Determination of the degree of collagen coiling by electron paramagnetic resonance

It has been shown that kinetics of the death of free radicals UV-induced at 77 degrees K in collagen is determined by two reactions having different rates. Such shape of the kinetic curve is substantiated by the spatial structure of macromolecules and permits to find easily the portion of peptide chains in the helical form and the portion of end peptides not incorporated in this structure. The degree of helical pattern of collagen from rat skin was shown to be 92%.     

Structural implications of electric-field induced dichroism of nucleic acids: Studies of alternating purine-pyrimidines

Transient and steady-state electric dichroism measurements of double helical poly(dG-dC) and its 5-methyl guanosine analogue and transient electric dichroism measurements of double helical poly(dA-dT) are shown to give the following information on the structural and dynamical properties of these molecular systems: (i) the Z form structure of the alternating guanosine-cytidine moieties has the same inter base-pair separation in solution as it does in the fibre and crystalline forms; (ii) the mean normal to the base pairs (and thus their average tilt and twist) of the B and Z forms of the guanosine-cytidine moieties is very nearly the same despite the large difference in their secondary structure; (iii) the alternating adenosinethymidine nucleic acid is at least twice as flexible as random-sequence DNA.     

Thermodynamic parameters of the helix-coil transition in polypeptide chains. III. Random copolymers of L-leucine and L-glutamic acid.

Conformational transitions induced by pH changes in random copolymers of leucine and glutamic acid have been studied. Significant differences were observed in the potentiometric titration curves of copolymers with small (up to 4%) and large leucine contents. The helical stability of copolymers with small leucine content, determined from titration curves by the Zimm and Rice method, decreases slightly with an increase in the leucine content, whereas the helical stability of copolymers with large leucine content increases sharply with an increase of the leucine content. It is shown that copolymers with large leucine content aggregate in the region of transition into the helical state, but the increase of their helical state stability is not connected with intermolecular aggregation, as it was also observed for a nonaggregating fraction isolated from one of the copolymers by gel chromatography. A conclusion is made that the helix–coil equilibrium constant s for leucine does not itself exceed the s constant for uncharged polyglutamic acid. The stabilization of the helical state in copolymers with large leucine content is due to intramolecular aggregation of helices in these copolymers. The analysis of the leucine residue distribution between helical and nonhelical regions in globular proteins also gives no real arguments to ascribe special helix-forming properties to leucine.     

Local mobility of nucleic acids as determined from crystallographic data. II. Z-form DNA

Directions and magnitudes of the local mobility of the Z-DNA hexamer duplex CpGpCpGpCpG have been determined by crystallographic refinement of anisotropic displacement parameters using the observed X-ray diffraction data. The cytidine and guanosine residues demonstrate different modes of mobility, implying that a dinucleotide is the smallest repeating unit in terms of flexibility as well as structure. Directions of librational and translational mobility of the cytidine and guanosine residues of Z-DNA are similar to those observed for the same nucleotides in B-DNA. This suggests that the local mobility of DNA is primarily determined by the individual nucleotide type and by the constraints of Watson-Crick base-pairing, rather than by helical form. Differences in the magnitudes of mobility may be responsible for some of the different physical properties of B-DNA and Z-DNA. The B to Z transition is discussed in terms of the observed flexibilities of these two helical forms.     

Electric birefringence studies on polyglutamic acid.

The electric birefringence for the aqueous solution of poly-L -glutamic acid (PGA) in the helical form was studied. PGA samples were fractionated by gel column chromatography. PGA showed a positive electric birefringence. The permanent dipole moment of the PGA molecule was suggested to be largely suppressed. The measurements of the intrinsic Kerr constants for various molecular lengths showed that the electric anisotropy (polarizability) of PGA is proportional to the 1.5 power of the length. The electric birefrigence measurement was also carried out in the helix–coil transition region. The Kerr constant of PGA was largely reduced on going from the helical form to the coiled form.     

Gelation of gellan gum aqueous solutions studied by polarization modulation spectroscopy

Circular birefringence (CB, or optical rotation) and linear birefringence (LB) were measured for gellan gum aqueous solutions with and without salt to examine the gelling system in the helical structure as well as in the orientation. It was found that gelling samples with salt show nonzero LB values, whereas LB is zero for the samples without salt even in the gel state. This difference can be explained by the thermal deformation of the system containing anisotropic aggregations of helices formed with the shielding effect of the added salt on the intramolecular and intermolecular electrostatic repulsions. Considering that the presence of LB in the system affects the estimation of CB, we developed an original procedure of the CB measurement to eliminate the contribution of LB. It was shown that our methods for eliminating the contribution of LB can improve the CB measurement for the gellan gum gel. The temperature dependence of [alpha] for the samples with salt in the gel state is quite different from that for the samples without salt, suggesting that the aggregates of helices in the samples containing a high concentration of salt form a supramolecular structure that contributes to CB.     

Influence of vitamin E on phosphatidylethanolamine lipid polymorphism

The effect of vitamin E, in its major form alpha-tocopherol and its synthetic analog alpha-tocopheryl acetate, on phosphatidylethanolamine lipid polymorphism has been studied by mean of differential scanning calorimetry and 31P-nuclear magnetic resonance techniques. From the interaction of these tocopherols with dielaidoylphosphatidylethanolamine it is concluded that both molecules promote the formation of the hexagonal HII phase at temperatures lower than those of the pure phospholipid. When the tocopherols were incorporated in the saturated dimiristoylphosphatidylethanolamine, which has been shown not to undergo bilayer to hexagonal HII phase transition, up to 90 degrees C, they induce the phospholipid to partially organize in hexagonal HII phase. From our experiments it is shown that alpha-tocopherol is more effective than its analog in promoting HII phase in these systems. It is also shown that, while alpha-tocopheryl acetate does not significantly perturb the gel to liquid-crystalline phase transition of dimirystoylphosphatidylethanolamine, alpha-tocopherol does so and more than one peak appears in the calorimetric profile, indicating that lateral phase separations are taking place.     

Role of substituents on the properties of some polysaccharides

This paper concerns the influence of the chemical structure on the physical properties of some polysaccharides. Especially, we proposed to discuss the role of the substituents on these properties. In some cases, non-carbohydrate substituents play a minor role on rheological properties in the presence of a salt excess as shown on xanthan and succinoglycan. The rheology of aqueous solution of these stereoregular polysaccharides is controlled by the conformation (helical conformation) whose stability is not largely influenced by these substituents. On the other hand, the interaction between galactomannan and xanthan depends on the presence of acetyl substituents on xanthan but also on the xanthan conformation. However, for polymers such as gellan, XM-6 or BEC 1615, complete deacetylation induces the ability to form physical gels in given thermodynamic conditions. The presence of carbohydrate substituents or short side chains was also examined. Especially in the gellan family, the role of position of substitution (position 3 on the glucose unit C or position 6 on the A glucose) was presented. It is concluded that the substituents giving the higher stability for the helical conformation (higher DeltaH and Tm values) also cause a lower salt sensitivity for the helical stability. The role of the substituents on the properties is also described for natural polymers and their chemically or enzymatically modified derivatives.     

Guanosine Deaminase and Guanine Deaminase from Tea Leaves

Guanosine deaminase and guanine deaminase were partially purified from tea leaves. The optimum activity of guanosine deaminase was observed at pH 7.5 and that of guanine deaminase was at pH 7.0–7.5 and 8.5. Guanosine deaminase was an unstable enzyme. The activities of these deaminases were significantly inhibited by heavy metals. Molecular weights of guanosine deaminase and guanine deaminase as measured by gel filtration were about 18,000 and 54,000, respectively. The K_m for the respective substrates, guanosine and guanine, were 9.5 μm and 41.7 μm. Guanosine deaminase was considered to catalyze the deamination of 2′-deoxyguanosine besides guanosine. It is suggested that guanosine deaminase as well as guanine deaminase in tea leaves not only acts on the catabolic pathway, but also is involved in the biosynthesis of caffeine from guanosine or guanine nucleotides.     

Polymorphism of sorbitol dehydrogenase and 6-phosphogluconate dehydrogenase in swine (Sus scrofa)

More than 300 kidneys from the local bacon factory were investigated and it was shown that the enzyme sorbitol dehydrogenase (EC 1.1.1.14) exhibits a genetically determined polymorphism. While homozygous individuals yield only a single enzyme band after starch gel electrophoresis, heterozygotes show multiple bands.
On the same material also 6-phosphogluconate dehydrogenase (EC 1.1.1.44) and lactate dehydrogenase were investigated, the former showed also clear genetic variants while the latter appeared only in one form.
Gene frequencies for different breeds and types of pigs are given and the results discussed.     

Ultrastructure of pig renal glutaminase. Evidence for conformational changes during polymer formation

Highly purified pig renal glutaminase has been examined by electron microscopy. It is demonstrated that the Tris·HCl form of the enzyme contains cylindrical particles with a diameter of about 60 Å and a length of about 82 Å. Treatment of the Tris·HCl form of the enzyme with sodium dodecyl sulphate and mercapto-ethanol, followed by polyacrylamide gel electrophoresis in sodium dodecyl sulphate, shows that the enzyme contains two types of sub units with molecular weights of 53,000 and 61,000. In agreement with earlier data, it is further demonstrated that the phosphate form is a simple dimer of the Tris·HCl form. Evidence that major conformational changes are involved in the formation of large, helical polymers of the enzyme described earlier, is also presented.     

Information transfer from peptide nucleic acids to RNA by template-directed syntheses.

Peptide nucleic acids (PNAs) are uncharged analogs of DNA and RNA in which the ribose-phosphate backbone is substituted by a backbone held together by amide bonds. PNAs are interesting as models of alternative genetic systems because they form potentially informational base paired helical structures. A PNA C10 oligomer has been shown to act as template for efficient formation of oligoguanylates from activated guanosine ribonucleotides. In a previous paper we used heterosequences of DNA as templates in sequence-dependent polymerization of PNA dimers. In this paper we show that information can be transferred from PNA to RNA. We describe the reactions of activated mononucleotides on heterosequences of PNA. Adenylic, cytidylic and guanylic acids were incorporated into the products opposite their complement on PNA, although less efficiently than on DNA templates.     

Synthesis of a new helical protein: the effect of secondary structure rearrangement on structure formation

A new helical protein was designed and synthesized to alter the sequential connectivity of the 4 helices in human growth hormone and to delete the long surface loop structures. The protein accumulated as an insoluble form in E. coli was solubilized and purified to apparent homogeneity in the presence of 7M urea, and refolded by the aid of 1% n-octyl-beta-D-glucopyranoside. The circular dichroism spectrum was typical of a highly helical protein. The molecular weight estimated by gel permeation chromatography and the red-shift of the fluorescence maximum by urea-induced denaturation suggest that the protein folds into a compact globular form. The new protein obtained, however, was destabilized relative to the original human growth hormone.     

Detection and characterization of the intermediate on the folding pathway of human alpha-lactalbumin

To discuss the relation between the folding mechanism and the chemical structure of proteins, the reversible unfolding reactions of human alpha-lactalbumin by acidification and by guanidine hydrochloride at 25 degrees C are studied by means of circular dichroism, difference spectra and pH-jump measurements and are compared with those for bovine alpha-lactalbumin. As shown previously for bovine alpha-lactalbumin, the folding process at neutral pH is not explained by a simple two-state mechanism but involves an intermediate form that has the same amount of helical structures as the native form. The transition between the intermediate and the fully denatured states is too rapid to be measured and corresponds to the helix-coil transition of the backbone. One of the differences of human alpha-lactalbumin from the bovine protein is the remarkable stability of the intermediate at neutral pH, which can be explained by differences in the primary chemical structure. Another difference is the existence at acid pH of an additional helical form, which is more helical than the native form. The transition from this to the intermediate or to the fully denatured one also is shown to resemble the helix-coil transition. The following folding scheme of human alpha-lactalbumin is proposed: formula: (see text). Here N is the native form, and the intermediate is a macroscopic state distributed around the state A3 at neutral pH, while the distribution in the acid and fully denautured states shifts toward Am and A-n, respectively.     

Polymeric Structures and Dynamic Properties of the Bacterial Actin AlfA

AlfA is a recently discovered DNA segregation protein from Bacillus subtilis that is distantly related to actin and the bacterial actin homologues ParM and MreB. Here we show that AlfA mostly forms helical 7/3 filaments, with a repeat of about 180 Å, that are arranged in three-dimensional bundles. Other polymorphic structures in the form of two-dimensional rafts or paracrystalline nets were also observed. Here AlfA adopted a 16/7 helical symmetry, with a repeat of about 387 Å. Thin polymers consisting of several intertwining filaments also formed. Observed helical symmetries of AlfA filaments differed from those of other members of the actin family: F-actin, ParM, or MreB. Both ATP and guanosine 5′-triphosphate are able to promote rapid AlfA filament formation with almost equal efficiencies. The helical structure is only preserved under physiological salt concentrations and at a pH between 6.4 and 7.4, the physiological range of the cytoplasm of B. subtilis. Polymerization kinetics are extremely rapid and compatible with a cooperative assembly mechanism requiring only two steps: monomer activation followed by elongation, making AlfA one of the most efficient polymerizing motors within the actin family. Phosphate release lags behind polymerization, and time-lapse total internal reflection fluorescence images of AlfA bundles are consistent with treadmilling rather than dynamic microtubule-like instability. High-pressure small angle X-ray scattering experiments reveal that the stability of AlfA filaments is intermediate between the stability of ParM and the stability of F-actin. These results emphasize that actin-like polymerizing machineries have diverged to produce a variety of filament geometries with diverse properties that are tailored for specific biological processes.     

Characterization of inherent curvature in DNA lacking polyadenine runs.

Sequence-directed DNA curvature is most commonly associated with AA dinucleotides in the form of polyadenine runs. We demonstrate inherent curvature in DNA which lacks AA/TT dinucleotides using the criteria of polyacrylamide gel mobility and efficiency of DNA cyclization. These studies are based upon two 21-base pair synthetic DNA fragments designed to exhibit fixed curvature according to deflections made to the helical axis by non-AA dinucleotide stacks. Repeats of these sequences display anomalously slow migration in polyacrylamide gels. Moreover, both sequences describe helical conformations that are closed into circles by DNA ligase at much smaller sizes than is typical of nondeformed DNA. Chemical cleavage of these DNA molecules with hydroxyl radical is also consistent with local variation in helical conformation at specific dinucleotide steps.     

A calorimetric study of the triple helix formation: interaction of poly(C) - guanosine - protonated poly(C).]

The triple helix formation of poly(C) - guanosine - poly(C+) was investigated by the help of an LKB scanning micro-calorimeter. The existence of the triple helix could also be shown by recording the melting curves. The ultraviolet absorption at different wave lengths namely 275 nm, 260 nm, and 245 nm was plotted as a function of the temperature. Furthermore formation of the triple helix was shown by plotting the ultraviolet absorption at 245 nm during the increasing addition of guanosine solution to a fixed amount of poly(C) in the solution. Finally the formation of the triple helix was demonstrated by plotting the ultraviolet absorption at 245 nm of a certain mixture of the components while the pH value of the solution was continuously lowered. All these methods show that the monomer interacts with the polymer double helix to form a triple helix. The calorimetric measurements show that the reaction enthalpy is concentration dependent. Above a threshold concentration a rapid increase of the reaction enthalpy is observed. This increase occurs in a very narrow concentration interval. Above this interval a final value of the reaction enthalpy is reached. The amount of the reaction enthalpy for the interaction of guanosine with poly(C) - poly(C+) double helix is 5.5 Kcal (mol base triplet)-1.     

Structure of the three-way helical junction of the hepatitis C virus IRES element

The hepatitis C virus internal ribosome entry site (IRES) element contains a three-way junction that is important in the overall RNA conformation, and for its role in the internal initiation of translation. The junction also illustrates some important conformational principles in the folding of three-way helical junctions. It is formally a 3HS₄ junction, with the possibility of two alternative stacking conformers. However, in principle, the junction can also undergo two steps of branch migration that would form 2HS₁HS₃ and 2HS₂HS₂ junctions. Comparative gel electrophoresis and ensemble fluorescence resonance energy transfer (FRET) studies show that the junction is induced to fold by the presence of Mg²⁺ ions in low micromolar concentrations, and suggest that the structure adopted is based on coaxial stacking of the two helices that do not terminate in a hairpin loop (i.e., helix IIId). Single-molecule FRET studies confirm this conclusion, and indicate that there is no minor conformer present based on an alternative choice of helical stacking partners. Moreover, analysis of single-molecule FRET data at an 8-msec resolution failed to reveal evidence for structural transitions. It seems probable that this junction adopts a single conformation as a unique and stable fold.     

Bulge loops used to measure the helical twist of RNA in solution.

Bulge loops are commonly found in helical segments of cellular RNAs. When incorporated into long double-stranded RNAs, they may introduce points of flexibility or permanent bend that can be detected by the altered electrophoretic gel mobility of the RNA. We find that a single An or Un bulge loop near the middle of a long RNA helix significantly retards the RNA during polyacrylamide gel electrophoresis if n greater than or equal to 2. The mobility of an RNA containing two A2 bulges various periodically with the number of base pairs between the bulges. We interpret this to mean that A2 bulges varies periodically with the number of base pairs between the bulges. We interpret this to mean that Z2 bulges form torsionally stiff bends in the helix; the gel mobility reaches a minimum when the total helical twist between the bulges rotates the arms of the molecule into a cis conformation. The gel mobilities are proportional to the predicted end-to-end distance of the RNA if the average RNA helical repeat is 11.8 +/- 0.2 bp/turn and there is no helical twist (3 +/- 9 degrees) associated with the bulge (data obtained in 0.15 M Na+). Other sizes and sequences of bulges have very different effects on RNA helix conformation and flexibility. U2 bulges bend the helix to a much smaller degree than A2 bulges, while longer A or U bulge sequences probably allow bends of 90 degrees or more; all of these may be fairly flexible joints.(ABSTRACT TRUNCATED AT 250 WORDS)     

Chemical forms of selenium in selenium containing proteins from human plasma

The chemical forms of selenium (Se) were determined in human plasma fractions. Human plasma was subjected to gel filtration using Sephadex G-150, and the first Se peak from this column was subsequently chromatographed on DEAE-Sephacel. The form of Se in the Se peak which eluted from this column was shown to be selenocysteine (SeCys). In a second approach human plasma was again subjected to gel filtration and the first Se peak was chromatographed on Affigel blue. SeCys was shown to be the form of Se in both the retained and unretained Se on this column. The second gel filtration Se peak was also chromatographed on Reactive Blue 2-Sepharose CL-6B and the form of Se which was not retained was also shown to be SeCys. However, the form which was retained was shown to be selenomethionine. Evidence is presented that there are three Se containing proteins in human plasma, which are selenoprotein P, glutathione peroxidase, and albumin.