bluuebunny/crossref_metadata_2025 huggingface dataset:
Normal vibrations of α‐glycylglycine
Authors: Dwivedi A. M. , Gupta V. D.
Published: December 2004

A complete normal coordinate analysis, infrared absorption, and inelastic neutron scattering studies on α‐glycylglycine are reported. A Urey‐Bradley force field which is also valid for N‐deuterated sample is obtained. Assignments in the low‐frequency region are based on inelastic neutron spectrum obtained in one phonon and cubic approximation.
Magnitude of a finite equilibration effect in analytical gel chromatography
Authors: Weiss George H. , Ackers Gary K.
Published: December 2004

Previous analyses of solute behavior in analytical gel chromatography1,2 have allowed for a finite equilibration time between stationary and mobile phases in estimating the magnitude of axial dispersion coefficients, but have ignored these effects in formulating the continuity equations for solute transport. We develop a more accurate theory including the equilibration effect, and show experimentally that it can be disregarded after approximately two minutes from the start of a small‐zone experiment.
On the conformation change attending the hydration of lyophilized cytochrome c
Authors: Aviram Irit , Schejter Abel
Published: December 2004

When lyophilized cytochrome c is disolved in pH 5 to 9 buffers, a spectroscopic change can be detected with a first‐order rate constant of 0.016 sec−1 at 23°, activation energy of 24.2 kcal/mole and entropy of activation of 11 e.u. The difference spectrum obtained by extrapolating the kinetic plots to zero time indicates that the form obtained by dissolving cytochrome c is in the low spin state and lacks the 695 nm band. It is proposed that the rate process observed corresponds to a conformation change in which the lysyl‐79 residue is displaced from iron coordination by the methionyl‐80 residue.
New banding species, with densities of phage‐ghost clusters, produced from lambda phage particles on storage
Authors: Costello R. C. , Baldwin R. L.
Published: December 2004

Density gradient analysis of purified lambda phage particles after storage reveals that minor species with new banding desities arise during storage. These have densities expected for phage‐ghost clusters containing integra rations of ghosts to phage particles. A lage numbersof new banding species has been observed.
The pH dependence of tyrosine cyanuration in proteins
Authors: Gorbunoff Marina J.
Published: December 2004

The pH, temperature, and reagent concentration dependences of the cyanuration of tyrosines within proteins are compared with those of the free amino acid. The results indicate that the mechanism of the cyanuration reaction is a nucleophilic aromatic substitution of the SN2 type, where the tyrosine oxygen acts as a nucleophile and the displacement takes places at a carbon atom which is part of the six‐membered ring of the s‐triazene. This reaction must compete with the hydrolysis of cyanuric fluoride in aqueous media. These competing reactions generate curves for the pH dependence of the reactivity of tyrosine with cyanuric fluoride whihc vary in a predictable manner with the extent of ionization of tyrosine and the concentration of cyanuric fluoride. In the case of proteins, the dependence of the degree of tyrosine reactivity on pH and temperature within the pH range of full reactivity of the free amino acid reflects constraints imposed by the microenvironment of these groups within the three‐dimensional structure of the macromolecule.
Study of the interaction of DNA and acridine orange by various optical methods
Authors: Fredericq E. , Houssier C.
Published: December 2004

The degree of binding of acridine orange to DNA, native or denatured, has been determined by equilibrium dialysis in 0.1M and 0.001M NaCl at 20°. The nature of the binding process has been investigated by studying various optical properties of the dye–DNA complexes and by relating them to the binding ratio. All these properties were found to vary quantitatively and qualitatively according to the successive stages of the process. These stages were assumed to be a strong binding of intercalated monomers followed by formation of bound dimers and finally by external binding of aggregates of native DNA.

Absorption spectra of the complexes could be interpreted on that basis.

Circular dichroism spectra were resolved into components: one band for intercalated monomers without interactions, two excition splittings for interacting monomers and bound dimers, respectively, weak bands and exciton splitting for external aggregates.

The fluorescence intensity was greatly enhanced in intercallated monomers; its quenching at higher binding ratio was quantitatively related to dimer fixation. The value of the anisotropy of fluorescence at low binding ratio suggested a limited mobility of intercalated monomers; the decrease of polarization at higher binding was attributed to energy transfer between monomers.

Electric dichroism displayed by the complexes in the dye absorption bands indicated an orientation of the bound molecules quite parallel to the base rings at low binding. In the range of fixation of dimers and external molecules, the dichroism was lower but still indicated an important degree of ordering.
Complexes of histone F1 with DNA in 0.15M NaCl. Circular dichroism and structure of the complexes
Authors: Šponar J. , Frič I.
Published: December 2004

Conditions were studied under which aggregated complexes of histone F1 with DNA display a circular dichroic spectrum of nonconservative type characterized by two intense negative maxima at 269 nm and 209 nm. It was found that the intensity of the longwave band depends directly on the content of guanine plus cytosine and inversely on the molecular weight of DNA. The same type of dependence was found for DNA's of eukaryotic and bacterial origin. It appears that the formation of the nonconservative spectrum which can be ascribed to a certain structural form of DNA is caused by orientation of the DNA molecules in the aggregated complex and by specific interactions of the bases of the guanine–cytosine pair. The possible mechanism of formation of nonconservative dichroic spectrum is discussed with respect to special properties of guanine.
Rapid kinetic studies on the conformation of single‐stranded DNA
Authors: Walz Frederick G.
Published: December 2004

The 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

Differential 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

Previous 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

The 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

By 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

Vacuum 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

The 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

The 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

The 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

The 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

Infrared 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

The 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

Conformational 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

The 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

The 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

A 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

Poly‐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

Reduced 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

Melting 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

The 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

The 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

A 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

By 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

An 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.
Polynucleotides. XIII. Stoichiometric and Thermodynamic Studies of Polynucleotide Helices with Non‐Complementary Residues
Authors: Lomant A. J. , Fresco Jacques R.
Published: December 2004

Stoichiometry and thermodynamic properties of polyadenylate–polyuridylate helices containing varying proportions of near‐randomly distributed non‐complementary uridine residues were charactrized from an analysis of their mixing curves and melting profiles measured at 259 nm and at appropriate longer wavelength isochromic points. The noncomplementary residues in this homopolymer–copolymer system (in which the homopolymer has the capacity to readjust with respect to the residues with which it is in opposition) show absolute preference for an extrahelical conformation even when situated in … AAUAA … sequences and must occur therefore as single loops. As the frequency of extrahelical residues in creases, the electrostatic energy of these complexes becomes greater, and is particularly severe for the three‐stranded helices. Thus, an adenyl‐ate‐uridylate copolymer containing 35.2 mole percent uridine residues does not form a three‐stranded complex with polyuridylate even in 0.7M Na+at O°C. The imperfections introduced into the helix lattice by extrahelical residues decrease the cooperativity of thermal denaturation as well as Tm. However, for the helices with extrahelical residues in low frequency (∼1 per helix turn) only small increases in concentration of charge‐neutralizing ions are required to bring Tm to the level of their perfect analogs. Two‐stranded helices with a higher density of extra helical residues (∼5 per helix turn) show [Na+] dependence of Tm characteristic of perfect three‐stranded helices. These findings together with the absence of an effect of these imperfections on the hypochromicity per base‐pair suggest only minimal disruption of helix continuity or distortion of stacking interactions that normally in volve the base pairs or triplets.
The application of surface tension measurements to the study of conformational transitions in aqueous solutions of poly‐L‐lysine
Authors: Neumann A. W. , Moscarello M. A. , Epand R. M.
Published: December 2004

The change in surface tension of solutions of poly‐L‐lysine in water has been studied as a function of temperature at various pH values. The changes at various temperatures have been correlated with changes in the circular dichroic spectra reflecting conformational change. In addition to the major transition at 50°C attributed to the conversion of the α‐helical → β conformation, two other transitions have been observed at 30°C and 80°C.

A minimum in the surface tension value was observed at pH 10, near the pK value for poly‐L‐lysine. It was concluded that at this pH the concentration of hydrophobic groups at the surface was a maximum.
An X‐Ray diffraction study of poly‐L‐ornithine hydrobromide
Authors: Suwalsky M. , De La Hoz L.
Published: December 2004

An X‐ray study has been made of the synthetic polypeptide poly‐L‐ornithine hydrobromide to investigate whether, like the chemically related polypeptides poly‐L‐lysine and poly‐L‐arginine hydrochlorides, it can undergo conformational changes merely from variations in its degree of hydration. X‐ray powder and fiber photographs of specimens with from half up to about three molecules of water per ornithine residue show features that suggest a “cross‐β‐pleated‐sheet” structure. Each pleated sheet is formed from parallel chains and the sheets are piled up along the b axis. The spacings, which do not vary appreciably with hydration, can be satisfactorily indexed in terms of an orthogonal unit cell with a = 4.60 Å, b = 30.2 Å, and c = 6.64 Å. These dimensions are shown by models to be compatible with the proposed structure. Removal of the last half molecule of water results in a very diffuse pattern but on rehydration the sharp pattern reappears. Specimens containing four to nine molecules of water per residue show a quite different pattern. Reflections other than equatorial are absent in oriented diagrams except for a 5.4 Å diffuse streak across the meridian which is suggestive of an α‐helical structure. Increasing the relative humidity from 86% to about 100% causes the a axis of the hexagonal unit cell to increase from 14.7 Å to 15.3 Å. On drying, the β structure reappears once again. These conformational changes are very similar to those observed in poly‐L‐lysine hydrochloride except that the latter shows a more stable α‐helical form. This difference may be explained in terms of stabilizing hydrophobic interactions between side chains, since ornithine has a shorter side chain than lysine.
Studies on the bacteriophage MS2. XXIV. Hydrodynamic properties of the native and acid MS2 RNA structures
Authors: Slegers H. , Clauwaert J. , Fiers W.
Published: December 2004

The molecular weight of native 26.6S MS2 RNA, of acidic 53.1S MS2 RNA and of formaldehyde‐treated 36.1S MS2 RNA was determined by light‐scattering studies. The three forms examined correspond to monomers. Also νv values were determined, and in conjunction with our previous estimates for S20,W and [η], led again to the conclusion that formaldehyde‐cross‐linked 37S MS2 RNA is a monomer. On the basis of the experimentally observed RG, [η], S20,W, and νv values, and taking a prolate ellipsoid as a model, the hydrodynamic volume, the solvation water and the axial ratio could be deduced for the three conformations. In the “native” 26S form the RNA occupies only 8.2% of the hydrodynamic volume. The formation of the 36S and the 53S structures correspond largely to a loss of solvation water.
Theory of oligonucleotide stabilization. I. The effect of single‐strand stacking
Authors: Appleby David W. , Kallenbach Neville R.
Published: December 2004

Certain theoretical difficulties present in the analysis of thermal transition properties of short complementary double‐stranded RNA oligomers can be resolved in part by introducing the stability of the component single‐stranded systems explicitly into the model. The stability constant S of the usual theories is redefined so as to contain double‐stranded pairing (τt) and single‐stranded stacking (ρ) contributions, and we analyze the statistics of two experimental systems—acid oligo(A) and oligo (An·Un) dimers—to exhibit the underlying stability parameters. We present a fitting procedure to extract values of the heats and entropies of the separated components when the required single‐strand data is unreliable or not available. The theory leads to length dependent heats and entropies for short single strands in a natural way, and permits a more accurate assessment of the contribution of partially bonded states in thermal transitions than has previously been possible.
Phase separation in the beta‐coil transition of poly‐S‐carboxyethyl‐L‐cysteine
Authors: Maeda Hiroshi , Ikeda Shoichi
Published: December 2004

The visible phase separation encountered in aqeuous system involving the β‐coil transition is investigated on poly‐S‐carboxyethyl‐L‐cysteine at a constant ionic strength of 0.2 molal. Solubility of the polymer decreases as the average charge density or pH is decreased, indicating that short‐range interactions favor the phase separation. The titration curve of the gel phase (i.e., of the pure β‐structure) is obtained by using the solubility data. Circular dichroism of the solution phase in equilibrium with the gel shows that the β‐structure is present in the solution phase. To isolate the two phases, centrifugal force is applied and it is demonstrated that the polymers in the two phases are in true equilibrium with each other. The effect of total concentration on the solubility of polymer and the degree of neutralization in each phase is interpreted in terms of the poly‐dispersity of the sample.
Optical and other properties of a hydrocarbon‐soluble polypeptide, poly‐γ‐(n‐dodecyl)‐L‐glutamate
Authors: Smith Jerry C. , Woody Robert W.
Published: December 2004

The polypeptide poly‐γ‐(n‐dodecyl)‐L‐glutamate (PDLG) is soluble in hydrocarbon solvents such as hexane, cyclohexane, and dodecane. The CD spectra of PLDG in these solvents are reported here. These spectra are typical α‐helix spectra and show none of the wavelength shifts and magnitude changes displayed by partially helical proteins in membrane preparations. This observation rules out the possibility that the membrane protein CD spectra result from solvent effects. The PDLG helix is stable in dodecane up to at least 70 °C. However, it is easily disrupted by trifluoroacetic acid, with the helix–coil transition centered at 3% TFA in hexane. Viscosity measurements of PDLG in dry dichloroacetic acid exhibit polyelectrolyte effects which can be suppressed by addition of several percent water.
Optical characterization of orientation of collagen
Authors: Chang E. P. , Chien James C. W.
Published: December 2004

The optical properties of reconstituted collagen were characterized in the frame‐work of a two‐phase model. The total birefringence is assumed to be the sum of form birefringence ΔF, of amorphous birefringence Δa, and of crystalline birefringence Δc. The contribution of ΔF has been determined as a function of strain. The intrinsic values of Δc and Δa were calculated to be 0.24 ± 0.06 and 0.055 ± 0.018, respectively. In the undeformed state, the observed birefringence is almost entirely due to the distortion of the electric field of the light at the phase boundary. Whereas there is a slight increase of form birefringence with increasing strain, the total birefringence shows much larger increments. The latter is attributable to orientation of the rodlike superstructures of the tropocollagen molecules.
Helix–coil transition and conformational studies of protamine–DNA complexes
Authors: Yu Sharon S. , Li Hsueh Jei
Published: December 2004

Protamine–DNA complexes prepared by the method of direct and slow mixing in 2.5 × 10−4M EDTA, pH 8.0, have been studied by thermal denaturation and circular dichroism. The complexes show biphasic melting with Tm at about 50 °C corresponding to the melting of free DNA regions and Tm′ at about 92 °C corresponding to the melting of protamine‐bound regions. In protamine‐bound regions there are 1.38 amino acid residues per nucleotide, indicating a nearly completely charge neutralization. Tm is increased but Tm′ is not when the ionic strength of the buffer is raised. This also supports a full charge neutralization in protamine‐bound regions. The circular dichroism of the complexes can be decomposed into two components, Δε0 of free DNA regions in B‐form conformation and Δεb of protamine‐bound regions in a characteristic conformation neither that of B‐ nor C‐form but somewhere between them.
Electric birefringence of native DNA in an alternating field
Authors: Miller Stephen J. , Wetmur James G.
Published: December 2004

The relaxation of the birefringence of native DNA in solution was investigated in a pulsed sine‐wave electric field. Relaxation times were calculated from the degree of damping of the birefringence signal and were studied as a function of the strength and frequency of the applied field, the molecular weight of the DNA, and the viscosity and ionic strength of the solvent. Relaxation times decrease with increasing field strength. For high‐molecular weight DNA (>106 daltons), the relaxation times decreased with frequency and increased less than linearly with viscosity. For low‐molecular‐weight DNA (<6 × 105 daltons), the relaxation times were independent of frequency, increased linearly with viscosity, and varied with the 1.65 ± 0.1 power of the molecular weight. The average birefringence of high‐molecular‐weight DNA decreased with frequency in 0.001M Na2 EDTA plus NaOH, pH 7.0, but is much less frequency‐dependent if the EDTA concentration is reduced tenfold, while the average birefringence of sonicated DNA increases in both solvents with increasing frequency.
Circular dichroism studies on the polymerization of N‐carboxy α‐amino acid anhydride
Authors: Akaike Toshihiro , Makino Tetsuya , Inoue Shohei , Tsuruta Teiji
Published: December 2004

The D and L copolymerizations of N‐carboxy γ‐benzyl glutamate anhydride (NCA) were carried out in a homogeneous solution with various D/L ratios, initiated by either n‐butylamine or sodium methoxide, and were followed directly by circular dichroism (CD) to observe the behavior of the secondary structure of growing polymer molecules. In the n‐butylamine system, the difference of the helical content between the righthanded and the lefthanded (Δα‐helix) gradually increased as the polymerization proceeded, while in the sodium methoxide system, the Δα‐helix had a tendency to decrease during the later stages of the polymerization. These results suggest a difference of the power of stereo‐selection of monomer antipodes by the growing chain end between these systems, the stereoselectivity by the growing chain end in the sodium methoxide system being higher than that in the n‐butylamine system.
Effect of ionic conditions on DNA melting curve parameters
Authors: Berestetskaya I. V. , Frank‐Kamenetskii M. D. , Lazurkin Yu. S.
Published: December 2004

Systematic experimental data for the dependence of melting range width ΔT for phage T2 and calf thymus DNA's on sodium ion concentration was obtained. A mathematical description of helix‐coil transition was given for the case of DNA with a block sequence of nucleotides (such as calf thymus DNA). This description predicts an almost linear dependence of ΔT for DNA from higher organisms on the value TGC‐TAT. On the other hand, ΔT is proportional to (TGC‐TAT)1.6 for DNA's with quasi‐random sequences (such as phage T2 DNA). Experimental data fully confirmed the theoretical predictions.

The dependence of TGC‐TAT on sodium ion concentration was determined. The most striking feature of this dependence is the sharp rise in TGC‐TAT in the region of low sodium ion concentration (< 3 × 10−3) up to 100°C. The dependence of TGC and of TAT on ionic strength was calculated separately. In the region of low ionic strength, these quantities show markedly different behavior.
Influence of magnesium ions on helix–coil transition of DNA determined by modified differential scanning calorimeter
Authors: Baba Yoshihiro , Kagemoto Akihiro
Published: December 2004

The thermal effect of magnesium ions on the helix–coil transition of DNA was studied calorimetrically by a modified differential scanning calorimeter (DSC). It was found that the transition temperature of DNA depends on both the DNA and magnesium ion concentrations. The dependence of the helix–coil transition of DNA on the mole ratio of magnesium ions to DNA(P) can be classified into two groups. When this mole ratio is less than 1, magnesium ions tend to stabilize the double‐helix DNA, so that the transition temperature increases linearly and the heat of transition increases significantly with increasing mole ratio. When the mole ratio is more than 1, magnesium ions tend to destabilize the double‐helix DNA, so that DNA precipitates when the temperature is raised above the transition temperature. In this case, both the transition temperature and the heat of transition decrease with increasing mole ratio.
Dielectric behavior of DNA—dye complex—II
Authors: Goswami D. N. , Gupta N. N. Das
Published: December 2004

The dielectric relaxation of native DNA and the effect of aminoacridine dyes, such as acridine orange (AO), proflavine (PF), and ethidium bromide (EB) have been investigated at different molar DNA phosphate (P) to dye (D) ratios in the frequency range 100 Hz–100 kHz. The static dielectric constant was observed to decrease with increasing binding of aminoacridines. This was interpreted as arising from the neutralization of the surface changes of the DNA molecules as a result of dye binding. At any P/D ratio the extent of charge neutralization was greatest for AO and least for the EB–DNA complex. The relaxation time (τ) for dye‐bound DNA was greater compared to that for native DNA. This increase in τ was ascribed to the increase in the length of the dye‐bound DNA. The maximum value of τ occurred at P/D = 20, 10, and 2 for AO‐, PF‐, and EB‐treated DNA, respectively. The variation of τ at various levels of binding gave a qualitative idea about the conformational changes of DNA due to its binding with the dyes.
The optical properties of alanine and proline diketopiperazines
Authors: Hooker Thomas M. , Bayley P. M. , Radding W. , Schellman John A.
Published: December 2004

The optical properties of the diketopiperazine chromophore of the cyclic dipeptides have been investigated as a function of molecular conformation. The rotatory strengths of L‐alanyl–L‐alanine diketopiperazine and L‐prolyl–L‐proline diketopiperazine have been calculated as a function of the angle of fold of the diketopiperazine ring. The results of these theoretical calculations have been compared with experimental circular dichroism and optical rotatory dispersion data. It is shown that the observed optical properties of these molecules can be explained only if their diketopiperazine rings are folded in opposite directions. The direction of fold is established for each molecule. In solution, the diketopiperazine ring of L‐alanyl‐L‐alanine diketopiperazine is folded in the direction opposite to that found by X‐ray diffraction analysis of crystals. It has been observed that the degree of conservatism of the π → π* couplet of L‐propyl–L‐proline diketopiperazine depends markedly upon the nature of the solvent that is used. In addition, a shoulder has been discovered in the CD spectrum of L‐alanyl–L‐alanine diketopiperazine, which may not be directly attributable to the n → π* and π → π* transitions of the peptide chromophores.