bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cooperative interactions in single‐strand oligomers of adenylic acid
Authors: Poland Douglas , Vournakis John N. , Scheraga Harold A. 
Published: December 2004

AbstractOptical rotatory dispersion measurements were made on the oligonucleotides (pA)2, (pA)4, and (pA)6 at neutral pH over the temperature range 5–85°C., and compared to similar data for polyriboadenylic acid. The data were interpreted in terms of a temperature‐dependent stacking of the bases in the single‐strand oligomers, with very little dependence of the degree of stacking on the chain length. These results can be explained by a theory of cooperative stacking. The degrees of freedom available per residue are rotations about the five backbone covalent bonds and the bond connecting the base to the ribose ring. To nucleate a stacking interaction between neighboring bases the backbone sequence must be ordered as must be the two bases. For this stack to grow by one base a backbone sequence must again be ordered, but only one additional base must be ordered. Thus, the degree of freedom of the base with respect to the ribose ring determines the extent of the cooperative effect and hence the effect of chain length. A matrix formulation of the partition function is presented which incorporates this cooperative nature of the interaction and is shown to be in fair agreement with the data. The entropy of ordering a base with respect to the ribose ring is found to be 0.68 e.u., which suggests that the purine has a torsional oscillation when unstacked, but does not have several isoenergetic positions of internal rotation available. The enthalpy of stacking is found to be −6.5 kcal./mole. A model involving neighbor and next‐nearest neighbor interactions could also account for the data. For all practical purposes, the stacking interactions of successive residues can be treated as independent, i.e., the state of one residue is essentially independent of the state of stacking of its neighbors.
The ultrasonic degradation of biological macromolecules under conditions of stable cavitation. I. Theory, methods, and application to deoxyribonucleic acid
Authors: Pritchard N. J. , Hughes D. E. , Peacocke A. R. 
Published: December 2004

AbstractSolutions of calf thymus DNA have been degraded in the presence of vibrating air bubbles in ultrasonic fields of low power which would not normally induce ultrasonic cavitation. The DNA was degraded to a limiting intrinsic viscosity, after which further irradiation by ultrasound had little or no effect. This limiting intrinsic viscosity decreased with increase in the ultrasonic intensity. Previously developed theories have‐been adapted to calculate the maximum velocity gradient associated with the streaming of the solution around such vibrating air bubbles. The tensile force which is induced and which acts on the DNA has been calculated on the basis of current theories of degradation by hydrodynamic shear. These calculations indicate that the degradation of the DNA by ultrasound under conditions of “stable cavitation” is mainly the result of the shearing forces engendered in the solution around the oscillating bubbles.
Computation of the sterically allowed conformations of peptides
Authors: Leach S. J. , Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractThe sterically permitted conformations for various di‐ and tripeptides have been described using mathematical and computer methods outlined in an earlier paper. The effects of variations in the size and shape of the side‐chain groups on the allowed conformations have been assessed. Steric restrictions, due to the backbone atoms alone, permit the peptide groups adjacent to glycyl residues to assume only about 50% of all conceivable conformations. An alanine side chain limits these to 16% and, with further side chain complexity, restrictions increase so that the backbone adjacent to valyl or isoleucyl side chains can take up only about 5% of all possible conformations. The results of the computations are therefore consistent with what is known of the ability of various residues to fit into α‐helical polypeptide chains, and of the comparative stabilities of the α‐helical forms of poly‐L‐alanine and polyglyeine. The rigid ring structures in prolyl peptides provide such severe steric restrictions that, a trans polyprolyl chain can exist only in a left‐handed helical form of the type observed experimentally for collagen II. Other factors which have been investigated are the effects of possible variations in the geometry of the planar amide backbone and in van der Waals' contact distances between atoms on the sterically permitted backbone conformations. The evaluation of steric restrictions emphasizes their important role as a determinant in protein conformation, and the results will lie useful in applying the computer techniques to the determination of the conformation of longer polypeptide chains.
Numerical solutions of the Lamm equation. II. Equilibrium sedimentation
Authors: Dishon Menachem , Weiss George H. , Yphantis David A. 
Published: December 2004

AbstractThe Lamm equation has been solved numerically for conditions corresponding to equilibrium runs for a nonlinear concentration dependence of the form s/s0 = (1 + kc)−1. It is shown that the approach to equilibrium is very close to being exponential (in time) as in the case k = 0. We also compare results for the nonlinear case given above with results obtained for linear c‐dependence of the form s/s0 = 1 – kc. For relatively high speeds the time required to attain equilibrium may be greatly underestimated by use of the latter approximation. Finally, we present analytic approximations for the concentration distribution at equilibrium and as a function of time.
Studies of the birefringence and birefringence dispersion of polypeptides and proteins
Authors: Oriel P. J. , Schellman John A. 
Published: December 2004

AbstractAn apparatus has been constructed which permits the polarimetric observation of streaming solutions of macromolecules. The apparatus is a streaming birefringence device allowing the usual measurements of birefringence parallel to the cylinder axis but which in addition transmits light in the radial direction. Installation of the apparatus between the polarizer and analyzer of a Rudolph polarimeter makes possible the measurement of changes in optical rotation, dichroism and birefringence. The present work is concerned with the latter effect. The systems studied were α‐helical polyglutamic acid, paramyosin, and collagen (ichthyocol). The combined measurements of radial and axial birefringence completely determines the refractive index ellipsoid of the streaming fluid. This result in turn permits the testing of the Peterlin‐Stuart distribution function for streaming in a Couette device, apart from a proportionality constant. The comparison between theory and experiment is very satisfactory provided the system is reasonably homogeneous with regard to molecular length and is sufficiently dilute. On the other hand, it is concluded that the Peterlin‐Stuart optical factor seriously overestimates the “form” birefringence in agreement with recent results and conclusions of Taylor and co‐workers. The apparatus permits the study of the dispersion of the birefringence in the radial direction. The dispersion of collagen follows a one‐term Sellmeier formula and is dominated by absorption bands in the neighborhood of 2000 A. On the other hand, the dispersion of the α‐helical systems is complex and requires a multiterm Sellmeier formula. This contrast between the two kinds of polypeptidc helices is similar to results obtained with other optical techniques and is attributed to the splitting of absorption bands in the α‐helix.
Effect of aggregation on the optical rotatory dispersion of poly(α,L‐glutamic acid)
Authors: Tomimatsu Y. , Vitello L. , Gaffield W. 
Published: December 2004

AbstractLight‐scattering measurements show that poly(α,L‐glutamic acid) (PGA) is strongly aggregated at the low pH's (4.0–4.3) usually used to measure the mean residue rotation at the trough, [R′]233, and that [R′]233 becomes more negative with aggregation. Concurrent weight‐average molecular weight measurements by light‐scattering and [R′]233 measurements by optical rotatory dispersion as a function of pH show that a maximum negative value for [R′]233 (unaffected by aggregation) is obtained at higher pH's (4.53–4.82). Precautions should be taken to insure that the Na‐PGA sample used as standard does not aggregate at the low pH's required for its complete conversion to the helical form. An Na‐PGA sample meeting the above requirements gives [R′]233 of −14,600° ± 1.5% over the pH range 4.53–4.82 in 0.05M NaCl.
Steady‐state kinetics of enzyme‐catalyzed copolymerization on primers
Authors: Bloomfield V. 
Published: December 2004

AbstractThe theory of the steady‐state kinetics of irreversible enzyme‐catalyzed homopolymerization and copolymerization on primers has been developed. The rate law for homopolymerization is of the Michaelis‐Menten form, but the kinetic parameters depend on primer concentration. Copolymerization has been treated for two monomers considering both terminal and penultimate effects and for four monomers considering terminal effects. The composition equations and conditional probabilities for monomer succession are identical for enzymatic and nonenzymatic processes, because the steady‐state approximation is used in both cases. The reactivity ratios and steady‐state velocities are different, however. Examination of published results for AU and UG copolymers synthesized by polynucleotide phosphorylase permits evaluation of reactivity ratios for the AU copolymer and indicates that penultimate effects may be operative in both cases.
Electro‐optical studies of conformation and interaction of polynucleotides
Authors: Jakabhazy S. Z. , Fleming S. W. 
Published: December 2004

AbstractMeasurements by the technique of electric birefringence with pulsed sinusoidal electric fields on polyriboadenylic acid (poly‐A) and polyribouridylic acid (poly‐U) indicate that the kinetics of the double‐stranded helix formation of poly (A + U) in the presence of Mg2+ is second order and consists of two steps: nucleation and propagation of base pairs from nuclei. The nucleation involves approximately 7 base pairs. It seems that the requirement of 7 base pairs to start the formation of a double‐stranded helix is not peculiar to poly (A + U) but is associated with double‐stranded helices of polynucleotides in general. This implies that it may be associated with spatial requirements of the phosphate‐sugar backbone, rather than with the particular bases linked to the backbone. The decline in rate of poly (A + U) formation observed above a critical temperature is the consequence of changes in the poly‐A conformation setting in at this critical temperature, rather than resulting from an increase in the reversibility of the base‐pair propagation step of double‐stranded helix formation. The dominant role of the conformation of poly‐A in the double‐stranded helix formation of poly (A + U) is further borne out by the pH dependence of the rate which completely parallels the conformation changes known to occur in poly‐A as a function of pH. This indirectly suggests that at neutral pH poly‐A is a single‐stranded helix. The rotary diffusion coefficients attest to the flexibility of this helix, while the stacked nature of the base pairs at low temperatures is revealed by the identical increments in the specific Kerr constant on going from poly‐A to poly (A + U) and from poly (A + U) to poly (A + 2U) helices. Results suggest that Mg2+ binds to the phosphate part of the backbone. Poly‐U binds Mg2+ more strongly than poly‐A; this difference in binding strength is attributed to differences in conformation (random coil versus helix). It is also borne out by the present results that the degree of order in the structure of poly‐U, even at low temperatures and neutral pH, is at best an order of magnitude smaller than that of poly‐A under similar conditions. Furthermore, the earlier proposed double‐stranded structure of poly‐U is called into question. A hairpinlike structure seems to agree with results of this investigation. Finally, the results support the contention that the ion atmosphere polarization is responsible for orientation of polyelectrolytes in the presence of alternating electric fields in the neighborhood of 25 kc./sec. frequency.
Potentiometric titration of poly(L‐glutamic acid) in aqueous solutions and binding of divalent cations
Authors: Kono Naoko , Ikegami Akira 
Published: December 2004

AbstractThe potentiometric titration of poly(L‐glutamic acid) was performed under conditions of varied ionic strength and concentration of added divalent cations. From these titration curves, the amount of divalent cations, especially magnesium, bound to poly(L‐glutamic acid) was determined using a new method of analysis based on polyelectrolyte theory. By comparison with the polyelectrolyte, poly(acrylic acid), it was found that there are no specific interactions between metal ion and poly(L‐glutamic acid) in either the helical or random coil conformation. The effect of these divalent cations on the conformation of poly(L‐glutamic acid) was also discussed.
Intramolecular steric effects and hydrogen bonding in regular conformations of polyamino acids
Authors: Leach S. J. , Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractA survey has been made, by using computer methods, of the types of helices which polypeptide chains can form, taking into account steric requirements and intramolecular hydrogen‐bonding interactions. The influence on these two requirements, of small variations in the bond angles of the peptide residues, or of small changes in the overall dimensions of the helix (pitch and residues per turn), have been assessed for the special case of the α‐helix. Criteria for the formation of acceptable hydrogen bonds have also been applied to helices of other types, viz., the 3, γ−, ω−, and π‐helices. It was shown that the NH … O and H … OC angles in hydrogen bonds are sensitive to changes in either the NCαC′ bond angle or in the rotational angles about the NCαand CαC′ bonds. However, the variants of the α‐helix observed experimentally in myoglobin can all be constructed without distortion of the hydrogen bonds. For α‐helices, the steric and hydrogen bonding requirements are more easily fulfilled with an NCαC′ bond angle of 111°, rather than 109.5°. The decreased stability observed for the left‐handed α‐helix relative to the right‐handed one forL‐amino acids is due essentially only to interactions of the Cβatom of the side chains with atoms in adjacent peptide units in the backbone, and interactions with atoms in adjacent turns of the helical backbone are not significantly different in the two helices. Restrictions in the freedom of rotation of bulky side chains may have significant kinetic effects during the formation of the α‐helix from the “random coil” state.
On the form of the partition function for the helix–coil transition of random copolymers
Authors: Crothers D. M. 
Published: December 2004

AbstractThe purpose of this paper is to examine and contrast several formulations of the partition function for the helix–coil transition of random‐sequence nucleic acids. In the exact approach, the sequence of bases in a given molecule is fixed, but this leads to expressions which are difficult to evaluate. Another approach is to make a summation over all possible sequences, each weighted by the probability of its occurrence, thereby in effect allowing all sequences to a given molecule. The error in this approach is that it does not guarantee that the average base sequence is random. This difficulty can, in principle, be overcome by applying successively increasing constraints on the system to ensure that all moments of the distribution are equal to the random‐sequence values. It is shown for the particular case of short molecules which melt only from the ends that the convergence of this method to the true solution is poor. The major conclusion is that composition fluctuations which cover a sizeable region of the molecule must be included in an accurate description of the melting transition.
Enthalpy changes in the helix‐coil transition of poly(γ‐benzyl L‐glutamate)
Authors: Karasz F. E. , O'Reilly J. M. 
Published: December 2004

AbstractThe helix‐coil transition temperature Tc of poly(γ‐benzyl L‐glutamate) in binary solvent mixtures of dichloroacetic acid and 1,4‐dichlorobutane, 1‐chlorooctane, or 1‐chlorododecane have been measured. A treatment is presented with which the transition enthalpy can be calculated from the observed dependence of Tc on solvent composition. Results are compared with previously obtained calorimetric data. The underlying assumptions of the calculation are discussed.
Molecular weight fractionation and the self‐suppression of complex coacervation
Authors: Veis Arthur , Bodor Edward , Mussell Shirley 
Published: December 2004

AbstractA marked molecular weight fractionation accompanies the demixing or phase separation resulting from the complex coacervation of mixtures of aqueous solutions of salt‐free isoionic unfractionated gelatins with pI's of 5 and 9. Viscosity studies show that the fractionation is such that the concentrated phase tends to maintain constant, homogeneous composition. A second feature, seen in phase volume and concentration measurements, is a marked self‐suppression of coacervation intensity with increasing mixing concentration. These data were interpreted in terms of a dilute‐phase aggregate model which assumes nearly equal electrostatic free energies of mixing in dilute aggregate and concentrated random phase. The driving force for phase separation is the entropy increase upon formation of the random phase but demixing also depends upon the polymer‐solvent interaction parameter χ, in the same fashion as in simple coacervation. The dilute‐phase aggregate model indicates that the sharp molecular weight selection takes place in the aggregate formation step and explains the self‐suppression. Phase equilibria studies utilizing fractionated, paucidisperse high molecular weight gelatins, emphasize the requirement for concentrated phase homogeneity and indicate that aggregates of different molecular weight may act as different components, so that χP1Q1,PkQk > 0, bringing about a separation of the system into three or more coexisting phases. The formation of several coexisting phases from a homologous polyelectrolyte system and the very marked requirement for phase homogeneity suggest that the phenomenon of complex coacervation is a very good model for some of the essential steps in the pre‐biologic organization of polymeric polyions.
Structure of branched poly‐α‐amino acids in dimethylformamide. II. Viscosity, sedimentation, and diffusion
Authors: Eliezer N. , Silberberg A. 
Published: December 2004

AbstractThe intrinsic viscosity, sedimentation and diffusion of a series of branched, multichain poly‐α‐amino acids having a poly(L‐lysine) backbone and poly(γ‐benzyl L‐glutamate) and poly (β‐benzyl L‐aspartate) side chains was studied at room temperature in dimethylformamide. The molecules were found to be extremely compact structures in which the molecular backbone is either lying along the major axis in a slightly twisted configuration (the longer the side chain the smaller the twist) or is coiled up in the form of a disk with backbone and side chains coplanar. Heat treatment (to 70°C.) introduces only small changes in the hydrodynamic parameters showing that the heat‐labile aggregates detected by light scattering are reversibly broken up during the hydrodynamic measurements. The above structural information concerns the initial metastable conformation of the molecules which is irreversibly destroyed by heat treatment.
Frictional coefficients of multisubunit structures. II. Application to proteins and viruses
Authors: Bloomfield V. , Van Holde K. E. , Dalton W. O. 
Published: December 2004

AbstractThe theory of Kirkwood for the translational frictional coefficients of structures composed of identical subunits has been extended in the previous paper to the case where nonidentical subunits are involved. In this paper, the theory is applied to particular proteins and viruses. It is found that the calculated sedimentation coefficients of various states of aggregation of the reversibly associating proteins hemocyanin and phycocyanin are in excellent agreement with experiment. The dimensions of the fibrinogen molecule obtained from electron micrographs do not give good agreement between calculated and experimental frictional coefficients. The frictional coefficient of tobacco mosaic virus calculated without explicit consideration of end effects is in good agreement with experiment if a hydrodynamic diameter of 18O A., corresponding to the maximum diameter from x‐ray studies, is used. Agreement is also good for the fast sedimenting form of bacteriophage T2 and the protein ghosts of bacteriophage λ but the slow form of T2 and whole λ have frictional coefficients considerably in excess of those calculated. Tail fiber configuration or head porosity are unable to account for the difference in sedimentation coefficients between the fast and slow forms of T2.
Interaction of metal ions with polynucleotides and related compounds. X. Studies on the reaction of silver(I) with the nucleosides and polynucleotides, and the effect of silver(I) on the zinc(II) degradation of polynucleotides
Authors: Eichhorn Gunther L. , Butzow James J. , Clark Patricia , Tarien Edward 
Published: December 2004

AbstractPotentiometric titration curves of the silver(I) complexes of cytidine, adenosine, and uridine show little uptake of base below pH 7, unlike the curve for silver(I)‐guanosine, which shows extensive base uptake at neutral pH. This observation is correlated with spectrophotometric data showing little difference between the silver complex spectra of adenosine, cytidine, and uridine and the spectra of uncomplexed nucleosides, except at high pH, but showing a great difference between the silver complex spectra of guanosine and inosine and the corresponding uncomplexed nucleosides even at pH 6. Similar comparisons of the silver complexes of poly A, poly C, poly I, and poly U, both by potentiometric titration and by spectrophotometry, show that poly I behaves like guanosine and inosine as expected, differing from poly A and poly C. However, poly U behaves like poly I and thus does not resemble uridine in its complexing behavior. There is thus a dichotomy between poly A and poly C on the one hand in silver complexing phenomena, compared with poly U and poly I on the other. When silver(I) is added to systems containing zinc(II) and various polynucleotides, the same dichotomy is noted. Silver(I) inhibits the degradation by zinc(II) of all four polynucleotides, but the degradation of poly I and poly U is prevented virtually completely. Silver(I) alone has no degradative effect on RNA and inhibits, the zinc(II) degradation of RNA. Polynucleotide complexes in which silver(I) and zinc(II) are simultaneously bound to different positions on the macromolecules are postulated as intermediates in the inhibited degradation reactions.
X‐Ray diffraction studies of the conformation of macromolecules in solution. III. The helix–coil transition
Authors: Brady George W. , Salovey R. 
Published: December 2004

AbstractThe procedure outlined in the previous paper of this series is applied to x‐ray diffraction patterns of labeled polytyrosine in dimethylformamide–trifluoroacetic acid solutions. The α‐helix appears to transform into the random coil conformation at a trifluoroacetic acid concentration between 40 and 42.5%. Comparison of these results with those measured in the same system by optical rotation are in essential agreement.