bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction during fibril formation of soluble collagen with cartilage proteinpolysaccharide
Authors: Disalvo Joseph , Schubert Maxwell
Published: December 2004

Precipitation of soluble forms of collagen from solutions containing the soluble protein‐polysaccharide (PP‐L) of bovine nasal cartilage, followed by centrifugation at 100,000 g, resulted in the formation of coherent elastic pellets whose wet weights increased with the concentration of PP‐L in the initial solution. Dry weights and uronic acid contents of these pellets showed that the amount of water held in the wet pellet was nearly constant for any one kind and concentration of collagen, and ranged from 20 to 100 mg./mg. PP‐L in the pellet. Soluble collagens from four different sources and PP‐L from three kinds of cartilage showed similar effects. Precipitation of soluble collagen in the presence of hyaluronate or dextran yielded pellets of much smaller size than those formed in the presence of PP‐L. The presence of chondroitin sulfate had only a slight effect on wet pellet weights. Wet weights of pellets formed in the presence of PP‐L decreased with increasing ionic strength. A model involving entanglement between insoluble collagen fibrils and the relatively stiff chondroitin sulfate chains of branched PP‐L seems qualitatively capable of accounting for these results.
Conformational change in poly‐L‐lysine on reaction with polyacids
Authors: Gratzer W. B. , McPhie P.
Published: December 2004

When solutions of poly‐L‐lysine and poly(acrylic acid) in salt solutions at neutral pH are mixed, complexes are formed. Optical rotatory dispersion studies of these complexes away from the equivalence point reveals the formation of α‐helices. The α‐helix content of the polylysine never rises above about 50%. On addition of 25% by volume of dioxane, the turbidity of the complex solutions disappears, and there is some enhancement of the α‐helix content. Poly(phosphoric acid) behaves essentially in the same way as poly(acrylic acid). Poly(uridylic acid) forms complexes with polylysine but with no detectable formation of α‐helix. The same is true of ribosomal RNA and native and denatured DNA. A number of other polyacid polybase systems involving basic proteins have been examined, but again no α‐helix formation is induced. The results are related to the case of biological nucleoproitein complexes, and the conformational specificity of these systems is discussed. The effect of scattering on measured optical rotation has been investigated and is shown to be unimportant up to quite high levels.
Optical rotatory dispersion of mononucleosides and 5′‐mononucleotides
Authors: Yang Jen Tsi , Samejima Tatsuya , Sarkar P. K.
Published: December 2004

Optical rotatory dispersions between 200 and 600 mμ are presented for mononucleosides and 5′‐mononucleotides in neutral, acid, and in some cases alkaline solutions. All display a single Cotton effect in the ultraviolet region (above 220–240 mμ); the purine ones are negative in sign and the pyrimidine ones positive, with the crossovers (zero rotations) in most cases close to the wavelengths of their respective absorption maxima. The visible rotatory dispersions obey the one‐term Drude equation, except for TMP and UMP, which show anomalous dispersions. The rotational strengths of the dichroic bands were estimated from the Cotton effect profiles; cytosine mononucleotides and mononucleotides show the strongest rotational strengths among the compounds studied.
Deuteration and solvent composition effects in the helix–coil transition of poly‐γ‐beiizyl‐L‐glutamate
Authors: Karasz F. E. , O'Reilly J. M.
Published: December 2004

The effects of deuteration and of changes in solvent composition on the thermo dynamics of the helix–coil transition have been studied by calorimetric and optical measurements in the poly‐γ‐benzyl‐L‐glutamate–dichloroacetic acid–1,2‐dichloro‐ethanc system. For a given solvent composition, deuteration of the polypeptide and of the acid lowers the transition temperature Tc, while an increase in the volume fraction of acid in the solvent raises Tc. A rise in Tc is accompanied by a decrease in both the van't Hoff and the calorimetric heats of transition, but at different rates. The result is a temperature dependency in the Zimm‐Bragg cooperation parameter σ. Possible causes of this result and its implications are discussed.
Molecular configuration of amylose and its complexes in aqueous solutions. Part II. Relation between the DP of helical segments of the amylose–iodine complex and the equilibrium concentration of free iodine
Authors: Szejtli J. , Richter M. , Augustat S.
Published: December 2004

The iodine which is added to an aqueous amylose solution is bound only partly by the amylose while forming the blue complex and partly remains free. The equilibrium normality of the free and the bound iodine at half‐saturation of amylose by iodine is designated as [If]v and [Ib]w, respectively. The stability of the poly iodine chain formed within the axis of amylose helices depends on its length, i.e., indirectly on the DP of the amylose helices: the greater this stability, the lower the [If]v value. The amylose molecule consists of helical segments. Such a molecule may behave as a random coil. The average length of the helical segments in freshly prepared amylose‐iodine complexes depends on temperature, pH, iodide concentration, the presence of other complex‐forming agents, and the DP of the amylose. This latter factor is investigated in the present paper. By the aid of an automatically recording photometrictitrating device the coherent values of [Ib] and [If] were determined. Plotting these values against DPn for mechanochemically degraded as well as for periodateo‐xidized amyloses resulted in curves consisting of two linear sections. The break of the curves occurred between DPn 110 and 130. It was concluded that below DPn = 100 the DP of helical segments (= sDPn) is identical to the DPn of the total molecule, i.e., the molecule consists of only a single, relatively stiff helix. Above this limit the molecule contains several helical segments. The DP of these helical segments can be calculated as follows: sDPn = 141.1 − 10.2 × 105[If]v. This equation is considered to be valid for 0.5–0.6 mg. amylose in 100 ml. 0.1N HCl at 20°C., λ = 650 mμ, euuvet diameter 3.4 cm., the feed rate of the iodate‐iodide titrating solution (in acid medium resulting in a 5 × 10−3N I2 solution with a molar iodide to iodine ratio of 1.5) is 0.4ml./min. Amylose molecules of, e.g., DPn = 1380 consist of an average of 11.4 segments having a DP of about 120 and consisting of an average of 15–18 helical turns.
α‐Helix formation by solvent–solvent interaction
Authors: Lotan Noah , Bixon Mordechai , Berger Arieh
Published: December 2004

The degree of helicity θ of a series of homologous polypeptides as a function of solvent composition was investigated. The polypeptides studied were: poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine (PHPG) as well as the corresponding 2‐hydroxyethyl and 4‐hydoxybutyl derivatives (PHKG and PHBG, respectively). PHPG, which is nonhelical in formic acid, attains helicity on addition of relatively small amounts of formates, formamide, and urea to its solution in formic acid. This demonstrates that the high acidity of pure formic acid is largely responsible for its helix‐breaking power‐probably through protonation of the peptide bonds. In formic acid‐water mixtures all three polymers show a maximum in degree of helicity at a mole fraction of about 0.3 formic acid. This is interpreted as being due to interaction between the two helix‐breaking solvents, which results in the formation of an inactive molecular species. It is shown that solvent‐induced transitions with helicity maxima are predicted by the Bixon‐Lifson treatment when applied to this system.
Polarisation de fluorescence des polypeptides portant un groupe terminal fluorescent
Authors: Frey M. , Weill G.
Published: December 2004

The polarization of fluorescence of a chromophore chemically bound on the NH2 end of a poly(L‐benzyl glutamate) molecule has been studied as a function of temperature, viscosity, and solvent. The relaxation times depend on both the overall rotation of the helix and the local rotation of the endgroup. In m–cresol the endgroup is rigidly bound and the rotational diffusion constant of the molecule is in good agreement with the values obtained by Kerr effect and dielectric relaxation. In other helicogenic solvents (DMF, DCE, etc.) the local rotation is nearly free. In m‐cresol‐DMF mixtures a sharp decrease of the polarization around a composition of 40% DMF can be interpreted as a change in the freedom of rotation of the endgroup. No discontinuity in the optical rotation is observed in the solvent mixture. The question of how a rapidly rotating endgroup could show an extrinsic Cotton effect as observed by Bloutand Yamaoka for the system Acridine Orange–PBLG in chloroform is then raised. Polarization of fluorescence measurements on this system show a nearly complete freedom of rotation of the dye and OH D measurements show no detectable Cotton effect in the dye absorption band.
Stability of helical polyamino acids in solution at high temperatures
Authors: Franzen James S. , Harry John B. , Bobik Caroline
Published: December 2004

Optical rotatory dispersion studies have been carried out at temperatures up to 150 °C. on poly(γ‐benzyl L‐glutamate) in α‐chloronaphthalene and N‐methylcaprolactam, and on poly‐ε‐carbobenzoxy‐L‐lysine, poly‐δ‐carbobenzoxy‐L‐ornithine, and poly(L‐glutamic acid) in N‐methylacetamide. The Moffitt‐Yang −b0 values were large in all cases, but significant decreases in −b0 were observed at the upper temperature limits of the study suggesting that a transition region was being entered. Polymer degradation generally precluded examination of the systems through the suggested transition region.
Extent and stability of the α‐helix in γ‐benzyl L‐glutamate–glycine copolymers
Authors: Block H. , Kay Josephine A.
Published: December 2004

Block and random copolymers of γ‐benzyl L‐glutamate and glycine were studied by optical rotatory dispersion methods in order to ascertain the extent and stability of the α‐helix formed by these polymers in appropriate solvent mixtures. Results indicate that when in solution such polymers do contain sections of α‐helix. However, it appears that glycine does not readily fit into the α‐helix which is largely due to the γ‐benzyl L‐glutamate segments. Further, there are indications that the helical sections in the random copolymers are due to the nonrandomness of the polymerization.
Effect of glycyl residues on the stability of the α‐helix
Authors: Fraser R. D. B. , Harrap B. S. , Macrae T. P. , Stewart F. H. C. , Suzuki E.
Published: December 2004

A series of polypeptides containing ordered sequences of glyeyl and γ‐ethyl L‐glutamyl residues has been synthesized. The properties of the polymers were investigated by x‐ray diffraction, infrared spectrophotometry, and optical rotator dispersion, and the results indicate that glycine appreciably reduces the stability of the γ‐ethyl L‐glutamate helix.
Polypeptides. LIII. Water‐soluble copolypeptides of L‐glutamic acid, L‐lysine, and L‐alanine
Authors: Morita K. , Simons E. R. , Blout E. R.
Published: December 2004

The synthesis and some of the physical‐chemical properties of tricopolymers of L‐glutamic acid, L‐lysine, and L‐alanine are reported here. The molar ratios of the glutamyl: lysyl: alanyl residues were 1:1:X or 3:2:X, where the alanyl content X was increased in regular steps. The α‐helix content calculated from the optical rotatory dispersion of the polypeptides is compared with a predicted helix content estimated from the composition of the polymers and the known behavior of the homopolypeptides at pH 3, 8, and 12. At pH 3 copolypeptides containing 20 mole‐% or more alanine exhibit a helix content equal to the sum of their alanyl and glutamyl residue contents. At pH 8 the helix content equals the alanyl content when the latter was 40 mole‐% or higher; at lower alanyl contents the electrostatic interaction between charged glutamyl and lysyl residues makes some contribution. At pH 12 the amount of helix observed is proportional to the mole ratio of alanine residues present in the polymer. The helix content of a tricopolymer containing 1:1:3 mole ratios of glutamyl: lysyl: alanyl residues was determined in solutions of lithium bromide and in urea solutions. Both reagents led to a decrease in helix content at pH 3 and 8 to a minimum of approximately 20% helix in 8M urea or 5.5M LiBr. The helix–random chain transition curves at pH 3 and 8 are parallel when the urea concentration is varied, but differ in shape when the lithium bromide concentration is varied at pH 3 and 8. The mode of action of these two “denaturing” reagents may thus be different. Heating the same tricopolypeptide at pH 3 or 8 from 5 to 80°C. also led to a helix–random chain transition centered at approximately 45°C.
Interaction of metal ions with polynucleotides and related compounds. IX. Unwinding and rewinding of poly(A + U) and poly(I + C) by copper(II) ions
Authors: Eichhorn Gunther L. , Tarien Edward
Published: December 2004

It is demonstrated that, poly(A + U) and poly(I + C) are both formed under low ionic strength conditions. Continuous variation studies indicate the formation of copper(II) complexes of poly A, poly C, and poly I, but not of poly U. Copper(II) in a 1:1 ratio to polynucleotide prevents the formation of poly(A + U) and brings about the dissociation of the poly (A + U) complex produced in the absence of the metal. Poly (I + C) is similarly dissociated by copper(II) ions. The addition of sufficient electrolyte reverses the copper(II) induced dissociation of poly(I + C). The effect of copper(II) on ordered synthetic polynucleotides is thus very similar to its effect on DNA.
Anti‐cooperative interactions in single‐strand oligomers of deoxyriboadenylic acid
Authors: Vournakis John N. , Poland Douglas , Scheraga Harold A.
Published: December 2004

Optical rotatory dispersion measurements were made on the deoxyribo nucleotides d(pA)2, d(pA)4, d(pA)6 and poly(deoxyriboadenylic acid) at neutral pH over the temperature range 5–80°C. and were compared to similar data for the analogous oligoriboadenylic acids. The data were interpreted in terms of a temperature‐dependent stacking of the bases in the single‐strand deoxyribo oligomers. The thermal transition curves show an inverted chain‐length dependence compared to the ribo oligomer curves. These results are explained by a theory of anti‐cooperative interaction, where the nucleation parameter σ is >1. The theory, based on a one‐dimensional Ising model involving both attractive nearest‐neighbor and repulsive next‐nearest‐neighbor interactions, predicts the inverse chain length dependence and agrees rather well with the experimental data. At and above the transition temperature, the deoxyribo polymer is seen to consist of isolated stacked base pairs separated by at least one unit of random coil, there being only a very small probability for the existence of sequences of stacked residues longer than one. The partition function is seen to undergo an irregular behavior as a function of chain length because of the anti‐cooperative phenomenon. It is necessary to use an enthalpy of stacking of −5.0 kcal./mole in order to fit the experimental data with the theory. This value, 1.5 kcal./mole more positive than the ΔH found for the ribo oligomers, is reasonable, since the 2′ hydroxyl group would be expected to stabilize the stacking interaction in the ribo oligomers. Various kinds of distribution functions are calculated and plotted graphically for this theoretical model. A physical rationale is presented for the use of a repulsive next‐nearest‐neighbor term in this theory for the deoxyribo oligomers.
Stability of the α‐helix in poly(γ‐benzyl L‐glutamate) and related polymers
Authors: Fraser R. D. B. , Harrap B. S. , Ledger R. , Macrae T. P. , Stewart F. H. C. , Suzuki E.
Published: December 2004

A series of poly(L‐glutamic acid) esters have been synthesized and studied by optical rotatory dispersion, x‐ray diffraction, and infrared spectrometry. The results obtained emphasize the importance of the outer portions of the side chains in determining both the stability and precise conformation of the α‐helix.
Conformational aspects of polypeptides. XXIV. Conformational energies of poly‐N‐methyl‐L‐alanine chains
Authors: Mark J. E. , Goodman Murray
Published: December 2004

Conformational energies of the poly‐N‐methyl‐L‐alanine chain have been calculated as a function of the rotational angles of its skeletal bonds, taking into account torsional potentials, van der Waals repulsions, and London attractions. Four pronounced minima in the energy were found; the relative magnitudes of the energies at these minima suggest that the preferred conformation of this chain is either a right‐handed, approximately threefold helix, or a slightly distorted, left‐handed α‐helix. Inclusion of an estimate of the dipolar contribution to the total conformational energy does not significantly affect this conclusion.
Viscolastic relaxations in solutions of poly(glutamic acid) and gelatin at ultrasonic frequencies
Authors: Wada Yasaku , Sasabe Hiroyuki , Tomono Makoto
Published: December 2004

Complex shear viscosity η* = η′ –iη″ of poly (L‐glutarmic acid) solution was measured by the torsional crystal method at 50 kc./sec. as a function of pH. A sharp peak was found at the midpoint of the helix‐coil transition region in both η′ and η″. The relaxation time is calculated from η′ and η″ assuming a single relaxation process and the peak value at the midpoint of transition is estimated at 10−6sec. Such behavior agrees well with the prediction from the theory of Schwarz. The attenuation of longitudinal sound waves at,3 Me./sec. was measured as a function of pH for solutions of poly(glutamic acid), glutamic acid, and gelatin. A small attenuation peak was observed for the three solutions, the peak height being almost, the same for them. The peak is interpreted in terms of the dissociation reaction of side chains.
Effect of ions on the dielectric relaxation of DNA
Authors: Takashima Shiro
Published: December 2004

The dielectric relaxation of DNA solutions has been investigated with and without extraneous ions covering a wide frequency range. The effect of monovalent ions such as Na, K, and Li as well as divalent ions such as Mg, Ca, and Hg have been included in the study. These ions are found to have a profound effect on the dielectric increment and the relaxation time without affecting the molecular dimension drastically. This dielectric effect is interpreted as indicating the importance of counterion fluctuation on the low frequency dielectric constant of DNA in solution. The effect of an organic ion, tetra‐methylammoniun bromide, has also been studied. This ion has no noticeable effect. A simple theory is derived on the basis of a microscopic model to account for the effect of external ions on the dielectric behavior of solutions of DNA.
Synthesis of poly‐O‐tert‐butyl‐L‐serine and poly‐L‐serine
Authors: Tooney Nancy M. , Fasman Gerald D.
Published: December 2004

The synthesis of polymers containing O‐tert‐butyl‐L‐serine, O‐tert‐butyl‐DL‐serine, L‐serine, and DL‐serine is reported. The N‐benzyloxycarbonyl‐(L or DL)‐serine benzyl ester was used to synthesize the corresponding N‐benzyloxycarbonyl‐O‐tert‐butyl‐(Lor DL)‐serine benzyl ester. Catalytic hydrogenation of this material gave O‐tert‐butyl‐(Lor DL)‐serine. The reaction of O‐tert‐butyl‐(Lor DL)‐serine with phosgene produced the corresponding N‐carboxyanhydrides. The kinetics of polymerization of N‐carboxyanhydrides were investigated to facilitate, the preparation of block copolymers. The O‐tert‐butyl blocking group was removed from polymers by treatment with HCl and HBr in benzene. Both high molecular weight (water‐insoluble) and low molecular weight (water‐soluble) homopolymers have been prepared, as well as water‐soluble block copolymers of the type (DL‐serine)x (L‐serine)y, (DL‐serine)z.
Comments on the one‐dimensional ising model and its application to the cis–trans equilibrium in poly‐L‐proline
Authors: Applequist Jon
Published: December 2004

A treatment of the Finite one‐dimensional Ising model is given in which four possible nearest‐neighbor interactions are taken into account, as well as the effect of the absence of neighbors at the ends of the chain. This represents the most general situation possible when interactions are limited to nearest neighbors and when the number of accessible states of a single residue is two. Some previous treatments of the Ising model are shown to be special cases of this problem. From the symmetry of the partition function it is found that the equilibrium transition curves for chains of all lengths intersect at their midpoints if and only if the free energy of both residue states is modified to the same extent when located at an end of the chain. The shift in transition midpoints with chain length generally observed for various one‐stranded systems is thus largely a measure of an end effect, and not a junction effect, as might seem to be the case from the theory of helix–coil equilibria. These considerations appear to be important in the cis—trans equilibrium in poly‐L‐proline, where the observations of Engel on short‐chain samples suggest that the effects at junctions and at chain ends must differ significantly. It is concluded from his observations that a cis unit at the end of a chain has a less favorable free energy than a trans unit at the end. This is attributed to the fact that there are no van der Waals contacts between three residues at the end of the relatively compact cis helix and the missing adjacent turn of the helix, while the residues in the relatively open trans helix are little affected by their location at the end of the chain.
A theory on the effect of low molecular salts on the dissociation of linear polyacids
Authors: Oosawa Fumio
Published: December 2004

A theoretical analysis is given on the effect of low molecular salts on the titration behavior of partially neutralized linear polyacids or polybases. On the basis of the additivity law experimentally and theoretically established on the activity of counterions in polyelectrolyte solutions containing salts, the chemical potential of alkali added for neutralization of polyacids is derived as a function of the salt concentration. The relation between the pH and the salt, concentration at constant degree of neutralization is expressed by pH(cs) − pH(0) = ({[∂ (γpCa)/∂Ca]/γos} − 1) ln [1 + (γosCs/γpCA)] where Ca is the concentration of alkali, C8, the concentration of salts, γp is the activity coefficient of counterions in the absence of salts and γos is that in the absence of polyelectrolytes. This relation is found to be in good agreement with experimental data obtained in synthetic linear polyelectrolytes as well as in rodlike charged proteins. Therefore, it is concluded that the titration behavior of linear polyions can be understood from the special feature of the integrated coulomb interaction between linear polyions and small ions which was essential for the additivity law. In addition, the screening effect of salts on the electric potential around the polyion is discussed.
Fluorescence of proflavine–DNA complexes: Heterogeneity of binding sites
Authors: Thomes J. C. , Weill G. , Daune M.
Published: December 2004

Measurements of the relative quantum yield of fluorescence of proflavine bound to DNA as a function of the number of bound dyes per nucleotide and the ionic strength allow the determination of the binding constants and respective number of the two types of sites previously postulated. It is demonstrated that 2–3% of the base pairs form sites where the dye is strongly bound and fluoresces normally while in the other set of sites the binding constant is 3–4 times weaker and the fluorescence completely quenched. Comparison with complexes of Pro with double stranded polynucleotides poly (A + U), poly (I + C), poly(G + C), confirm that the strong binding sites correspond to A‐T‐rich regions of the DNA while the quenched sites seem to require the presence of a neighboring guanine. The role of charge transfer in quenching of fluorescence and mutagnic action is considered. An original method for the determination of free dye and bound dye, based upon the use of an external quencher is described in the Appendix.
Optical properties of polypeptides in the β‐conformation
Authors: Woody Robert W.
Published: December 2004

The rotational strengths and oscillator strengths of the nπ* band and ππ* exciton bands have been calculated for antiparallel and parallel β‐structures of varying length and width. The results are compared with experiment and with previous theoretical treatments of β‐structures. The generally good agreement of calculations on the antiparallel β‐structure with experimental results on poly‐L‐lysine and poly‐L‐serine indicates that these systems are indeed in the antiparallel conformation. It is found that the exciton component strongest in absorption shifts to longer wavelengths as the width of an antiparallel structure increases, and it is suggested that the position of the ππ* absorption band may be a useful criterion of sheet width. The results also reconcile the linear dichroism measurements of Rosenheck and Sommer on poly‐L‐lysine films with an anti‐parallel structure. Calculations on parallel β‐structures indicate that the CD spectra of this form will be rather similar to that of the antiparallel form. However, the major absorption band in the antiparallel form is associated with a small positive CD band, while in the parallel form it coincides with a large negative CD band. Finally, it is pointed out that the large positive CD bands predicted for single‐stranded parallel and antiparallel β‐structures at about 200 mμ render unlikely the suggestion that random‐coil polypeptides contain a substantial fraction of extended chain.
Some optical properties of myosin and tropomyosin
Authors: Rainford Patricia , Rice Robert V.
Published: December 2004

The optical rotatory dispersion (ORD), and to a lesser extent the circular dichroism (CD) of the proteins tropomyosin and myosin have been extensively studied. The effect of aging and of certain reagents on these optical properties, relating to helical contents, were observed. As expected, spectra typical of right‐handed, α‐helices were found, with helical contents of 60–65% for myosin and 97–100% for tropomyosin. Studies were made to find which aqueous salt solutions would permit rotation observations in the far ultraviolet and also dissolve these proteins. The presence or absence of sulfhydryl groups (SH) were found to have no effect on helicity, and it is suggested that both proteins have an identical helical portion of 40%.
Optico‐hydrodynamic properties of high molecular weight DNA from steady‐state flow birefringence and viscosity at extremely low velocity gradients
Authors: Harrington Rodney K.
Published: December 2004

The flow birefringence, extinction angles, and shear‐dependent viscosity over a velocity gradient range of approximately 0.1–3 sec−1 have been obtained for T2 bacteriophage DNA at low concentration in neutral aqueous buffer. The data are found to be interpretable and self‐consistent in terms of subchain dynamical theory, including hydrodynamic, interactions and excluded volume, and the parameters characterizing these phenomena are in good agreement with the results of other hydrodynamic experiments and theoretical calculations. No necessity for modification of the subchain model in terms of limited extensibility or internal viscosity is found for high molecular weight DNA at the velocity gradients studied, although the latter cannot be ruled out on the basis of the present data. The Kuhn statistical segment length is determined from the intrinsic optical anisotropy and is estimated as 930 Å. Implications of these findings and their relation to appropriate dynamical models for DNA are discussed.
Investigations on the resolving power of hydroxyapatite columns
Authors: Kawasaki Tsutomu , Bernardi Giorgio
Published: December 2004

An investigation on the resolving power of hydroxyapatite columns is reported. The macromolecules chosen for this investigation have been five proteins endowed with a rigid structure and of different sizes: cytochrome c, lysozyme, β‐lactoglobulin A, collagen, and T2 phage. The following points have been investigated in detail: (1) the dependence of the elution molarity upon column length and slope of the gradient; (2) the dependence of the elution molarity and the width of the protein peak upon the load and the presence of other chromatographic components; (3) the optimal conditions for the resolution of macromolecules having the same size or different sizes.
Heterogeneity of tropocollagen as investigated by chromatography on hydroxyapatite columns
Authors: Kawasaki Tsutomu , Bernardi Giorgio
Published: December 2004

The chromatography of native acid‐soluble tropocollagen from calf skin on hydroxyapatite columns has been investigated. Resolution of a number of chromatographic peaks has been obtained by using shallow slopes of the eluting phosphate gradient. The results obtained suggest a heterogeneity of tropocollagen molecules which might be due to different distributions of absorbing sites on the molecules. The results obtained have also been used to study the mechanism of chromatography of proteins on hydroxyapatite and the resolving power of the columns.
Interlocked DNA rings. II. Physicochemical studies
Authors: Wang James C.
Published: December 2004

Several species of topologically interlocked λb2b5c DNA rings (catenanes) have been prepared in vitro. The sedimentation behavior of dimeric catenanes containing 0, 1, or 2 covalently closed duplex rings has been studied as a function of the superhelical density of the covalently closed ring or rings. In general, if XtpY represents rings X and Y topologically interlocked, the sedimentation coefficient of this species, SXtpY, is related to the sedimentation coefficients SX and SY of the component rings by the empirical relationship SXtpY/SY = [(MX + MY)/MY] [1 + (MX/MY)1.78(SY/SX)1.78]−0.56

This equation can also be extended to the case where three monomeric rings are topologically linked in a chain. For two topologically interlocked monomeric rings with neither ring covalently closed, the sedimentation coefficient is 1.35 times that of the monomeric ring. This is different from results reported for mitochondrial and P22 catenanes by others. Several possibilities are discussed to account for this discrepancy. The sedimentation coefficient of a species containing one covalently closed duplex ring and a single‐stranded ring was also measured in an alkaline medium. This species, which can be easily derived from a dimeric catenane containing two covalently closed duplex rings, is particularly useful for the identification of covalently closed dimeric catenanes. Some electron microscopic studies of these interlocked rings are presented in an accompanying paper.
Location of proline derivatives in conformational space. II. Theoretical optical activity
Authors: Madison Vincent , Schellman John
Published: December 2004

The coupling of theoretical optical calculations with experimental data provides a check of the validity of the theory or provides conformational information. The theory was validated by studies in which the approximate conformation was located independently. These studies have shown that a theory restricted to the two lowest energy transitions for each chromophore gives qualitative agreement with experiment. On the other hand, for some of the proline derivatives, the theoretical treatment allows detailed conformational assignments. Both successes and failures in correlating theory with experiment are discussed. The results presented provide a basis for assessing the prospects for relating protein and polypeptide optical activity to their conformations.
Cooperativity of the helix–random coil transition determined from hydrodynamic data
Authors: Hagnauer Gary , Miller Wilmer G.
Published: December 2004

The approximations in the equation relating the viscosity of partially helical molecules to the cooperativity of the helix–random coil transition are investigated. Of the several approximations considered, only the neglect of long‐range intramolecular interactions in the random coil leads to significant error. This is a result of the inverse fourth‐power relationship between the assumed expansion factor and the cooperativity determined from analysis of experimental data. Upon approximately accounting for the random coil expansion, the experimental data of Ptitsyn et al. yield an ionic strength‐independent cooperativity in agreement with other methods.
Solution properties of synthetic polypeptides. VI. Helix–coil transition of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine
Authors: Okita K. , Teramoto A. , Fujita H.
Published: December 2004

A new procedure for evaluating u and σ characterizing σ‐helix‐forming polypeptides in solution was derived from Nagai's theory for the helix–coil transition of such polymers. Here u is the activity for helix formation from random coil, and σ is the helix initiation parameter. The necessary data are the helical content fN at fixed solvent and temperature as a function of N, where N is the degree of polymerization of the polypeptide sample. Such data were obtained from ORD measurements on a number of fractionated samples of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine (PHPG) in mixtures of water and methanol covering the complete range of composition and at various termperatures (5–40°C). When analyzed in terms of the proposed procedure, they yielded values of σ which were in the range (3.2 ± 0.6) × 10−4, substantially independent of solvent composition and temperature. These values were much larger than those obtained recently for σ of poly(β‐benzyl‐L‐aspartate) in m‐cresol and in a mixture of chloroform and DCA. The data for [η] and s0 (limiting sedimentation coefficient) as functions of molecular weight indicated that the molecular shape of PHPG in pure methanol is essentially rodlike, whereas that in pure water is not entirely randomly coiled but rather may be regarded as an interrupted helix. These indications were consistent with the results from ORD measurements. When plotted against the corresponding values of fN, the values of [η] and [s0] for PHPG in mixtures of water and methanol of various compositions and temperatures formed smooth composite curves, and we attributed these phenomena to the fact that σ of PHPG was nearly constant under these solvent conditions. Here [s0] stands for a reduced limiting sedimentation coefficient which is equal to the inverse friction factor of the solute molecule.
Effect of side‐chain hydrophobic bonding on the stability of homopolyamino acid α‐helices: Conformational studies of poly‐L‐leucine in water
Authors: Ostroy Sanford E. , Lotan Noah , Ingwall Richard T. , Scheraga Harold A.
Published: December 2004

The conformational properties of block copolymers of poly‐L‐leucine in water have been examined. The degree of polymerization of the poly‐L‐leucine block was 11 and 21, respectively, for samples prepared by the Merrifield procedure, and 56 for a sample prepared by the polymerization of leucine N‐carboxyanhydride. The optical rotatory dispersion parameter b0 was used to obtain the helix content θh at various temperatures. Application of the Lifson‐Roig theory gave the following parameters for the transition of a residue from a coil to a helical state: v = 0.05–0.011, ΔH = +100 cal/mole, ΔS = +0.70–1.00 e. u. These parameters, as well as those for other polyamino acids, are accounted for by hydrophobic bonds involving the nonpolar side chains in the helical and randomly coiled forms. From the data for poly‐L‐alanine and theoretical values of the thermodynamic parameters for hydrophobic bond formation, the parameters for formation of a polyglycine helix are computed. By separating the contributions of the backbone, it is possible to obtain a set of thermodynamic parameters for the side‐chain contributions of a number of polyamino acids. Increased size of the nonpolar side chain (with a larger contribution from hydrophobic bonding) makes a larger contribution to the stability of the α‐helix which is reflected, among other ways, in a higher helix content at given temperature.
Sedimentation of ribosomal ribonucleic acid from ribonuclease treated and untreated ribosomes
Authors: Rodgers A.
Published: December 2004

The formation of a slowly sedimenting form of 23‐S ribosomal RNA from E. coli has been investigated by analytical ultracentrifugation and thermal denaturation in aqueous solution and in formamide. Evidence is presented that the slow form of 23‐S arises as a result of nucleate damage to the RNA in the 50‐S ribosome. The 30‐S ribosome (and 16‐S RNA), is unaffected. The slow form of 23‐S RNA cannot be demonstrated under conditions of complete denaturation in formamide, but only by partial denaturation in aqueous solution of low ionic strength (< 0.01M Na). Apparent maintenance of the integrity of 23‐S RNA in formamide after nuclease treatment suggests that this may not be a simple linear molecule. An alternative model is suggested containing a circular element in the structure.
Studies on the viscosity of solutions of bovine liver glutamate dehydrogenase and on related hydrodynamic models; effect of toluene on enzyme association
Authors: Reisler E. , Eisenberg H.
Published: December 2004

The viscosity of bovine liver glutamate dehydrogenase solutions was studied at 10 and 20° C in 0.2.M sodium phosphate buffer at pH 7, in the concentration range 0.1–8 mg/ml. A method for the study of the viscosity of very dilute solutions of associating enzymes is described. It was found that the reduced specific viscosity ηsp/c of glutamate dehydrogenase continuously increases with increasing enzyme concentration, from about 4 ml/g at the lowest concentrations to about 16 ml/g at 8 mg/ml. In the presence of 10−3M GTP and 10−3M NADH the viscosity increase is much smaller and the results can be extrapolated to zero enzyme concentration to yield an intrinsic viscosity [η] = 3.2. The values of ηsp/c in phosphate buffer alone apparently extrapolate to the same value of [η], or to a value close to it. We also observe that, in the presence of toluene ηsp/c increases very much more with enzyme concentration: ηsp/c already equals 16 ml/g at a concentration of 0.75 mg/ml. These observations are in good agreement with the hypothesis that the active oligomer of glutamate dehydrogenase (MW = 312,000) associates with increasing enzyme concentration to form linear rodlike polymers of indefinite length. This association is strongly diminished by the addition of 10−3M GTP, 10−3M NADH. Toluene, on the other hand, promotes reversible association to linear polymers of very high molecular weight. The transverse and axial rotary frictional coefficients of macroscopic bodies, similar to a physical model for the structure of glutamate dehydrogenase recently advanced, were determined. Assuming that the viscosity of the model is equal to that of an ellipsoid of rotation with identical frictional coefficients, we calculate [η] = 3.26 ml/g according to Kuhn and 3.20 ml/g according to Simha, for the glutamate dehydrogenase oligomer, in good agreement with the result derived from the study of enzyme solutions.
Surface chemistry of poly(β‐beiizyl L‐aspartate)
Authors: Malcolm B. R.
Published: December 2004

Molecular monolaycrs of poly(β‐benzyl L‐aspartate) spread at. an air‐water interface have been studied. The results obtained both by direct observations on the monlayer and from examination of collapsed films with polarized infrared spectroscopy and electron diffraction are consistent with the presence of right handed α‐helices in the mono‐layer when the molecular weight is high. When 1% (v/v) isopropanol is present in the subphase the right‐handed helix prevails, provided that the monolayer is first spread on water. Monolayers of low molecular weight polymer appear to form the crossed‐β structure. Orientated collapsed films of high molecular weight polymer can be converted to the left‐handed α‐helical and to the ω‐conformation, and the mechanisms are discussed. The surface chemistry of this polymer is compared with that of related polymers and a consistent pattern of behavior emerges.
Electric dichroism studies: Interaction of trifluoroacetic acid with poly(gamma;‐benzyl L‐glutamate)
Authors: Milstien Julie B. , Charney Elliot
Published: December 2004

Electric dichroism studies on poly(γ‐benxyl L‐glutamate) show that the addition of small amounts (up to 5%) of trifluoroacetic acid causes complete disappearance of dichroism in contrast to the electric birefringence, which drops to an observable plateau at 20% of its initial value. This loss of dichroism cannot be explained simply by a decrease in the effective dipole moment of the benzyl ester side chains, and the nature of this interaction is explored by nuclear magnetic resonance and infrared spectral studies. Theories of the helix‐coil transition which require an initial protonation of the helix backbone to form a more flexible rod consisting of helical segments interrupted by regions of random coil are shown to be inadequate to describe the changes in poly(γ‐benzyl L‐glutamate) effected by small amounts of trifluoroacetic acid. Rather, trifluoroacetic acid in small amounts interacts with the ester carbonyl oxygen in the side chain, either by hydrogen bonding or protonation, before there is evidence of any effect on the backbone or of loss of helix content.
Kinetics for the transition between cis‐ and trans‐helices in poly‐L‐proline
Authors: Rifkind Joseph M.
Published: December 2004

The kinetics for the cis‐trans isomerization of long‐chain poly‐L‐proline has been studied as a function of pressure, temperature, and solvent composition in the acetic acid + n‐propanol solvent system. Our complete kinetic curves were fitted by Monte Carlo techniques, and rate constants for nucleation, growth, and termination were estimated. It was found that for the formation of a cis‐helix, high pressure, low temperature, and increased acetic acid content of the solvent, lowered the rate of nucleation relative to growth. The inverse seems to be t rue for the formation of a trans‐helix. Molecular models suggest that this behavior of the kinetic constants can be due to the exposure of peptide units to solvent in the transition state for trans nucleation, and the burying of peptide units in the transition state for cis nucleation. It is further suggested from our analysis of complete kinetic curves that at least one of the assumptions usually made in the analysis of relaxation kinetics is invalid for poly‐L‐proline.
Electrophoretic charge of a cylindrical macroion in aqueous 1 : 1 electrolyte
Authors: Mills R. A.
Published: December 2004

The potential problem is formulated for rodlike macroions and reduced to a single dimensionless equation with appropriate boundary conditions. A method of solution based on piecewise linearization of the potential equation is detailed and compared with two other approaches. It is suggested that the present method yields improved estimates of macroion charges. Some numerical results are included, and the relation between electrophoretic charge and macroion charge is considered.
Heats of water vapor sorption in swelling biopolymers
Authors: Bettelheim Frederick A. , Block Allan , Kaufman Leslie J.
Published: December 2004

Heats of water vapor sorption by three biopolymers, polygalacturonic acid, sodium hyaluronate, and calcium salt of bovine submaxillary mucin, were determined calorimetrically. These calorimetric heats of sorption were compared with the isosteric heats of sorption as a function of water uptake. Maxima in both of these functions occur at “monolayer” coverage. The differences between the calorimetric and isosteric heats are explained in terms of the irreversibility of the sorption process, especially in terms of the structural changes that occur in the biopolymers during swelling.
An obligatory α‐helical amino acid residue
Authors: Burgess Antony W. , Leach Sydney J.
Published: December 2004

Stereochemical studies predict that α‐amino isobutyric acid, one of the amino acids found in antibiotics, can fold only into left‐ or righthanded α‐helical conformations. Such residues will direct chain folding and should be useful in synthetic analogs of protein sequences to increase helix stability.
Elution properties of inhomogeneous chromatographic systems
Authors: Weiss George H. , Dishon Menachem
Published: December 2004

The first two moments of residence time in an inhomogeneous column are calculated by means of first passage time theory. These can be used to find the resolving power of the column for nearly equal amounts of protein. A recently developed perturbation theory allows the calculation of approximate elution profiles.
Analysis of the 1H‐NMR spectra of ferrichrome peptides. I. The non‐amide protons
Authors: Demarco Antonio , Llinás Miguel , Wüthrich Kurt
Published: December 2004

The thus far unexplored aliphatic region of the proton magnetic resonance spectra of ferrichrome peptides was investigated at 360 MHz. Six isomorphic diamagnetic analogues of the ferric cyclohexapeptide differing in the coordinated cation (AL3+ or Ga3+) and the amino acid composition were studied in d6‐DMSO solution. By use of a novel resolution enhancement technique which applies a sinusoidal half‐wave window to the free induction decay combined with multiplication by an increasing exponential, the proton chemical shifts and spin‐spin couplings were accurately measured. Homonuclear decoupling combined with Fourier difference spectroscopy was used to selectively extract resonances out of crowded spectral regions. The spectra revealed unique features of fine structure in the proton resonance lines. Thus, the conformation‐dependent geminal coupling constants of glycyl α‐protons were found to be constant throughout the suite of analogue peptides. A similar invariance was observed for the vicinal coupling constants between α‐, β‐, γ‐, and δ‐protons in the ornithyl side chains. Comparison of the proton spin–spin coupling constants with the crstallographic dihedral angles led to a unique stereochemical assignment of the side‐chain resonances. The combined data sets of x‐ray atomic coordinates and 1H‐nmr spin‐spin coupling parameters have been used to calibrate the coefficients for a Karplus curve related to the torsional x angles in amino acid side chains:

Structurial information was also obtained for the seryl residues, where the multiplet structures of the OH resonances indicate preferred spatial arrangements of the side chains.
The effects of aqueous neutral‐salt solutions on the melting temperatures of deoxyribonucleic acids
Authors: Gruenwedel Dieter W. , Hsu Chi‐Hsia , Lu Don S.
Published: December 2004

The helical stability of a variety of DNA samples, ranging in base composition from 0 to 72 mole‐% GC, has been studied by heat denaturation at neutral pH in increasing concentrations of LiCl, NaCl, KCl, CsCl, Li2SO4, and K2SO4. The variation of melting temperature with average base composition, dTm/dXGC, was found to decrease drastically in the concentrated salt media, e.g., from 41°C in 0.006M LiCl to 29°C in 3.2M LiCl, and from 39°C in 0.003M Li2SO4 to 18°C in 1.6M Li2SO4. At the same time, the thermal transition is much more cooperative in the concentrated salt solutions than at low ionic strength. Indeed, at limiting salt concentrations, the transition breadth seems to reach a minimum value irrespective of the compositional heterogeneity of the DNA samples. Attempts to correlate the observed decrease of dTm/dXGC with predicted changes in the enthalpy of melting, deduced from a simple theoretical treatment, experimental data on the binding of counterions and water to DNA, and experimental data on thermal denaturation, were unsuccessful. However, the strongly reduced composition dependence of the melting temperature can be understood in terms of a destabilizing effect of the concentrated salt media on GC‐base pairs. It is suggested, though not proven, that the destabilization involves the displacement of water molecules from the DNA helix.