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A 13C nuclear magnetic resonance study of gel-forming (1 goes to 3)-beta-d-glucans. Evidence of the presence of single-helical conformation in a resilient gel of a curdlan-type polysaccharide 13140 from Alcaligenes faecalis var. myxogenes IFO 13140.

A 13C nuclear magnetic resonance (NMR) study of a resilient gel of a curdlan-type polysaccharide 13140, a (1 goes to 3)-beta-D-glucan, from Alcaligenes faecalis var. myxogenes IFO 13140, was performed in an effort to understand the gel structure. It was found that very broad 13C resonance peaks of line widths ca. 150 (C-1-C-5) and 50 HZ (C-6) are able to be seen in the gel state. Because of a fivefold increase of the peak intensities with respect to those in an aqueous suspension by gelation, these peaks are unequivocally ascribed to certain regions relevant to the gel structure. Those 13 C NMR peaks, however, account for only 20-30 (as viewed from C-1-C-5) and 60% (from C-6) of the total gel, the peak areas of the rest being lost. With respect to those of the disordered low molecular weight acid degraded fraction, fraction II, and laminaran, downfield displacements of C-1, C-3, and C-4 signals are found to take place by amounts of 2.8, 3.2, and 0.9 ppm, respectively, while the remaining peaks (C-2, C-5, and C-6) are unchanged. In view of similar differences of chemical shifts between cyclodextrins and linear (1 goes to 4)-alpha-D-glucans (Colson, P., Jennings, H.J., and Smith, I.C.P. (1974), J. Am. Chem. Soc. 96, 8081-8087), the observed downfield 13C shifts of the glucosidic bonds in the gel are explained by the presence of the fixed conformation of the preferred dihedral angles, in which internal rotations around the glucosidic bonds are not allowed. Combined with the results of theoretical prediction and the downfield shift of C-4 signals, which is consistent with the presence of an O-4'...O-5 intramolecular hydrogen bond, the observed 13C peaks are ascribed to a region of single helical conformation, whereas the peak-loss portion of 13C NMR signals (70-80 and 40% from C-1 and C-6, respectively) is presumably ascribed to the multiple-helical junction zones for the gel structure and their vicinities. The variation of the line widths as well as the peak positions is also found to take place by stepwise addition of NaOH (greater than 0.22 M). The onset of the conformational transition, helix to random coil, is in good agreement with the change of viscosity, specific rotation, optical rotatory dispersion, and absorption maximum shift by complex formation with Congo Red reported by Ogawa et al. (Ogawa, K., Watanabe, T., Tsurugi, J., and Ono, S. (1972), Carbohydr. Res. 23, 399-405).

Alcaligenes↗

Physicochemical and kinetic properties of iodinated yeast 3-phosphoglycerate kinase.

The present studies have established that there is a critical tyrosyl residue in yeast 3-phosphoglycerate kinase. The iodination of this enzyme results in an inactivation following first-order kinetics. The extent of the modification is limited to only one tyrosyl residue. The monoiodotyrosine formation which leads to inactivation of the enzyme does not induce any significant conformational change as evidenced by hydrogen exchange and optical rotatory dispersion. The role of this tyrosine in the action of the yeast 3-phosphoglycerate kinase is studied. An effective protection against inactivation is observed with 3-phosphoglycerate, and the characteristic spectral effect of 3-phosphoglycerate binding cannot be detected in the modified enzyme. It is concluded that the essential tyrosyl residue may play a role in substrate binding.

Amino Acids↗

Histone interactions in solution and susceptibility to denaturation.

Histone interactions in solution may depend upon treatments used for purification. Optical rotatory dispersion and sedimentation-velocity measurements have been made in a reference solvent, before and after exposure to various treatments, to investigate histone susceptibility to irreversible denaturation. Some acid conditions and urea and guanidine solutions may denature. Interaction studies performed on nondenatured histones indicate that the dimer, (H4)(H3), and tetramer, (H4)2(H3)2, dissociate to monomers at low ionic strength. Sedimentation-velocity experiments suggest a model for the (H4)2(H3)2 tetramer, with a compact semispherical center and four protruding amino-terminal regions. Fractions H2a and H2b interact to form the mixed dimer in equilibrium with monomers. Fraction H2a self-associates readily to dimers, tetramers, and octamers, while fraction H1 associates only weakly to form dimers.

Acetates↗

Enzymic and physicochemical properties of Streptomyces griseus trypsin.

Streptomyces griseus trypsin has been isolated from Pronase by ion-exchange chromatography on CM-Sephadex and SE-Sephadex. The isolated enzyme was homogeneous by the criteria tested except for a low degree of contamination by an enzyme with nontryptic activity. The latter could be partially resolved by chromatography on Bio-Rex 70. The molar absorbancy at 280 nm was found to be 3.96 times 10-4 M-1/cm and the E1cm1% was found to be 17.3. The molecular weight was 22,800 plus or minus 800. The enzyme was found to be stable at 0 degrees from pH 2 to 10. At 30 degrees the enzyme was maximally stable at pH 3-4 and significantly stabilized in the neutral and alkaline range by 15 mM Ca2+. Some evidence was obtained for a reversible denaturation of the enzyme at pH 12.0 and 2.0. The K-m for N-alpha-benzoyl-L-arginine ethyl ester at pH 8.0 in 20 mM CaCl2-0.1 M KCl-10 mM Tris-HCl buffer at 30 degrees was found to be 7.7 plus or minus 1.9 times 10-6 M and the esterase activity was observed to be dependent on an ionizing group with pK-a equals 5.85. In 2H2O this pKa was increased to 6.35 and the rate of hydrolysis dicreased threefold. The rate of hydrolysis was independent of pH between 8 and 10. The inhibition of the enzyme with L-1-chloro-3-tosylamido-4-phenyl-2-butanone was shown to be associated with the alkylation of its single histidine residue. This residue is present in a homologous amino acid sequence as the active-site histidine in trypsin and chymotrypsin. Optical rotatory dispersion and circular dichroism measurements over the pH range 5.3-10.5 indicated no significant conformational change until the pH was increased above 10.1. The observation that, under the conditions tested, acetylation and carbamylation of the NH2-terminal valine were incomplete is consistent with the view that this group is buried as an ion pair and only becomes available for deprotonation and reaction upon denaturation of the enzyme at pH values greater than 10.0.

Acetylation↗

Structural characterization of alpha-zein.

A variety of published physical measurements, computational algorithms, and structural modeling methods have been used to create a molecular model of 19 kDa alpha-zein (Z19). Zetaeins are water-insoluble storage proteins found in corn protein bodies. Analyses of the protein sequence using probability algorithms, structural studies by circular dichroism, infrared spectroscopy, small-angle X-ray scattering (SAXS), light scattering, proton exchange, NMR, and optical rotatory dispersion experiments suggest that Z19 has approximately 35-60% helical character, made up of nine helical segments of about 20 amino acids with glutamine-rich "turns" or "loops". SAXS and light-scattering experiments suggest that in alcohol/water mixtures alpha-zein exists as an oblong structure with an axial ratio of approximately 6:1. Furthermore, ultracentifugation, birefringence, dielectric, and viscosity studies indicate that alpha-zein behaves as an asymmetric particle with an axial ratio of from 7:1 to 28:1. Published models of alpha-zein to date have not been consistent with the experimental data, and for this reason the structure was re-examined using molecular mechanics and dynamics simulations creating a new three-dimensional (3D) structure for Z19. From the amino acid sequence and probability algorithms this analysis suggested that alpha-zein has coiled-coil tendencies resulting in alpha-helices with about four residues per turn in the central helical sections with the nonpolar residue side chains forming a hydrophobic face inside a triple superhelix. The nine helical segments of the 19 kDa protein were modeled into three sets of three interacting coiled-coil helices with segments positioned end to end. The resulting structure lengthens with the addition of the N- and C-terminal sections, to give an axial ratio of approximately 6 or 7:1 in agreement with recent experiments. The natural carotenoid, lutein, is found to fit into the core of the triple-helical segments and help stabilize the configuration. Molecular dynamics simulations with explicit methanol/water molecules as solvent have been carried out to refine the 3D structure.

Models, Molecular↗

Sequential polypeptides. 2. Helix--coil transition in poly(gamma-benzyl epsilon-carbobenzoxy-L-lysyl-L-glutamate).

Helix--coil transitions of an alternating copolypeptide poly(gamma-benzyl epsilon-carbobenzoxy-L-lysyl-L-glutamate) (poly[Lys(Z)-Glu(OBzl)]) in binary mixtures of dichloroacetic acid (DCA) and ethylene dichloride (EDC) were investigated by optical rotatory dispersion (ORD). The ORD data obtained were analyzed to evaluate the equilibrium constant s for helix formation and the cooperativity parameter sigma. The values of sigma1/2 are substantially independent of temperature and solvent composition, yielding 0.4 X 10(-2) on the average. The transition enthalpy deltaHc at the transition point decreases from 291 to 154 cal mol-1 as the DCA content is increased from 56 to 64 vol%. At about 20 degrees C and at 58 vol% DCA, poly[Lys(Z)-Glu(OBzl)] in binary mixtures of DCA and EDC undergoes a solvent-induced transition. This DCA content is intermediate between those for poly(gamma-benzyl L-glutamate) and poly(epsilon-carbobenzoxy-L-lysine) in the same binary solvent and close to that of an equimolar random copolymer of the two peptides. However, the s of poly[Lys(Z)-Glu(OBzl)] is not a geometrical mean of those of the parent homopolypeptides. This fact suggests that the helical conformation of the copolypeptide is stabilized by a conformational induction operative between adjacent residues.

Benzyl Compounds↗

Verticillane derivatives from Bursera suntui and Bursera kerberi.

The stems of Bursera suntui afforded two new verticillane derivatives, (1S,3Z,7E,11S,12S)-(+)-verticilla-3,7-dien-12,20-diol (1) and (1S,3Z,7E,11S,12S)-(+)-verticilla-3,7-dien-12,20-diol 20-acetate (2), together with (1S,3E,7E,11R)-(+)-verticilla-3,7,12(18)-triene (3), (1R,3E,7E,11R,12Z)-(+)-verticilla-3,7,12-triene (4), (1R,7E,11Z)-(-)-verticilla-4(20),7,11-triene (5), and (1S,3E,7E,11S,12S)-(+)-verticilla-3,7-dien-12-ol (6). Compounds 3 and 4 are new enantiomerically pure natural products whose racemic mixtures, derived from synthetic approaches toward the taxane skeleton, were obtained previously. The stems of Bursera kerberi afforded the new (1S,3E,7E,11S,12R)-(+)-verticilla-3,7-dien-12-ol (7) together with 3-5. This is the first time that verticillane derivatives have been isolated from the genus Bursera. Their structures and stereochemistry were elucidated by 1D and 2D NMR data, including COSY, NOESY, HSQC, and HMBC experiments, while the absolute configuration was determined by comparison of the optical rotatory dispersion data with that of recently revised (1S,3E,7E,11S,12S)-(+)-verticilla-3,7-dien-12-ol (6), obtained from Sciadopitys verticillata, and those of (1R,3E,7E,11R,12R)-(-)-verticilla-3,7-dien-12-ol (8) and (1R,3E,7E,11R,12S)-(-)-verticilla-3,7-dien-12-ol (9), isolated from the liverwort Jackiella javanica. The conformational preferences of 1-7 were studied by molecular mechanics modeling employing the Monte Carlo protocol.

Bursera↗

The composition and physicochemical properties of hyaluronic acids prepared from ox synovial fluid and from a case of mesothelioma.

1. Materials containing hyaluronic acid have been prepared by filtration (Ogston & Stanier, 1950) from ox synovial fluid and from a protein-rich human mesothelioma fluid. The ox material has been deproteinized by treatment with chloroform and pentanol and by gradient elution on DEAE-Sephadex; several fractions were obtained by the latter method. These materials can be stored in solution at -20 degrees without change of properties. The ox material contained 21% of protein; all other preparations contained less than 6% of protein. 2. The two materials have been compared by sedimentation and viscosity and shown to be closely similar. Treatment of the ox material with neuraminidase caused no change in its viscosity behaviour. 3. Information about the molecular configuration of the ox material has been obtained from measurements of light-scattering and viscosity. The results, though consistent with a highly extended configuration, are not consistent with a linear random-coil configuration. It is tentatively suggested that the structure may have some degree of branching and of cross-linking, which give it a rigidity with respect to expansion of the molecular domain that would not be possessed by a random coil. 4. The deproteinized material recovered from DEAE-Sephadex, though polydisperse, showed unchanged average molecular weight; however, the average radius of gyration was greater than before this treatment. 5. Acidification to approx. pH3 resulted in a contraction of the structure, with only a slight degree of expansion when the pH was restored to 6.8-7.0. 6. Measurements of optical rotatory dispersion qualitatively support a structure less simple than a linear random coil. 7. Colloid osmotic pressures of mixed solutions of bovine serum albumin and of hyaluronic acid prepared by filtration from ox synovial fluid have been measured. The results agree approximately with those of Laurent & Ogston (1963) but are in quantitative disagreement with the partition measurements of Ogston & Phelps (1960). The relationships between thermodynamic quantities in a quaternary system of electrolytes are discussed in Appendix 2. 8. Refractometric measurements have been made in connexion with light-scattering measurements, as the basis for a convenient method of determining the concentrations of solutions of hyaluronic acids, and to measure the partition of sodium chloride in dialysis experiments. The theory of the last use is discussed in Appendix 1. 9. Sedimentation measurements on the ox preparation have been made up to a concentration of 1.4x10(-2)g./ml. The form of the sedimentation coefficient-concentration relationship is discussed. The value of the sedimentation coefficient at higher concentration is the basis of an illustration of the likely effect of hyaluronic acid on the flow of water through narrow channels in connective tissue. 10. Available colorimetric methods have been shown to give low estimates for glucuronic acid when applied to highly polymerized materials, as compared with estimates by decarboxylation. A spectrophotometric titration with cetylpyridinium bromide has been shown to give estimates of carboxyl groups that agree well with those of decarboxylation when applied to preparations of hyaluronic acid under suitable conditions; the results are not affected by the presence of protein. 11. Estimates of glucosamine (Ogston, 1964) have been found to be low compared with those of total acetyl, independently of the presence of protein. The magnitude of the discrepancy is characteristically different for preparations from ox synovial fluid and from mesothelioma. 12. Sialic acid was estimated in several preparations. It is likely that this forms part of the protein. 13. Analyses of preparations for total nitrogen, amino acids, total acetyl, glucuronic acid (by decarboxylation) and ash account for at least 95.7% of the dry weight in terms of N-acetylglucosaminyl, glucuronyl, protein and metal ions. Previously published analyses of hyaluronic acids are reviewed. 14. The estimated molar ratios of glucuronic acid to glucosamine were all significantly greater than unity. 15. The analytical results are interpreted as agreeing with the physicochemical measurements in suggesting a more complex structure, for at least some hyaluronic acids, than that of an alternate linear copolymer in random-coil configuration.

Animals↗

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.

Journal Article↗

Conformational changes and the regulation of glutamate-dehydrogenase activity.

1. The effect of NADH and the non-competitive inhibitor GTP on the optical-rotatory-dispersion properties of glutamate dehydrogenase has been studied. 2. Analysis of the data in terms of the a(0) and b(0) parameters of the Moffitt-Yang equation indicates that a conformational change is induced either by NADH or by GTP in the presence of small amounts of NADH. 3. Sedimentation measurements under comparable conditions showed that the enzyme reversibly dissociates into sub-units but that this dissociation is only secondary to the conformational changes. 4. Fluorescence measurements showed that the binding constant of NADH and the number of binding sites on the enzyme increased in the presence of GTP. 5. This is confirmed by studies of fluorescence polarization, which in addition showed that the movement of NADH on the enzyme surface is more restricted in the presence of GTP. 6. The relation of these results to possible regulatory mechanisms is discussed.

Chemical Phenomena↗

Magnesium ions and the structure of Escherichia coli ribosomal ribonucleic acid.

1. The effect of removing Mg(2+) from a purified high-molecular-weight (1.07x10(6)) fraction of Escherichia coli ribosomal RNA was examined by ultracentrifugation, thermal denaturation and optical rotation. 2. At moderate I (0.1m-sodium chloride), EDTA at 2-50mm has little effect on RNA; at low I, 0.01-0.04 (with tris as counter-ion), two boundaries appear. 3. The leading boundary, S(20,w) about 20s, is identified with the original material with counter-ion Mg(2+) (;ionic atmosphere') removed, leading to an expanded form. 4. The slow boundary, 15-16s, is associated with a further loss of Mg(2+) and a further expansion, sensitive to EDTA concentration: it is proposed that this Mg(2+) is localized on the polynucleotide chain, i.e. ;site-bound'. 5. I is important and the EDTA effect at low I is reversible if Na(+) is added immediately after the EDTA: this Na(+) reversibility is lost on standing at 0 degrees . It is suggested that changes in the tertiary structure may be associated with this loss of reversibility. 6. Thermal-denaturation studies show that there is no loss of secondary structure associated with these changes: change in the optical-rotatory-dispersion spectrum in the region of the Cotton effect may be associated with this change in tertiary structure.

Chemical Phenomena↗

Further studies on the thiol groups of human haemoglobin.

When the SH groups of various derivatives of human haemoglobin are converted into their mercuric mercaptides small changes are observed in the optical rotatory dispersion in the range 385-294mmu. These changes are proportionately greater for the reactive than for the unreactive SH groups. These observations have been interpreted in terms of the conformational changes that are likely to occur in the haemoglobin molecule on modification of the SH groups.

Journal Article↗

Purification and properties of an acidic protein from chromaffin granules of bovine adrenal medulla.

1. A soluble protein has been purified from an aqueous extract of bovine adrenal chromaffin granules by chromatography on Sephadex G-200. This protein comprises 25% of the total protein of the granules and gave a single band on gel electrophoresis. 2. The protein is unusually rich in acidic amino acids, notably glutamic acid (26.0%, w/w); it is also relatively rich in proline (8.6%, w/w) but poor in cystine (0.35%, w/w). 3. A molecular weight of 77000 was obtained from sedimentation and diffusion measurements on the protein, and approach-to-equilibrium measurements gave apparent molecular weights of the same order. 4. A molecular weight 7 times that given above was estimated from the results of chromatography on a column of Sephadex G-200 that had been calibrated with globular proteins. However, good agreement between the ultracentrifuge and Sephadex experiments was obtained on the assumption that Sephadex chromatography depends on the effective hydrodynamic radii of proteins and not on their molecular weights. 5. The hydrodynamic properties of the protein differed from those of a typical globular protein. Thus the protein had a high intrinsic viscosity, a high frictional ratio and a large effective hydrodynamic volume. 6. The hydrodynamic properties of the protein, but not its molecular weight, were dependent on the ionic strength of the solvent. Increasing the ionic strength caused an increase in the sedimentation and diffusion coefficients, but a decrease in the intrinsic viscosity and in the frictional ratio of the protein. 7. Optical-rotatory-dispersion measurements indicated that only a small part of the polypeptide chain was in an alpha-helical conformation. 8. These results are compatible with the protein's having a conformation approaching that of a random-coil polypeptide, the volume occupied by the molecule being determined by electrostatic repulsion between the excess of negative charges.

Adrenal Medulla↗

New evidence for the structure of myxinol.

1. Preliminary spectroscopic examination of a second component of hagfish bile salts suggested that it might be 3beta,7alpha,26(27)-trihydroxy-5alpha-cholestane. 2. Impure reduction products of the 3beta,26(27)-dihydroxycholestane-7,16-dione previously made from myxinol disulphate appeared also to have the 5alpha-configuration. 3. Infrared, nuclear-magnetic-resonance and mass-spectrographic as well as optical-rotatory-dispersion measurements on 3beta,26(27)-dihydroxycholestane-7,16-dione showed that it was a 5alpha-compound. 4. Myxinol is thus 3beta,7alpha,16alpha,26(27)-tetrahydroxy-5alpha-cholestane; new nuclear-magnetic-resonance measurements on myxinol tetra-acetate at higher resolution confirm this structure.

Animals↗

Sedimentation equilibrium and other physicochemical studies on the lysine-rich fraction of calf thymus histones.

1. The lysine-rich fraction (Ia+Ib, or f1) of calf thymus histones was isolated as the sulphate by acid extraction. 2. Sedimentation-equilibrium measurements with interference optics showed that this fraction was monodisperse with a molecular weight of 19500+/-2000. 3. The ;apparent molecular weight' calculated from the sedimentation-equilibrium studies varied markedly with concentration. The large second virial coefficient implied by such variation was attributed to the very high charge/mass ratio of this relatively small protein. Estimates of the charge were made from the values of this virial coefficient. 4. The very large value of the virial coefficient explains anomalies in the earlier reports of the molecular weight of this histone and also why the z-average molecular weight can appear to be lower than the weight-average molecular weight. 5. The differences of the specific refractive increments, and the partial specific volumes, between dialysed and undialysed solutions of this histone fraction could also be attributed to its high molecular charge, which was estimated from these differences and agreed, within the expected limits, with the value deduced from the second virial coefficient. 6. Sedimentation-velocity measurements combined with the known molecular weight imply that lysine-rich histone has a high frictional ratio and an extended shape. Optical-rotatory-dispersion measurements indicated that it had a low helical content.

Animals↗

Desensitization of glutamate dehydrogenase by reaction of tyrosne residues.

1. The reaction of glutamate dehydrogenase with N-acetylimidazole and with tetranitromethane leads to modification of tyrosine residues. 2. Modification of 1 tyrosine residue/subunit does not affect the enzymic activity but decreases the response of the enzyme to the allosteric inhibitor, GTP. 3. The physical properties of the enzyme (sedimentation coefficient and optical rotatory dispersion) remain unaltered. 4. GTP partially protects against desensitization. 5. The diminished responses of the modified enzymes to GTP are also detected by using the fluorescence of 1-anilinonaphthalene-8-sulphonate as a conformational probe. 6. Difficulties that generally arise in chemical modifications from inhomogeneous distributions of products are discussed.

Aniline Compounds↗