bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational geometry and vibrational frequencies of nucleic acid chains
Authors: Brown Ellen B. , Peticolas Warner L.
Published: December 2004

Normal coordinate analysis of diethyl phosphate has been made, which predicts all observed Raman frequencies in the range 170–1300 cm−1. The force constants from this calculation have been transferred to a vibrational calculation for a simplified model of the backbone of nucleic acids, which also involves the OPO2−O phosphate group and the C5′C4′C3′linkage of the ribose. The coordinates of these atoms are those recently given by Arnott and Hukins, which place the ribose ring of B‐DNA in a C3′‐exo conformation. This simple polymer model appears to be able to describe adequately the frequency‐dependent changes observed in the Raman spectra arising from the backbone vibrations of nucleic acid in going from the B‐ to A‐form. The symmetric OPO diester stretch increases in frequency from about 787 cm−1 in the B‐form to 807 cm−1 in the A‐form. The increased frequency characteristic of the A‐form is due to the combining of the diester stretch with vibrations involving the C5′, C4′, and C3′ nuclei. The frequency of the symmetric OPO diester stretch is shown to be very dependent on the conformation of the ribose ring, indicating that in polynucleotides the ribose ring takes on one of two rigid conformations: C3′‐endo for A‐form or C3′‐exo for B‐form and “disordered” polynucleotides. The calculation lends confirmation to the atomic coordinates of Arnott and Hukins since the use of other geometries with the same force constants failed to give results in agreement with experimental evidence. The calculations also demonstrate the lowering effect of hydration on the anionic PO stretching frequencies. Experimental results show that the 814‐cm−1 band observed in the spectra of 5′GMP gel arises from a different vibrational mode than that of the 814‐cm−1 band of A‐DNA.
A bead and spring model for the stiffness of DNA
Authors: De La Torre J. García , Freire Juan J. , Horta Arturo
Published: December 2004

The chain stiffness of linear native DNA is represented by a generalized bead and spring model recently proposed. It incorporates molecular rigidity by means of springs between beads, which are second neighbors along the contour of the chain. These springs are equivalent to elastic forces having longitudinal and transversal contributions. The model is compared with existing experimental data of sedimentation and low‐angle light scattering to obtain the statistical parameters of DNA. The value of the statistical length obtained with this model is 1300 Å. The same value is obtained with the wormlike chain. Throughout this analysis, excluded volume is left out as a simplifying assumption.
Sequence‐dependent properties of DNA. Optimization of empirical parameterizations
Authors: Pysh Eugene S.
Published: December 2004

Some physical properties of DNA can be expressed reasonably as an expansion of the interaction among base pairs. For strictly random sequences, the terms of the expansion can be rearranged in such a way that an empirical parameterization of the nearest neighbor truncation is in fact correct to all orders. A parameterization obtained from data on real native DNA's is shown to be more accurate than the term “nearest neighbor approximation” implies. When synthetic polynucleotide duplexes are used in the parameterization, the degree of its accuracy depends on the selection of duplexes. It is shown here how to optimize such a parameterization for a given set of available duplexes.
On the application of polyelectrolyte limiting laws to the helix–coil transition of DNA. III. Dependence of helix stability on excess univalent salt and on polynucleotide phosphate concentration for variable equivalent ratios of divalent metal ion to phosphate
Authors: De Marky Nancy , Manning Gerald S.
Published: December 2004

Using the free energy difference between double‐helix and random‐coil forms of DNA as a measure of the stability of the double helix, we calculate the dependence of the stability on excess univalent cation concentration and on polynucleotide phosphate concentration, both as functions of the equivalent ratio r of divalent cation‐to‐phosphate concentrations. The theoretical tool is merely to compare the free energy of one polyelectrolyte solution, characterized by the polyelectrolyte linear charge density, with the free energy of another, characterized by a different value of the charge density. It is assumed only that the charge density of the double helix is greater than that of the coil form. The calculation represents the only molecular theory given to date (for r ≠ O) for these aspects of helix stability.

We find that, as excess univalent cation concentration increases, the helix stability increases if r is small but decreases if r is large (i.e., of the order of unity). Moreover, as the concentration of nucleotide phosphate increases, the helix stability does not change for small values of r but increases for large values. For both effects, a continuous transition as a function of r bridges the low‐r and high‐r behaviour.
Computer analyses of characteristic infrared bands of globular proteins
Authors: Rüegg Max , Metzger Virginia , Susi H.
Published: December 2004

Infrared spectra of myoglobin, ribonuclease, lysozyme, α‐chymotrypsin, α‐lactalbumin, and β‐lactoglobulin A were obtained in deuterium oxide solution in units of absorbance versus wavenumber from 1340 to 1750 cm−1. The spectra were resolved into Gaussian components by means of an iterative computer program. Resolved characteristic absorption peaks for the two infrared active amide I′ components of antiparallel chain‐pleated sheets (β‐structure) were obtained. The characteristic amide I′ peaks of α‐helical regions and apparently unordered regions overlap in D2O solution. Absorptivity values for the resolved β‐structure peak around 1630 cm−1 were estimated on the basis of the known structure of ribonuclease, lysozyme, and β‐chymotrypsin. The β‐structure content of β‐lactoglobulin was estimated to be ca. 48% of α‐lactalbumin ca. 18%, and of αs‐casein close to zero. The results are in general agreement with conclusions drawn from circular dichroism and optical rotatory dispersion studies.
Classical potential energy calculations for ApA, CpC, GpG, and UpU. The influence of the bases on RNA subunit conformations
Authors: Broyde Suse B. , Wartell Roger M. , Stellman Steven D. , Hingerty Brian , Langridge Robert
Published: December 2004

Classical potential energy calculations have been made for the ribodinucleoside monophosphates ApA, CpC, GpG, and UpU. Van der Waal's, electrostatic, and torsional contributions to the energy were calculated, and the energy was minimized with the seven backbone conformational angles as simultaneously variable parameters. At the global minimum, ApA and CpC have conformations like double helical RNA: the angles ω′ and ω are g−g−, the sugar pucker is C3′‐endo, and the bases are anti. GpG and UpU, on the other hand, have the ω′,ω angle pair g−t at the global minimum, and for GpG the bases are syn. Energy contour maps for ω′ and ω show two broad, low energy regions for ApA, CpC, and UpU: one is g−g−, and the second encompasses g−t and g+g+ within a single lowenergy contour. The two regions are connected by a path at 10–13 kcal./mole. For GpG, with bases syn, however, only a small low‐energy region at g−t is found. The helical ‘A’ RNA conformation is 8.5 kcal/mole higher for this molecule. Thus, the base composition is shown to influence the conformations adopted by dinucleoside phosphates. Comparison of calculations with experimetal data, where available, show good agreement.
Thermodynamic parameters of the helix–coil transition in polypeptide chains. III. Random copolymers of L‐leucine with L‐glutamic acid
Authors: Bychkova V. E. , Gudkov A. T. , Miller W. G. , Mitin Yu. V. , Ptitsyn O. B. , Shpungin I. L.
Published: December 2004

Conformational transitions induced by pH changes in random copolymers of leucine and glutamic acid have been studied. Significant differences were observed in the potentiometric titration curves of copolymers with small (up to 4%) and large leucine contents. The helical stability of copolymers with small leucine content, determined from titration curves by the Zimm and Rice method, decreases slightly with an increase in the leucine content, whereas the helical stability of copolymers with large leucine content increases sharply with an increase of the leucine content. It is shown that copolymers with large leucine content aggregate in the region of transition into the helical state, but the increase of their helical state stability is not connected with intermolecular aggregation, as it was also observed for a nonaggregating fraction isolated from one of the copolymers by gel chromatography. A conclusion is made that the helix–coil equilibrium constant s for leucine does not itself exceed the s constant for uncharged polyglutamic acid. The stabilization of the helical state in copolymers with large leucine content is due to intramolecular aggregation of helices in these copolymers. The analysis of the leucine residue distribution between helical and nonhelical regions in globular proteins also gives no real arguments to ascribe special helix‐forming properties to leucine.
Conformational studies of poly(L‐tyrosine). A helix–coil transition in dimethyl sulfoxide–dichloroacetic acid mixtures
Authors: Wen Kuo‐Jung , Woody Robert W.
Published: December 2004

Poly(L‐tyrosine) is a random coil in dimethyl sulfoxide. Upon addition of dichloroacetic acid, poly(L‐tyrosine) undergoes a conformational transition centered at about 10% dichloroacetic acid. The transition is nearly complete at 20% dichloroacetic acid. Further addition of dichloroacetic acid leads to precipitation of poly(L‐tyrosine). We have characterized this transition by optical rotation, viscosity, circular dichroism, and infrared. The optical rotation at 350 nm and the intrinsic viscosity increase sharply to values that are consistent with a transition to the α‐helix conformation. The circular dichroism of poly(L‐tyrosine) in dimethyl sulfoxide and in dimethyl sulfoxide/dichloroacetic acid (80:20 v/v) agrees with previous reports for random‐coil and α‐helix conformations, respectively. The infrared spectrum of poly(L‐tyrosine) in dimethyl sulfoxide/dichloroacetic acid (80:20 v/v) shows no evidence of β‐structure. We conclude that the transition on going from dimethyl sulfoxide to 20% dichloroacetic acid in dimethyl sulfoxide is a coil → α‐helix transition. The amide‐I band of poly(L‐tyrosine) in dimethyl sulfoxide/dichloroacetic acid (80:20) is found to be at 1662 cm−1. It has been suggested that this high frequency may be indicative of a left‐handed α‐helix. However, this high amide‐I frequency is consistent with conformational energy calculations of Scheraga and co‐workers. The mechanism of the dichloroacetic acid‐induced transition to an α‐helix is discussed. Dichloroacetic acid and dimethyl sulfoxide interact strongly and the transition presumably involves a marked decrease in the ability of dimethyl sulfoxide to solvate the peptide backbone and aromatic side chains upon complex formation with dichloroacetic acid.
Immobilization of polyribonucleotides in agarose gels at high ionic strength
Authors: Petrović S. L. , Novaković Milka B. , Petrović Jelena S.
Published: December 2004

Purine polyribonucleotides poly(A), poly(G), and poly(I) associate reversibly with agarose gels at high NaCl molarities over the pH range 6–10, at 20°−40°C. Pyrimidine polyribonucleotides poly (C) and poly(U) could not be immobilized in agarose gels under the above conditions. However, poly(C) could be immobilized in agarose without precipitation between pH 3.2 and 4.0.

Association of poly(G) and poly(I) with agarose appears to decrease progressively with deprotonation of their purine residues, and both polymers interact with the gel very weakly above pH 10 regardless of NaCl concentration. The binding to agarose of these polymers at pH 7.5 is also strongly influenced by temperature in the range 20°−40°C. The association of single‐stranded poly(A) is only shifted toward higher NaCl molarities by increased pH; its binding is also little affected by temperature in the above range.

At NaCl molarities effecting the saturating retention in agarose and at neutral pH, the immobilization of several polynucleotides could be prevented by urea in a concentration‐dependent manner. The corresponding profiles of urea molarity appear to disclose a number of hydrophobic interactions between polynucleotides and agarose, some of which could be relatively strong, especially in the case of poly(A).
The association reaction of collagen model polypeptides (Pro‐Pro‐Gly)n
Authors: Shaw Barbara Ramsay , Schurr J. Michael
Published: December 2004

The characterization of recently synthesized (Pro‐Pro‐Gly)n, n = 7, 8 is described, along with melting profile studies of its association equilibrium, and thermal quenching studies of the kinetics of its association reaction. The order of the kinetic reaction is about 3, implying that three peptide chains are involved in the activated state of the rate‐limiting step. The reaction rate was found to exhibit a negative temperature coefficient. With the (Pro‐Pro‐Gly)7 peptide, the concentration dependence of the (Pro‐Pro‐Gly)n association equilibrium was observed for the first time.

Detailed thermodynamic analysis for these n = 7, 8 data, together with literature data for n = 10, 15, 20 were carried out for both the simple “all‐or‐none” binding model and for a series of complex equilibrium models. For the latter, all of the (Pro‐Pro‐Gly)n data (in 10% acetic acid) are fit best with a maximally cooperative near‐neighbor model with a standard enthalpy change ΔH = −650 cal/mole of residues, and a standard entropy change ΔS = −14.63 −10/n cal/deg‐mole of residues, wherein the −10 eu represents an end‐effect contribution to the binding free energy.

With regard to optical rotatory properties and thermodynamic parameters, the data for the new n = 7, 8 peptides match rather well with the literature data for the n = 10, 15, and 20 peptides.

The enthalpic stabilization per residue of the triple‐helical form of (Pro‐Pro‐Gly)n was nearly an order of magnitude smaller than the enthalpic stabilization per additional proline obtained from direct calorimetric measurements on native collagens of different (and much lower) proline contents by Privalov and Tiktopulo. [Biopolymers (1970) 9, 127–139.] Possible explanations for this phenomenon are discussed.
Kinetics of proton transfer reactions of lysozyme with p‐nitrophenol near neutral pH—a study of dynamic properties of Glu 35 and His 15
Authors: Segawa Shin‐Ichi , Husimi Yuzuru , Wada Akiyoshi
Published: December 2004

Kinetics of proton transfer between lysozyme and a pH indicator p‐nitrophenol (p‐Np) were measured by the temperature‐jump method in a pH range of 6.0–7.0. Two well‐defined relaxation processes were observed. The fast process (τ ≃ 15 μsec) was also observed for a lysozyme derivative succinylated at the terminal α‐amino group of Lys 1. Therefore, the fast process was found to be attributable to the proton transfer reaction of His 15 with p‐Np. The slow process (τ ≃ 50 μsec) was found to be characteristic of the proton transfer reaction of Glu 35, because it disappeared completely in solution containing a lysozyme derivative having an ester crosslink between the carboxyl group of Glu 35 and indol C‐2 of Trp 108. The rate constants for proton transfer from Glu 35 and His 15 to p‐Np were found to be 9 × 106/sec/M (±65%, 23°C) and 3 × 108/sec/M (±20%, 25°C), respectively. These data indicate that the proton of the carboxyl group of Glu 35 is kinetically stabilized in lysozyme.
Studies on cytochrome c. X. Synthesis of Nα‐benzyloxycarbonyl‐[Thr107]‐dotetracontapeptide (sequence 67–108) of baker's yeast iso‐1‐cytochrome c
Authors: Moroder Luis , Filippi Bruno , Borin Gianfranco , Marchiori Fernando
Published: December 2004

Synthesis of nonapeptide hydrazide (sequence 93–101), [Thr107]‐decapeptide (sequence 99–108), [Thr107]‐tridecapeptide (sequence 96–108), [Thr107]‐hexadecapeptide (sequence 93–108), [Thr107]‐heptacosapeptide (sequence 82–108), and Nα‐benzyloxycarbonyl‐[Thr107]‐dotetracontapeptide (sequence 67–108) of the proposed primary structure of baker's yeast iso‐1‐cytochrome c are described. Evidence is presented to indicate that these materials are sequentially homogeneous.
Studies on cytochrome c. XI. Circular dichroism studies on synthetic peptides related to the C‐terminal region of baker's yeast iso‐1‐cytochrome c
Authors: Moroder Luis , Filippi Bruno , Borin Gianfranco , Marchiori Fernando
Published: December 2004

Circular dichroism studies on synthetic peptides related to the C‐terminal region of yeast iso‐1‐cytochrome c were carried out and compared with conformational studies on horse cytochrome c fragments. Evidence is presented for a weaker predisposition for ordered structure in the former peptides when compared with the corresponding region in horse cytochrome c. These findings agree with theoretical predictions and with observations that yeast and other mammalian type cytochromes c differ in several minor respects.
Raman spectroscopic study of poly (β‐benzyl‐L‐aspartate) and sequential polypeptides
Authors: Frushour B. G. , Koenig J. L.
Published: December 2004

Poly‐β‐benzyl‐L‐aspartate (poly[Asp(OBzl)]) forms either a lefthanded α‐helix, β‐sheet, ω‐helix, or random coil under appropriate conditions. In this paper the Raman spectra of the above poly[Asp(OBzl)] conformations are compared. The Raman active amide I line shifts from 1663 cm−1 to 1679 cm−1 upon thermal conversion of poly[Asp(OBzl)] from the α‐helical to β‐sheet conformation while an intense line appearing at 890 cm−1 in the spectrum of the α‐helix decreases in intensity. The 890 cm−1 line also displays weak intensity when the polymer is dissolved in chloroform–dichloroacetic acid solution and therefore is converted to the random coil. This line probably arises from a skeletal vibration and is expected to be conformationally sensitive. Similar behavior in the intensity of skeletal vibrations is discussed for other polypeptides undergoing conformational transitions.

The Raman spectra of two cross‐β‐sheet copolypeptides, poly(Ala‐Gly) and poly(Ser‐Gly), are examined. These sequential polypeptides are model compounds for the crystalline regions of Bombyx mori silk fibroin which forms an extensive β‐sheet structure. The amide I, III, and skeletal vibrations appeared in the Raman spectra of these polypeptides at the frequencies and intensities associated with β‐sheet homopolypeptides. Since the sequential copolypeptides are intermediate in complexity between the homopolypeptides and the proteins, these results indicate that Raman structure–frequency correlations obtained from homopolypeptide studies can now be applied to protein spectra with greater confidence.

The perturbation scheme developed by Krimm and Abe for explaining the frequency splitting of the amide I vibrations in β‐sheet polyglycine is applied to poly(L‐valine), poly‐(Ala‐Gly), poly(Ser‐Gly), and poly[Asp(OBzl)]. The value of the “unperturbed” frequency, V0, for poly[Asp(OBzl)] was significantly greater than the corresponding values for the other polypeptides. A structural origin for this difference may be displacement of adjacent hydrogen‐bonded chains relative to the standard β‐sheet conformation.
Stability of proteins in guanidine·HCl solutions
Authors: Bull Henry B. , Breese Keith
Published: December 2004

A new method has been described for the study of the denaturation of proteins by guanidine·HCl. The pH of an unbuffered solution of protein is monitored as Gu·HCl solution at a constant rate is run into the protein solution. As the protein undergoes the transition from the native to denatured state a significant and fairly abrupt change in the pH is observed. The behaviour of 14 proteins has been explored. Lysozyme, pepsin, α‐lactalbumin, lima bean trypsin inhibtor, and insulin failed to yield satisfactory transitions by this method. The method is entirely satisfactory with the other proteins. The maximum stabilities of the proteins in respect to Gu·HCl concentration and pH, and at zero rate (by extrapolation) of delivery of Gu·HCl have been studied. The relative stabilities of the proteins differ greatly. The stabilities are not related in a simple way to any known parameter.

To supplement the pH change method outlined, the viscosities of nine proteins have been studied as a function of Gu·HCl concentration. A useful empirical equation relating the viscosity of a Gu·HCl solution to its molar concentration has been developed. The linear relationship between the relative fluidity and protein concentration has been confirmed and the intrinsic viscosities of the proteins have been calculated. The viscosities of the proteins vary significantly in respect to Gu·HCl concentration. All of the proteins undergo transitions from the native to the denatured state as shown by increases in the viscosities of their solutions. These transitions coincide closely with those found by the pH change method in respect to Gu·HCl concentration and pH. After the initial transition, the proteins continue to expand (viscosity increases) as the Gu·HCl concentration increases, indicating that the denatured state consists of many molecular configurations likely differing little in their energy content. The presence of disulfide bonds tends to limit the expansion of the protein molecules.
Cu(II)–poly(L‐arginine) complexes. Potentiometric and spectral characterization of amine and peptide nitrogen ligands
Authors: Garnier Arlette , Tosi Lucia
Published: December 2004

The study of Cu(II)–poly(L‐arginine) complexes by potentiometric titration, as well as by optical, circular dichroism, and infrared spectra, provides information about the nature of ligands and the coordination sphere around the metal ion. Three different complexes have been identified. The first, which is formed below pH 8, contains two guanidinium nitrogens and two water molecules at the corners of the coordination square. The constant of the overall process as determined by the Gregor method equals 2.0 ± 0.1 × 10−9. The two other complexes form between pH 8 and 10.5 and they contain two guanidinium and two peptide nitrogens as nearest ligands. One of them is a monomer and the other probably a dimer, which differ in the symmetry of the coordination sphere around the cupric ion. The optical spectra of the three complexes show an absorption band at 260 nm that we have assigned to a charge‐transfer transition between a σ metal nitrogen (amine) molecular orbital and a dx2−y2 metal orbital. The spectra of the two complexes containing peptide nitrogens exhibit another absorption band at 320 nm, which we have assigned to a charge transfer from a π orbital of the amide group to the dx2−y2 metal orbital.
Synthesis of protected oligo (γ‐methyl‐L‐glutamates) and study of their conformation in solution and at the air–water interface
Authors: Caspers J. , Hecq W. , Loffet A.
Published: December 2004

Oligopeptides having the general formula N‐carbobenzoxy(γ‐methyl‐L‐glutamyl)n‐dimethyl‐L‐glutamate (with n = 1, 3, 5, 7, 11) were prepared, using both solid‐phase synthesis and conventional peptide couplings in solution. The appearance of an ordered structure with increasing chain length was studied in organic solvents and at the air–water interface. The results obtained by thin‐layer chromatography were interpreted. All the studies have demonstrated a very similar behaviour of this type of oligopeptide in solution and in monolayers.
Equilibrium mechanisms of length regulation in linear protein aggregates
Authors: Wagenknecht Terence , Bloomfield Victor A.
Published: December 2004

Statistical thermodynamic theories have been developed in order to explore the consequences of two prominent models of length regulation in linear protein aggregates: the length‐determining factor model and the cumulated strain model. In the former, the possibility that the final subunit is bound with extra stability has been incorporated. Calculations explore the dependence of the sharpness of the onset of extensive polymerization, and the breadth, shape, and most probable value of the distribution as functions of concentrations of template and polymerizing subunit, of subunit association constant, of the strain free energy, and of the maximum length and extra stability of the last subunit in the length‐determining factor model. Numerical calculations are made with particular reference to the parameters of bacteriophage T4 tail‐core polymerization. Both models predict suitably narrow length distributions with plausible values of the thermodynamic parameters. The length‐determining factor model may exhibit highly cooperative behaviour, with either fully polymerized or very short aggregates being observed as the product K[C] of association constant and free monomer constant is varied. This cooperativity is accentuated as binding of the final subunit becomes more stable. Species of intermediate length will be observable only if the length‐determining factor is shortened. In the cumulated strain model, if K[C] is lowered at constant strain free energy per subunit, shorter aggregates will be observed; but increasing K[C] will not yield appreciably longer polymers. As [C] is lowered, the distribution will remain narrow.
The structure of fibrin. An electron microscopic investigation
Authors: Conio G. , Dondero G. , Troglia C. , Trefiletti V. , Patrone E.
Published: December 2004

An electron microscopic investigation on the structure of fibrin is reported. Fibrin morphology was investigated in a wide variety of experimental conditions, and by carefully controlled staining procedures. Two main band patterns A (230‐Å‐spaced main dark bands) and B (230‐Å‐spaced main light bands) are observed for stained fibrin; it is shown that the former results from the superimposition of both positive and negative staining, and the latter is given by positive staining. By suitable denaturation experiments, it was found that the fiber is composed of a regular alternation of lose and dense regions along the axis.

We have assumed that the monomer of fibrin is described by the three‐nodular model of Hall and Slayter, as supported by recent investigations. The monomers are arrayed according to a head‐to‐tail sequence along the fiber, and to a staggered lateral association. This model accounts for all the experimental observations, and predicts well the high‐resolution band pattern of fibrin. It further agrees with the results of a recent work on the early stages of the fibrinogen‐to‐fibrin conversion.
Acceleration of DNA renaturation rates
Authors: Wetmur James G.
Published: December 2004

The rate of renaturation of DNA may be increased by altering the effective solvent volume available for DNA in solution. Accelerations are demonstrated when neutral and anionic dextran polymers are used to exclude volume in DNA solutions. The logarithm of the DNA renaturation rate constant is shown to be proportional to the concentration of dextran polymer and to be proportional to the intrinsic viscosity of a series of dextran polymers of identical chemical composition. A theory is proposed to account for these results.
The interaction of glutaraldehyde with poly(α,L‐lysine), n‐butylamine, and collagen. II. Hydrodynamic, electron microscopic, and optical investigations on the reaction products
Authors: Swenson M. K. , Meir E. , Yanai P. , Zvilichovsky B. , Blauer G.
Published: December 2004

Interactions of glutaraldehyde with either n‐butylamine, poly(α,L‐lysine), or collagen resulted in a fast release of protons in dilute aqueous solutions at various pH values, followed by much slower changes. The latter reactions, which extended over hours and days, were followed spectrophotometrically and revealed the formation of distinct absorption bands in the visible and near‐ultraviolet regions in all the above systems. The visible‐range bands disappeared upon treatment with sodium borohydride. A qualitative relationship between oxygen uptake by the system n‐butylamine–glutaraldehyde and the slow formation of colored products has been established, while the chemical nature of the reaction products has not been determined.

Sedimentation velocity, viscosity, and optical rotation measurements on the products of interaction between poly(L‐lysine) and glutaraldehyde in aqueous solution indicated large conformational changes in the polyamino acid present in excess (in residues) over the dialdehyde. In particular, the intrinsic viscosity dropped considerably after interaction, indicating intramolecular crosslinking. At molar ratios of 1:1 between polylsine residues and aldehyde groups, intermolecular crosslinking of polylysine was obtained at pH 8.6.

Electron microscopic examinations of collagen samples treated by glutaraldehyde at various pH values indicated changes from unordered to more ordered structures upon treatment with glutaraldehyde, in particular at pH 10.

The present structural and optical investigations are considered to be relevant to tanning processes of hides and to fixation procedures.
Circular dichroism of corticotropin, fragment 1–24, and model compounds. An assessment of the contributions of the peptide chromophore and aromatic residues
Authors: Holladay Leslie A. , Puett David
Published: December 2004

The far‐ultraviolet circular dichroic spectrum of the 39‐residue peptide hormone porcine corticotropin and the biologically active fragment corticotropin 1–24 is negative from 250 nm to 195 nm in water, but in 6M guanidinium chloride a positive band appears at about 225 nm. The temperature and guanidinium chloride dependence of this spectral transition indicates the absence of any stable ordered secondary structure in corticotropin and the spectrum is seen to be in only partial agreement with results using the model peptide chromophore, Ala‐Ala‐Ala. Using oligopeptides containing aromatic amino acid residues sandwiched between glycyl residues, it is shown that the shape and intensity of the corticotropin 225 nm positive band which appears in 6M guanidinium chloride is in agreement with the far‐ultraviolet transitions of the aromatic chromophores in the hormone. Curve resolution of the near‐ultraviolet circular dichroic spectrum of corticotropin and comparison of the rotational strengths of the phenylalanyl and tyrosyl bands reveals no evidence for increased rotational freedom in 6M guanidinium hydrochloride. Spectral changes are observed, however, in the transitions arising from the single tryptophan. This study suggests that corticotropin in aqueous solution may serve as a better model for the circular dichroic spectrum of the aperiodic regions in globular proteins than either synthetic homopolypeptides or reference proteins for which spectral and X‐ray diffraction data are available.
Binding of proflavin to T2L bacteriophage and its DNA
Authors: McCall Philip J. , Bloomfield Victor A.
Published: December 2004

We have measured the binding equilibria of proflavin to T2L bacteriophage, in both “slow” and “fast” sedimenting forms, and to free T2L DNA. Measurements were carried out by difference spectroscopy at 430 nm at temperatures from 13 to 43°C and at pH 5.6 and 7.6. We found no significant difference in the binding parameters of the two phage forms. Also, the fraction of nucleotides available as binding sites for proflavin was the same for both free and intraphage DNA. However, the binding constant is about an order of magnitude lower for encapsulated than for free T2L DNA, due to the decreased exothermicity of the binding reaction within the phage head.
Electric mobility of bivalent cations in the presence of an anionic polysaccharide
Authors: Magdelénat H. , Turq P. , Chemla M. , Para B.
Published: December 2004

The electrophoretic mobilities of bivalent cations (Ca++ and Sr++) were measured in the presence of a linear anionic polysaccharide extracted from cartilage—chondroitin sulfate. The experimental results were analyzed according to Manning's treatment which involves only the charge‐density parameter ξ related to the structure of the polyion and the charge of the counterion. The comparison between the electrophoretic mobility and the self‐diffusion coefficient enabled us to determine the apparent charge of the counterions in the different domains of concentration.
On the application of polyelectrolyte limiting laws to the helix–coil transition of DNA. IV. Dependence of helix stability on the concentration of divalent metal ions
Authors: De Marky Nancy , Manning Gerald S.
Published: December 2004

The molecular theory of the previous paper in this series is extended to determine the effect of divalent metal ions on helix stability relative to coil at fixed ionic strength and nucleotide phosphate concentration. Specification of the state of condensed counterions, as well as their concentration, is essential for the solution of this problem, and it is assumed that they translate freely within a thin cylindrical shell close to the polynucleotide. As a function of divalent counterion concentration m the relative stability of the helix is highly nonlinear. Although the overall trend is that the helix stability increases with addition of divalent metal ion, there is a narrow concentration range for which it decreases slightly. The behavior of the relative stability as a function of m is determined by the translational degrees of freedom of the counterions, both univalent and divalent, both condensed and uncondensed. Detailed comparison of the theory with data is not given here, but it is pointed out that the calculated values of the relative stability are consistent with the order of magnitude of the observed effect Mg2+ on the melting temperature.
Proton and phosphorus nmr studies of d‐CpG(pCpG)n duplexes in solution. Helix–coil transition and complex formation with actinomycin‐D
Authors: Patel Dinshaw J.
Published: December 2004

The Watson–Crick imino and amino exchangeable protons, the nonexchangeable base and sugar protons, and the backbone phosphates for d‐CpG(pCpG)n, n = 1 and 2, have been monitored by high‐resolution nmr spectroscopy in aqueous solution over the temperature range 0°–90°C. The temperature dependence of the chemical shifts of the tetramer and hexamer resonances is consistent with the formation of stable duplexes at low temperature in solution. Comparison of the spectral characteristics of the tetranucleotide with those of the hexanucleotide with temperature permits the differentiation and assignment of the cytosine proton resonances on base pairs located at the end of the helix from those in an interior position. There is fraying at the terminal base pairs in the tetranucleotide and hexanucleotide duplexes. The Watson–Crick ring imino protons exchange at a faster rate than the Watson–Crick side‐chain amino protons, with exchange occurring by transient opening of the double helix. The structure of the d‐CpG(pCpG)n double helices has been probed by proton relaxation time measurements, sugar proton coupling constants, and the proton chemical shift changes associated with the helix–coil transition. The experimental data support a structural model in solution, which incorporates an anti conformation about the glycosyl bonds, C(3) exo sugar ring pucker, and base overlap geometries similar to the B‐DNA helix. Rotational correlation times of 1.7 and 0.9 × 10−9 sec have been computed for the hexanucleotide and tetranucleotide duplexes in 0.1 M salt, D2O, pH 6.25 at 27°C. The well‐resolved 31P resonances for the internucleotide phosphates of the tetramer and hexamer sequences at superconducting fields shift upfield by 0.2–0.5 ppm on helix formation. These shifts reflect a conformational change about the ω,ω′ phosphodiester bonds from gauche‐gauche in the duplex structure to a distribution of gauche‐trans states in the coil structure. Significant differences are observed in the transition width and midpoint of the chemical shift versus temperature profiles plotted in differentiated form for the various base and sugar proton and internucleotide phosphorous resonances monitoring the d‐CpG(pCpG)n helix–coil transition. The twofold symmetry of the d‐CpGpCpG duplex is removed on complex formation with the antibiotic actinomycin‐D. Two phosphorous resonances are shifted downfield by ∼2.6 ppm and ∼1.6 ppm on formation of the 1:2 Act‐D:d‐CpGpCpG complex in solution. Model studies on binding of the antibiotic to dinucleotides of varying sequence indicate that intercalation of the actinomycin‐D occurs at the GpC site in the d‐CpGpCpG duplex and that the magnitude of the downfield shifts reflects strain at the O‐P‐O backbone angles and hydrogen bonding between the phenoxazone and the phosphate oxygens. Actinomycin‐D is known to bind to nucleic acids that exhibit a B‐DNA conformation; this suggests that the d‐CpG(pCpG)n duplexes exhibit a B‐DNA conformation in solution.
ESR investigation of the binding of acidic biopolymers to synthetic apatite
Authors: Peckauskas R. A. , Termine J. D. , Pullman I.
Published: December 2004

The interaction between synthetic crystalline calcium phosphate (apatite) and acidic macromolecules (sodium polyacrylate, sodium poly(L‐glutamate), chondroitin sulfate, phosvitin) was investigated by electron spin resonance spectroscopy of mineral‐macromolecule complexes doped with vanadyl ion (VO++) as a paramagnetic probe. Changes in magnetic parameters were interpreted in terms of bonding between mineral and macromolecule. The VO++ probe data indicated that polymer acidic functional groups were bound to mineral surfaces in all cases.
Infrared spectra and resonance interaction of amide‐I vibration of the parallel‐chain pleated sheet
Authors: Chirgadze Yu. N. , Nevskaya N. A.
Published: December 2004

Resonance vibrational interactions of amide I for the parallel‐chain pleated‐sheet structure have been treated on the basis of the perturbation theory in a dipole–dipole approximation. The infinite sheet and finite fragments of different types have been considered. The possibility of experimental observation by infrared spectra of parallel‐chain pleated‐sheet fragments in globular proteins is discussed.
Infrared spectra and resonance interactions of amide‐I and II vibrations of α‐helix
Authors: Nevskaya N. A. , Chirgadze Yu. N.
Published: December 2004

Amide‐I and II vibrations of α‐helix have been treated on the basis of the perturbation theory in a dipole–dipole approximation. The infinite helix and its finite fragments have been considered as models. The calculated infrared spectra for the infinite helix are in good agreement with the spectra of synthetic polypeptides. In the case of finite fragments of the α‐helix, the characteristic contours of the amide‐I and II bands appear when the nuimber of peptide groups is about 10 and 6, respectively.
Electron diffraction of Valonia cellulose. A quantitative interpretation
Authors: Claffey W. , Blackwell J.
Published: December 2004

The crystal structure of native cellulose (Valonia) has been analyzed by electron diffraction. Possible models for the structure were refined by rigid‐body least squares methods, which incorporated parameters defining the preferred orientation of the fibrils around their long axes in the cell wall lamellae. The structure was found to consist of an array of chains having the same sense (i.e., parallel), with packing parameters similar to those recently determined by X‐ray diffraction. The eight‐chain unit cell could be approximated adequately by a two‐chain monoclinic unit cell with dimensions a = 8.18 Å, b = 7.84 Å, c = 10.38 Å (fiber axis), and γ = 97.04°; the space group is P21.
Raman spectroscopic study of the proteins of egg white
Authors: Painter P. C. , Koenig J. L.
Published: December 2004

The Raman spectra of ovalbumin, ovomucoid, and conalbumin are reported. Spectral shifts in the conformationally sensitive amide I and amide III lines as a result of thermal denaturation indicate the formation of intermolecular β‐ sheets. A medium intensity line at 1260 cm−1 in the spectra of ovomucoid and ribonuclease is demonstrated to contain a substantial contribution from tyrosine residues.
Dynamic light scattering from collagen solutions. I. Translational diffusion coefficient and aggregation effects
Authors: Fletcher Guy C.
Published: December 2004

Solutions of native collagen extracted from rat tail tendons in neutral salt solution have been studied by dynamic light scattering. The spectra obtained are consistent with the presence in solution of both single rod‐shaped collagen molecules and aggregates of molecules. No contribution to the spectrum has been detected at any scattering angle from rotational diffusion of single molecules, although a measurable broadening effect is expected at high angles. The translational diffusion coefficient D of single molecules, calculated from the broader spectral component, shows an anomalous dependence on collagen concentration with a maximum value of D20,w = 8.6 ± 0.2 × 10−12 m2/sec near the concentration 0.04% by weight. Above 0.05% D falls linearly with increasing concentration and takes the value D 20,w = 8.1 ± 0.2 × 10−12 m2/sec at 0.064% collagen.
Investigation of the formation of triple helices between (pro‐pro‐gly)n's of different degrees of polymerization using gel filtration
Authors: Kobayashi Yuji , Suezaki Yukio , Inouye Katsuhiko , Tanaka Kaori , Kakiuchi Kinji , Kyogoku Yoshimasa
Published: December 2004

The properties of triple‐helix formation of (Pro‐Pro‐Gly)n were studied. The probability of hybridization between the polytripeptides (Pro‐Pro‐Gly)n, of different degrees of polymerization was investigated by gel filtrations of mixed solutions of them. Using samples selectively labeled with radioactivity, the elution pattern was detected by uv absorption and liquid scintillation counting. The hybridization was found only when the difference of polymerization is small. The amount of heterohelices (triple helices of the polypeptide chains with different degrees of polymerization) measured by integrated intensity of elution pattern was comparable to the theoretical value of Suezaki and Go. Concentration dependence of the helix–coil transition temperature of (Pro‐Pro‐Gly)n was also measured by the use of optical rotation and discussed with the theoretically expected values.
Kinetic analysis of the annealing period in the formation of the poly(A)·2poly(U) triple helix
Authors: Spodheim Melanie , Neumann Eberhard
Published: December 2004

The slow kinetics of annealing processes in multistranded nucleic acids is spectrophotometrically investigated using poly(A)·2poly(U) as a model system. The absorbance changes at specific wavelengths show that double‐helical (A·U) base pairs appear as transient intermediates. The annealing process is identified by the enlargement of triple‐helical sequences at the cost of (A·U) base pairs and unpaired (U) residues. A large time range in the reorganization of mismatched chain configurations is characterized by a logarithmic dependence on time. This observation is quantitatively described by a kinetic model developed by Jackson. In Jackson's model the rate‐limiting process in the slow annealing phase of maximizing triple‐helical sequences, is the removal of strand entanglements, knots, and hairpin loops by complete unwinding of those helical stretches which stabilize the mismatched configurations. The results of the present study are briefly discussed in terms of optimum conditions for hybridization experiments and for the preparation of polynucleotide complexes commonly used to produce interferons.
Conformational behavior of polyethylenimine derivatives revealed by fluorescence spectroscopy
Authors: Pranis Robert A. , Klotz Irving M.
Published: December 2004

Conformation behavior of polyethylenimine has been examined by studies of the fluorescence characteristics of derivatives of the polymer containing pyrenyl ligands. Excimer formation within the macromolecular matrix serves as a sensitive probe of group proximities. The experimental observations combined with nearest neighbor analyses lead to quantitative assessments of the extent of interaction between polymer side chains.
An X‐ray diffraction study of poly(L‐lysine hydrobromide)
Authors: Suwalsky M. , Llanos A.
Published: December 2004

A structural study of the synthetic polypeptide poly(L‐lysine hydrobromide) has been made by X‐ray fiber techniques. The investigation was undertaken to determine whelther this polymer undergoes conformational transitions as a function of hydration in a manner similar to other chemically related basic polypeptides. Specifically, a comparison with the previously reported structures of the hydrochloride form of poly(L‐lysine) was sought. Homogeneous powder mixtures with various amounts of water and oriented fibers of poly(L‐lysine hydrobromide) at different relative humidities were X‐ray photographed. Reversible transitions amorphous state ⇌ β‐pleated sheet ⇌ α‐helix ⇌ isotropic solution as a function of increasing/decreasing degrees of hydration were found. The β‐pleated‐sheet conformation was observed between 33% and 76% relative humidities (containing about one and three molecules of water per residue, respectively). Each pleated sheet was formed by “antiparallel” chains, and the sheets were piled up along the b‐axis. The spacings of this conformation did not vary appreciably with hydration. The observed reflections at 52% relative humidity (1.4 molecules of water per residue) could be indexed satisfactorily in terms of an orthorhombic unit cell, of space group P21221, with a = 9.52 Å, b = 16.44 Å, and c = 6.80 Å. These dimensions were shown by models to be compatible with the proposed structure. The α‐helix conformation was present in specimens photographed at 76% relative humidity and up, and containing between three and fifteen molecules of water per residue. The helices were packed parallel to each other in a hexagonal array but randomly along or about their lengths. Increasing the hydration from five to fifteen molecules of water per residue causes the a‐axis to increase from 16.9 to 20.8 Å. Twenty molecules of water per residue produced an isotropic solution. Despite some structural differences between the hydrobromide and hydrochloride forms it is concluded that the role played by the anions is mainly related to determining the water content levels at which conformational changes occur. Therefore, the anions do not significantly influence the prevailing conformation in this particular system, but might affect the packing arrangement of the polypeptide chains.
Synthesis of linear stereoregular glucomannan heteropolysaccharides
Authors: Kobayashi Kazukiyo , Eby Ronald , Schuerch Conrad
Published: December 2004

A series of stereoregular α‐(1 → 6) linked glucomannans have been prepared by Lewis acid‐catalyzed copolymerization of anhydro sugar derivatives followed by debenzylation. The products have been characterized for mole fraction of the individual monomer, and sequence lengths have been calculated from copolymerization data. The viscosity, specific rotation, and 13C nmr spectra have been correlated with the structure of the various copolymers.