bluuebunny/crossref_metadata_2025 huggingface dataset:
Frictional coefficients of multisubunit structures. II. Application to proteins and viruses
Authors: Bloomfield V. , Van Holde K. E. , Dalton W. O.
Published: December 2004

The 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

Potentiometric 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

The 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.
Molecular conformation of poly‐S‐carboxytmethyl‐L‐cysteine in aqueous solutions
Authors: Ikeda Shoichi
Published: December 2004

Poly‐S‐carboxymethyl‐L‐cysteine has been prepared by debenzylation of poly‐S‐carbobenzoxymethyl‐L‐cysteine with hydrogen bromide in acetic acid. By the infrared spectroscopic method the polymer is found to be in the extended β‐conformation with an antiparallel arrangement of polypeptide chains in solid film, if it has been regenerated from dimethyl sulfoxide solution. Aqueous solutions of the polymer have been investigated by measurements of optical rotatory dispersion and viscosity. Various properties sharply change around pH 5 at different ionic strengths. By combining these with infrared studies in D2O solutions, it has been shown that the polymer exists in the random coil conformation at higher ionization but associates into the intermolecular β‐conformation at lower ionization. At the lowest pH attainable in solution, the β‐form is partly converted into the random coil as the temperature is raised. The rotatory dispersion of the polymer is described by the Moffitt equation. While the random coil form has a large negative a0 value and a zero b0 value, the β‐form is characterized by a positive a0 value and a negative b0 value, −130°.
Volume change on formation of native collagen aggregate
Authors: Cassel James M. , Christensen Richard G.
Published: December 2004

The volume change which occurs in dilute tropocollagen solution as a result of the phase transition producing the “native” form of collagen aggregate has been measured dilatometrically. A volume increase of 0.8 × 10−3 ml./g. collagen in phosphate buffer (pH 7–7.5) was determined. The volume expansion is attributed to a reduction in the organization of water molecules around nonpolar surfaces of the individual tropocollagen units. This volume expansion is consistent with a previous hypothesis that hydro‐phobic bonding is the driving force in this collagen aggregation.
X‐Ray diffraction of oriented amylose fibers. I. Amylose dimethyl sulfoxide complex
Authors: French A. D. , Zobel H. F.
Published: December 2004

The amylose–dimethyl sulfoxide complex has been investigated with the aid of x‐ray diagrams of oriented fibers. The amylose occurs in a six‐residue helix with alternate “up” and “down” chains packed in a square array, that is, pseudo‐tetragonal. A unit cell is proposed with a = b = 19.21 A. and c = 8.12 A.
Interaction of polynucleotides with aromatic hydrocarbons
Authors: Isenberg I. , Baird S. L. , Bersohn R.
Published: December 2004

DNA in its native and denatured form and yeast RNA complex individual aromatic hydrocarbon molecules but single‐stranded poly A does not. The degree of complexing appears to depend on molecular dimensions; it is appreciable for phenanthrene, pyrene, and benzpyrene but very small or undetectible for coronene, tetracene, pentacene, and 20‐methylcholanthrene.
Influence of counterions radius on the polymerization of actin
Authors: Botré C. , Borghi S. , Marchetti M. , Baumann M.
Published: December 2004

The G–F transformation of actin was studied in terms of an interaction between different counterions and actin. macroion by means of electrometric measurements. Due to the polyelectrolyte‐structure of the actin molecule, the electrostatic interactions must play a predominant role. In this sense the influence of the counterion radius has been investigated.
Infrared absorption of tyrosine side chains in proteins
Authors: Bendit E. G.
Published: December 2004

Poly‐L‐tyrosine absorbs strongly at 1515 cm.−1, and a band at this frequency has been found in a number of proteins and has been assigned to the tyrosine residue. The assignment was confirmed by examination of spectra of deuterated proteins, which usually exhibit a residual band at 1513 cm.−1. In proteins, this band correlates linearly with known tyrosine content, but the point corresponding to poly‐L‐tyrosine itself does not fall on the correlation line. The possibility and limitations of using the infrared method for tyrosine determinations is discussed.
Conformation of horse heart ferricytochrome c. III. Comparative optical rotatory dispersion study of the protein with its derivative heme undecapeptide
Authors: Saludjian P. , Shechter E.
Published: December 2004

The optical rotatory dispersion of horse heart ferricytochrome c and of a ferri heme undecapeptide have been determined under various conditions. Analysis of the Soret region makes it possible to characterize three different states of ferricytochrome c. the native state (superposition of a negative and a positive Cotton effect); an intermediate state (single positive Cotton effect whose magnitude Δ[M] is equal to 55,000); a denatured state (single positive Cotton effect whose magnitude Δ[M] is equal to 115,000) in which compared to both the native and intermediate states a more or less important decrease in helix content is observed. The optical rotatory dispersion spectra of the Soret region of the monomeric ferri heme undecapeptide is similar to that of denatured ferricytochrome c. The multiplicity of Cotton effects observed under certain conditions for the hemopeptide is a consequence, resulting from a polymerization, of intermolecular interactions. The comparison of the optical rotatory dispersion spectra of ferricytochrome c and the ferri heme undecapeptide indicates that in the intermediate state interactions remain between the heme group and the portion of the poly pep tide chain absent in the hemopeptide. These interactions disappear in the denatured state.
Influence of reductants upon optical characteristics of the DNA–Cu2+ complex
Authors: Minchenkova L. E. , Ivanov V. I.
Published: December 2004

The addition of reducing agents, i.e., ascorbic acid or sodium borohydride, to a DNA solution containing Cu2+ ions causes changes in the DNA absorption spectra which are due to a new absorption band with a maximum at 280 mμ assigned to a DNA base–Cu1+ complex. The stoichiometry of the complex is one Cu1+ ion per four bases of DNA. The DNA–Cu1+ complex has an increased melting temperature and rather different circular dichroism curve as compared with DNA itself. It is inferred that the above effects are caused by proton transfer along the hydrogen bond from guanine to cytosine under complexing of Cu1+ ions with the N7 atom of the guanine of DNA.
Hydrophobic fluorescent group coupled to Taka‐amylase A. Change of its environment accompanying splitting of disulfide bonds
Authors: Takagi Toshio , Nakanishi Yoshiko , Okabe Nobuo , Isemura Toshizo
Published: December 2004

Native Taka‐amylase A (α‐amylase produced by Asp. oryzae) was coupled with 1‐dimethylaminonaphthalene‐5‐sulfonyl chloride. When disulfide bonds of the modified enxyme were split by reduction or by reduction and subsequent carboxymethylation, its fluorescent properties changed markedly. It was suggested that the hydrophobic dye group is incorporated into a hydrophobic region as the consequence of the flexibility gained by the polypeptide chain by the cleavage of disulfide bonds.
Conformations of copoly(γ‐benzyl L‐glutamate–O‐benzyl‐L‐serine)
Authors: Imahori Kazutomo , Inouye Hiroshi
Published: December 2004

Four samples of copolymers of γ‐benzyl is L‐glutamic (BLG) and O‐benxyl‐L‐serine (BLS) were synthesized by changing the mixing ratio of two monomer anhydrides. The conformations of these copolymers in CHCl3, containing very small amount of dichloroacetic acid (DCA) necessary to dissolve the sample, were determined by their compositions; the copolymer which is rich in BLG is mostly helical and one which is rich in BLS is mostly in the β conformation. However, in DCA solution the conformations of these copolymers are independent of their composition. The interesting observation was that the copolymer which has least con tent of BLS is richest in β‐conformation.
Transient distributions arising from initially sharp boundaries in the ultracentrifuge
Authors: Charlwood P. A.
Published: December 2004

An infinite series solution to the Mason‐Weaver equation is presented for the case in which a synthetic boundary is formed originally between solution and solvent. Digital computations based on this series, and confirmed independently, have been made for a range of parameters. For given conditions, the maximum rate of change of concentration at the meniscus and the time at which it occurs can be easily estimated by means of the curves presented. In equilibrium experiments which commence with formation of a sharp boundary, this enables the fringes to be identified with certainty.
Kerr effect study of the aqueous solutions of three globular proteins
Authors: Riddiford C. L. , Jennings B. R.
Published: December 2004

A Kerr effect study is reported in which measurements have been made on the magnitudes of both the steady maxima and the decays of the birefringence of solutions of ovalbumin, bovine γ‐globulin, and β‐lactoglobulin. For each protein, results are presented on solutions covering the concentration range of 0.3–1.7 g./100 ml. in order to obtain by extrapolation, values of the specific Kerr constant Ksp, and the birefringence relaxation time τ25, w at zero concentration. The relaxation times thus obtained for ovalbumin (18.3 nsec.) and γ‐globulin (157 nsec.) have been shown to be compatible with molecular models and dimensions presented in the literature. All experiments showed the need for careful extrapolation to zero concentration if reliable parameters are to be obtained: for example a 1% solution of ovalbumin or l.5% solution of γ‐globulin, would give values for τ which are 50% too high when compared with the true value at infinite dilution. The gradual fall in τ for γ‐globulin as the pH was lowered from 6.7 to 3.0 was also studied for three solvents. Fisher's generalized model for the arrangement of the polar residues around the outside of a globular protein has been developed to account for ellipsoidal particles and has been used to demonstrate the suitability and usefulness of this treatment in predicting the conformation and dimensions of these proteins. Rather unusual birefringence traces for β‐lactoglobulin were obtained, which may indicate the dissociation of aggregates, or of the parent molecule into its subunits, under the influence of strong electric fields.
Effect of binding on melting transitions in polymer–diluent systems
Authors: Orofino T. A. , Ciferri A. , Hermans J. J.
Published: December 2004

An expression is derived for the melting point of a polymer when in equilibrium with a solution in which binding of low molecular weight compounds to the polymer takes place. Allowance is made for the possibility that the crystalline polymer itself is a complex. The argument is a purely thermodynamic one and is based on a consideration of the change in free energy as a result of a change in binding. Allowance is made also for non‐specific polymer–solvent interactions, in which the mixture of low molecular weight solvents is treated as a single solvent. Special attention is paid to “inverted” melting transitions, i.e., cases in which the melting point increases with increasing dilution of the polymer. It is shown that as a rule this is accompanied by a corresponding, inverted effect of the solvent composition on the melting point. It is further shown that‐in the absence of binding, “normal” behavior at the critical point (i.e., phase separation is induced by lowering the temperature) is always accompanied by “normal” melting behavior (i.e., a decrease in melting point when the polymer is diluted). Also, “inverted” melting always implies that phase separation at the critical point is induced by heating, but the reverse is not necessarily true.
Calculated optical properties of 64 trinucleoside diphosphates
Authors: Cantor Charles R. , Tinoco Ignacio
Published: December 2004

The optical rotatory dispersion and ultraviolet absorption spectra of the 64 trinucleoside diphosphates containing the bases A, U, C, and G have been calculated by using a simple semiempirical approach. These calculations accurately predict the optical properties of the nine trimers for which extensive experimental results are available. The computed optical data should be useful in the identification of oligonucleotides obtained in the course of sequence determination of ribonucleic acids and should simplify the determination of the concentration of oligonucleotides in aqueous solution. Additional calculations indicate that it should be possible to analyze most, mixtures of sequence isomers of trinucleoside diphosphates by direct, measurement of the ORD of the mixture at neutral pH.
Thermal transition of DNA measured by NMR spin‐echo technique
Authors: Lubas Barbara , Wilczok Tadeusz , K.‐Daszkiewicz Olgierd
Published: December 2004

The thermal helix–coil transition of DNA can be studied by means of the spin‐echo technique. The longitudinal spin–lattice relaxation time T1 and the transvense spin–spin relaxation time T2 of the DNA sample show a similar phase transition as observed spec‐trophotometrically with increasing and decreasing temperatures. Four slopes on the T1 and T2 temperature relationship curves were found and interpreted as functions of nonrelational hydration of the DNA molecule. The T1 and T2 values differ depending on the native or denatured state of the DNA molecule. The importance of the dynamic equilibrium between water molecules in the hydration lattice and steps in the denaturation of the DNA molecule are discussed. This phenomenon may be directly related to the nonrotational hydration.
Sedimentation coefficient of polyoma virus DNA
Authors: Gray Horace B.
Published: December 2004

The sedimentation coefficient of the twisted circular form of polyoma virus DNA is calculated from the Kirkwood sedimentation–diffusion equation, the structure being assumed to be a rigid double superhelix. Agreement with the experimental sedimentation coefficient can be obtained, with the use of an experimental value for the number of superhelical turns, when the pitch of the superhelix is intermediate between its minimal and maximal possible values. Another model, which has been proposed for polyoma DNA at low ionic strengths, may be visualized as a superhelical structure wound about a torus. Calculations of sedimentation coefficients for this model agree qualitatively with experimental data at ionic strengths Below 10−2M.
Kinetics of biopolymerization on nucleic acid templates
Authors: MacDonald Carolyn T. , Gibbs Julian H. , Pipkin Allen C.
Published: December 2004

The kinetics of biopolymerization on nucleic acid templates is discussed. The model introduced allows for the simultaneous synthesis of several chains, of a given type, on a common template, e.g., the polyribosome situation. Each growth center [growing chain end plus enzyme(s)] moves one template site at a time, but blocks L adjacent sites. Solutions are found for the probability nj(t) that a template has a growing center that occupies the sites j — L + 1,…, j at time t. Two special sets of solutions are considered, the uniform‐density solutions, for which nj(t) = n, and the more general steady‐state solutions, for which dnj(t)/dt = 0. In the uniform‐density case, there is an upper bound to the range of rates of polymerization that can occur. Corresponding to this maximum rate, there is one uniform solution. For a polymerization rate less than this maximum, there are two uniform solutions that give the same rate. In the steady‐state case, only L = 1 is discussed. For a steady‐state polymerization rate less than the maximum uniform‐density rate, the steady‐state solutions consist of either one or two regions of nearly uniform density, with the density value(s) assumed in the uniform region(s) being either or both of the uniform‐density solutions corresponding to that polymerization rate. For a steady‐state polymerization rate equal to or slightly larger than the maximum uniform‐density rate, the steady‐state solutions are nearly uniform to the single uniform‐density solution for the maximum rate. The boundary conditions (rate of initiation and rate, of release of completed chains from the template) govern the choice among the possible solutions, i.e., determine the region(s) of uniformity and the value(s) assumed in the uniform region(s).
Vacuum ultraviolet absorption spectra of sublimed films of nucleic acid bases
Authors: Yamada Takenori , Fukutome Hideo
Published: December 2004

Measurements of the optical absorption spectra of the sublimed films of adenine, guanine, cytosine, thymine, and uracil were extended down to 120 mμ at room temperature. Several remarkable absorption peaks were found to exist below 190 mμ in addition to the already known ones near 260 mμ and 200 mμ. The intensities of these peaks were comparable to or, in some cases, even larger than those near 260 mμ and 200 mμ. It was found that the relative intensities of the absorption peaks differed considerably from sample to sample for all five bases, probably due to variation in the arrangement of the bases in the sublimed films. It was found also that the absorption spectra of the sublimed films change with aging on standing in vacuo at room temperature. On comparing the spectra of several fresh samples it was found that the intensities of the transitions with wavelength longer than 160 mμ of adenine, guanine, and uracil films are inversely correlated with those of the transitions shorter than 160mμ.
A theory on the effect of low molecular salts on the conformation of linear polyions
Authors: Oosawa Fumio
Published: December 2004

The effect of low molecular salts on the conformation of linear polyions is analyzed on the basis of the additivity law for the thermodynamic properties of polyelectrolytes in the presence of salts. In the case of flexible polyions the theory shows that the logarithm of the conformation parameter changes proportional to A ln (1 + γs0Cs/γpCp) as a function of the salt concentration cs, where cp is the concentration of counterions from polyelectrolytes and γp and γs0 are the activity coefficient of counterions from polyelectrolytes in the absence of salts and from salts in the absence of polyelectrolytes, respectively. In the case of the discontinuous transition of the conformation of polyions, it is shown that the change of the transition point by salts is proportional to the same factor as the above. The constant A, which determines the magnitude of the effect of salts, is proportional to the sensitivity of the activity coefficient to the conformation of polyions in the absence of salts. A similar analysis is made for the conformational change due to dilution by the addition of solvent. These theoretical results are found to be in good agreement with experimental data on the viscosity of flexible polyions and on the helix–coil transition of biopolymers. The interrelation between these conformational changes and various thermodynamic properties of polyelectrolytes with salts is discussed.
Acid–base behavior of poly (vinylpyrrolidone–vinylimidazole) copolymers
Authors: Klotz Irving M. , Lyndrup Mark L.
Published: December 2004

Copolymers of vinylimidazole and vinylpyrrolidone containing 0.7–24% of the former residue have been prepared. Titration behavior was examined over a range of temperature and at several ionic strengths. Intrinsic pK's, corrected for electrostatic effects, arc independent of mole fraction of imidazole residue in the copolymer. Nevertheless they are about 1.15 pK units lower than in the corresponding model small molecule, N‐ethylimidazole. Enthalpies and entropies of ionization in the copolymer are changed by ionic strength. It is apparent that the charged state of an N‐ethylimidazole residue placed in a macromolecular matrix is destabilized relative to the uncharged state because of changes in the local polymer or solvent environment.
Esterolytic activity of vinylimidazole–vinylpyrrolidinone copolymers
Authors: Kopple Kenneth D.
Published: December 2004

Copolymers of vinylimidazoles and vinylpyrrolidinone, dilute in imidazole residues, have been prepared; their reactivity in the hydrolysis of p‐nitrophenyl acetate has been examined. The catalytic activity of imidazole residues in these copolymers is comparable to that of nonpolyineric imidazoles of the same basicity, and no kinetic effects of preassociation of polymer with substrate ester of p‐nitrophenol were detected. It is suggested that although polyvinylpyrrolidinone probably does bind these substances, they are sequestered from the catalytic, side chains.
Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units
Authors: Venkatachalam C. M.
Published: December 2004

The general conformations of a system of three linked peptide units are studied, and it is found that there are three types of conformations which contain NH…O hydrogen bonding between the first and the third units. One of them is part of a 310‐helix, while the other two arc nonhelical. The two nonhelical conformations are very similar, and in both the cases the peptide chain turns around, reversing the direction of progress. Such a conformation can therefore occur in the region where a polypeptide chain folds back on itself, as in the cross‐β structure. The method of representing these interesting tripeptide conformations in a (ϕ,ψ) map is described. Examples of such hydrogen‐bonded, nonhelical conformations which occur in peptides and proteins are discussed—e.g., in cyclohexaglyeyl, an open tetrapeptide Gly‐L‐Pro‐L‐Leu‐Gly, and in parts of the lysozyme chain.
Gel–water relationships: Dielectric dispersion
Authors: Masuzawa Mitsunobu , Sterling Clarence
Published: December 2004

At low frequencies, the dielectric constant of gels of agar, carboxymethyl cellulose, gelatin, mid maize starch is much higher than that of water. It decreases continuously as the frequency increases, tending to level off at about 108 cps. The dielectric constant is lower the higher the concentration of polymer; it increases in the order: carboxymethyl cellulose, agar, starch, and gelatin. Results are most reasonably explained by assuming a more solid structure of water the lower the dielectric constant.
Studies on conformational changes in the DNA structure induced by protonation: Reversible and irreversible acid titrations and sedimentation measurements
Authors: Zimmer Ch. , Triebel H.
Published: December 2004

Reversible and irreversible conformational changes in the acid‐induced denaturation of DNA were studied by spectrophotometric titration, sedimentation, and melting measurements. A GC‐rich DNA (72 mole‐%) shows complete or partial reversibility of the titration profiles within the pH region of transition from helix to coil, while AT‐rich DNA (29 mole‐%) is irreversible in its titration behavior at each acid pH below the onset of the transition. The results for GC‐rich DNA further indicate distinct differences in the titration behavior, which can be attributed to differences in the frequency of GC clusters along the DNA molecule. Plots of the sedimentation coefficient and the parameter asapp against pH lead to the conclusion that conformational changes occur before the onset of the acid‐induced helix–coil transition. These alterations are more pronounced upon protonation of larger GC‐rich domains than of smaller ones, as concluded from very marked differences observed in the sedimentation–pH behavior of two GC‐rich DNA's. An acid denaturation scheme for a GC‐rich DNA segment is suggested. Reversibility of the acid denaturation is explained by the existence of stable, protonated, single GC base pairs in nonprotonated stacked single‐stranded domains formed in the acid‐induced transition region.
Time‐dependent fluorescence depolarization and Brownian rotational diffusion coefficients of macromolecules
Authors: Tao Terence
Published: December 2004

Using a distribution function formalism, we have derived relations between the time‐dependent fluorescence polarization anistropy r(t) = [I‖(t) − I⟂(t)]/[I‖(t) + 2I⟂(t)] and the Brownian rotational diffusion coefficients of macromolecules. It is shown that in the most general case of a completely asymmetric body, five exponentials appear in r(t). Reduction to previously obtained simpler expressions are presented and discussed. Experiments were performed to measure r(t) for the complex of 1‐anilino‐8‐naphthalene sulfonate (ANS) and apomyoglobin. The results revealed a spherical geometry, with a radius of 20.8 Å. Similar experiments were performed on the ANS–apohorse radish peroxidase complex. The results were inconclusive towards the geometry of the complex, but when assumed to be spherical, the radius was estimated to be 29.6 Å, consistent with the larger molecular weight of horse radish peroxidase.
In vitro incorporation of tritium into native DNA
Authors: Doppler‐Bernardi Françoise , Felsenfeld Gary
Published: December 2004

An exchange method is described for producing tritium‐labeled native DNA in vitro with minimal physical damage to the DNA. Tritium‐labeled calf thymus DNA prepared in this way has a specific activity of about 100 μCi/mmole of nucleotide (i.e., about 2 × 108 dpm/mmole). Sedimentation velocity at neutral and alkaline pH indicate that the product has an average of two single strand breaks per duplex molecule of molecular weight 6 × 106 daltons. The optical and thermal denaturation properties of the product are those of native DNA. The method should be particularly useful for labeling DNA from organisms that cannot be labeled conveniently in vivo.
Bindings of RNAse to denatured and native deoxyribonucleic acids
Authors: Raju E. V. , Davidson N.
Published: December 2004

The binding of pancreatic ribonuclease‐A by denatured DNA, native DNA, poly‐dA, and poly‐dT, has been studied by a gel filtration method. With denatured DNA at pH 7.5, ionic strength 0.053M, there is one binding site per 12 nucleotides and the equilibrium binding constant per site is 9.7 × 104 l./mole. The binding constant increases by a factor of 8 as the pH is decreased from 8 to 7. The strength of the binding of denatured DNA increases with decreasing ionic strength. At pH 7.5, native DNA binds about ⅛ as strongly as does denatured DNA. The binding affinity increases in the order poly‐dA, denatured DNA, and poly‐dT. These results support the view that the binding of denatured DNA involves both electrostatic interactions between the negatively charged polynucleotide and the positively charged protein, and an interaction of the protein with a pyrimidine residue of the denatured DNA, and thus that the binding is basically similar to that between RNAse and its substrate RNA.
Theoretical evaluation of polytripeptide collagen models
Authors: Hopfinger A. J. , Walton A. G.
Published: December 2004

The influence of inserting certain residues (X) into a polytripeptide sequence conformed into a poly‐L‐proline II helix is examined theoretically. It is found that for sequences such as ‐Gly‐Pro‐X‐ and ‐Gly‐X‐Pro‐, the introduction of glycyl, L‐alanyl or L‐seryl residues in the X position destabilizes the helix so that it is no longer the most stable intramolecular form. On the other hand, L‐prolyl and L‐hydroxyprolyl residues cause the PP II helix to be most stable. Of the many stable intramolecular forms, the majority will not pack efficiently to form fiber or solid‐state structures. The Rich‐Crick and Ramachandran collagen model structures were examined in terms of a Gly‐Pro‐Ala sequence, the Ramachandran, one‐hydrogen‐bond structure, being the most stable. However, another triple‐strand structure for (Gly‐Pro‐Ala)n, is much more energetically favorable. Hence, it may be concluded that none of the aforementioned is an entirely satisfactory collagen model. The new triple helix conformation proposed by Traub, Yonath, and Segal for (Gly‐Pro‐Pro) is found to give a more favorable intramolecular conformation for (Gly‐Pro‐Ala)n than those derived from other collagen models. It is concluded that the collagen molecule derives its stability from interchain interactions in proline‐sparse regions and intrachain stability in proline‐rich regions.
Syntheses of poly[γ‐(l)‐menthyl L‐ and D‐glutamates] and their secondary structures
Authors: Yamamoto Hiroyuki , Kondo Yoshiyuki , Hayakawa Tadao
Published: December 2004

γ‐(l)‐Menthyl L‐ and D‐glutamates were prepared by a fusion reaction of N‐phthalyl‐L‐ and D‐glutamic anhydrides with l‐menthol, followed by hydrazinolysis. The monomers were polymerized to poly[γ‐(l)‐menthyl L‐ and D‐glutamates] by the N‐carboxyanhydride method. These polymers were soluble in many organic solvents, such as ethyl ether, chloroform, tetrahydrofuran, and n‐hexane. From the results obtained by a study of the infrared absorption spectra, the x‐ray photographs, the optical rotatory dispersions and the circular dichroisms, poly[γ‐(l)‐menthyl L‐glutamate] was found to be a right‐handed α‐helix in the solid state and in solution. Similarly, poly[γ‐(l)‐menthyl D‐glutamate] was a left‐handed α‐helix. The helix‐coil transition of these polymers was observed in the vicinity of 40% dichloroacetic acid in a chloroform–dichloroacetic acid mixture.
Diamide model for the optical activity of collagen and polyproline I and II
Authors: Madison Vincent , Schellman John
Published: December 2004

A diamide, N‐acetyl‐L‐proline‐N,N‐dimethylamide (AcProDMA), in water solution has optical rotatory dispersion (ORD) and circular dichroism (CD) spectra very similar to those of poly‐L‐proline II and the fibrous protein collagen. In contrast, AcProDMA in cyclohexane solution has optical activity resembling that of poly‐L‐proline I. Conformational analysis shows that AcProDMA is confined by steric constraints to either of two narrow regions of conformational space. The trans isomer of AcProDMA assumes conformations near those of polyproline II and collagen nearest neighbors, while cis‐AcProDMA assumes conformations near that of polyproline I nearest neighbors. Nuclear magnetic resonance (NMR) experiments show that an equilibrium mixture of the cis and trans isomers of AcProDMA is present in solution. The trans isomer predominates in aqueous solution, but the equilibrium shifts to favor the cis isomer in nonpolar organic solvents such as cyclohexane. Analysis of the ORD spectra in terms of two basic spectra reveals a solvent dependent isomerization which parallels that observed by NMR. The optical activity of the pure isomers of AcProDMA can be derived from the ORD, CD and NMR data. A comparison of component cotton effects confirms the similarity in optical activity of trans‐AcProDMA, polyproline II, and collagen on the one hand, and of cis‐AcProDMA and Polyproline I on the other.
Cooperative transition between two helical conformations in a linear system: Poly‐L‐proline I ⇌ II. I. Equilibrium studies
Authors: Ganser V. , Engel J. , Winklmair D. , Krause G.
Published: December 2004

The solvent‐induced conformational transition between the two helical forms of poly‐L‐proline is studied as a model for cooperative order ⇌ order transitions. The chain length dependent equilibrium data in two solvent systems are described by Schwarz's theory, which is based upon the most general formulation of the linear Ising model with nearest neighbor interactions. The parameter σ which describes the difficulty of nucleation of a I (II) residue in an uninterrupted II (I)‐helix is 10−5 in both solvent systems. The ratios of the nucleation difficulties of states I and II at the ends of the chains β′ and β″ are very different in the two systems. Nucleation difficulty within the chain is interpreted as being due to unfavorable excess interaction energies at the I–II and II–I junctions, which add up to 7 kcal/mole of nuclei as calculated from the σ value. A similar value is computed from the atomic interactions at the junctions. In contrast to this intrinsic properly of poly‐L‐proline, the energies of I and II residues at the ends are heavily influenced by interactions of the endgroups with the solvent. The above values of the nucleation parameters are determined by a new least‐square fitting procedure which does not necessitate the assumption of the dependence of the equilibrium constant s for propagation upon the external parameters, but yields this function from the experimental transition data. A quantitative explanation of this experimental s function through the binding of solvent is attempted. In the transition region a very small free energy change (about 0.1 kcal/mole), arising from a preferential binding of solvent molecules to one of the conformational states, is sufficient for a complete conversion from one helical form to the other.
Simplified quantitative electron microscopy of biopolymers
Authors: Lang D. , Mitani Michiko
Published: December 2004

Shape and molecular weight of DNA can be obtained with a new method involving spontaneous surface adsorption of DNA or of other macromolecules from a solution which contains formaldehyde and a critical amount of cytochrome c. Subsequent transfer to specimen grids and electron microscopy shows individual molecules suitable for quantitative evaluation. Adsorption of DNA and fd bacteriophages is proportional to (time)0.75. Contour lengths of double‐stranded DNA are not influenced by formaldehyde. A modification of this method requires only 2 × 10−5 μg DNA.
Chemical fixation of chymotrypsin to water‐insoluble crosslinked dextran (Sephadex) and solubilization of the enzyme derivatives by means of dextranase
Authors: Axén Rolf , Myrin Per‐Åke , Janson Jan‐Christer
Published: December 2004

Catalytically active chymotrypsin derivatives can be synthesized from cyanogen bromide‐activated Sephadex G200. In most cases the apparent catalytic activity of the covalently fixed enzyme appears to be considerably decreased in comparison to the activity of the free enzyme. However, by proper choice of the reaction conditions for the activation, enzyme conjugates with high activity, even toward a high molecular substrate, can be synthesized. These latter derivatives may be of practical value for the digestion of proteins. Crosslinked dextran as carrier was chosen because of the possbility, of digesting it enzymatically by dextranase. Sephadex G200, if activated at or below pH 10.3, will combine with chymotrypsin to yield digestable products. Changes of apparent kinetic properties of the fixed enzyme can accordingly be studied during the degradation process. On the solubilization of the insoluble conjugate, a total recovery of activity of the fixed enzyme can be obtained in cases the carrier has been activated by a sufficiently mild procedure. The high apparent Michaelis constant Km of insoluble chymotrypsin–Sephadex toward N‐acetyl‐L‐tyrosine ethyl ester shifts back on solubilization to the value of free chymotrypsin. We therefore propose that the decreased activity of an insoluble chymotrypsin–Sephadex is due to diffusional effects shown by the gel matrix toward the substrate. Similarly observed shifts in optimum pH are explained by accumulation of hydrogen ions in the gel. The organic chemical reaction used for coupling the enzyme to the polymer can therefore be performed without decreasing the inherent catalytic activity of the enzyme. The route described for fixing chymotrypsin to Sephadex followed by solubilization of the products may be useful as a synthetic method for binding proteins, peptides, and other amino group‐containing substances to soluble carriers, e.g., for the modification of pharmaceuticals.
Stability of the helical conformation of random L‐alanine–L‐lysine copolymers in aqueous solution
Authors: Sugiyama Hiroyuki , Noda Haruhiko
Published: December 2004

The potentiometric titration of random copolymers of L‐lysine and L‐alanine containing 0–35% alanine was carried out. The standard free‐energy change for the transition of coil to helix was calculated from the titration curve, and was treated by taking account of first‐neighbor interactions. For uncharged lysine ΔG° = −140 cal/mole, and for alanine ΔG° = −50 cal/mole in 0.06M NaBr at 25°C, indicating that the alanine helix is thermodynamically less stable than the lysine helix. The randomness in co‐polymerization was confirmed by trypsin treatment.
Raman spectra of L‐alanine oligomers
Authors: Sutton P. , Koenig J. L.
Published: December 2004

The Raman spectra have been obtained of di‐, tri‐, tetra‐, penta‐, and hexa‐L‐alanine in the solid state. Raman spectra of the dimer and trimer in aqueous solution are also reported. The oligomers of alanine exist as zwitterions in the solid state and aqueous solution. Spectral differences between the dipeptide, and other oligomers arise primarily from the conformationally sensitive amide modes. The dipeptide exists as a nonplanar structure in the solid state and the other oligomere as β conformations. Comparison of Raman spectra of tri‐L‐alanine in the solid state and in aqueous solution suggests a conformational change to a random coil upon dissolution.
Cooperative binding of adenosine by polyuridylic acid: A further analysis
Authors: Schmitz Kenneth S. , Schurr J. Michael
Published: December 2004

The dialysis data of Huang and Ts'o for the cooperative binding of adensine to polyuridylic acid are analyzed here using a grand‐partition function Ising model method similar to that originally employed for polyelectrolytes by Rice and Nagasawa. An appropriate modification permitting the treatment of the sliding degeneracy of the two polyuridylic acid strands is also included. In addition to the previously estimated stacking energy of about −6 kcal/mole one also obtains the free energy change F̄ for the transfer of a single adenosine molecule from a fixed site in solution to a fixed site on the polyuridylic acid. This binding energy falls in the range F̄ = −140 to +620 cal/mole, indicating that binding in the 1:2 (purine: pyrimidine) complex is either very weak or repulsive. The absence of any comparable cooperative stacking of adenosines in solution at the same concentration together with the likely repulsive character of the binding implies that the stacking energy must contain a significant contribution from other processes than simple stacking of adenosines. A generalization of the theory to treat multicomponent binding and longer‐range interactions is effected, and the form applicable to simultaneous binding of both adenosine and guanosine by polyuridylic acid is presented.
Interaction of nucleic acids. VI. Interaction of purine with nucleic acids
Authors: Sander Christian , Ts'o Paul O. P.
Published: December 2004

The interaction of purine with DNA, tRNA, poly A, poly C, and poly A. poly U complex was investigated. In the presence of purine, the nucleic acids in coil form (such as denatured DNA, poly A and poly C in neutral solutions, or tRNA) have lower optical rotations. In addition, hydrodynamic studies indicate that in purine solutions the denatured DNA has a higher viscosity and a decreased sedimentation coefficient. These findings indicate that through interaction with purine, the bases along the poly‐nucleotide chain are unstacked and are separated farther from each other, resulting in increased assymmetry (and possibly volume) of the whole polymer. Thus, the de‐naturation effect of purine reported previously can be explained by this preferential interaction of purine with the bases of nucleic acids in coil form through a hydrophobic‐costacking mechanism. Results from studies on optical rotation and helix‐coil transition show that the interaction of purine is greater with poly A than with poly C. The influence of temperature, Mg++ concentration, ionic strength, and purine concentration on the effect of purine on nucleic acid conformation has also been investigated. In all these situations the unraveling of nucleic acid conformation occurs at much lower temperatures (20–40°C lower) in the presence of purine (0.2–0.6M).
Configurational statistics of polysaccharide chains. Part II. Cellulose
Authors: Yathindra N. , Rao V. S. R.
Published: December 2004

The characteristic ratio of unperturbed cellulose chain was computed as a function of the angle τ at, the bridge oxygen atom and the degree of polymerization. Very high values of the order of 40 or more, depending on the angle at the bridge oxygen atom, have been obtained for this ratio, indicating that cellulose chains are highly extended. The average dimensions of cellulose chains are found to be sensitive even for small changes in the angle at the bridge oxygen, and these chains attain the character of a random coil in very high molecular weight range (degree of polymerization greater than 2000). The large differences in the unperturbed dimensions of cellulosic chains observed in different solvents have been attributed to the possible small changes in the angle τ caused by specific solvent, interactions.
Ionic polysaccharides. IV. Free‐rotation dimensions for disaccharide polymers. Comparison with experiment for hyaluronic acid
Authors: Cleland Robert L.
Published: December 2004

The root‐mean‐square end‐to‐end distance has been calculated for a model allowing free rotation about glycoside bonds for the general case of polysaccharides having a disaccharide repeating unit. Numerical estimates are given for several naturally occurring structures based on an idealized pyranose unit in the C1 chair conformation. Extrapolation procedures which make use of the intrinsic viscosity [η] in good solvents to obtain unperturbed dimensions do not represent, data for hyaluronic acid very well, especially at low molecular weights. However, order‐of‐magnitude estimates suggest that this polymer behaves similarly to other polysaccharides, and probably has stiffer local structure than typical non‐ionic synthetic polymers. A double logarithmic plot of the product of [η] and M̄w, the weight‐average molecular weight, against the degree of polymerization in the range for M̄w of 104 to 2 × 104 permits a straight‐line fit of available data for all the glycosaminoglycans, including heparin and the chondroitin sulfates, as well as sodium carboxymethyl cellulose. This result suggests similarity of short‐chain hydrodynamic behavior of these polymers.
Experimental thermodynamics of the helix–random coil transition. III. Determination of the transition enthalpies of the helical complexes poly(I + C) and poly I in solution
Authors: Hinz H.‐J. , Haar W. , Ackermann Th.
Published: December 2004

The enthalpies of the helix‐coil transitions of the ordered polynucleotide systems of poly(inosinic acid)–poly(cytidylic acid) [poly(I + C)], (helical duplex), and of poly (inosinic acid) [poly(I + I + I)], (proposed secondary structure: a triple‐stranded helical complex), were determined by using an adiabatic twin‐vessel differential calorimeter. Measuring the temperature course of the heat capacity of the aqueous polymer solutions, the enthalpy values for the dissociation of the helical duplex poly (I + C) and the three‐stranded helical complex poly(I + 1 + 1), respectively, were obtained by evaluating the additional heat capacity involved in the conformational change of the polynucleotide system in the transition range. The ΔH values of the helix‐coil transition of poly (I + C) resulting from the analysis of the calorimetric measurements vary between the limits 6.5 ± 0.4 kcal/mole (I + C) and 8.4 ± 0.4 kcal/mole (I + C). depending on the variation of the cation concentration ranging from 0.063 mole cations kg H2O to 1.003 mole cations/kg H2O. The calorimetric investigation of an aqueous poly I solution (cation concentration 1.0 mole/kg H2O) yielded the enthalpy value ΔH = 1.9 ± 0.4 kcal/mole (I), a result which has been interpreted qualitatively following current models of inter‐ and intramolecular forces of biologically significant macromolecules. Additional information on the transition behavior of poly(I+ C)Was obtained by ultraviolet and infrared absorption measurements.
Enthalpy of helix–coil transitions from heats of solution. II. Poly‐ε‐carbobenzoxy‐L‐lysine and copolymers with L‐phenylalanine
Authors: Giacometti Giovanni , Turolla Angklo , Boni Renzo
Published: December 2004

The heal of solution of Poly‐ε‐carbobenzoxy‐L‐lysine and of a series of its copolymers with phenylalanine was measured as a function of solvent composition. The enthalpy change of the helix‐to‐coil transition was estimated for the various cases. The previous findings that side chains do not greatly affect the transition enthalpy is confirmed also in cases having much larger differences in helix stability.