bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid kinetic studies on the conformation of single‐stranded DNA
Authors: Walz Frederick G. 
Published: December 2004

AbstractThe conformational states of single‐stranded calf thymus DNA were probed using the tmeperature‐jump kinetic technique. A rapid decrease in transmission at 260 nm followed by a broad relaxation spectrum was observed for single‐stranded DNA at 0.15M KCI, pH, 6.5 at 25°. The relaxation spectrum could also be detected as a hydrogen ion release. Sonicated samples of 103,000 daltons showed identical relaxation kinetics as unsonicated samples. The relaxation kinetics were studied as a function of temperature, pH, and salt concentration and could be interpreted as representing the melting of short, isolated folded segments. The rapid process that could not be kinetically resolved is interpreted as single‐strand unstacking. Upon the addition of excess MgCl2 at pH 7.0, a hydrogen ion release from single‐stranded DNA was observed that was 3.5 times greater than that observed for a comparable sample of native DNA. Evidence is presented which indicates that charge‐pairs exist in folded segments that are A‐T rich. There was no kinetic evidence of structures in single‐stranded DNA other than single‐stranded stacking and short isolated folded regions.
Calorimetric investigations of crystalline 3′,5′‐cyclic nucleotides
Authors: Bryan A. M. , Olafsson P. G. 
Published: December 2004

AbstractDifferential enthalpic analysis of a series of 3′,5′‐cyclic nucleotides indicates that homolytic cleavage of the six‐membered phosphate ring occurs either immediately prior to or concurrent with decomposition of the crystal lattice. Homolysis is followed by a rapid polymerization to yield oligonucleotides. The enthalpies of these reactions have, with the exception of guanosine 3′,5′‐cyclic phosphate, almost identical values of 25 kcal/mole. The anomalous case is attributed to a more stabilized phosphate ring as a result of hydrogen bonding through the two position of the purine ring. The pair of overlapping exothermic peaks observed in each of the thermograms for cAMP and cIMP is related to the presence of two conformational arrangements within the unit cell of each compound.
Thermodynamics of ligand binding on dilute polymer molecules in solution: Complementary monomers and oligomers on polynucleotides
Authors: Hill Terrell L. 
Published: December 2004

AbstractPrevious work on the thermodynamics of small systems is applied to the binding of ligands on dilute polymer molecules in solution, and especially to the binding of complementary monomers and oligomers on polynucleotides. Topics emphasized are: binding isotherms, optical melting curves, calorimetric melting and mixing studies, role of the activity of the ligand, quasi phase transitions, the polymer phase diagram, and interrelations between these subjects. The one‐dimensional Ising model (linear and circular) is used to illustrate some of the thermodynamics. An Appendix shows how the ligand activity in salt solution may be found from vapor pressure osmometry measurements.
Studies on cytochrome c. Part IV. Synthesis of the protected dodecapeptide (sequence 45–56) of Baker's yeast iso‐1‐cytochrome c
Authors: Borin Gianfranco , Moroder Luis , Marchiori Fernando , Scoffone Ernesto 
Published: December 2004

AbstractThe synthesis is described for the N‐benzyloxycarbonyldodecapeptide tert‐butoxycarbonylhydrazide corresponding to the sequence 45–56 of baker's yeast iso‐1‐cytochrome c by fragment condensation using the Rudinger modified azide procedure for the assembly of the small subunits.
Extended conformations of polypeptides and proteins in urea and guanidine hydrochloride
Authors: Tiffany M. Lois , Krimm S. 
Published: December 2004

AbstractBy analyzing the effect of urea and guanidine hydrochloride on the circular dichroism of many polypeptides and proteins, it is concluded that under conditions of high concentration of the perturbant and at low temperatures the resultant state approached is that of a local extended helix structure instead of a completely random coil. Intensification by urea and guanidine hydrochloride of the circular dichroism bands of poly‐L‐proline II leads to the proof that the mechanism of interaction of urea and guanidine hydrochloride with proteins is through hydrogen bonding to the backbone carbonyl group.
Vacuum ultraviolet spectroscopy of poly‐α‐amino acids
Authors: McMillin C. R. , Rippon W. B. , Walton A. G. 
Published: December 2004

AbstractVacuum ultraviolet spectra are reported for a series of poly‐α‐amino acids which were film cast onto lithium fluoride discs. The solvents used for film casting were chosen such that chain conformations representative of those normally found for polypeptides were produced. Comparison of the spectra obtained suggests that the peptide group has at least one conformationally sensitive transition in the vacuum ultraviolet region at ∼165 nm. For the β, or extended, form of the polymers, the intensity of this transition appears to be greater than that found for the monomer units, whereas the formation of a more compact helix results in a reduction in the intensity of this transition relative to that found for the monomers.
Action of hemoglobin. The energy of interaction
Authors: Saroff H. A. 
Published: December 2004

AbstractThe energy of interaction is developed for three of the models applied to the action of hemoglobin. Evaluation of an energy of interaction requires a model defining the unperturbed or statistical process from which the real system is derived. The shape of a ligand binding curve by itself does not yield an energy of interaction since a steepened ligand binding curve may result from either a negative or positive energy of interaction.
The rate of γ‐benzyl‐L‐glutamate NCA polymerizations
Authors: Williams Fred D. , Brown Ronald D. 
Published: December 2004

AbstractThe primary amine initiated homopolymerization of γ‐benzyl‐L‐glutamate NCA in dioxane at 25°C, 35°C, 50°C, and 65°C has been investigated. The reactions were virtually independent of temperature indicating an activation energy of less than 1 kcal/mole. The entropy of activation was estimated to be −65 entropy units at 300°K. The reaction proceeded in two stages. The first stage was zero‐order with respect to monomer, whereas the second was first‐order with respect to monomer. Both stages were first‐order with respect to initiator. These results were interpreted by assuming that the rate constant for propagation was not independent of the degree of polymerization up to the point where a conformational transition to α‐helix occurred.
Studies on cytochrome c. Part VII. Synthesis of the protected undecapeptide (sequence 82–92) of Baker's yeast iso‐I‐cytochrome c
Authors: Moroder Luis , Borin Gianfranco , Marchiori Fernando , Scoffone Ernesto 
Published: December 2004

AbstractThe synthesis is described of the N‐benzyloxycarbonylundecapeptide tert‐butoxycarbonylhydrazide corresponding to the sequence 82–92 of baker's yeast iso‐I‐cytochrome c.
Polynucleotides. XI. Thermodynamics of (A)N·2(U)∞ from the dependence of TmN on oligomer length
Authors: Blake R. D. , Fresco Jacques R. 
Published: December 2004

AbstractThe variation in the helix‐coil transition temperature, TmN, with oligomer length, N, for the system

has been examined. The results for N = 4‐13, measured in 0.2M Na+, have been analyzed in terms of the expression of Blake (1972):

where cm is the free oligomer concentration at TmN, and Vrf is the thermodynamic free volume available to a helical base‐triplet residue. The correlation coefficient for the fit to expression (II) of data obtained over a 50° temperature range is 0.997 when ΔHr = −12.6 kcal/mole of base‐triplets (independent of oligomer length (N ⪖ 4) or temperature), the value previously obtained from both calorimetry of (A)∞·2(U)∞ and (A)4 concentration dependence of Tm. It is found that Vrf = 8.0 × 10−4 1/mole (± 30%) or 1.33 Å3 per helical base‐triplet, and is constant with temperature. A maximum value for Vrf of 21.0 × 10−4 1/M (± 1.3%), equivalent to 3.54 Å3 per helical basetriplet is obtained by the same treatment of the helix‐coil transition data for the three‐stranded helix formed by adenosine (N = 1) and 2(U)∞ obtained by Davies and Davidson (1971).
The vibrational spectra and structure of poly (rA‐rU). Poly (rA‐rU)
Authors: Morikawa Kosuke , Tsuboi Masamichi , Takahashi Seizo , Kyogoku Yoshimasa , Mitsui Yukio , Iitaka Yoichi , Thomas George J. 
Published: December 2004

AbstractInfrared and Raman spectra of aqueous poly(rA‐rU)·poly(rA‐rU), the double‐helical complex containing strands of alternating riboadenylate and ribouridylate residues, display significant differences from one another and from corresponding spectra of poly(rA)·poly(rU), the double‐helical complex of riboadenylate and ribouridylate homopolymers. Parallel studies on the copolymer and homopolymer complexes by cesium sulfate density gradient centrifugation, ultraviolet absorption spectroscopy, hydrogenion titration, 1‐N oxidation of adenine residues by monoperphthalic acid and X‐ray diffraction reveal, however, that the geometry of base pairing between adenine and uracil is closely similar in each complex and apparently of the Watson‐Crick type. Therefore the differences observed between vibrational spectra of poly (rA‐rU)·poly (rA‐rU) and poly(rA)·poly(rU) are not due to different base‐pairing schemes but may be attributed to differences in vibrational coupling between vertically stacked bases. Vibrational coupling may also account for the differences between infrared and Raman spectra of the same complex. Thus, the present results indicate that infrared and Raman frequencies of RNA in the region 1750–1550 cm−1 should be dependent on the base sequence.
Effect of residual side chain blocking groups and side chain charge on polypeptide conformation in aqueous solution
Authors: Rao S. P. , Miller W. G. 
Published: December 2004

AbstractThe circular dichroism (CD) spectrum of poly‐L‐lysine and poly‐L‐glutamic acid has been investigated in the presence of a small percent of side‐chain blocking groups. The blocking groups benzyl, methyl, and carbobenzoxy show qualitatively similar effects. Less than five mole percent of aromatic blocking groups alters the CD spectrum. Consequently, unsuspected blocking groups may account for the variation observed in CD spectra of these polymers. A weak CD band at 235–240 nm was observed for the disordered unblocked polymer even in the absence of electrolyte. Viscosity data indicate that in salt‐free solutions these chains at neutral pH still behave as random coils though with reduced conformational freedom, in contrast to some polyelectrolytes which behave as rigid rods in the absence of electrolyte. The viscosity data bring into question the relevance of isolated molecule conformational calculations to experimental CD spectra.
Electrostatic interactions in polyglutamic acid
Authors: Rai J. H. , Miller W. G. 
Published: December 2004

AbstractConformational energy estimates were made for completely charged polyglutamic acid with different assumptions concerning the placement of side chain charge. Viewed as a helix, the minimum energy structure is somewhat affected by the side‐chain charge placement. The average energy of the chain viewed as a random coil is equal to or less than the average energy of the chain viewed as a helix. Unlike the polyacrylate chain, nearest‐neighbor charge interaction is shown to increase the chain dimensions. Although the calculations are approximate there is little evidence to suggest that isolated polyglutamate molecules in the absence of added electrolyte should behave as rods or that there are significant amounts of locally ordered structures. Presently no experimental results exist under conditions appropriate to isolated molecular calculations.
A proton magnetic relaxation study of human ferrihaemoglobin in aqueous salt solutions
Authors: Pifat G. , Maričič S. , Grandja Š. 
Published: December 2004

AbstractThe proton magnetic relaxation time, T1, has been measured at 29 MHz in 0.1M KH2PO4 and 0.1M NaCI (both pH 6) aqueous solutions of human ferrihaemoglobin, the protein concentrations ranging from 0.5 to 5 mM per haem. The linear dependence on protein concentration of the enhancement in relaxation rates, Δ(1/T1), due to the presence of the paramagnetic iron in haemoglobin was confirmed at 34°C and at ∼10°C. In the middle temperature range there is a thermally activated process, whose energy of activation depends on protein concentration. This dependence is different for the two salt solutions; Ea increases with cHb for 0.1M KH2PO4 and decreases for 0.1M NaCI.The model of water‐proton exchange between the bulk solvent and the sixth coordination site of the haem iron was used to calculate the distance from the “liganded” water protons to the haem iron. This yields distances much larger than those determined by X‐ray crystal structure analysis. A model is proposed which reconciliates both types of data. The low‐temperature relaxation rates cannot be used in deriving quantitative stereochemical data for the haem pocket because of its special shape. Irrespective of the molecular model adopted, the experimental results show clearly that, both at low (∼10°C) and higher (>34°C) temperatures, the interaction of paramagnetic haem iron with water protons is practically the same for the two aqueous solutions. The dynamic state of the haemoglobin molecule, as indicated by the middle‐temperature range, is completely different in 0.1M KH2PO4 and 0.1M NaCl, pH 6.
The solution behavior of poly‐L‐proline: I. Light scattering studies in water and concentrated aqueous neutral salt solutions
Authors: Schleich Thomas , Yeh Yin 
Published: December 2004

AbstractThe solution bebavior of poly‐L‐proline Form II has been studied in water and aqueous salt solutions by both elastic and quasi‐elastic light ‐scattering techniques. The results of this study suggest that polyproline Form II can exist in water at 24 °C as an associated polymer complex and that certain salts which do not appear to affect the helix integrity, e.g., guanidinium‐HCl, resutl in dissociation of the aggregate. Other neutral salts, of the variety effective in mediating unfolding of the Form II helix (e.g., 4M NaClO4) also induce aggregate dissociation, but 4M CaCl2 results in enhanced aggregation of polyproline. Kinetic experiments indicate that a time of 20 hours is necessary for the completion of the “large” to “small” transformation (at 22°C) which is induced by the addition of 4M NaClO4. Thus it appears that neutral salts additives in aqueous solutions of polyproline influence both the state of aggregation and the conformation of this polymer.
The effect of alkali and alkaline earth salts on the structure of hydrated collagen fibers as studied by deuterium NMR
Authors: Fung B. M. , Wei Shirley C. 
Published: December 2004

AbstractA detailed study on the deuterium NMR of hydrated collagen in the presence of alkali and alkaline earth salt is reported. The effect of different salts in reducing the deuteron quadrupole splitting are similer at low molar content of salt. At higher salt contents, larger ions are more effective. The ressults are explained by the blocking of water binding sites to collagen by hydrated ions. When the temperature is reduced, only part of the adsorbed water iss frozen, and the amount of “unfreezable water” decreases with the increase in ionic sizes(LiCl < MgCl2 < KCL < KCNS). The freezing temperature is also lowered in the presence of salts. A description of the structure of hydrated collagen based upon the observed facts is given.
Conformational studies of anthrax polypeptide, subtilis polypeptide, and synthetic poly‐γ‐Lglutamic acid
Authors: Balasubramanian D. , Kalita C. C. , Kovacs J. 
Published: December 2004

AbstractPoly‐γ‐L‐glutamic acid has been synthesized by the activated pentachlorophenyl ester polymerization method and the molecule weight of the polymer was found to be 16,000. Comparative conformational studies on the synthetic and on the native polyglutamic acid mbtained from B. anthracis and B. subtilis were carried out using optical rotatory dispersion, circular dichroism, peptide absorption spectrum, and titration data. These results show that poly‐γ‐glutamic acid does not exhibit any conformational order under the conditions of investigation. At low degrees of ionization, restriction of conformational freedom via random “hypercoiling” of the chain appears likely.
The viscosity behavior and conformations of low‐molecular‐weight poly‐γ‐benzyl‐L‐glutamate in various solvents
Authors: Imae Toyoko , Ikeda Shoichi 
Published: December 2004

AbstractReduced viscosity and infrared spectra of low‐molecular‐weight poly‐γ‐benzyl‐L‐glutamate (which was prepared by polymerization of the N‐carboxyanhydride with n‐hexylamine initiation at [A]/[I] 3, 4, and 8) have been measured in various organic solvents. Infrared spectra indicate that the polypeptide molecules consist of a series of residues of two forms, the solvated σ‐form and the hydrogen‐bonded β‐form, and relative abundance of the two forms depends on solvent species and polypeptide concentration. An approximate method is developed for estimating the content of β‐structure from a single spectrum of dissolved polypeptide. The reduced viscosity of some solutions is scarcely dependent in polypeptide concentration, in which a single conformation is predominantly kept over the concentration range. In the other solutions the reduced viscosity displays a strong concentration dependence or some anomalous behavior. The observed viscosity behavior has been attributed to the changes in size and shape of aggregates, which are determined by the number of hydrogen bonds in the aggregate. This unusual behavior is exhibited by solutions of the polypeptides which have a moderate content of β‐structure at a finite concentration. Both the content of β‐structure and the extent of association increase in the following solvents, ranked in order of effectiveness: dimethylformamide, trifluoroethanol < trimethyl phosphate < chloroform < dioxane < ethylene dichloride < ethylene dibromide. Infrared spectra suggest that the conformation of the polypeptide in dichloroacetic acid differs from either the σ‐ or the β‐conformation.
Thermal transitions in E. coli tRNAfMet and two of its molecular fragments
Authors: Kallenbach N. R. , Ma R. I. , Ofengand J. , Siddiqui M. A. Q. 
Published: December 2004

AbstractMelting curves of tRNAfMet and two fragments derived from this molecule by limited ribonuclease T1 digestion (i.e., the anticodon arm and loop [K fragment] and the larger fragment representing three‐fourths of the tRNA chain from the 3′ terminus including two potential limbs of the cloverleaf structure [L fragment]) are presented. The profiles observed are consistent with the presence of base paired structures in all those molecules. At low salt concentration (0.02M Na+) the stabilities of these molecules measured by the apparent midpoints of the denaturation profiles are in the order K > L > tRNA. The relative stabilities approach each other at 0.2M Na+ (the tRNA profile being biphasic), while at high salt (2M) the L fragment seems to be more stable than either K or t‐RNA fMet. Estimation of the enthalpy of denaturing the K structure in 0.02M Na+ gives a value of 40 ± 3 kcal/mole corresponding to an enthalpy per effective G.C. base pair disrupted of 10 ± 1 kcal/mole.
Solvent dependence of the helix–coil transition of poly‐γ‐benzyl‐L‐glutamate. A PMR study
Authors: Ferrara Luciano , Temussi Piero A. 
Published: December 2004

AbstractThe coil to helix conformational transitions undergone by poly‐γ‐benzyl‐L‐glutamate in solutions of haloacetic acids and various cosolvents were studied by means of proton magnetic resonance. The results indicate a very small solvent dependence of the α‐CH Helix–coil chemical shift difference. The helical stabilities of PBLG in different solvent mixtures were interpreted in terms of modifications of the “solvent structure.”
Cooperative nonenzymic base recognition. Thermodynamics of the helix—coil transition of a monomer—polymer double helix
Authors: Hoffman Geoffrey W. , Pörschke Dietmar 
Published: December 2004

AbstractThe double‐helical complex formed from m6m9A and poly U has been characterized by circular dichroism and u.v. spectrophotometry. The circular dichroism of the complex is similar to that of the double‐helical poly A poly U complex both in shape and in magnitude and thus indicates a quite similar structure. The double Helix–coil transition has been studied at various nucleotide concentrations and at three different ionic strengths. As expected for the binding of a base to a polymer, the Helix–coil transition is shifted to higher temperatures by increasing nucleotide concentrations, but is not affected by changes of the ionic strength. The melting curves are analyzed according to a linear Ising model taking the stacking of the monomers into account. At 0°C the equilibrium constant for nucleation is found to be 2–5 M−1 and that for chain growth is 500 M−1. The enthalpy change associated with chain growth is −11.2 ± 1 kcal M−1.
Conformational analysis of dipeptides in aqueous solution. II. Molecular structure of glycine and alanine dipeptides by depolarized rayleigh scattering and laser Raman spectroscopy
Authors: Avignon M. , Garrigou‐Lagrange C. , Bothorel P. 
Published: December 2004

AbstractA new approach to the experimental conformational analysis of peptides in aqueous solution is presented and discussed. The basic idea is to combine laser Raman spectroscopy and depolarized Rayleigh scattering in order to interpret scattering properties of the dissolved molecule in terms of both local and global structure. We outline a simple method (anisotropic perturbation treatment) appropriate for solving conformational problems in large molecules by studying together slightly perturbed homologous compounds. This method is applied to the study of the molecular structure of simple glycine and alanine dipeptides. The preferred conformation for such molecules is the seven‐membered chelated ring (C7) additionally stabilized by two intermolecular hydrogen bonds involving one molecule of water.
Hydration‐dependent α–β transconformation of sodium poly‐L‐glutamate as observed by X‐ray diffraction
Authors: Mitsui Yukio 
Published: December 2004

AbstractBy X‐ray diffraction method, an originally almost dry oriented fiber of sodium poly‐L‐glutamate was shown to undergo transconformation from β‐structure to α‐helices when its water content was gradually increased by equilibrating with the helium gas of 64% relative humidity. The observation is correlated to the corresponding infrared spectroscopical study made by Blout et al.
Conformational energy and circular dichroism computed for cyclo‐(Pro‐Gly)3
Authors: Madison Vincent 
Published: December 2004

AbstractAn analytic cyclization procedure has allowed the complete specification of c‐(Pro‐Gly)3 conformation by three dihedral angles. Utilizing this simplification, the intramolecular potential energy of c‐(Pro‐Gly)3 has been computed over all of conformational space. Conformers with all peptide bonds trans have the lowest total potential energy. Circular dichroism spectra calculated for the low‐energy regions provide the basis for the interpretation of experimental CD spectra.