bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing a hypothesis: Native cellulose elementary fibrils are formed with metastable structure
Authors: Stöckmann Volker E. 
Published: December 2004

AbstractAny spinning of high‐polymeric solutions and any extruding of high‐polymeric melts produce fibrillar textures built‐up of folded molecules with a predominantly uniform period. Because data strongly suggest extended molecules within native cellulose elementary fibrils, spinning or extruding as potential fibrillar growth mechanisms must be considered unlikely. Among the crystallization conditions known to produce extended chain structures, crystallization with simultaneous polymerization appears the most plausible mechanism for forming elementary fibrils. The mechanism yields a structure distinguished by uniformity of lateral order along the fibrillar length axis with the lateral order being paracrystalline. Because thermodynamic equilibrium requires a fibrillar structure of alternating crystalline and amorphous regions, a newly grown elementaryfibril is hypothesized to be in a thermodynamically unfacorable state. Intermolecular forces “freezing‐in” the unfavorable state provide metastability. Whenever the intermolecular cohesion is weakened, a structural transformation of the paracrystalline fibril is predicted, which consists of the creation of distinctly disordered and distinctly well‐or‐dered phases. Because disorder is created, a transforming fibril contracts longitudinally. The transformation must be expected to be gradual, which gives rise to a series of intermediate metastable structures of decreasing free energy levels. With lattice type I, a fibril, however, is believed unable to reach the stable state. The equilibrium structure characterized by coexistence of perfectly ordered crystallites with completely disordered regions is thought associated with lattice type II.
Far‐ultraviolet optical activity of saccharide derivatives. II. Dextran, amylose, and mycodextran acetes; dextran and amylose xanthates
Authors: Mukherjee S. , Sarko A. , Marchessault R. H. 
Published: December 2004

AbstractThe ultraviolet ORD and CD spectra of amylose, dextran, and mycodextran acetates and some of thier oligomers were recorded in trifluoroethanol solution in the 300–185nm wavelength range. Similarly, the spectra of amylose and dextran xanthates in water solution were obtained in the 400–200 nm range. In the amylose acetate series, the monomer and dimer both show a normal acetyl n → π* transition in CD, while the trimer and the polymer both exhibit an additional, shorter wavelength peak. The latter is presumed to arise from a helical conformation of the amylose chain. This interpretation is substantiated by a helix–coil type transition of the CD spectra of amylose triacetate at elevated temperatures and a reversion of the anomalous CD to the normal CD upon partial deacetylation. By contrast, neither dextran acetates nor mycodextran acetate exhibit any conformational effects. The CD of dextran acetates is quite sensitive to β‐1,6 and branch linkages. The ORD and CD of amylose xanthate are complex, suggesting the presence of organized structure in solution. The dextran xanthate shows only a simple ORD spectrum and no observable CD.
Effwct of temperature on the circular dichroism spectra of polypeptides in the extended state
Authors: Tifany M. Lois , Krimm S. 
Published: December 2004

AbstractThe circular dichroism (CD) spectra of poly‐L‐proline and of poly‐L‐glutamic acid and poly‐L‐lysine in their charged states have been studied as a function of temperature. The variation of CD spectra with temperature is inconsistent with the assignment of the spectrum of such charged polypetides to an unordered chain conformation, but does support our earlier assignment to a locally ordered structure—what we have called the extended helix conformation. These results also strengthen our previous assignment of the CD spectrum of an unordered chain, and indicate that three conformational states (α‐helix, extended helix, and unordered) should be incorporated in our thinking about conformational transitions in polypeptides.
Correlation between the backbone and side chain conformations in 5′‐nucleotides. The concept of a ‘rigid’ nucleotide conformation
Authors: Yathindra N. , Sundaralingam M. 
Published: December 2004

AbstractConformational energies of the 5′‐adenosine monophosphate have been computed as a function of χ and ψ, of the torsion angles about the side‐chain glycosyl C(1′)–N(9) and of the main‐chain exocyclic C(4′)–C(5′) bonds by considering nonbonded, torsion, and electrostatic interactions. The two primary modes of sugar puckering, namely, C(2′)‐endo and C(3′)‐endo have been considered. The results indicate that there is a striking correlation between the conformations about the side‐chain glyocsyl bond and the backbone C(4′)–C(5′) bond of the nucleotide unit. It is found that the anti and the Gauche–Gauche (gg), conformations about the glycosyl and the C(4′)–C(5′) bonds, respectively, are energetically the most favored conformations for 5′‐adenine nucleotide irrespective of whether the puckering of the ribose is C(2′)‐endo or C(3′)‐endo. Calculations have also shown that the other common 5′‐pyrimidine nucleotides will show similar preferences for the glycosyl and C(4′)–C(5′) bond conformations. These results are in remarkable agreement with the concept of the “rigid” nucleotide unit that has been developed from available data on mononucleotides and dinucleoside monophosphates. It is found that the conformational ‘rigidity’ in 5′‐nucleotides compared with that of nucleosides is a consequence of, predominantly, the coulombic interactions between the negatively charged phosphate group and the base. The above result permits one to consider polynucleotide conformations in terms of a “rigid” C(2′)‐endo or C(3′)‐endo nucleotide unit with the major conformational changes being brought about by rotations about the P–O bonds linking the internucleotide phosphorus atom. IT is predicted that the anti and the gg conformations about the glycosyl and the C(4′)–C(5′) bonds would be strongly preferred in the mononucleotide components of different purine and pyrimidine coenzymes and also in the nucleotide phosphates like adenodine di‐ and triphosphates.
Showing up the thermal transconformation of Na–DNA in solution by noise spectrography
Authors: Vasilescu Dane , Teboul Maurice , Kranck Hubert , Camous Bernard 
Published: December 2004

AbstractMeasuring the equivalent noise resistance of Na–DNA solutions in NaCl provides in formation about the free ino atmosphere. In an Arrhenius type diagram, the helix → coil transition is clearly brought Out. A Calculation of the number of free ions in the solution as function of temperature, reveals once more the process of ejection of compensating Na+ ions form the macromolecules during the thermal transconformation.
Studies on cytochrome c. Part VIII. Synthesis of the protected hexadecapeptide (sequence 93–108) of Baker's yeast iso‐1‐cytochrome c
Authors: Moroder Luis , Marchiori Fernando , Borin Gianfranco , Scoffone E. 
Published: December 2004

AbstractThe synthesis is described of the protected hexadecapeptide corresponding to the C‐terminal sequence 93–108 of baker's yeast iso‐I‐cytochrome c. The cysteine residue in position 107 of the natural sequence has been substituted by a threonine residue. The rationale of this substitution as well as the synthetic route to the preparation of the hexadecapeptide derivative is discussed.
Electrophoretic light scattering as a probe of reaction kinetics
Authors: Berne B. J. , Giniger Rina 
Published: December 2004

AbstractA new method is proposed for determining chemical rate contants in dimerization reactions of globular proteins. Light scattering from a solution of charged macromolecules in and applied electric field gives a series of bands whose widths can be used to deduce the reaction rate contants. This method should be applicable to other types of peactions. First order reactions are also considered.
Optical absorptions of aliphatic amino acids in the far ultraviolet
Authors: Inagaki T. 
Published: December 2004

AbstractThe far ultraviolet absorptions of aliphatic amino acids such as glycine, alanine, aminobutyric acid, valine, and leucine were measured with their solid thin films down to 120 nm. Four absorption bands arising from the carboxyl group were observed in the 200–140 nm region. It was found that the band positions and intensities vary systematically according to the number of carbon atoms in the aliphatic side chain. This result may be interpreted as a phenomenon similar to the hyper‐and hypochromisms of aliphatic homopolypeptides in far ultraviolet region.
Sedimentation and intrinsic viscosity behavior of PM2 bacteriophage DNA in alkaline solution
Authors: Ostrander Daryl A. , Gray Horace B. 
Published: December 2004

AbstractThe sedimentation coefficient and intrinsic viscosity of nicked and closed circular PM2 bacteriophage DNA have been measured as a function of pH in the alkaline region. A gradual increase in the sidimentation coefficient, and a corresponding decrease in the intrinsic viscosity, are observed for the superhelical (closed) circle in the pH region from 10.5 to about 10.9. This has been tentatively interpreted in terms of the known dependence of sedimentation coefficient upon the number of superhelical turns. At slightly higher pH values, the curve passes through the minimum (sedimentation coefficient) and maximum (intrinsic viscosity) expected when the superhelical turns present at neutral pH are unwound by partial alkaline denaturation. Sedimentation studies of the relaxed (nicked) circular species have revealed the existence of DNA forms in the pH region from 11.27 to 11.37 which sediment considerably faster than the closed circle in the same pH region. These have been identified as partially denatured nicked circles, in which varying fractions of the duplex structure have undergone alkaline denaturation, but strand separation has not yet occurred. Varying fractions of a slower species, either undenatured or completely denatured nicked circles, are also observed in some of these experiments. A corresponding result is observed in the intrinsic viscosity vs. pH curve.When nicked circular PM2 DNA is exposed to various alkaline pH's, rapidly neutralized, and sedimented at neutral pH, the expected sharp transition from native to denatured (strand‐separated) molecules is seen. However, a very narrow pH range is noted in which native and denatured forms coexist in a single experiment. The above experiments carried out upon the closed form also reveal a narrow pH range in which the bulk of the transition from native closed circles to the collapsed cyclic coil takes place, in acccord with an earlier study on a different DNA. This transition is shown never to be completely effected, however, as there is a fraction (7–8%)of the closed circles which renature to the native form, regardless of the alkaline pH employed. This same phenomenon was not observed in the case of artificially closed λb2b5c DNA circles. Possible explanations for some of the above results are discussed.
Conformation of cyclic dipeptides from empirical energy calculations
Authors: Chandrasekaran R. , Lakshminarayanan A. V. , Mohanakrishnan P. , Ramachandran G. N. 
Published: December 2004

AbstractEmpirical energy calculations on cyclo‐Gly‐X with X‐ Phe, Tyr, Val, and Leu as a function of the side‐chain torsion angles χ indicate that the conformation of minimum energy are characterized by χ1 = 60°, χ2 = 90° for Phe and Try, χ1 = −60° for Val and χ1 = −60°, χ2 = 180° and χ1 = 60° and χ2 = 150° for Leu. The minimum energy conformation of cyclo‐Gly‐Phe and cyclo‐Gly‐Val have the side chains of Phe and Val stacked over the poperazinedione ring as suggested by NMR and found for cyclo‐Gly‐Tyr crystal structure. In contrast, the Leu side chain is expected to exist in an extended or a quasi‐folded form.
Polymerization of DL‐phenylalanine NCA initiated by copolymer of sarcosine and DL‐phenylalanine
Authors: Imanishi Yukio , Sugihara Toshiharu , Higashimura Toshinobu 
Published: December 2004

AbstractPolymerizations of DL‐phenylalanine NCA by block copolymers of sarcosine and DL‐phenylalanine, designated by (Phe)m(Sar)n and capable of reaction at the phenylalanyl terminal, were investigated in nitrobenzene solution at 25°C. With increasing n for constant m (m = 0, 1, 2, and 5), the polymerization rate greatly increased. Previously the acceleration of the initiation reaction in the polymerization of DL‐phenylalanine NCA by polysarcosine (m = 0) was reported. The present results showing the acceleration by the copolymers of sarcosine and DL‐phenylalanine indicate the presence of the polymer effect in the propagation reaction as well. However, the polymer effect was most marked with polysarcosine (m = 0), and decreased with increasing m.The same polymerizations by sequential copolymers composed of ten sarcosine units and two DL‐phenylalanine units were also investigated. Again with these copolymer catalysts the polymerization rate was larger than that by monomeric amines. But the polymer effect decreased sharply when the phenylalanine units take positions near the terminal amine group of the copolymer catalyst.These two deteriorating effects of the phenylalanine unit have been interpreted in terms of the decrease of the flexibility of polymer chain, caused possibly by an intramolecular hydrogen bond of the phenylalanine unit.
Rotational relaxation of macromolecules determined by dynamic light scattering. II. Temperature dependence for DNA
Authors: Schmitz Kenneth S. , Schurr J. Michael 
Published: December 2004

AbstractCorrelation functions have been determined for the fluctuating intensity of the depolarized component of forward‐scattered laser light from solutions of DNA. The molecular correlation function of calf thymus DNA (mol wt ∼15 × 106) appears to exhibit a longest relaxation time (τ25,w, ∼ 18 msec) close to what one would predict from the flowdichroism measurements of Callis and Davidson and, in addition, manifests a spectrum of faster times down to tenths of milliseconds. Furthermore, a major fraction of the amplitude of fluctuations in the angular distribution of segment axes is relaxed on a very much shorter time scale (of the order of 20 microseconds) that appears to be relatively insensitive to molecular weight of the DNA, or to near‐melting temperatures.The temperature profile of the longest relaxation time has been obtained and found to exhibit a peculiar spike near Tm, which, together with the absence of a corresponding spike in the (high shear) viscosity, has been interpreted as indicative of an increase in the molecular weight of the DNA in a narrow temperature region near Tm. Correlation functions for polarized light scattered at finite angles were obtained in an attempt to determine the temperature dependence of the translational diffusion coefficient. Although the data contain an extremely slow component that does not admit a simple interpretation, there is some indication of a decrease in the translational diffusion coefficient near Tm, thus supporting the notion of an aggregation occurring near Tm. Finally, a “counterion escape” mechanisn is proposed for the apparent aggregation.
On the interaction of lithium salts with model amides
Authors: Balasubramanian D. , Shaikh Rashid 
Published: December 2004

AbstractResults of a study of the interaction of alkali metal salts on model aliphatic amides are reported. Lithium salts appear to interact more strongly with amides than those of other alkali metals. Spectroscopic investigations suggest that Li+ ion binds to the amide group at the carbonyl oxygen, causing a change in the spectroscopic properties and the geometry of the amide. Such binding of ions to amide groups may be of importance when one studies the spectral and conformational changes of polypeptides and proteins in high salt media.
The contribution of proton fluctuation to dielectric relaxation in protein solutions
Authors: South G. P. , Grant E. H. 
Published: December 2004

AbstractEquations are derived which account for the effect of an applied electric field on the fluctuation of protons associated with a macromolecule. The contribution of this proton polarization to the complex permittivity of the macromolecules is evaluated in terms of its effect on both the dispersion due to proton fluctuation and the dispersion caused by dipolar rotation. An expression for the fluctuation correlation time τiδ is derived in terms of the mean lifetimes of the ionised and unionised state τ0 and τ+. If τiδ is very much less than the dipolar correlation time τi, the fluctuation dispersion will occur at much higher frequencies than the dispersion due to orientation polarization; hence the dispersions will be well separated. If τiδ » τi the two regions would overlap and would be indistinguishable as separate entities. At present insufficient data are available to test rigorously these conclusions but the potentialities of the theory in relation to small globular proteins is shown.
Occurrence of β‐chain conformation in poly‐γ‐methyl glutamate membranes
Authors: Nakajima Akio , Fujiwara Takashi , Hayashi Toshio , Kaji Keisuke 
Published: December 2004

AbstractMolecular chain conformations of poly‐γ‐methyl‐L‐glutamate, poly‐γ‐methyl‐D‐glutamate, and poly‐γ‐methyl‐D,L‐glutamate in membranes prepared by using mainly trifluoroacetic acid and formic acid as solvents were investigated by infrared, X‐ray diffraction, and optical rotatory dispersion measurements. It was pointed that these polymers exist in the α‐helix form in membranes cast from trifluoroacetic acid solutions, but in the β‐chain form in membrances swollen in formic acid. The β‐chain structure was also observed in crystals precipitated from dilute solutions including formic acid. The formation of the β‐chain structure was discussed.
Structure of guanosine‐3′,5′‐cytidine monophosphate. I. Semi‐empirical potential energy calculations and model‐building
Authors: Stellman S. D. , Hingerty B. , Broyde S. B. , Subramanian E. , Sato T. , Langridge R. 
Published: December 2004

AbstractThe conformation and packing scheme for guanosine‐3′, 5′‐cytidine monophosphate, GpC, were computed by minimizing the classical potential energy. The lowest energy conformation of the isolated molecule had dihedral angles in the range of helical RNA's and the sugar pucker was C3′ endo. This was used as the starting conformation in a packing search over orientation space, the dihedral angles being flexible in this step also. The packing search was restricted by constraints from our x‐ray data, namely, (1) the dimensions of the monoclinic unit cell and its pseudo‐C2 symmetry (the real space group is P21), (2) the location of the phosphorous atom, and (3) the orientation of the bases. In addition, a geometric function was devised to impose Watson‐Crick base pairing. Thus, a trial structure could be sought without explicit inclusion of intermolecular potentials. An interactive computer graphics system was used for visualizing the calculated structures.The packing searches yielded two lowest energy schemes in which the molecules had the same conformation (similar to double‐helical RNA) but different orientations within the unit cell. One of these was refined by standard x‐ray methods to a discrepancy index of 14.4% in the C2 pseudocell. This served as the starting structure for the subsequent refinement in the real P21 cell.5
Conformational analysis of a cyclic nucleotide: 3′−5′‐Adenosine monophosphate. A study based on the extended Hückel theory
Authors: Lespinasse Jean Noël , Vasilescu Dane 
Published: December 2004

AbstractThe extended Hückel theory (EHT) was used as a quantum mechanical approach for the determination of the best conformation of cyclic AMP. Both geometrical and quantum mechanical studies were necessary to ascertain the configuration of the sugar ring and phosphate ring. This was due to the fact that no crystallographic data are known for the ribose phosphate part of this nucleotide.The calculations have shown that the sugar ring takes a 3T4 (C3′‐endo–C4′‐exo) configuration while the phosphate ring exhibits a chair form. Once the geometry of the rigid ribose–phosphate block is resolved, the problem of the determination of the best conformation for cyclic AMP is reduced to the determination of the position of the adenine base with respect to this ribose phosphate part.The study of the rotation of the adenine base around the glycosidic bond C1′–N9 revealed that the two conformations anti (χ = 30°) and syn (ξ = 210°) are possible with an energy difference of only 1 kcal × mole−1. This theoretical calculation is in good agreement with experimental data.
Calorimetric investigation of the helix–coil conversion of polyuridylic acid
Authors: Heinecke Marion , Bode Diedrich , Schernau Ulrich 
Published: December 2004

AbstractThe heats of the conformational conversion ΔHc of polyuridylic acid (polyU) in the presence of various cations were determined using a differential scanning microcalorimeter and an isothermal mixing calorimeter. The first method yields a value of ΔHc = 5.2 kcal/mol of base pairs, the second one a value of ΔHc = 6.4 kcal/mol of base pairs. Knowing ΔHc and the maximal slope of the degree of conversion, which was determined from the temperature dependence of the absorbance of polyU solutions at 260 nm, we were able to evaluate the parameter of cooperativity σ. From the relation σ = e the stacking free energy ΔFstack could be calculated. Dividing the apparent enthalpy of conversion by the calorimetrically measured enthalpy yields the cooperative length N0 of one helical segment at the midpoint of conversion. The results show that the type of the cation has no influence on the magnitude of ΔHc, whereas the cooperativity of polyU is influenced by the various cations.
Raman spectra of copoly(D,L‐alanines)
Authors: Itoh Koichi , Hinomoto Tetsu , Shimanouchi Takehiko 
Published: December 2004

AbstractRaman spectra in the region 1000–150 cm−1 were measured for copoly(D,L‐alanines) with the D‐residue contents, 3, 7, 10, and 20%, and compared with the spectrum of the α‐helical poly‐L‐alanine. The 532‐ and 378‐cm−1 peaks were assigned to the L‐residues with a right‐handed α‐helix‐like local conformation or to the D‐residues with a left‐handed α‐helix‐like local conformation. From the intensity of the latter peak the contents of these local conformations were estimated as a function of the D‐residue contents for the copolymers. The 264‐cm−1 peak, which has been assigned to the breathing vibration of the α‐helical poly‐L‐alanine, shows a marked decrease in its intensity upon the introduction of the D residues. This result suggests that the overall deformation vibration of the α‐helix arises from rather long sequences of the L‐ and D‐alanine residues with the α‐helical conformation and that the intensity of this vibration depends on the content of these sequences in the copolymers.
The infrared absorption spectrum of dextran and its bound water
Authors: Heyn Anton N. J. 
Published: December 2004

AbstractAlmost complete assignments are presented for the infrared absorption spectrum of dextran. These assignments were made by normal group analysis of the subaltern bands within the broad composite bands constituting the spectrum, and by examining the conclusions in the light of normal coordinate analysis of the repeat unit of this polymer.The α‐1,6‐glycosidic linkages in dextran have been found to result in lower intermolecular hydrogen bonding than in other glucans and this explains many features of the spectrum, including the occurrence of a variety of bands originating from different types of bound water. Particularly, a very strong band at 800 cm−1 corresponding to the libration vibration of ice, which occurs in the spectrum of freeze‐dried dextran, is of great interest and has been ascribed to “organized” water.