolayers to hydrolysis by pancreatic lipase yielded kinetic data which, together with the physical studies, support a model for monolayer glyceride molecules undergoing discrete changes of state. In the absence of bile salt, the relatively expanded state exhibits an area of 75 A2/diglyceride molecule and is not a substrate for pancreatic lipase B. The more condensed state exhibits an area of 38 A2/diglyceride molecule and is hydrolyzed at a rate proportional to its concentration in the monolayer. Taurodeoxybholate at 0.05 to 0.60 mM shifts the apparent area of the expanded state to 360 A2/diglyceride molecule.     

Conformation of viroids.

Viroids are uncoated infectious RNA molecules (MW 107 000-127 000) known as pathogens of certain higher plants. Thermodynamic and kinetic studies were carried out on highly purified viroid preparations by applying UV-absorption melting analysis and temperature jump methods. The thermal denaturation of viroids is characterized by high thermal stability, high cooperativity and a high degree of base pairing. Two relaxation processes could be resolved; a process in the sec range could be evaluated as an independent all-or-none-transition with the following properties: reaction enthalpy= 550 kcal/mol, activation enthalpy of the dissociation = 470 kcal/mol; G : C content = 72 %. These data indicate the existence of an uninterrupted double helix of 52 base pairs. A process in the msec range involves 15 - 25 base pairs which are most probably distributed over several short double helical stretches. A tentative model for the secondary structure of viroids isproposed and the possible functional implications of their physicochemical properties are discussed.     

Two-state vs. multistate protein unfolding studied by optical melting and hydrogen exchange

A direct conflict between the stabilization free energy parameters of cytochrome c determined by optical methods and by hydrogen exchange (HX) is quantitatively explained when the partially folded intermediates seen by HX are taken into account. The results support the previous HX measurements of intermediate populations, show how intermediates can elude the standard melting analysis, and illustrate how they confuse the analysis when they are significantly populated within the melting transition region.     

Changes in size and shape of liposomes undergoing chain melting transitions as studied by optical microscopy

Changes in the shape and size of dipalmitoylphosphatidylcholine liposomes at the phase transition at 41.5°C have been monitored by light microscopy. All liposomes change size or shape at the transition and those with simple topologies such as spheres and cylinders can be readily measured. The surface area of these is some 24% greater above the transition than below. This surface area change is virtually identical to that predicted by crystallographic measurements on this system. Also, the rate of transition from one state to another is seen to proceed more rapidly in the smaller liposomes. Optical microscopic observation provides a rapid simple method for monitoring the dependence of the lipid bilayer area on temperature.     

Solution and membrane structure of enkephalins as studied by infrared spectroscopy

The backbone conformation of the two opioid pentapeptides Leu5-enkephalin and Met5-enkephalin was studied by the technique of resolution-enhanced infrared spectroscopy. In aqueous solution, the conformation-sensitive amide I bands of the two peptides are identical. The positions of these bands are consistent with the view that in aqueous solution both enkephalins exist as an ensemble of largely unfolded conformers. Interaction of Leu5- and Met5-enkephalins with bilayer membranes of ditetradecylphosphatidylcholine results in a substantial refolding of the peptide backbones. The conformation stabilized by the membrane environment is a hydrogen-bonded turn structure. Conformational transitions in enkephalins induced by a lipid environment may play a role in the specific interactions between these hormones and their receptor sites.     

Internal structure of ovomacroglobulin studied by electron microscopy.

As a model for the molecular structure of proteins belonging to the alpha 2-macroglobulin family, ovomacroglobulin of reptilian origin was studied by electron microscopy in the original tetrameric form as well as in the dissociated forms into half- and quarter molecules. The following aspects of the molecular internal structure which had previously not been known for the homologous human alpha 2-macroglobulin or chicken ovomacroglobulin were revealed. First, the negatively stained tetrameric native protein gave an appearance of a collection of four semi-circular strings placed on the four corners of a molecule. They were connected to each other in the center of a molecule through a set of globular domains which formed a cross-figured subunit contact region. Second, two kinds of active half-molecules prepared either by the reduction of intersubunit disulfide bonds or by the disruption of noncovalent subunit interface had similarly elongated forms having semi-circular units on the two ends, indicating quasi-equivalent subunit arrangement in the two kinds of half-molecules. We thus concluded that the structure of native ovomacroglobulin can be represented by four circular strings each equipped with an extra domain to form the central intersubunit contact region. The results may also be adapted to the internal structure of human alpha 2-macroglobulin because it was sometimes possible to observe similar ring-like internal structure in the human protein.     

Conformational structure of bombesin as studied by vibrational and circular dichroism spectroscopy

Raman and Fourier transform infrared (FTIR) spectroscopies and circular dichroism (CD) have been applied to investigate the secondary structure of bombesin in the solid state and in phosphate buffer solution (pH 3.8). At concentrations around 10⁻⁵ M, circular dichroism reveals that bombesin exists as an irregular or disordered conformation. However, the secondary structure of the peptide appears to be a mixture of disordered structure and intermolecular β-sheets in 0.01 M sodium phosphate buffer when the peptide concentrations are higher than around 6.5 mM. The tendency of bombesin to form aggregated β-sheet species seems to be originated mainly in the sequence of the residues 7–14, as supported by the Raman spectra and β-sheet propensities (P_β) of the amino-acid residues. It is the hydrophobic force of this amino-acid sequence, and not a salt bridge effect, that is the factor responsible for the formation of peptide aggregates.     

Interdigitated structure of phospholipid-alcohol systems studied by x-ray diffraction.

In the interdigitated structure of phosphatidylcholine/alcohol systems, the one-dimensional electron density profile in the direction normal to the membrane surface is generated from the x-ray diffraction pattern. The membrane thickness for these systems is expressed by the sum of the hydrocarbon chain lengths of phosphatidylcholine and alcohol molecules. For this study, various sets of phosphatidylcholines and 1-alcohols were used; a phosphatidylcholine has a carbon number from 14 to 18 in a hydrocarbon chain, and an alcohol has a carbon number from 1 (methanol) to 4 (1-butanol). Based upon the results, we propose a model for the interdigitated structure in which 1) two alcohol molecules occupy a volume whose surface is surrounded interstitially by the headgroups of phosphatidylcholine molecules, and 2) the methyl ends of both hydrocarbon chains in alcohol and phosphatidylcholine molecules face each other at the bottom of the volume.     

Relationship between medium pH and that of the lysosomal matrix as studied by two independent methods.

1. The method of estimating the intralysosomal pH by measuring the distribution of [14C]methylamine in lysosomes isolated from the livers of Triton WR 1339-treated rats has been critically examined. 2. In lysed lysosomes, methylamine is bound to the membrane fragments, but this binding can be completely suppressed by increasing the concentration of monovalent cations in the medium. 3. In intact lysosomes, the binding of [14C]methylamine is only partly inhibited by monovalent cations at 25 degrees C. 4. THe accumulation of [14C]methylamine in intact lysosomes is progressively inhibited as the concentration of methylamine is increased. A similar inhibition of [14C]methylamine accumulation is obtained with NH4Cl. 5. Similar values for the intralysosomal pH were obtained from measurements of the distribution of methylamine, dimethylamine and trimethylamine, which are accumulated in the lysosomes, and of 5,5-dimethyloxazolidinedione-2,4, which is excluded. 6. The breakdown of endocytosed 123I-labelled bovine serum albumin by intact isolated lysosomes is much less sensitive to the pH of the medium than the breakdown of added protein by lysed lysosomes. 7. The intralysosomal pH has been estimated by comparing the rate of breakdown of endocytosed 125I-labelled albumin in intact lysosomes as a function of medium pH with that of added 125I-labelled albumin by lysed lysosomes at different pH values. The values obtained agree well with those calculated from the distribution of [14C]methylamine. 8. Methylamine and NH4Cl inhibit the breakdown of 125I-labelled albumin in intact lysosomes, particularly at high medium pH, but have no effect on the breakdown by lysed lysosomes. 9. It is concluded that a pH difference across the lysosomal membrane (more acidic inside than outside) is maintained by the presence of indiffusible negatively charged groups within the lysosomes, and by the permeation across the lysosomal membrane of protons together with permeant anions (or of OH- in exchange for anions).