bluuebunny/crossref_metadata_2025_split huggingface dataset:
Raman spectra of D and L amino acid copolymers. Poly‐DL‐alanine, poly‐DL‐leucine, and poly‐DL‐lysine
Authors: Frushour B. G. , Koenig J. L. 
Published: December 2004

AbstractThe Raman spectrum of poly‐DL‐alanine (PDLA) in the solid state is interpreted in terms of the disordered chain conformation, in analogy with the spectrum of mechanically deformed poly‐L‐alanine. The polymer is largely disordered with only a small α‐helical content in the solid state. When PDLA is dissolved in water, the spectra suggest that short α‐helical segments are formed upon dissolution. These helical regions might be stabilized by hydrophobic bonds between side‐chain methyl groups. Addition of methanol to the aqueous PDLA solutions results in a Raman spectrum resembling that of solid PDLA. This result suggests that the methanol disrupts the helical regions by breaking the hydrophobic bonds.The Raman spectra of poly‐DL‐leucine (PDLL) and poly‐L‐leucine (PLL) are compared and only slight differences are observed in the amide I and III regions, indicating that PDLL does not have an appreciable disordered chain content. Significant differences are observed in the skeletal regions. The 931‐cm−1 lines in the PLL and PDLL spectra are assigned to residues in α‐helical segments of the preferred screw sense, i.e., L‐residues in right‐handed segments and D‐residues in left‐handed segments (in PDLL). On the other hand, the 890‐cm−1 line in the spectrum of PDLL is assigned to residues not in the preferred helical sence, i.e., L‐residues in left‐handed segments and D‐residues in right‐handed ones. The Raman spectra of poly‐DL‐lysine and poly‐L‐lysine in salt‐free water at pH 7.0 are compared. The Raman spectra of the two polymers are very similar. However, this does not negate the hypothesis of local order in poly‐L‐lysine because the distribution of the residues in poly‐DL‐lysine probably tends towards blocks, and the individual blocks may take up the 31 helix.
Characterization of rodlike DNA fragments
Authors: Thomas M. Record , Woodbury Charles P. , Inman Ross B. 
Published: December 2004

AbstractNative calf thymus DNA was sheared by sonication in a viscous solvent to the molecular‐weight range from 3 × 104 to 3 × 105 daltons, and fractionated by gel chromatography. Number and weight average molecular weights (M̄n and M̄w) were determined for individual fractions by electron microscopy; the ratio M̄w/M̄n for the peak fraction is approximately 1.1. Sedimentation coefficients (s020,w) of these fractionated samples show an approximately linear dependence on the logarithm of the molecular weight M̄w. This behavior is that expected for rodlike molecules, and is in quantitative agreement with the theory of Yamakawa and Fujii [(1973) Macromolecules 6, 407–415] for the sedimentation coefficient of a wormlike chain with a persistence length of 625 Å, a diameter of 25 Å, and a mass per unit length of 195 daltons/Å. It appears that the wormlike coil model, without excluded volume, can represent the sedimentation behavior of DNA over the entire conformational range from rigid rod to flexible coil, using the above parameters.Equilibrium melting curves were determined for various fractions in aqueous 2.4 M tetraethylammonium bromide. A substantial broadening of the transition and decrease of the melting temperature were observed with decreasing molecular weight. Empirical expressions have been obtained relating both the transition temperature and breadth in this solvent to molecular weight.
Raman spectroscopic study of the structure of antibodies
Authors: Painter Paul C. , Koenig J. L. 
Published: December 2004

AbstractThe Raman spectra of human IgG, IgM, and rabbit IgG in lyophilized form and solution are reported. The spectral results indicate that the predominant structure in these immunoglobulin proteins is the antiparallel β‐sheet. The Raman spectra have also been obtained of rabbit anti‐ovalbumin, and this antibody molecule precipitated with its respective antigen. The spectra reflect a conformational change on binding of antibody with antigen. The conformational change occurs in the direction of disordering.
Helix–coil transition of poly(γ‐benzyl‐L‐glutamate) in the dioxane–dichloroacetic acid mixture
Authors: Gupta A. K. , Dufour C. , Marchal E. , Benoit H. 
Published: December 2004

AbstractThe thermal helix–coil transition of four samples of poly(γ‐benzyl‐L‐glutamate) in the dioxane–dichloroacetic acid (DCA) mixture was studied by optical rotatory dispersion method. The transition occurred at very high DCA content (97.5% by weight) in this system. The transition parameters have been evaluated by two methods based on the theories of Zimm and Bragg and of Nagai. The values of the helix initiation parameter and of the enthalpy of transition were found to be (4.4 ± 0.4) × 10−5 and 340 cal/mole, respectively. The range of validity and equivalence of the two methods is discussed.
Condensed states of nucleic acids. II. Effects of molecular size, base composition, and presence of intercalating agents on the Ψ transition of DNA
Authors: Cheng Sheau‐Mei , Mohr Scott C. 
Published: December 2004

AbstractCircular dichroism spectroscopy has been used to investigate the influence of DNA molecular size, base composition, and the presence of intercalating agents upon the Ψ transition of DNA brought about by high concentrations of poly(ethylene oxide) and salt (Lerman (1971) Proc. Natl. Acad. Sci. (U.S.) 68, 1886–1890). A molecular weight of 0.15–3.0 × 106 daltons yields maximum formation of Ψ‐DNA. Both the amplitude of the large negative CD band at 265 nm—a chief characteristic of the Ψ state—and the thermal stability of Ψ‐DNA increase linearly with increasing mole fraction of guanine plus cytosine in the DNA sample. Either ethidium or proflavine, at concentrations where approximately one dye is bound per 5–10 nucleotide residues, can prevent the transition completely. Striking similarities between the Ψ‐DNA produced by poly(ethylene oxide) + salt and the complexes formed between DNA and lysine‐rich histone f1 suggest the presence of similar nucleic acid–nucleic acid interactions in both types of condensed phase.
Estimation of amino acid residue side‐chain absorption in the infrared spectra of protein solutions in heavy water
Authors: Chirgadze Yu. N. , Fedorov O. V. , Trushina N. P. 
Published: December 2004

AbstractThe values of maximum frequencies, intensities, and other spectral parameters of the main absorption bands of amino acid residue side‐chain groups have been obtained in the 1500–1800‐cm−1 region for solutions in heavy water at pD 1–12. It is shown that absorption of residues of asparagine, glutamine, aspartic and glutamic acids, arginine, and tyrosine must be taken into account in quantitative studies of the infrared spectra of polypeptide and protein solutions in heavy water. Examples of separating out the amide I band for ribonuclease A in heavy water are given.
Influence of the sugar configuration on the structure of RNA by conformational analysis of the ribose‐phosphate unit
Authors: Broch H. , Cornillon R. , Lespinasse J. N. , Vasilescu D. 
Published: December 2004

AbstractThe conformation of the ribose‐phosphate unit for the four principal configurations of the sugar ring has been studied using the extended Hückel theory and the Lennard–Jones empirical potential. Initially, the oxygen atoms of the p3 and p5 groups were not taken into account. With this restriction, the energy of this residue with regard to the structure of RNA has been minimized for the rotational angles ψ and ϕ′.The equivalence of the sugar puckering C2′endo ≃ C3′exo and C3′endo ≃ C2′exo has been confirmed. We find that the role of the sugar configuration is important and that there is a difference in the rotations around the bond C3′‐O3′ (ϕ′ angle) according to this configuration. The C3′endo sugar form seems to be energetically preferred for this residue of RNA.The oxygen atoms and the electrostatic interactions were then introduced into the empirical potential. The variation of the energy when varying ϕ′ for different positions of the p5 group was studied for the main C3′endo and C2′endo configurations of the sugar; in this condition the ϕ′ rotation is considerably restricted but the allowed regions continue to differ according to the configuration of the sugar considered.
Neutron‐scattering spectroscopy of the α‐ and β‐ forms of poly‐L‐alanine. Motion of the methyl side chain
Authors: Drexel Winfried , Peticolas Warner L. 
Published: December 2004

AbstractDetailed inelastic, incoherent neutron‐scattering (INS) spectra are presented for poly‐L‐alanine in both the α‐helical and β‐sheet form. Assignments are made from previous normal coordinate calculations. Of particular interest is the methyl torsion at 230 cm−1, which is the strongest peak in the spectrum and is independent of backbone conformation. The height of the potential barrier for methyl group rotation is calculated to be 14 kJ mol−1.
Studies on cyclic peptides. II. Synthesis of cyclic peptides containing sarcosine
Authors: Sugihara Toshiharu , Imanishi Yukio , Higashimura Toshinobu 
Published: December 2004

AbstractCyclic peptides containing sarcosine, cyclo‐(Pro‐Sar‐Gly)2, cyclo‐(Sar‐Sar‐Gly)2, cyclo‐(Sar4), and cyclo‐(Sar6) have been synthesized by the cyclization of the p‐nitrophenyl ester of linear peptides. The tert‐butoxycarbonyl group was used as the Nα‐protecting group, which was removed by acid. Benzyl ester was used to protect the C‐terminal. tert‐butoxycarbonylpeptide was obtained by the stepwise elongation of the peptide bond by the carbodiimide method. Deblocking and cyclization of the linear peptides gave the cyclic peptides.
A 13C spin‐lattice relaxation study of dipeptides containing glycine and proline: Mobility of the cyclic proline side chain
Authors: Fossel E. T. , Easwaran K. R. K. , Blout E. R. 
Published: December 2004

AbstractMolecular dynamics of the cyclic dipeptides cyclo(Gly‐L‐Pro), cyclo‐(L‐Pro‐L‐Pro), and cyclo(L‐Pro‐D‐Pro) and the linear dipeptides L‐Pro‐Gly and cis and trans Gly‐L‐Pro were studied in neutral aqueous solution by 13C nuclear magnetic resonance. Spinlattice relaxation times (T1) were determined for each individual carbon atom. The correlation times, τ, were derived from a semiquantitative analysis of the T1 data. The correlation times of the proline ring carbons, β, γ, and δ suggest that the cyclic dipeptides have more restriction of conformational freedom in the proline ring than the linear dipeptides. This effect is most pronounced on the γ carbon.
Hill's equation applied to reconstituted contractile collagen
Authors: Balmer R. T. , Soto R. J. 
Published: December 2004

AbstractA new type of automatic force‐displacement recording myograph has been developed to measure the contraction–relaxation characteristics of contractile systems. The device produces a polytonic (variable‐force) load and therefore provides a more realistic measurement than either isometric or isotonic apparatus. Measurements on collagen that was first well ground and then extruded into a reconstituted thin tape show contraction and relaxation behaviour that can be characterized by a slightly modified form of Hill's 1938 equation. The characteristic parameters of the Hill equation determined for the reconstituted collagen were remarkably similar to those of intact muscle tissue.
Ion–polyelectrolyte interactions. Comparison between Manning's electrostatic theory and the multiple equilibrium theory of Scatchard in the case of linear polyelectrolytes and bivalent counterions
Authors: Magdelenat Henri , Turq Pierre , Chemla Marius 
Published: December 2004

AbstractManning's and Scatchard's models for the description of ion–polyelectrolyte interactions are compared in the case of linear polyelectrolytes and bivalent counterions, where “condensation” of the counterions is known to occur for certain concentration ratios of the two species in solution. This comparison leads to the definition of certain conditions on Scatchard's parameters for a precise structural interpretation of Scatchard's plots to be valid. Experimental data obtained with both models are compared and found in good agreement under such conditions.
Nmr study of the structure of short‐chain peptides in solution
Authors: Gupta‐Bhaya Pinaki 
Published: December 2004

AbstractThe electron‐mediated spin–spin coupling constant J between the amide NH and the α‐CH protons in the dipeptide fragment CαCO(NHCαH)RC′ONHCα is dependent on the dihedral angle of rotation (Φ) around the NC bond. Measurement of J in a series of zwitterionic dipeptides H3N+CHR1CONHCHR2CO2− (which is conformationally similar to the dipeptide fragment) in TFA solution shows that J is independent of R1, but dependent on the steric bulk of R2. The data are interpreted in terms of a model that assumes that what we measure is an average value of Ja thermal average over all the possible rotamers. The groups R1 and R2 are, in most cases, sterically kept apart by the trans and planar amide bonds, and hence the independence of J of R1. This model is consistent with the theoretical calculations done on the dipeptide fragment. The effect of the structural characteristics of the side chains (e.g., the effect of lengthening and branching the side chains) on the J values in dipeptides is discussed in the light of the existing results of theoretical calculations.Study of 〈J〉 values in tripeptides (C6H5CH2OCONHCHR1CONHCHR2CO2CH3, essentially three linked peptide units) shows that electrostatic interaction between the two amide bonds modifies the potential energy surface and the 〈J〉 value of a dipeptide subunit in the tripeptides. Also in some cases, direct steric interaction between the two side chains in the two adjacent dipeptide subunits in the tripeptide affects the potential energy surfaces of the individual dipeptide subunits and hence the 〈J〉 values. The influence of the structural characteristics of the side chains of individual amino acids on structure formation at or beyond the dipeptide level is discussed at various points.The J(NHαCH) values of CH3CONHCHRCONH2 and CH3CONHCHRCO2CH3 with the same R are quite different for R = valine, leucine, phenylalanine, methionine, but equal for R = glycine. This, coupled with the fact that one of the carboxamide NH resonances has a chemical shift different from its counterpart in simple amides like CH3CONH2 and the other carboxamide NH has the same chemical shift as its counterpart in CH3CONH2, suggest the presence of a hydrogen bond in dipeptide CH3CONHCHRCONH2 with carboxamide NH as the donor. Theoretical evidence for two seven‐membered hydrogen‐bonded rings with the carboxamide NH as donor and the acetyl oxygen as acceptor is summarized. Our data cannot suggest the number of such hydrogen‐bonded rings, nor can they conclude the relative proportion of these rings in a particular dipeptide. A discussion of the difficulty of interpretation is presented and the data are discussed under certain simplifying assumptions.
On the various types of circular dichroism induced on acridine orange bound to poly(S‐carboxymethyl‐L‐cysteine)
Authors: Imae Toyoko , Ikeda Shoichi 
Published: December 2004

AbstractCircular dichroism and absorption spectra are measured on mixed solutions of acridine orange and poly(S‐carboxymethyl‐L‐cysteine) at different pH and P/D mixing ratios. The observed circular dichroism spectra are classified into several types, mainly based on the number and sign of circular dichroic bands in the visible region. Three of them are associated with the absorption spectra characteristic of dimeric dye or higher aggregates of dye. Type I is observed with solutions, of which the pH is acid and P/D is higher than 4, and it has an unsymmetrical pair of positive and negative dichroic bands at 470 and 430 nm. This type is induced on the dye bound to the polymer in the β‐conformation. Types II and III are considered to be characteristic of randomly coiled polymers. Type II is exhibited by solutions of P/D higher than 1 at pH 5–7 and has two dichroic bands around the same wavelengths as Type I but with opposite signs and an additional positive band at 560 nm. Type III, shown by solutions of P/D 2–0.6 at pH 6–10.5, has three dichroic bands around the same wavelengths as Type II but with signs opposite to it. The other two types of circular dichroism, induced for the solutions of P/D less than 1 at slightly acid pH, are associated with the absorption spectra of monomeric dye and are observed with disordered or randomly coiled polymer. They have a pair of dichroic bands at 540 and 425 nm, and the signs of these bands are opposite to each other in these two types.
Basic polypeptides as histone models. Synthesis, conformation, and interaction with DNA of statistical copolymers (Lysx,Alay)n
Authors: S̆okrová S̆. , Šponar J. , Havránek M. , Sedláček B. , Bláha K. 
Published: December 2004

AbstractStatistical copolymers (Lysx,Alay)n were synthesized by copolymerization of N‐carboxyanhydrides of L‐amino acids. The conformation of copolymers in aqueous solutions was investigated using circular dichroism (CD). Calculations based on the CD data showed that polymers (Lysx,Alay)n can exhibit a random conformation, an α‐helix, and a β‐structure in various ratios. CD spectra of complexes of copolymers with DNA prepared by gradual dialysis from a high ionic strength to 0.15 M NaCl can be correlated with the copolymer conformation in medium and high ionic strength. For copolymers forming an α‐helix and β‐structure, these spectra show resemblance with similar spectra of complexes of those histones that are able to exhibit ordered conformations.
Conformational geometry and vibrational frequencies of nucleic acid chains
Authors: Brown Ellen B. , Peticolas Warner L. 
Published: December 2004

AbstractNormal 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

AbstractThe 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

AbstractSome 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

AbstractUsing 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

AbstractInfrared 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.