bluuebunny/crossref_metadata_2025 huggingface dataset:
Distribution and cycle of arsenic compounds in the ocean
Authors: Santosa Sri Juari , Wada Satoshi , Tanaka Shigeru
Published: January 2005

In order to understand the distribution and the cycle of arsenic compounds in the marine environment, the horizontal distributions of arsenic(V) [As(V)], arsenic(III) [As(III)], monomethylarsonic acid (MMAA) and dimethylarsinic acid (DMAA) in the Indian Pacific Oceanic surface waters have been investigated. This took place during cruises of the boat Shirase from Tokyo to the Syowa Station (15 November–19 December 1990), of the tanker Japan Violet from Sakai to Fujayrah (28 July–17 August 1991) and of the boat Hakuho‐maru from Tokyo to Auckland (19 September–27 October 1992). Vertical distributions of arsenic in the west Pacific Ocean have also been investigated.

The concentration of As(V) was found to be relatively higher in the Antarctic than in the other areas. Its concentration varied from 340 ng dm−3 (China Sea) to 1045 ng dm−3 (Antarctic). On the other hand, the concentrations of the biologically produced species, MMAA and DMAA, were extremely low in the Antarctic and southwest Pacific waters. Their concentrations in Antarctic waters were 8 ng dm−3 and 22 ng dm−3 and those in the southwest Pacific were 12 ng dm−3 and 25 ng dm−3. In the other regions the concentration varied from 16 ng dm−3 (China Sea) to 36 ng dm−3 (north Indian Ocean) for MMAA and from 50 ng dm−3 (east Indian Ocean) to 172 ng dm−3 (north Indian Ocean) for DMAA. As a result, with the exception of Antarctic and southwest Pacific waters, the percentages of each arsenic species in the surface waters were very similar and varied from 52% (east Indian Ocean) to 63% (northwest Pacific Ocean) for As(V), from 22% (northwest Pacific Ocean) to 27% (east Indian Ocean) for As(III) and from 15% (northwest Pacific Ocean) to 21% (north and east Indian Oceans) for the methylated arsenics (MMAA+DMAA). These percentages in Antarctic waters were 97%, 0.2% and 2.8%, respectively, and those in the southwest Pacific Ocean were 97% for As(V)+As(III) and 3% for MMAA+DMAA. The very low concentrations of the biologically produced species in Antarctic waters and that of methylated arsenic in southwest Pacific waters indicated that the microorganism communities in these oceans was dominated by microorganisms having a low affinity towards arsenic. Furthermore, microorganism activity in the Antarctic was also limited due to the much lower temperature of the seawater there.

The vertical profile of inorganic arsenic was 1350 ng dm−3 in surface waters, 1500 ng dm−3 in bottom waters with a maximum value of 1700 ng dm−3 at a depth of about 2000 m in west Pacific waters. This fact suggested the uptake of arsenic by microorganisms in the surface waters and the co‐precipitation of arsenic with hydrated heavy‐metal oxides in bottom waters. The suggested uptake of inorganic arsenic and subsequent methylation was also supported by the profile of DMAA, with a high concentration of about 26 ng dm−3 in surface water and a significant decrease to a value of 9 ng dm−3 at a depth of 1000 m.
Identification of extracellular arsenical metabolites in the growth medium of the microorganisms apiotrichum humicola and scopulariopsis brevicaulis
Authors: Cullen William R. , Li Hao , Hewitt Gary , Reimer Kenneth J. , Zalunardo Nadia
Published: January 2005

The separation and identification of some of the arsenic species produced in cells present in the growth medium when the microorganisms Apiotrichum humicola (previously known as Candida humicola) and Scopulariopsis brevicaulis were grown in the presence of arsenicals were achieved by using hydride generation–gas chromatography–atomic absorption spectrometry methodology (HG GC AA). Arsenite, monomethylarsonate, dimethylarsinate and trimethylarsine oxide were detected following incubation with arsenate. With arsenite as a substrate, the metabolites were monomethylarsonate, dimethylarsinate and trimethylarsine oxide; monomethylarsonate afforded dimethylarsinate and trimethylarsine oxide, and dimethylarsinate afforded trimethylarsine oxide. Trimethylarsine was not detected when the arsenic concentration was 1 ppm.
Methylation of arsenic by anaerobic microbial consortia isolated from lake sediment
Authors: Bright D. A. , Brock S. , Reimer K. J. , Cullen W. R. , Hewitt G. M. , Jafaar J.
Published: January 2005

Anaerobic enrichment cultures, isolated from arsenic–contaminated lake sediment in the Canadian sub–arctic and grown in five selective media, methylated arsenate/arsenite to produce mono−, di− and tri–methyl arsenicals. The extent of methylation and methylarsenic species produced varied with the type of enrichment. Iron–reducing, manganese–reducing, sulfate–reducing and broad–spectrum anaerobic heterotrophic mixed cultures all produced methylarsenicals. Sulfate–reducing cultures produced higher concentrations of methylarsenicals (especially trimethyl species) than iron‐ or maganese–reducers. There is evidence that several of the methylarsenicals, which were hydride–reactive at pH 6, were methylarsenic(III) thiols. The organoarsenicals produced by enrichment cultures were the same as those detected in the porewater of the lake sediments used to initiate the enrichment cultures. Overall, this study demonstrates that microbes from anaerobic lake sediments can methylate (and demethylate) arsenic, a capability shared by manganese−, iron−, and sulfate–reducing microbial consortia.
Working Methods Paper: Critical considerations with respect to the identification of tin species in the environment
Authors: Quevauviller Philippe , Ritsema Rob , Morabito Roberto , Dirkx Wilfried M. R. , Chiavarini Salvatore , Bayona José M. , Donard Olivier F. X.
Published: January 2005

Biogeochemical pathways of tin species in the environment are still controversial, e.g. with regard to methylation and transmethylation phenomena, owing to the fact that the identification of methylated tin‐compounds is often difficult. The previous tentative identification of a mixed methylbutyltin compound in sediment and biological samples by GC/AAS after hydride generation gave an illustration of this problem. This compound was previously identified in sediments by other authors and also suspected to occur in a contaminated sediment sample from the Boyardville Marina, France. The retention time obtained by GC/AAS corresponded to the actual retention time of a mixed methylbutyltin calibrant. However, additional checks demonstrated that the compound detected was actually monophenyltin. This evidence was produced by a thorough analysis of a selected sediment sample by alternative techniques such as GC/AAS and GC/AES after pentylation, GC/FPD and GC/MS. The results presented highlight the need for a full identification of compounds to avoid mis‐interpretation.
Quality control in the speciation analysis of butyltin compounds in marine biological samples by hydride generation–cold trapping and on‐line quartz furnace atomic absorption spectrometry
Authors: Pannier F. , Astruc A. , Astruc M.
Published: January 2005

The determination of tributyltin (TBT) in sea food (mussel, oyster, fish) by a hydride generation–cold trapping–quartz furnace atomic absorption spectrometry procedure has been studied with emphasis on quality control. Large amounts of spiked materials have been prepared and stored either frozen, or frozen after freeze‐drying. Extraction of TBT by 0.1 M hydrochloric acid in methanolic solution is efficient (88–96%) for wet samples or freeze‐dried samples. It is also efficient with freshly spiked materials. Consumption of sodium borohydride by the matrix makes it necessary to use quite large amounts of reagent to obtain optimal sensitivity. Analysis of a fish‐tissue Certified Reference Material seems to indicate a partial debutylation of TBT during transport and/or storage of this material.
Certified reference material (CRM 462) for the quality control of dibutyl‐ and tributyl‐tin determinations in coastal sediment
Authors: Quevauviller Ph. , Astruc M. , Ebdon L. , Desauziers V. , Sarradin P. M. , Astruc A. , Kramer G. N. , Griepink B.
Published: January 2005

Determinations of tributyltin (TBT) species, along with the degradation products mono‐ and dibutyltin (MBT and DBT), are routinely carried out by a number of laboratories to ascertain the level of organotin contamination of the marine enviroment, particularly in water, sediment and biota. In order to improve and control the quality of such analyses the EC Community Bureau of Reference, BCR (Measurements and Testing Programme), has organized two interlaboratory studies on TBT in water and TBT in a spiked sediment which were followed by a certification campaign for butyltins in a coastal sediment (CRM 462). This material was collected in the Arcachon Bay (France), then carefully prepared (controlled oven drying) and its homogeneity and long‐term stability were verified. This paper presents the certification work performed. The certified values for TBT and DBT are 70±14 ng g−1 (as TBT cation) and 128±16 ng g−1 (as DBT cation), respectively.
Organotin(IV) complexes with tetraethyl ethylene‐ and propylene‐diphosphonates
Authors: Grigoriev E. V. , Yashina N. S. , Prischenko A. A. , Livantsov M. V. , Petrosyan V. S. , Massa W. , Harms K. , Wocadlo S. , Pellerito L.
Published: January 2005

The series of organotin halide complexes with tetraethyl ethylene‐ and propylene‐diphosphonates RnSnX4–n,˙L [n=0, X=Cl; n=1, R=Me, X=Cl, Br; n=1, R=Ph, X=Cl; n=2, R=Me, Et, Bu, X=Cl, Br; n=2, R=Ph, X=Cl; L=(EtO)2P(O)CH2CHR'P(O)(OEt)2, R'=H, Me] were synthesized and characterized by means of NMR and Mössbauer spectroscopy. The crystal structure of the complex of diphenyltin dichloride with propylenediphosphonate was determined. The complex consists of polymer chains with bridging bidentate ligands and an octahedral tin environment containing two types of phosphoryl fragments. All of the R2SnX2 adducts have trans‐R2SnX4 geometries of tin coordination octahedra according to the quadrupole splitting values in the Mössbauer spectra. The 31P and 119Sn NMR studies at low temperatures revealed that RSnHal3 complexes in solution form isomers with different mutual orientations of phosphoryl ligands and organic groups in the coordination sphere. The diethyltin dichloride adduct with ethylene‐diphosphonate appeared to be active against lung cancer NCI‐H522 cells.
Some applications of the diels–alder reaction in organosilicon chemistry
Authors: Qiu Huayu , Yu Weiyong , Du Zuodong
Published: January 2005

A review of advances in the applications of the Diels–Alder reaction in organosilicon chemistry in our laboratory is presented. Using this reaction, we have synthesized a series of organosilicon monomers and polymers with polyphenyl groups and condensed rings and established a novel vulcanization system for silicone rubber. In addition, we discuss the influences of the large aromatic groups on the properties of the polymers.
Detection of polypeptide helix‐coil transitions by nuclear magnetic resonance
Authors: Goodman Murray , Masuda Yukio
Published: December 2004

We have studied the helix coil transition for poly‐γ‐ethyl‐L‐glutamate (PELG) in the mixed solvent system: trifluoroacetic acid‐trifluoroethanol by high resolution nuclear magnetic resonance spectroscopy. At 25°, the transition occurs over a range of solvent compositions between 62–64% trifluoroacetic acid. In addition, we have assigned τ‐values to the various types of protons in PKLG.
Theory of inactivation and reactivation of transforming DNA
Authors: Bresler S. E. , Kalinin V. L. , Perumov D. A.
Published: December 2004

A simple quantitative theory of inactivation of transforming DNA has been formulated. It is based on the idea that genetic recombination of the molecule of transforming DNA with the bacterial genome is possible only, from the point mutation of the gene up to the nearest hit or point of damage on the corresponding DNA molecule. Our data and the data of other authors on the kinetics of inactivation by HNO2 or U.V. light or both are consistent with these theoretical predictions. Theoretical predictions were made concerning the extent of reactivation by fusion mid annealing of damaged DNA with a diluting genetically inactive DNA. These estimates have been reasonably confirmed by our experimental results.
On the discrimination between symmetric pentapeptides
Authors: Oesper Peter , Scheinok Perry A.
Published: December 2004

Patchornik has pointed out that identification of the dipeptides AC, GC, GA, and AG is insufficient information to allow one to distinguish between the pentapeptide sequences ACGAG and AGACG. The present study proposes a probabilistic approach which will sometimes allow one to distinguish between the parent pentapeptides when all the dipeptides have been determined quantitatively. For the case when the free amino acids have also been quantitatively determined, necessary and sufficient conditions are established for unambiguous discrimination.
Contraction–relaxation of collagen fibers in LiBr–water–acetone solutions
Authors: Sherebrin M. H. , Oplatka A.
Published: December 2004

Studies have been made of the contraction of collagen fibers in acetone due to the action of LiBr. No contraction occurs unless a small amount of water is added; on further increase of the water concentration, the fibers relax. The first contraction is irreversible. The effect of water is discussed in terms of hydrate formation.
Computation of molecular weight averages for DNA molecules containing both preformed and randomly induced single‐strand breaks
Authors: Crothers Donald M. , Spatz H.‐CH. , Elson Elliot
Published: December 2004

We derive equations for calculating the number‐, weight‐, and z‐average lengths between single‐strand breaks in DNA molecules. Provision is made for the existence of preformed breaks under genetic control: these are assumed to be fixed in number in each molecule, but may be variable in position. Breaks due to random degradation may be superimposed on the pre‐existing breaks. An example is given for illustrative purposes.
Equilibrium sedimentation of a polyelectrolyte in a density gradient of a low‐molecular weight electrolyte. I. DNA in CsCl
Authors: Daniel Ezra
Published: December 2004

Previous work had indicated that the molecular weight calculated from the equilibrium distribution of DNA in a CsCl density gradient appears to be one half the estimated value of the true molecular weight. In the present study, the sedimentation equilibrium of a polyclectrolyte in a density gradient generated by a low molecular weight electrolyte is treated in terms of the representation according to which a constant fraction of the counterions is considered permanently immobilized and the remaining fraction completely free. Equations for the preferential hydration and the molecular weight are obtained. The validity of the treatment is tested by applying it to experimental data on the equilibrium sedimentation of ϕX 174 DNA in CsCl, and it is found that the molecular weight calculated in this way is in agreement with the accepted value for this molecule. Also, recalculation of published data on density gradient centrifugation of T2 DNA in CsCl according to the present treatment brings up the molecular weight to within the range of values given by other methods.
Enthalpy of helix–coil transition from heat of solutions. III. Poly‐N‐δ‐carbobenzoxy‐L‐ornithine and poly‐N‐γ‐carbobenzoxy‐L‐α,γ‐aminobutyric acid
Authors: Giacometi G. , Turolla A. , Verdini A. S. , Snam
Published: December 2004

The helix‐to‐coil transition in dichloroethane–dichloroacetic acid (DCE–DCA) mixtures for poly‐N‐δ‐carbobenzoxy‐L‐ornithine (PCBO) and for poly‐N‐γ‐carbobenzoxy‐Lα,γ‐aminobutyric acid (PCBBA) have been studied by ORD and the “heat of solution” method. The results provide strong evidence for the existence of a very specific side‐chain/side‐chain interaction in PCBBA, which is discussed on the basis of a detailed structural model. The main sources of enthalpy and entropy changes in helix‐coil transitions of uncharged homopolypeptides in DCE–DCA mixtures are also discussed briefly.
Interaction between chondroitin‐6‐sulfate and poly‐L‐arginine in aqueous solution
Authors: Gelman R. A. , Glaser D. N. , Blackwell J.
Published: December 2004

The interactions between chondroitin‐6‐sulfate and poly‐L‐arginine in aqueous salt solution have been investigated by circular dichroism techniques. In the presence of chondroitin‐6‐sulfate, at neutral pH, poly‐L‐arginine adopts the α‐helical conformation rather than “charged coil” form observed in the absence of mucopolysaccharide. This interaction is at a maximum when the ratio of arginine to disaccharide residues is 2:1. Elevation of the temperature leads to a sharp melting transition at 76.0 ± 1.0°C. This behavior is in marked contrast to that for poly‐L‐lysine‐chondroitin‐6‐sulfate interactions, which are at a maximum at a 1:1 residue ratio and have a melting transition at 47.0 ± 1.0°C. These results indicate a stronger interaction for poly‐L‐arginine than for poly‐L‐lysine. The positive arginine side chains appear to interact with both the negative sulfate and carboxyl residues, while those of the lysines are involved only with the sulfates. Poly‐L‐ornithine at neutral pH shows no conformation directing interaction with chondroitin‐6‐sulfate, although a small proportion of α‐helix is formed on dilution of the mixture with methanol. The extent of the interaction of cationic polypeptides with chondroitin‐6‐sulfate increases in the order poly‐L‐ornithine, poly‐L‐lysine, poly‐L‐arginine, i.e., in the order of increasing side‐chain length.
Thermodynamics and kinetics of the helix‐coil transition of oligomers containing GC base pairs
Authors: Pörschke D. , Uhlenbeck O. C. , Martin F. H.
Published: December 2004

Absorbance‐temperature profiles have been determined for the following self‐complementary oligonucleotides or equimolar paris of complementary oligonucleotides containing GC base pairs: A2GCU2, A3GCU3, A4GCU4, A6CG + CGU6, A8CG + CGU8, A4G2 + C2U4, A5G2 + C2U5, A4G3 + C3U4, and A5G3 + C3U5. In all cases cooperative melting transitions indicate double‐helix formation. As was found previously, the stability of GC containing oligomer helices is much higher than that of AU helices of corresponding length. Moreover, helices with the same length and base composition but different sequences also have quite different stabilites. The melting curves were andlyzed using a zipper model and the thermodynamic parameters for the AU pairs determined previously. The effect of single‐strand stacking was considered separately. According to this model, the formation of a GC pair from unstacked single strands is associated with an ethalpy change of −15 kcal/mole. Due to the high degree of single‐strand stacking at room temperature the enthalpy change for the formation of GC pairs from unstacked single strands is only −5 to −6 kcal/mole. (The corresponding parameters for AU pairs are −10.7 kcal/mole and −5 to −6 kcal/mole.) The sequence dependence of helix stability seems to be primarily entropic since no differences in ΔH were seen among the sequence isomers.

The kinetics of helix formation was investigated for the same molecules using the temperature jump technique. Recombination of strands is second order with rate constants in the range of 105 to 107M−1 sec−1 depending on the chain length and the nucleotide sequence. Within a series of oligomers of a given type, the rates of recombination decrease with increasing chain length. Oligomers with the sequence AnGCUn recombine six to eight times slower than the other oligomers of corresponding chain length. The experimental enthalpies of activation of 6 to 9 kcal/mole suggest a nucleation length of one or two GC base pairs. The helix dissociation process has rate constants between 0.5 and 500 sec−1 and enthalpies of activation of 25 to 50 kcal/mole. An increase of chain length within a given nucleotide series leads to decreased rates of dissociation and increased enthalpies of activation. An investigation of the effect of ionic strength on AnGCUn helix formation showed that the rates of recombination increase considerably with increased ionic strength.
Solution properties of synthetic polypeptides. XV. Helix–coil transition in poly (ε‐carbobenzyloxy L‐lysine)
Authors: Matsuoka Mikio , Norisuye Takashi , Teramoto Akio , Fujita Hiroshi
Published: December 2004

Helix–coil transitions of poly(ε‐carbobenzyloxy L‐lysine) (PCBL) in m‐cresol and in mixtures of dichloroacetic acid (DCA) and ethylene dichloride (EDC) were investigated by optical rotation measurements, with special interest in the molecular‐weight dependence of helical content. The data obtained were analyzed according to an approximate expression for the helical content of Okita et al. The values obtained for the cooperativity parameter σ and transition enthalpy ΔHε (at the transition temperature) were: √σ = (0.25 ± 0.06) × 10−2 and ΔHc = 930 ± 130 cal/mole in m‐cresol, and √σ = (0.49 ± 0.10) × 10−2, and ΔHc = 350 ± 150 kcal/mole in a DCA–EDC mixture (33 vol % DCA). The ΔHc value in the DCA–EDC mixture is much smaller than that derived by Giacometti et al. from heat of solution measurements. The transition in m‐cresol was extremely sharp. This was attributed to the unusually small value of √σ and the moderately large value of ΔHc obtained.
Solution properties of synthetic polypeptides. XVI. Hydrogen bonding in helix–coil transitions of poly(β‐benzyl L‐aspartate)
Authors: Norisuye Takashi , Misumi Kozo , Teramoto Akio , Fujita Hiroshi
Published: December 2004

Helix–coil transition of polypeptides in solution involves two elementary processes: unfolding of an α‐helical polypeptide chain and interaction of the unfolded chain with solvent molecules which are capable of forming hydrogen bonds. Optical rotation data for poly(β‐benzyl L‐aspartate) in mixtures of dichloroacetic acid and carbon tetrachloride are analyzed according to the procedure developed by Sayama et al., who explicitly took these processes into theoretical account; and the enthalpy changes, ΔH0 = −650 ± 200 cal/mole and ΔHa = −5.2 ± 1.6 kcal/mole. The latter value is favorably compared with heats of association (per hydrogen bond) of various amides and lactams in CCl4. There is excellent agreement with −5.15 kcal/mole for δ‐valerolactam in CCl4. In analogy with amides in non‐polar solvents, the difference between ΔH0 and ΔHa may be attributed to the fact that the former is associated with intramolecular hydrogen bonding, whereas the latter is associated with intermolecular hydrogen bonding.
Spherical trigonometry and the structure of valinomycin
Authors: Max Nelson L.
Published: December 2004

A new method of computing the geometry of a cyclic polymer from internal coordinates is discussed, which is particularly useful if the molecule has a center of inversion symmetry. When applied to the structure of valinomycin, the calculation is reduced to solving one transcendental equation in one variable.
Cooperative nonenzymic base recognition. Kinetics of the binding of a base monomer to a complementary polynucleotide template
Authors: Hoffman Geoffrey W. , Pörschke Dietmar
Published: December 2004

The kinetics of double‐helix formation by poly U and the complementary monomer N‐6,9‐dimethyladenine (m6m9A) has been measured using a new fast temperature‐jump apparatus. The cooperative binding kinetics are complicated by the extensive self‐association of the monomers, but a satisfactory analysis using average relaxation times was possible in terms of three different models. Application of a model which considers only monomer binding yields the upper limit for the binding rate constant of an m6m9A monomer next to an already bound monomer on a poly U strand: (2 ± 0.4) × 108 M−1sec−1. A lower limit is found by using a model which allows for binding of all m6m9A stacks to poly U with equal rate constants: (3 ± 0.3) × 107 M−1sec−1. A third model with “weighted” rate constants consistent with the data: (7.5 ± 1.0) × 107 M−1sec−1. The rate of cooperative binding of m6m9A to the trimer UpUpU has also been measured. The rate constants obtained with the trimer agree with those obtained with the polymer for each of the three models within experimental error.
Electro‐optical properties of carboxymethylcellulose. I. Concentration and ionic strength dependence
Authors: Hanss M. , Roux B. , Bernengo J. C. , Milas M. , Rinaudo M.
Published: December 2004

The experimental conditions for studying the electro‐optical properties of a natural, modified polyelectrolyte, carboxymethylcellulose (DS 1.3; DP 180) were determined. The transient Kerr effect was found to be a function of CMC concentration, field strength, and ionic strength, I. If the concentration and I were low enough (c < 20 mg.l−1), saturation was obtained for field strengths of approximately 15 kV.cm−1. The optical anisotropy was shown to be independent of I; the electrical anisotropy decreased sharply when I increased. These results are discussed in connection with polarization theories of polyelectrolytes. The molecular dimensions of carboxymethylcellulose, calculated from the birefringence kinetics, suggest that the molecule is a rigid rod.
Nucleic acid–solvent interactions: Temperature dependence of the heat of solution of thymine in water and ethanol
Authors: Alvarez José , Biltonen Rodney
Published: December 2004

The heats of solution of thymine in water and ethanol have been determined calorimetrically as a function of temperature. These data, along with solubility data, have been used to calculate the thermodynamic quantities (ΔGt, ΔHt, ΔSt and ΔCp,t) associated with the transfer of thymine from ethanol to water. Since ΔSt = −2 cal/mole deg and ΔCp,t = 0, it has been concluded that hydrophobic bonding does not play an important role in the thermocynamic stability of nucleic acids.

However, large heat capacities of solution of thymine are observed in both solvents (ΔC°p2 = 45 ± 4 cal/mole deg). This is explained in terms of temperature variation in the degree of solvent–solute hydrogen bonding. It is our proposal that the components of macromolecules (i.e., nucleic acid bases and amino acids) do not make all possible hydrogen bonds with the solvent in the vicinity of room temperature. Thus the thermodynamic contribution of hydrogen bonding to the stability of macromolecules in aqueous solution must be reassessed.
The evaluation of standard sedimentation coefficient in band sedimentation of macromolecules
Authors: Belli Mauro
Published: December 2004

Standardization in the calculation of the sedimentation coefficient of macromolecules by means of band techniques is discussed. When a sample of macromolecules suspended in a solvent is layered on to a denser bulk solution, the macromolecules do not sediment in this solution alone, but sediment in a mixture of bulk solution and sample solvent. This is caused by the diffusion between sample solvent and bulk solution.

Experimental evidence of this process is shown during band sedimentation of ribosomes when the variation of the density and the viscosity along the cell is measured. The calculation shows that in the experimental conditions frequently used, standardization made in the usual way leads to a sedimentation coefficient which is largely overestimated; while standardization yields the correct coefficient if the diffusion effect of the sample solvent in to the bulk solution is taken into account, together with possible deuteration effects.

A method to calculate the standard coefficient with the aid of a computer is proposed.
Structural components of alginic acid. II. The crystalline structure of poly‐α‐L‐guluronic acid. Results of X‐ray diffraction and polarized infrared studies
Authors: Atkins E. D. T. , Nieduszynski I. A. , Mackie W. , Parker K. D. , Smolko E. E.
Published: December 2004

A structural investigation of the marine algal polysaccharide poly‐α‐L‐guluronic acid is described. The molecular chains consist of 1 → 4 diaxially linked L‐guluronic acid residues in the 1C chair conformation and are stabilized in a twofold helix conformation by an intra‐molecular O(2)H … O(6)D hydrogen‐bond. The X‐ray fiber diffraction photograph has been indexed to an orthorhombic unit cell in which a = 8.6 Å, b (fiber axis) = 8.7 Å, c = 10.7 Å.

A structure corresponding to the space group P212121 is proposed, in which all intermolecular hydrogen bonds interact with water molecules and in which all oxygen atoms except for the inaccessible bridge oxygens are involed. The relationship between the shape and structure of the polyguluronic acid molecule and its biological function is discussed.
Über die Adsorption von DNA in der Grenzfläche Quecksilber–Elektrolyt. III. Reaktionen der DNA in der Grenzfläche Quecksilber–Elektrolyt
Authors: Flemming Joachim
Published: December 2004

The adsorption of deoxyribonucleic acid in the mercury‐electrolyte interface was investigated. The effect of this adsorption on the differential capacity of the electrical double layer at the interface between a stationary mercury drop electrode (HMDE) and a buffered aqueous sodium chloride solution was measured. The dependences of this differential capacity on potential, time, and pH was studied in the presence of native and also of denatured DNA. These results were compared with the adsorption of model compounds and with the general theory of the adsorption of polymers. The structure of the adsorbed DNA molecules corresponds to an alternating arrangement of two‐dimensional, totally adsorbed sequences and three‐dimensional loops extending into the solution. The adsorbed sequences and loops consist of several segments with a specific free‐energy change of adsorption. Essentially this energy determines the distribution of the segments between adsorbed sequences and loops. The absolute value of this energy change per segment is fairly large in the case of negatively charged poly‐electrolyte DNA at the weakly positively charged interface near the electrocapillary maximum (ECM). The fraction of totally adsorbed segments is relatively large in this potential region. The more negative the potential the lower is the absolute value of free energy change of adsorption per segment. Under the conditions unfavorable for the adsorption, only a few segments can be adsorbed. Most of the segments of the adsorbed DNA molecules extend into the solution and therefore fairly high interface concentrations can be reached. Thus, the arrangement of DNA molecules in the electrode surface is changed when the potential is altered from values near the ECM to more negative ones. This change should produce the wave on the differential capacity curves at a little more negative potential than that of ECM. At a more negative potential, intermolecular interactions between the loops extending into the solution may occur. The adsorption tendency of the resulting associates is higher than that of the isolated molecules. Therefore the isolated molecules desorb at sufficient negatively charged interface producing a round wave while the associates stay adsorbed. At this potential it is impossible for native DNA to generate associates because they are formed from the isolated molecules. This explains the hysteresis loop of the curves of differential capacity vs. potential by using the HMDE. The desorption of the associates is indicated by a sharp wave at much more negative potential. For denatured DNA the associates arise from the very few isolated adsorbed molecules at this potential; therefore, no hysteresis loop occurs. The association constant of denatured DNA must be much higher than that of the native DNA. The reasons for this are discussed.
Studies on the bacteriophage MS2. XXIII. Fixation of the MS2 RNA acid structure by formaldehyde
Authors: Slegers H. , Fiers W.
Published: December 2004

When MS2 RNA is heated at low pH in the presence of formaldehyde, a fast‐sedimenting conformation is irreversibly formed. This species is homogeneous and stable at neutral pH. Its formation further requires Mg++ ions and low ionic strength. The most compact form sediments at 46S and is obtained after short reaction times at high temperature or after long reaction times at 35°C. Melting curves suggest that the specific acid conformation is not destabilized by the formaldehyde addition reaction. The pH at which this acid conformation is formed depends on the MgC12 concentration. At 10−2M MgCl2 the midpoint is pH 5.3. Removal of more than half of the bound formaldehyde has no effect on the compactness of the molecule, although most of the original secondary structure has not yet re‐formed.
Polymerization of L‐ and DL‐phenylalanine N‐carboxyanhydride by poly(N‐methyl‐L‐alanine)
Authors: Imanishi Yukio , Kugimiya Kazuya , Higashimura Toshinobu
Published: December 2004

Polymerizations of L‐ and DL‐phenylalanine N‐carboxyanhydride in nitrobenzene by poly (N‐methyl‐L‐alanine) of varying degrees of polymerization (n = 1–30) were investigated. Poly(N‐methyl‐L‐alanine) was prepared by the polymerization of N‐methyl‐L‐alanine NCA with N‐methyl‐L‐alanine diethylamide and the degree of polymerization was controlled by the molar ratio [NCA]/[Catalyst] + 1. This polymer was shown to be an asymmetrically selective catalyst which polymerized L‐phenylalanine NCA at a faster rate than DL‐phenylalanine NCA. With increasing degree of polymerization the stability of the secondary structure of poly(N‐methyl‐L‐alanine) increased. This was confirmed by circular dichroism spectra. However, the degree of asymmetric selection did not increase as the stability of the secondary structure of poly(N‐methyl‐L‐alanine) increased. These findings indicate that the interaction of a growing polypeptide in an ordered structure with NCA molecules prior to the reaction does not lead to an asymmetric selection, and that the mechanism of the asymmetric selection by poly(N‐methyl‐L‐alanine) should be different from those proposed so far.
Nmr studies of poly‐γ‐benzyl‐L‐glutamate in trifluoroacetic/deuterochloroform solutions: Temperature dependence
Authors: Brosio E. , Delfini M. , De Paolis A. , Paci M. , Conti F.
Published: December 2004

The helix–random‐coil transition process for poly‐γ‐benzyl‐L‐glutamate (PBG) in solvent mixtures trifluoroacetic acid/deuterochloroform (TFA/CDCl3) at different temperatures has been studied by nmr. The chemical shift behavior of the α‐CH resonances of the peptide chain and of the TFA carboxylic protons is reported.
The formation of the triple helix in a mixed solution of (Pro‐Pro‐Gly)n and (Pro‐Pro‐Gly)n′. A model of molecular size recognition
Authors: Suezaki Yukio , Gō Nobuhiro
Published: December 2004

A theoretical analysis is given of the triple‐helix–random‐coil transition in a mixed solution of poly(Pro‐Pro‐Gly)n with two different but defined degrees of polymerization n and n′. Because of the highly cooperative nature of this helix–coil transition, each polypeptide chain tends to form a triple helix with other polypeptide chains with the same degree of polymerization (size recognition). Occurrence of triple helices consisting of polypeptide chains with different degrees of polymerization (error in recognition) is studied in detail as a function of the cooperativity, and n and n′. Implication of this analysis for molecular recognition in general is discussed.
Synthesis of a novel fluorescent polyriboadenylic acid analog by polynucleotide phosphorylase
Authors: Tsou K. C. , Yip K. F.
Published: December 2004

Poly(1,N6‐etheno‐2‐aza‐adenylic acid) [poly(2‐aza‐εA)] was synthesized from 1,N6‐etheno‐2‐aza‐adenosine 5′‐diphosphate (2‐aza‐εADP) and Escherichia coli polynucleotide phosphorylase. The values Km = 1.02 mM, V = 1.06 μmol hr−1 enzyme unit−1 were found for the polymerization reaction. In contrast to polyadenylic acid, this novel fluorescent polymer has a random structure in solution. The application of the 2‐aza‐εADP for localization of polynucleotide phosphorylase was also described.
Solution properties of synthetic polypeptides. XVII. Stability of the α‐helical conformation of poly(γ‐benzyl L‐glutamate) in helicogenic solvents
Authors: Matsumoto Tadao , Teramoto Akio
Published: December 2004

The Zimm–Bragg parameters s and σ were determined for poly(γ‐benzyl L‐glutamate) (PBLG) in m‐cresol and in dimethylformamide (DMF) from ORD data as a function of molecular weight. It was found that, within the temperature range between 10 and 55°C and on the average, s = 1.61 ± 0.1 and √σ = 0.04 ± 0.01 in m‐cresol and s = 1.65 ± 0.05 and √σ = 0.045 ± 0.015 in DMF. The values of s in m‐cresol decreased with increasing temperature, while the values of σ in the same solvent increased. This result for s suggests that PBLG in m‐cresol will undergo a thermal helix–coil transition of normal type. The parameters in DMF showed no appreciable trend to vary with temperature. Aside from the difference between the two solvents, our results are consistent with existing data for various conformation‐dependent properties such as light‐scattering radius, intrinsic viscosity, and dipole moment, each indicating that the polypeptide chain has some flexibility in helicogenic solvents.
Conformations of cyclic 2′,3′‐nucleotides and 2′,3′‐cyclic‐5′‐diphosphates. Interrelation between the phase angle of pseudorotation of the sugar and the torsions about the glycosyl C(1′)–N and the backbone C(4′)C(5′) bonds
Authors: Yathindra N. , Sundaralingam M.
Published: December 2004

Semiempirical potential energy calculations have been carried out for cyclic 2′,3′‐nucleotides and their 5′‐phosphorylated derivatives, which are the intermediates in the hydrolysis of RNA. Calculations have been performed for both purine and pyrimidine bases for the observed O(1′)‐endo, O(1′)‐exo and the unpuckered planar sugar ring conformations. It is found that the mode of sugar pucker largely determines the preferred conformations of these molecules. For cyclic 2′,3′‐nucleotides themselves, the O(1′)‐endo sugars show a preference for the syn glycosyl conformation while the O(1′)‐exo sugars exclusively favor the anti conformation regardless of whether the base is a purine or pyrimidine. For the unpuckered planar sugar, the syn conformation is favored for purines and anti for pyrimidines. Both the gauche (+) (60°) and trans (180°) conformations about the C(4′)C(5′) bond are favored for O(1′)‐endo sugars, while the gauche (−) (300°) and trans (180°) are favored for O(1′)‐exo sugars. On the contrary, the 5′‐phosphorylated cyclic 2′,3′‐nucleotides of both purines and pyrimidines show a preference for the anti‐gauche (+) conformational combination about the glycosyl and C(4′)C(5′) bonds for the O(1′)‐endo sugars and the anti‐trans combination for the O(1′)‐exo sugars. The correlation between the phase angle of the sugar ring and the favored torsions about the glycosyl and the backbone C(4′)C(5′) bonds as one traverses along the pseudorotational pathway of the sugar ring is examined.
Conformation of histidine model peptides. I. Conformational energy calculations for L‐alanyl‐L‐histidine diketopiperazine
Authors: Grebow Peter E. , Hooker Thomas M.
Published: December 2004

Semiempirical conformational energy calculations were carried out for the cyclic dipeptide L‐alanyl‐L‐histidine diketopiperazine. The results indicate that electrostatic effects are probably significant in determining the conformation assumed by this molecule. When the imidazole group is in its uncharged state the most stable conformations of the molecule are those with the imidazole ring folded over the diketopiperazine ring (χ1 = 60°). Upon protonation of the imidazole group the folded conformation may be destabilized relative to conformations characterized by χ1 positions near 180°.
The physical properties and molecular structure of Ligamentum Nuchae elastin
Authors: Mukherjee Debi P. , Hoffman Allan S. , Franzblau Carl
Published: December 2004

The swelling and equilibrium stress–strain behavior of elastin in formamide and in its aqueous solution shows a “loosening” effect on the structure of elastin. The nature of the changes are irreversible even after the solvent has been leached out. The possible reason for such structural changes may relate to hydrophobic bonding and hydrogen bonding. Enzymatic studies on the hydrolysis of formamide treated and untreated elastin confirm these same observations.
Raman studies of the crystalline, solution, and alkaline‐denatured states of β‐lactoglobulin
Authors: Frushour B. G. , Koenig J. L.
Published: December 2004

The Raman spectra of β‐lactoglobulin in the crystalline, freeze‐dried, and solution states are compared. The spectra of the freeze‐dried and crystalline proteins were practically identical. The conformationally sensitive amide III line appearing at 1242 cm−1 increased in intensity 30% upon dissolution of the protein in water which is interpreted as a conformational change in the disordered chains of the protein. This result appears to be a phenomenon for globular proteins containing a large disordered chain fraction.

The alkaline denaturation of β‐lactoglobulin was studied. When the pH was increased from 6.0 to 11.0, the amide III line shifted from 1242 to 1246 cm−1, broadened, and decreased in intensity. This is consistent with the conversion of β‐sheet regions in β‐lactoglobulin to the disordered conformation, as has been proposed by other investigators. At pH 13.5 the amide III shifts to 1257 cm−1 characteristic of a completely disordered protein, indicating that any remaining “core” of β‐sheet has been randomized.

Several changes in the intensities of the tyrosine and tryptophan vibrations accompany the denaturation. As the pH is increased from 6.0 (native state) to 11.0 (denatured state) the intensity ratio of two tyrosine ring vibrations, I855 cm−1/I830 cm−1, decreases from 1.0:0.9 to 1.0:1.3. The same ratio for a copolymer consisting of 95% glutamic acid and 5% tyrosine at pH 7.0, where the polymer forms a random coil exposing the tyrosine to the aqueous environment, is 1.0:0.62. This ratio more closely resembles that corresponding to β‐lactoglobulin at pH 6.0 (native state) than pH 11.0 (denatured state) suggesting that the average tyrosine in the denatured state may be in a more hydrophobic environment than in the native state. A time‐dependent polymerization of the denatured protein reported by other investigators and observed by us may account for the change in the tyrosine environment.

A tryptophan vibration appearing at 833 cm−1 in the spectrum of the native state becomes weak as the pH is increased to 11.0. The intensity of this line may also reflect the local environment of the tryptophan residue.
Studies on deoxyribonucleoprotein structure. Small‐angle X‐ray scattering in solutions of various ionic strengths
Authors: Aleksanyan V. I. , Vorob'ev V. I. , Fedorov B. A.
Published: December 2004

The cross‐sectional radius of gyration of the deoxyribonucleoprotein (DNP) threads was measured by small‐angle X‐ray scattering in a wide range of ionic strengths (from 0.0005 to 2 M NaCl). For DNP in a solution of low ionic strength, this value is 30 Å. The increase of ionic strength results in partial deproteinization of DNP, while the cross‐sectional radius of gyration varies from 25 Å for DNP in 0.7 M NaCl to 10 Å for DNP in 2 M NaCl. It is suggested that gradual deproteinization by the increase of NaCl concentration causes conformational changes, which are associated with the alteration of the DNP superstructure. The data are interpreted on the basis of the superhelical model of DNA packing in DNP; however, the coexistence of superhelical and unfolded regions in the DNP structure is also a possibility.
Gel formation from solutions of single‐chain gelatin
Authors: Finer E. G. , Franks F. , Phillips M. C. , Suggett A.
Published: December 2004

The changes in conformation undergone by α‐gelatin molecules on quenching aqueous solutions to below the temperature at which they can gel have been monitored by nuclear magnetic resonance and dielectric relaxation techniques. The relative rates of these conformational transitions are compared with changes in rheological properties. The nmr spectral intensity changes for 0.2 and 0.5% w/v α‐gelatin solutions correspond to a unimolecular process with k ∼ 10−2 min−1 at 15°C; this process occurs independently of whether or not the solution is concentrated enough to form a gel. The process involves a slow intramolecular nucleation step, followed by a rapid conformational change of the whole molecule from random coil to a rigid stage. Comparison with other data suggests that the transition gives rise to a triple collagen‐like helix. In dilute solution (but above the critical concentration for gel formation, e.g., 0.5% w/v), the gelatin process follows the formation of the rigid molecular species. It probably involves the formation of junction zones consisting of three polypeptide chains in a collagen‐like triple‐helical conformation. These junctions may form, at low concentrations, from a reorganization of previously formed, intramolecular, triple helices. Solutions below a concentration of about 0.4% w/v α‐gelatin cannot gel by this mechanism, and only form viscous liquids.
Synthesis of poly(L‐Tyr‐L‐Glu‐L‐Ala‐Gly) and poly(L‐Glu‐L‐Lys‐L‐Ala) and their circular dichroism spectra in aqueous solution
Authors: Zeiger Allen R. , Lai Chang‐Hai , Maurer Paul H.
Published: December 2004

Two sequential polypeptides, poly(O‐benzyl‐L‐Tyr‐γ‐benzyl‐L‐Glu‐L‐Ala‐Gly) and poly(ε‐benzyloxycarbonyl‐L‐Lys‐L‐Glu‐L‐Ala), were synthesized, the former by the pentachlorophenyl ester of the tetrapeptide monomer and the latter by the azide of the tripeptide monomer. After deprotection and dialysis, poly(L‐Tyr‐L‐Glu‐L‐Ala‐Gly) was obtained in 71% yield and had a molecular weight of 53,000. The circular dichroism spectra (CD) of the polymer at pH's 7.2, 10.5, and 11.8 and of oligomers and of the monomer at pH 7.2 indicated that the polymer exists in an α‐helical conformation.

After deprotection, poly(L‐Lys‐L‐Glu‐L‐Ala) was obtained in 37% yield and had a molecular weight of 3000. The CD spectra of the polymer at pH 7.2 and 2.8, and of the monomer at pH 7.2, indicated that the polymer is in a randomly coiled configuration.
Potentiometric studies of hydrophobic effect on ion binding of ionic dextran derivatives
Authors: Gekko Kunihiko , Noguchi Hajime
Published: December 2004

In order to clarify the effect of degree of substitution of ionic and hydrophobic group on the polyelectrolytic behavior of polysaccharides, potentiometric titration and activity measurement of counterions were made for carboxymethyldextran (Cm‐dextran) having various degrees of substituted carboxyl group and for carboxymethylbenzyldextran (Cm‐Bzl‐dextran) containing various degrees of substituted benzyl group. From the shape of titration curve, no conformational change was observed for both Cm‐dextran and Cm‐Bzl‐dextran. The pK0 value of Cm‐dextran was independent of the degree of the degree of substituted carboxy group. However, the pK0 of Cm‐Bzl‐dextran increased with an increasing degree of substituted benzyl group. The suppression of dissociation of a carboxyl group, caused by the surrounding hydrophobic groups, was discussed mainly in terms of the change of water structure around such groups. From the results of activity measurement for counterions of these dextran derivatives, we proposed the possibility of ion selectivity based on the hydrophobicity.
Conversion of fibrinogen to fibrin. The correlation between clotting kinetics and morphology of fibrin polymerized in different solvent media
Authors: Conio G. , Trefiletti V. , Troglia C. , Patrone E.
Published: December 2004

The morphology of fibrin strongly depends on solvent medium, as shown by clotting experiments carried out in the presence of different salts. The clots were characterized by electron microscopy and spectrophotometric methods; the kinetics of gelation were determined.

In the presence of electrolytes which strongly delay clotting, the strands are thin and few branching points are observed; opposite morphological changes are induced by salts which act as accelerating agents. On the basis of this correlation, and of previous data on the structure of fibrin, a kinetic model of the self‐assembly process is outlined. It accounts well for the observed solvent effects on the morphology of the network.

An important result emerging from our experiments is that the fibers undergo branching prior to gelation. Branching points arise from the defective growth of the fibers; a simple explanation of the occurrence of branching may be obtained by our self‐assembly model.