bluuebunny/crossref_metadata_2025 huggingface dataset:
Anisotropic scattering by single starch granules. II. Layered granule structure
Authors: Finkelstein R. S. , Sarko A.
Published: December 2004

The study of anisotropy light scattering from tapioca and potato starches has continued with the recording of more detailed experimental single‐granule Hv scattering patterns and, for the first time, single‐granule Vv patterns. Quantitative analysis of the higher order scattering maxima to the granule morphology, permitting an analysis of the latter in terms of a lyered structure. For tapioca starch, this analysis indicates that if layering is present at all, the layer thickness is comparable to the wavelength of the incident radiation, and most likely is considerably less than 0.5 μ in thickness. On the other hand, the potato starch morphology is characterized by a relatively coarse layering with few layers and considerable difference in the anisotropy between successive layers. The models for the two starches in best agreement with experimental data are as follows: almost perfectly spherulitic anisotropic structure with very thin shell‐like layers—if any—for tapioca, and alternating layers of varying anisotropy several microns in thickness and probably simultaneously present with an isotropic center, for potato starch. The Vv pattern for tapioca starch is in agreement with this model, although its information content is lower owing to the experimental difficulty of recording higher order maxima. Suggestions for further morphological study of starches are presented.
Dynamic studies of the unwinding of a DNA‐like strand
Authors: Ree Francis H. , Chay Teresa Ree
Published: December 2004

Following Simon and Zimm's recent work, both molecular dynamic and Monte Carlo methods are used to simulate on a computer the unwinding of a DNA‐like (N + 1)‐unit helical strand. The strand unwinding is assumed to obey (N + 1)‐coupled Langevin equations of motion (N = 10–50). The present computer “experiment” was done to elaborate dependence of unwinding behavior of the helix upon (i) configurations of its complementary strand [represented here by a square cylinder (Simon‐Zimm model), a circular cylinder, and a fixed helix (double‐helical model)]; (ii) interstrand potentials (a hard‐cylinder potential, an inverse twelfth‐power soft repulsion with or without an inverse third‐power attractive tail); (iii) amplitudes of the Brownian motions, and (iv) the molecular weights of the unwinding strand.

We found that (i) the Brownian motions strongly couple with the interstrand potentials to produce a shorter “unwinding time” (τ0) (which characterizes an expotential decay of the unwinding) for a longer renged repulsive potential (without the Brownian motions, no such effect was present); (ii) addition of an attractive tail to the repulsive potentials further reinforces the unwinding, thereby giving a reduced value of τ0; (iii) τ0 can be expressed as a product of two factors–unwinding time for a one‐dimensional spring‐bead model, which mostly accounts for the N 2‐dependence in τ0, and a factor which depends on the Brownian motions and the interstrand potentials; (iv) among the three models described above, under similar situations, the three‐dimensional double‐helical model has the smallest τ0; and (v) unless the maximum Brownian displacement exceeds a certain value, the unwinding around a square cylinder takes place in a (unrealistic) stair‐step manner whose τ0 decreases with increase in the Brownian displacements.

The N 2‐dependence of τ0 agrees with the Simon and Zimm's machine results as well as Crother's experimental data on T2 DNA; however, it contradicts experimental data of Massie and Zimm, and others. Further possible improvements in connection with the computer simulation are suggested.
The conformation fo poly‐L‐alanine in hexafluoroisopropanol
Authors: Parrish Joseph R. , Blout Elkan R.
Published: December 2004

High‐molecular‐weight poly‐L‐alanine dissolved in hexafluoroisopropanol exhibits infrared, ultraviolet, circular dichroism, and optical rotatory dispersion spectra which are unique and unlike any other previously reported polypeptide spectra. Strong evidence that a helical conformation is present is shown by the high degree of hypochromism in the 187mμ absorption peak and by the positions of the amide infrared bands. The CD and ORD spectra are also similar to those of α‐helical polypeptides, though important qualitative and qualitative differences are observed. To explain the novel spectra, which are not mixtures of the spectra of previously reported polypeptide conformations, a new α‐helix‐like conformation is proposed. The postulated conformation (a doubly hydrogen‐bonded helix) is a distorted α‐helix in which the peptide carbonyl groups point slightly out from the helix axis and are hydrogen bonded simul taneously both to the NH of the fourth peptide residue to the carboxyl terminal side (as in the classical α‐helix), as well as to a solvent molecule's hydroxyl hydrogen.
Infrared spectroscopy of human amyloid fibrils and immunogolbulin proteins
Authors: Termine J. D. , Eanes E. D. , Ein D. , Glenner G. G.
Published: December 2004

The presence of the antiparallel‐β‐pleated sheet coformation io isolated human amyloid protein fibrils has been confirmed by infrared spectroscopy. In most amyloid samples, this conformation was enhanced by acidic solution conditions. Infrared spectroscopy (Amide I and Amide V absorption bands) and x‐ray diffraction methods were also used to examine the immunoglobulin molecule for solid state‐β‐structure. It was found that both heavy chains and Bence Jones proteins exhibited some β‐pleated sheet content upon acid and/or heat treatment. Furthermore, pepsin digests comprising either the variable‐rich region (Fd′) of the immunloglobulin heavy chain or in particular, filamentous variable segments of κ and λ Bence Jones proteins were, as isolated, very similar to amyloid in β‐structure content. Data from other immunoglobulin‐derived sample did not exhibit extensive β‐pleated sheet content. On the other hand, most amyliod and immunoglobulin‐derived samples did display some β‐structure when cast from 50% HCOOH solution. Under these conditions, however, filamentous light chain‐variable segments exhibited well‐defined infrared patterns rich in antiparallel‐β‐pleated sheet structure and gave a “cross‐β” x‐ray diffraction pattern.
Limiting sedimentation and diffusion coefficients of polyelectrolytes. The charge effect
Authors: Varoqui R. , Schmitt A.
Published: December 2004

General expressions relating the sedimentation and diffusion constants of polyelectrolytes to the friction properties of ionic components in multicomponent systems have been derived. A quantitative explanation of the charge effect with respect to the addition of a low‐molecular‐weight salt is given; special attention is laid on limiting laws according to the salt‐to‐polymer concentration ratio. The theory is applied to a simple model, the infinitely long rod‐like model, to illustrate the peculiar aspect of the charge effect in presence of salt.
Far‐infrared spectra of copoly(‐α‐amino acids)
Authors: Itoh Koichi , Oya Masanao , Shimanouchi Takehiko
Published: December 2004

Far‐infrared spectra in the region from 700 to 200 cm−1 were measured for the copolymers of L‐alanine and glycine, those of L‐alanine and L‐valine, those of L‐alanine and L‐leucine, and those of L‐alanine and L‐phenylalanine. The observed spectra were interpreted on the basis of the analysis of the far‐infrared spectra of the corresponding homopolymers, and the correlation between the conformations of the copolymers and the kinds of the component amino acids was discussed.
A Molecular Model for the Inversion of the CD Spectra of Actinomycin D in the Presence of gem‐diols
Authors: Ascoli F. , Desantis P. , Lener M. , Savino M.
Published: December 2004

A molecular model for the inversion of the CD spectra of actinomycin D in the presence of gem‐diols is proposed, in terms of the inversion of chirality of the peptide groups directly connected to the phenoxazone ring.
The Structures and Properties of Poly‐5‐methylcytidylic Acid
Authors: Warshaw Myron M. , Noe Ralph
Published: December 2004

The optical rotatory dispersion properties of poly 5MeC, poly diMeC, and 5MeCMP‐(5′) in 0.1M Na+ have been studied at various pH values and temperatures. Poly 5MeC and poly diMeC have optical properties which are similar to those for poly C; however, poly 5MeC has a biphasic melting profile in the pH range from 3.8 to 5.4 similar to that observed for poly 51C. Using titration, ionic strength, and pH dependence measuements, the data for poly 5MeC are interpreted in terms of the following scheme at pH 4.0 and 0.1 ionic strength: triple‐strand helix 37°C double‐strand helix 79°C single‐strand coil. Support for this scheme is discussed. The effect of the methyl group is discussed in terms of similar structural possibilities for other polymers of cytidylic acid.
Chain conformation of poly‐L‐alanine in dichloroacetic acid
Authors: Nakajima Akio , Murakami Masahiko
Published: December 2004

The chain conformation of poly‐L‐alanine in dichloroacetic acid has been investigated by combining experimental data on optical rotatory dispersions, intrinsic viscosities, and sedimentation equilibria. Comparison of experimentally obtained characteristic ratio with that predicted from theory leads to the conclusion that poly‐L‐alanine molecules exist as interrupted helices in dichloroacetic acid.
tRNA structure and binding sites for cations
Authors: Danchin Antoine
Published: December 2004

Equilibrium dialysis and electronic and nuclear resonance spectroscopy show that tRNA cooperatively binds divalent metal ions at very low concentrations (free metal concentration 3 × 10 −6 M). The first two methods show that different purified tRNAs have a very similar behavior, including initiator tRNAFmet. tRNAs with an extra arm in the clover‐leaf model, however, appear to have a slightly different behavior.

The binding can be described in terms of two classes of sites. The cooperative association of divalent ions binding first does not parallel a cooperative change in the hyperchromism of the tRNA, while the non‐cooperative association of the second class of divalent ions corresponds to the concentrations needed to obtain a cooperative melting of the tRNA.

The temperature dependence of the number of binding sites and of their binding constants is also presented.

The nature of the divalent ion gives the following efficiency: for the cooperativity Co++>Mg++>Mn++ for the weak binding sites Mn++>Co++>Mg++
Structure of β,D(1–>4′)‐xylan hydrate
Authors: Nieduszynski I. A. , Marchessault R. H.
Published: December 2004

A structure is proposed for xylan hydrate as a result of investigations by x‐ray fiber diffraction and computer‐aided chain‐packing methods. The unit‐cell dimensions are a = b = 9.16 Å, c (fiber axis) = 14.85Å, γ = 120° and the proposed anti‐parallel chain arrangement corresponds to a space group symmetry of P3221. Left‐handed threefold screw helices are stabilized in this conformation by their interaction with chains of water molecules, so that a satisfactory hydrogen‐bonding scheme is achieved. The proposed structure provides an explanation of the changes in the x‐ray diagram with relative humidity and yields a very good structure factors agreement. An x‐ray fiber diagram corresponding to a higher hydrate (xylan dihydrate) is presented. Comments are made on the possible role of xylan in nature and in technological processes.
An analysis of the results for the binding of formaldehyde to polyuridylic acid
Authors: Aylward N. N.
Published: December 2004

Spectrophotometric measurements were made on the extent of binding of formaldehyde to polyuridylic acid under conditions of varying temperature and formaldehyde concentration. The data is interpreted in terms of a temperature‐dependent stacking of the bases in poly U at 20°, but not at 40°C. A theory of cooperative stacking is developed which considers the base residues to be either non‐bonded, non‐bonded and methylolated, or stacked. The results indicate essentially non‐cooperative base stacking under these conditions with an equilibrium constant for base stacking of 0.92 at 20°C.
Studies on spin‐labeled polyriboadenylic acid
Authors: Bobst Albert M.
Published: December 2004

Spin‐labeled samples of poly rA, poly rU, and poly rG have been prepared, and physicochemical properties primarily of labeled poly rA are reported. The nitroxide radical, 4‐(2‐iodoacetamido)‐2,2,6,6‐tetramethylpiperidinooxyl, is incorporated to a greater extent in poly rA and poly rU, as compared to poly rG. No incorporation is observed in the case of poly rC. Special attention has been paid to the separation of the covalently attached labels from the free labels, and to the preservation of the integrity of the chain length of the labeled polymers. The determination of molar extinction coefficients of the three labeled polymers indicates virtually no difference from those known for the chemically unpertubed polyribonucleotides. The correlation times for the spin‐labeled single stranded poly rA and poly rU have been calculated. More mobile building blocks are found in poly rU as compared to poly rA. Conformational properties of labeled poly rA in aqueous solutions have been investigated using electron spin resonance, circular dichroism, and absorption spectroscopy. The objective of the study of labeled poly rA was to examine its conformational transitions upon the uptake of protons by the adenine bases. Based on electron spin resonance data there is strong evidence that the single strand‐double strand transition can take place in three steps. In addition to the already known two forms of double‐stranded poly rA in acidic solution, called A and B, it is suggested that a third phase, consisting possibly of large aggregates, is involved in the transition of the less protonated double strands to those of complete protonation.
Simple sequential model for the kinetics of conformational transitions of oligomeric helices and proteins
Authors: Elson Elliot L.
Published: December 2004

A simple sequential model is developed which is applicable to the kinetics of melting of some types of oligomeric helices and as an idealization to the kinetics of unfolding of some protein molecules. A procedure is presented for calculating the concentrations of all conformational species as functions of time. The time course of experimentally observable quantities which depend on these concentrations may then be computed.

One of the most characteristic features of the model is the distinction between a transient and a steady‐state phase. During the latter all molecular parameters change at the same rate, which depends strongly on the difficulty of nucleation and the length of the sequence. Simple approximations to the steady‐state rate are discussed in terms of the exact solution. Rates of transient processes dependless strongly on the rate of nucleation and the number of steps and are a more direct reflection of the rates of the rates of the elementary process of propagation. The value of experimental observation of transient process is emphasized.
Electrophoretic behavior of poly‐L‐glutamic acid and poly‐L‐lysine
Authors: Prokopová E. , Ciferri A.
Published: December 2004

Two electrophoretic components have been detected on the ascending boundary in unbuffered solutions of polyglutamic acid and polylysine under certain experimental conditions. If the conditions are favorable to aggregation, another maximum, the third in order, is formed on this boundary. We attribute this maximum to the formation of aggregates. The behavior of both boundaries and all components at various pH, concentrations, and temperature of solutions and at different molecular weights of polymers was described.
Electric and hydrodynamic properties of polypeptides in solution. III. Aggregation of poly(L‐glutamic acid) in aqueous methanol solvents studied by electric birefringence
Authors: Matsumoto Mitsuhiro , Watanabe Hiroshi , Yoshioka Koshiro
Published: December 2004

The rise and decay of electric birefringence for poly(L‐glutamic acid) (PLGA) in aqueous solvents containing 20 and 10 vol % methanol have been found to be unusual. The decay curves have been analyzed on the assumption that there exist two kinds of particles, namely, one (component I) with a shorter relaxation time exhibiting positive birefringence and the other (component II) with a longer relaxation time exhibiting negative birefringence at low fields. From the field strength dependence of the steadystate birefringence the permanent dipole moment, the anisotropy of electric polarizability, and the saturation value of birefringence have been determined for each component. Furthermore, from the relaxation time the length of component I and the diameter of component II have been computed on the models of cylindrical rod and oblate ellipsoid, respectively. The dipole moment, the anisotropy of electric polarizability, and the relaxation time of component II are much larger than those of component I. Both the anisotropy of electric polarizability and the optical anisotropy factor are positive in sign for component I and negative for component II. It is concluded that component I is the helical PLGA molecule itself and component II is the side‐by‐side (antiparallel) aggregate composed of many helical PLGA molecules. The optical anisotropy factor of each component has been discussed on the basis of Peterlin‐Stuart theory.
The absence of an isotope effect on the stability of the poly‐β‐benzyl‐L‐aspartate α‐helix in aprotic solvents
Authors: Dubin P. , Karasz F. E.
Published: December 2004

Optical rotatory dispersion measurements were used to follow the transition from the helical to the random coil conformation of poly‐β‐benzyl‐L‐aspartate as induced by changes in temperature and solvent composition in mixtures of dioxane and dimethylsulfoxide. Within experimental error, there is no difference in the stability of the helical state as measured in this way for the protonated and deuterated forms of the polypeptide. This result is considered in terms of previous attempts to study the isotope effect on conformational transitions of helical biological macromolecules and polypeptides. The conclusion is drawn that the apparent changes in conformational stability observed in these previous systems arise from alteration of the properties of the solvent. Speculations are advanced regarding the contribution of the interpeptide bond to the stability of the helical state.
Conformational aspects of polypeptide structure. XLI. Crystal structure of S‐thiazolidine‐4‐carboxylic acid and helical structure of poly[(S)‐thiazolidine‐4‐carboxylic acid]
Authors: Goodman Murray , Chen Vera , Benedetti Ettore , Pedone Carlo , Corradini Paolo
Published: December 2004

The helical structures of poly[(S)‐thiazolidine‐4‐carboxylic acid], in the cis and trans forms, were redetermined by using the new sets of bond angles and bond lengths established by X‐ray diffraction analysis of L‐thioproline. Calculations of the helical structures of poly‐L‐proline and poly[(S)‐oxazolidine‐4‐carboxylic acid] were also repeated. As a result of these energy calculations, it is suggested that, in contrast to poly‐L‐proline and poly[(S)‐oxazolidine‐4‐carboxylic acid], poly[(S)‐thiazolidine‐4‐carboxylic acid] should not mutarotate from the trans to the cis form. This result is due to the fact that the energy barrier for the conversion is most likely too high. Previous experimental work is consistent with this finding.
Normal vibrations of crystalline polyglycine I
Authors: Abe Yasuaki , Krimm S.
Published: December 2004

A valence force field has been refined for crystalline polyglycine I using its known antiparallel chain pleated‐sheet structure and without replacing the CH2 group by a point mass. Polyglycine I and four of its isotopic derivatives were used in the refinement. The calculated frequencies are in good agreement with the observed, except for the amide I modes. It is shown that this is a consequence of the fact that no reasonable force field predicts a large D10 term of the Miyazawa perturbation treatment. The amide I splittings can, however, be satisfactorily accounted for by introducing a direct interaction force constant between adjacent CO groups in neighboring chains. This can reasonably arise from transition dipole coupling and corresponds to the heretofore neglected D11 term.
The conformation of polycytidylic acid, polyguanylic acid, polyinosinic acid, and their helical complexes in aqueous solution from laser Raman scattering
Authors: Brown Kenneth G. , Kiser Ernest J. , Peticolas Warner L.
Published: December 2004

The Raman spectra of the double helical complexes of poly C–poly G and poly I–poly C at neutral pH are presented and compared with the spectra of the constituent homopolymers.

When a completely double‐helical structure is formed in solution a strong sharp band at 810–814 cm−1 appears which has previously been shown to be due to the A‐type conformation of the sugar–phosphate backbone chain. By taking the ratio of the intensity of the 810–814 cm−1 band to the intensity of the 1090–1100 cm−1 phosphate vibration, one can obtain an estimate of the fraction of the backbone chain in the A‐type conformation for both double‐stranded helices and self‐stacked single chains. This type of information can apparently only be obtained by Raman spectroscopy.

In addition, other significant changes in Raman intensities and frequencies have been observed and tabulated: (1) the Raman intensity of certain of the ring vibrations of guanine and hypoxanthine bases decrease as these bases become increasingly stacked (Raman hypochromism), (2) the Raman band at 1464 cm−1 in poly I is asigned to the amide II band of the cis‐amide group of the hypoxanthine base. It shifts in frequency upon base pairing to 1484 cm−1, thus permitting the determination of the fraction of I–C pairs formed.
Potentiometric titration studies on globular proteins
Authors: Nitta Katsutoshi , Sugai Shintaro
Published: December 2004

A power series method was applied to solve the Poisson‐Boltzmann equation for the spherical polyelectrolyte model and numerical calculation with an electronic computer was performed to obtain surface electric potential on rigid globular proteins. Deviation from the ideal linear relationship in Linderstrom‐Lang's plot was found to become noticeable as the surface charge density and the radius of protein increases and ionic strength decreases. The calculated surface potential was compared with potentiometric titration data of several proteins whose radii have been analyzed. Assuming the radius of the counterions to be equal to about 1.0 Å, the data for phenolic groups in ribonuclease and for carboxyl groups in conalbumin were interpreted. Reversible intramolecular transformation was found for α‐lactalbumin by comparing the present results with the potentiometric titration data for carboxyl groups. The molecular size of each protein was discussed.
Theoretical calculation of the circular dichroism of unordered polypeptide chains
Authors: Ronish E. W. , Krimm S.
Published: December 2004

A calculation has been done of the circular dichroism (CD) spectrum of an unordered polypeptide chain. This has been based on a Boltzmann averaging over a dipeptide conformational CD map. This is shown to be valid by comparing the CD spectra of 28‐mer oligopeptides with those generated by summing dipeptide CD spectra. The calculated CD spectrum of an unordered polypeptide chain is found to agree with the assignment proposed by Tiffany and Krimm from experimental studies.
An ordered precipitate of polyadenylic acid formed by freezing at acidic pH: Comparison of X‐ray diffraction and other properties of the precipitate with those of fibers or direct acid‐precipitates
Authors: Zimmerman Steven B. , Coleman Norma F.
Published: December 2004

Poly A was found to precipitate upon freezing acidic solutions at pH values where it is normally soluble; this precipitate tends to have the form of small thin plates of irregular outline (“plates”). The X‐ray diffraction pattern and solubility properties of the “plates” were compared with those of poly A precipitated solely by exposure to lower pH values, and with fibers drawn from acidic solution. There is considerable molecular order in each of these three types of preparation. In all cases, the diffraction patterns are consistent with the presence of the double‐stranded helical structure proposed by Rich, Davies, Crick, and Watson (J. Mol. Biol., 3, 71 (1961)) based on fiber diffraction data. The diffraction pattern from the “plates” is compared in detail with that of the fibers, and is shown to be in accord with a packing scheme having the chain axis of the molecular structure confined to the plane of the “plate,” but oriented randomly in that plane.
The thermodynamic effects of exposing nucleic acid bases to water: Solubility measurements in water and organic solvents
Authors: Scruggs Robert L. , Achter Eugene K. , Ross Philip D.
Published: December 2004

In order to examine the thermodynamic effects of exposing nucleic acid bases to water, we have measured the solubility of adenine, cytosine, and uracil in water and in organic solvents as a function of temperature. Transfer of a nucleic acid base from an organic environment into water is characterized by positive values for ΔH and for ΔS. We conclude from this result that the overall interaction between nucleic acid bases and water cannot be hydrophobic. If the effect we observe represents structure breaking in water by nucleic acid bases, this process would account for a major portion of the large, positive melting entropy of DNA, and would also contribute substantially to the melting enthalpy.
Ultrasonic absorption and relaxation spectra in aqueous bovine hemoglobin
Authors: White R. D. , Slutsky L. J.
Published: December 2004

Measurements of the frequency and pH dependence of acoustic absorption at 0°C in aqueous solutions of freshly prepared bovine oxyhemoglobin are reported. The role of ionization and possible direct proton‐transfer between proximal pairs in determining the characteristic times for the relaxation of the internal charge distribution is discussed. It is concluded that treatments which consider various classes of residues as ionizing independently will not give approximately correct relaxation spectra. A model which takes into account the coupling between the degrees of ionization of the various residues is found to give rough agreement with the observed acoustic absorption in the pH range in which the native conformation is stable.
Effect of organic solvents on the properties of the complexes of DNA with proflavine and similar compounds
Authors: Löber G. , Schütz H. , Kleinwächter V.
Published: December 2004

In order to obtain information on the binding forces involved in the formation of the complex proflavine–DNA by the stronger process I, the stability of the complexes was investigated in the presence of various organic solvents, methanol, ethanol, n‐propanol, isopropanol, formamide, dimethyl sulfoxide, p‐dioxane, glycerol, and ethylene glycol. Quantitative data on binding in terms of K/n and r were obtained by means of absorption and fluorescence spectra, as well as by a thermal denaturation technique.

All organic solvents used decrease the binding ability of the dye. The effectiveness of the solvents increases with their hydrocarbon content, but can hardly be related to their dielectric constant. The complex formation is effectively suppressed by organic solvent concentrations, in which DNA still preserves its double‐helical conformation. These results demonstrate the importance of hydrophobic forces in the formation of the complex proflavine–DNA in aqueous solution.

The similarity in spectroscopic properties of proflavine bound to DNA by process I and the same dye dissolved in an organic solvent make it possible to interpret the observed red shift of the long‐wavelength absorption peak as being due to the interaction of the dye molecules with the less polar environment.

The same behavior was found for other dyes capable of intercalation like purified trypaflavine, phenosafranine and ethidium bromide. However, intercalation is not a necessary condition, as it was shown in the case of pinacyanol, which binds only at the surface of DNA.
Synthesis and conformation of poly(L‐lysyl‐L‐alanyl), a sequence‐ordered water‐soluble copolymer
Authors: Yaron A. , Tal (Turkeltaub) N. , Berger A.
Published: December 2004

The sequence‐ordered copolymer poly‐(Lys‐Ala‐Ala) was synthesized by polycondensation of the N‐hydroxysuccinimide ester of ε,Z‐Lys‐Ala‐Ala and deprotection of the polymerization product. A fraction of molecular weight 13,000 obtained by ion‐exchange chromatography was investigated. The polymer is freely soluble in water at all pH values, and is completely digested by trypsin and elastase. From CD and ORD data it was concluded that in water at 1°C the ionized form (at pH 6.5) of the polymer is helical. On heating, helix‐coil transition curves were obtained with a midpoint, Tm, depending on salt concentration. In salt‐free water Tm = 12.3°C and in 0.2M NaCl Tm = 28.5°C. Adding MeOH, causes an increase in the helical content of the polymer (half helicity at 20% MeOH, without salt, at 29°C). Guanidine·HCl was shown to decrease the helicity. At 1°C half helicity. The nonionized polymer helix is more stable (Tm∼90°C). At the high pH, at 60°C, when concentration of the polymer is higher than 1.9 × 10‐2M, a precipitate is formed which redissolves on cooling with the original helicity. This does not occur in the presence of 50% MeOH. By comparison with polylysine it was concluded that replacing two‐thirds of the lysine residues in polylysine by alanine leads to a polymer forming a more stable α‐helix, when fully ionized. This is essentially due to the diminished coulombic repulsion. Uncharged lysine residues are comparable to alanine residues in their helix‐forming tendency since the sequential polymer as well as one‐third ionized polylysine are helical to approximately the same extent at room temperature.
Raman scattering of chymotrypsinogen A, ribonuclease, and ovalbumin in the aqueous solution and solid state
Authors: Koenig J. L. , Frushour B. G.
Published: December 2004

The Raman spectra of three globular proteins, beef pancreas chymotrypsinogen A, beef pancreas ribonuclease, and hen egg white ovalbumin have been obtained in the solid state and aqueous solution. X‐ray diffraction and circular dichroism evidence have indicated that these proteins have a low α‐helical content and a large fraction of the residues in the unordered and β‐sheet conformation. The frequencies and intensities of the amide I and amide III lines are consistent with assignments based on the Raman spectra of polypeptides. The intense amide III lines observed in all the spectra would be expected for proteins with a low fraction of the residues in the α‐helical conformation. Several spectra changes occur upon dissolution of the proteins in water and may be associated with further hydration of the proteins. The spectrum of thermally denatured chymotrypsinogen is presented. A 3 cm–1 decrease in the frequency of the amide I line of the protein dissolved in D2O upon heating was observed. This observation is consistent with a denaturation mechanism allowing only slight changes in the secondary structure but an increase in solvent penetration upon going from the native to the reversibly denatured state.
Thermal transitions in gelatin: Optical rotation and enthalpy changes
Authors: Macsuga D. D.
Published: December 2004

Enthalpy changes [as determined by differential scanning calorimetry (DSC)] and optical rotation changes over the helix → coil transition were measured for various gelatin solutions and films. From these studies it has been concluded that: (1) a linear correlation between ΔH and Δ[α] exists for gelatin solutions, independent of the temperature at which gelation occurred; (2) the amount of triple helical structure regained when a melted gelatin solution is quenched can be calculated from DSC data, but the values obtained will be dependent on assumptions about the number and strength of hydrogen bonds; (3) the anomalously high levorotation values found for cold‐dried films of gelatin do not reflect the presence of an extraordinarily large amount of triple helical structure; rather, the large rotations appear to be the result of orientation of helices in the plane of the film.
Effect of chemical structures of acridine and triphenylmethane dyes on the induced optical activity of DNA–dye complexes
Authors: Yamaoka Kiwamu
Published: December 2004

Fifteen symmetrically substituted acridine dyes, all of which are interrelated by their chemical structures, each belonging to a C2v symmetry, and three triphenylmethane dyes with amino or dimethylamino substituents are utilized to study necessary conditions for the appearance of extrinsic Cotton effects upon their binding to native and heat‐denatured deoxyribonucleic acid (DNA). Three different kinds of the DNA–dye complexes, i.e., (1) dye added to native DNA, (2) heat‐denatured DNA–dye complex, and (3) dye added to preheated DNA, were examined for each dye at a fixed P/D value of about 4. Optical activity was always observed for the compelexes of type (1) in each absorption band of the dyes in the visible and near‐ultraviolet region. Two exceptions are 9‐acetamido‐ and 9‐hydroxyacridine, both being nonionic in aqueous solution at a pH range of 6. Acridinium chloride was unable to exhibit any definite extrinsic Cotton effect for complexes (2) and (3). Thus, the monocationic form of a dye due to the protonation or quaternization of the ring nitrogen in acridines or exonuclear amino nitrogen in triphenylmethane dyes is concluded to be an essential factor for extrinsic Cotton effect to appear. Changes in the absorption spectra upon complex formation are also related to the structure of dyes. Hypochromism and bathochromism are associated with the induced optical activity in all cases in the presence of native and denatured DNA.
Hydrodynamic shear breakage of DNA
Authors: Bowman Ray D. , Davidson Norman
Published: December 2004

The rate of breakage of duplex DNA molecules by laminar flow through a capillary has been studied. For λb2b5c DNA (molecular wt., M = 25 × 106) the point at which breakage occurs is normally distributed around the center of the molecule with a standard deviation of 12.5% of the molecular length. At constant shear stress or shear rate, the breakage rate is independent of ionic strength. Thus, shear induced local denaturation is not a rate limiting, preliminary step in breakage. In experiments at constant temperature with varying solvent viscosity (controlled by added sucrose) the breakage rate is a function of shear rate, not of shear stress. The rate of opening of hydrogenbonded circles into linear molecules by hydrodynamic shear is also shown to be a function of shear rate and not of shear stress. The breakage rate at constant shear rate is not greatly dependent on temperature. The shear rate required to achieve breakage is inversely proportional to M1,2. The breakage rate constant, k varies as a very high power of the shear rate; at 25°C, d In k/d In Gm ∼ 15; at 10°C, d In k/d In Gm ∼ 26, where Gm is the maximum shear rate at the capillary wall. The unexpected result that breakage rate is mainly dependent on shear rate, not shear stress, supports a model in which the DNA molecule is distorted with a driving force which depends on the hydrodynamic shear stress, ηG, but the rate limiting step is segment diffusion into a highly extended configuration. The characteristic time to achieve this configuration is proportional to solvent viscosity, η, hence the breakage rate is dependent on ηG/η or G, the shear rate.
Intramolecular conformational transitions “random coil–helix–folded structure” in polypeptides
Authors: Adonts V. G. , Birshtein T. M. , Elyashevich A. M. , Skvortsov A. M.
Published: December 2004

A general theory has been developed for conformational intramolecular transitions in a single macromolecule with a high degree of polymerization (an infinite length model) capable of forming two types of ordered structures: the α‐helix and the folded β‐structure, as well as acquiring the random coil conformation. The phase diagram analysis of this system has shown that the regular β‐structure state is separated from all other states of the chain by the phase boundary line. Any intersection of the phase boundary is a phase transition which can be either of the first order or second order, depending on values of the energy parameters of the system. Mechanisms of intramolecular rearrangements: β‐structure–random coil and α‐helix–β‐structure have been discussed. It has been shown that there exist two different mechanisms for each of these rearrangements, and the regions of parameter variation corresponding to each mechanism have been specified.
Calculation of the molecular parameters of the α‐helix–coil and β‐structure–coil transitions
Authors: Birshtein T. M. , Skvortsov A. M. , Alexanyan V. I.
Published: December 2004

Monte‐Carlo calculations of geometric and thermodynamic characteristics of the α‐helix and the β‐structure of polypeptides have been carried out. To describe a hydrogen bond both the Lippincott–Schroeder and Morse potentials were used. The internal rotation angles φ and ψ in the α‐helix have been shown to fluctuate in the range of ±7°. The distribution functions on angles φ and ψ and on hydrogen bond lengths and angles in the α‐helix have been computed and compared with those in myoglobin and lysozyme. Thermodynamic characteristics of the α‐helix calculated in different approximations with the two forms of the hydrogen bond potentials have also been compared. The data obtained are close to the experimental values for polypeptides in neutral solution.

Some geometric and thermodynamic characteristics of the regular parallel and antiparallel and irregular antiparallel β‐structure have been found. In the β‐structure the internal rotation angles vary within the interval ±15–20°. An increase in the cross and longitudinal dimensions of the β‐structure only slightly influence both the geometric and thermodynamic characteristics.
The use of moment index displacement in analyzing fluorescence time‐decay data
Authors: Small Enoch W. , Isenberg Irvin
Published: December 2004

Moment index displacement automatically corrects a number of significant nonrandom instrumental errors in fluorescence time‐decay measurements. Three‐component data, obtained by measuring the fluorescence decay of three different species mixed in the same solution, were used as a test sample. It was shown, as predicted by theory, that moment index displacement corrects three nonrandom instrumental errors: (1) the presence of scatter in the data; (2) time origin shifts between lamp and fluorescence data; and (3) lamp drift, or time‐dependent changes in the shape of the excitation curve. The data clearly show that the use of the method of moments with moment index displacement to analyze fluorescence decay data is not a curve‐fitting procedure. This procedure will accurately obtain decay parameters for multiple‐exponential decays from certain badly distorted data, yielding a calculated curve very different from the actual data.
Catalysis by polymer complexes. I. Enhanced esterolytic reactivity of hydroxamate–polymer complexes
Authors: Kunitake Toyoki , Shinkai Seiji , Hirotsu Sumio
Published: December 2004

N‐methylmyristohydroxamic acid (1) bound to polymer micelles of laurylated poly(2‐ and 4‐vinylpyridines) (lauryl group contet: 2VP‐L, 30 mol%; 4VP‐L, 33 mol%) quantitatively reacted with p‐nitrophenyl acetate (NpAc) within a few seconds at 30°C, pH 8.95. Second order rate constants ka were 34,000 M−1 sec−1 for 1–2VP‐L and 11,400 M−1 sec−1 for 1–4VP‐L at μ = 0.5, and they were pronouncedly improved by a decrease in ionic strength (ka = 27,500–80,200 M−1 sec−1 at μ = 0.08). In contrast, poly(N‐ethyl‐4‐vinylpyridinium bromide) hardly affected the nucleophilicity of the hydroxamate ion. Therefore, the enhancement was considered to be associated with some micellar characteristics. Typical saturation phenomena of the reaction rate were observed for p‐nitrophenyl hexanoate (NpOCOPe) and 3‐nitro‐4‐acetoxybenzoic acid (NpAcCOOH). It was suggested that binding of NpOCOPe is caused by the hydrophobic interaction, while that of NpAcCOOH is probably induced by the electrostatic interaction. It is demonstrated that the cationic polymer micelle enormously activates the bound hydroxamate anion, and these complexes would be of much interest as a biomimetic system for enzyme catalysis.
Spatial electron distribution and population analysis of amides, carboxylic acid, and peptides, and their relation to empirical potential functions
Authors: Hagler A. T. , Lapiccirella A.
Published: December 2004

The properties of the electron distribution in amides, peptides, and carboxylic acids, obtained from ab‐initio molecular orbital calculations using both minimal and extended basis sets have been studied. These properties are discussed in terms of some of the common assumptions made in empirical conformational calculations of biomolecules. In particular, population analyses of 15 compounds in these families were carried out with both the minimal and extended basis sets, and compared with results of CNDO/2 calculations. It is suggested that population analysis is a useful tool for recognizing patterns of charge distributions, and investigating the transferability of parameters of different functional groups. However, its use for providing partial charges for conformational analysis is a questionable procedure.

A more detailed analysis of the charge distribution was carried out by calculating the spatial electron distribution in the four compounds, N‐methylacetamide, acetic acid, diketopiperazine, and N‐acetyl‐N′‐methylalanine. Both total electron‐density maps and differencedensity maps are presented. The properties of the overall shape of the molecule and the atoms in the molecule, are discussed in terms of the former along with three‐dimensional shape plots of the total density. The distortion accompanying molecular formation, resulting in such features as the lone pair orbital and “bonding deensities” is discussed in terms of the difference maps. Semiquantitative estimates of the bonding and orbital densities resulting from the integration of the densities are also presented. Finally, one of the novel features of the study is the presentation of three‐dimensional surfaces of constant difference densities from which the shapes of the orbitals and bonding densities emerge.
Spectroscopic properties of complexes of acridine orange with glycosaminoglycans. I. Soluble complexes
Authors: Salter Mary K. , Rippon W. Barton , Abrahamson E. William
Published: December 2004

The interaction of acridine orange with dermatan and chondrotin sulfates results in the formation of complexes containing bound dye molecules ordered into dissymmetric arrays. Complexes containing an excess of available disaccharide residues compared to dye are completely soluble, and exhibit biphasic circular dichroism bands. Analysis of the dependence of the extrinsic circular dichrosim on dye aggregation indicates the presence of extended dye stacks bound to the glycosaminoglycan. Complexes formed in solutions containing an excess of dye are only partially soluble, and exhibit circular dichroism spectra having band shifts and intensity changes relative to the soluble complexes. The latter complexes show a sharp drop in induced circular dichroism with temperature, due to a cooperative change in the structure of the complex. The structural order of the dye–glycosaminoglycan complex may differ from the intrinsic structure of the glycosaminoglycan itself in dilute solution.
Conformational properties of the sequential polyproline analogs poly(Pro‐Aze‐Pro) and poly(Aze‐Pro‐Aze)
Authors: Boni R. , Di Blasi R. , Farina A. , Verdini A. S.
Published: December 2004

The lack of the positive band at around 226 nm in the CD spectra of poly(prolyl‐azetidine‐2‐carbonyl‐proline) in trifluoroethanol and of poly(azetidine‐2‐carbonyl‐prolyl‐azetidine‐2‐carboxylic) acid in F3EtOH and water, the hyperchromism of the absorption maximum at about 202 nm, and the extremely small intensity of the Cβ‐Pro, Cγ‐Pro, and Cβ‐Aze signals for the cis peptide bonds in the 13C nmr spectrum of poly(Pro‐Aze‐Pro) in F3EtOH indicate that both polyproline analogs exist as disordered chains in this solvent, the trans peptide group being maintained. The disordering of the chains is attributed to an increase in the accessible range of ψ due to the reduced dimensions of the square ring of L‐azetidine‐2‐carboxylic acid residue relative to the pyrrolidine ring of proline and to strong interactions of the haloalcohol with the peptide groups of the chains.
Frictional properties of nonspherical multisubunit structures. Application to tubules and cylinders
Authors: McCammon J. A. , Deutch J. M.
Published: December 2004

Methods are described for numerical calculation of the anisotropic components of the translational and rotational friction coefficient tensors and of the intrinsic viscosity for rigid multisubunit structures in dilute solution. The methods apply to assemblies of any shape, provided that translation–rotation coupling is negligible.

Application is made to short cylindrical and tubular structures. Anomalous results arise when the Oseen tensor is used to describe the hydrodynamic interaction of the subunits, but these are corrected by use of a modified tensor. Transport coefficients for hollow tubules with typical supramolecular dimensions are found to be nearly the same as those for the corresponding solid cylinders. The Scheraga–Mandelkern equation is found to be useful for the determination of the molecular weights of such structures. For long hollow structures such as microtubules, use of the corresponding solid cylinder or wormlike chain equations should be adequate for interpreting hydrodynamic studies.
Vibrational spectrum of the unordered polypeptide chain: A Raman study of feather keratin
Authors: Hsu S. L. , Moore W. H. , Krimm S.
Published: December 2004

Raman spectra of native and solubilized feather keratin have been obtained, and the amide I and amide III regions have been analyzed by band resolution techniques. The amide I region of the native form indicates that at least 64% of the protein has an antiparallel chain pleated sheet structure, the remainder being unordered. For the solubilized keratin all of the protein is in an unordered state. The amide III region is not as easily analyzed into component contributions. Normal vibration analyses on N‐acetyl‐L‐alanine‐N‐methylamide support the conclusion that the amide III region is not as satisfactory as the amide I region in characterizing unordered structures. Even in the latter case caution must be used, since the observed amide I band is an average over the conformational distribution in the particular unordered system.