bluuebunny/crossref_metadata_2025 huggingface dataset:
Co‐oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. VI. Circular dichroism studies of co‐oligopeptides of L‐phenylalanine, L‐tryptophan, and glycine
Authors: Rizzo Vincenzo , Luisi Pier Luigi , Straub Barbara , Guarnaccia Rocco
Published: December 2004

The circular dichroic properties of H‐Gly‐Phe‐(Gly)n‐Trp‐Gly‐OH (II, n = 0,1,2) and of related simpler peptides, such as H‐Phe‐Gly‐OH, H‐Gly‐Phe‐OH, H‐Gly‐Phe‐Gly‐OH, H‐Phe‐Trp‐OH, H‐Phe‐Trp‐Gly‐OH, and H‐Gly‐Phe‐Trp‐OH in water and trifluoroethanol solutions are investigated. Peptides containing only one phenylalanyl residue show markedly different near‐uv dichroic signals depending on whether this residue is in the N‐terminal position or not. The possible origin of this feature is discussed. The study of the oligopeptides II (n = 0,1,2) shows that no strong intramolecular interaction between the two aromatic rings is present. However, the dichroic properties of II (n = 0) are clearly anomalous, and the analysis of H‐Gly‐Phe‐Trp‐OH, H‐Phe‐Trp‐Gly‐OH, and of H‐Phe‐Trp‐OH at different pH's, confirms that the presence of two adjacent aromatic residues may bring about chiroptical properties which indicate a restriction in the conformational equilibrium of the molecule. The limits, and the possible generalization of this finding, are discussed.
Theory of protein molecule self‐organization. III. A calculating method for the probabilities of the secondary structure formation in an unfolded polypeptide chain
Authors: Finkelstein A. V.
Published: December 2004

A mathematical model is developed adequately describing an unfolded polypeptide chain without long‐range interactions in which fluctuating hydrogen‐bonded α‐helices, β‐bends, fragments of helices 310, and other local structures are formed. The obtained model is a modification of a one‐dimensional Ising model for a heteropolymer and allows one to determine the probability of formation of different secondary structures in various parts of a polypeptide chain, provided the whole set of structural thermodynamic parameters exists.
Dynamic light‐scattering studies of DNA. I. The coupling of internal modes with anisotropic translational diffusion in congested solutions
Authors: Lee Wylie I. , Schmitz Kenneth S. , Lin Sung‐Chang , Schurr J. Michael
Published: December 2004

A model for the coupling between internal modes, or molecular rotation, and anisotropic translational diffusion in congested solutions is proposed to account for the anomalously slow component that has appeared ubiquitously in reported autocorrelation functions of Rayleigh scattered light from solutions of DNA's with molecular weights greater than about 107. The predicted existence of an anomalously slow mode in addition to a faster “normal” mode, as well as the predicted relative amplitudes of both fast and slow components, are qualitatively in agreement with the observations. For sufficiently long‐wavelength fluctuations all of the amplitude appears in the slower mode, which then exhibits an appropriately averaged translational diffusion coefficient.

In support of the model it is shown in the Appendix that nonideal central interactions between macromolecules are by themselves insufficient to generate isolated internal mode relaxation terms in the autocorrelation function, unless translational ordering of the macromolecules extends over the illuminated observation region.
Nuclear magnetic resonance studies of exchangeable protons. II. The solvent exchange rate of the indole nitrogen proton of tryptophan derivatives
Authors: Waelder Susan F. , Redfield Alfred G.
Published: December 2004

The exchange rate of the indole nitrogen proton with solvent water protons was measured as a function of pH and temperature for tryptophan, N‐methyl tryptophan, glycyl tryptophan, tryptophanamide, tryptophylglycine, and tryptophylglycyl glycine. The nmr observation was by long‐pulse Fourier transform methods, and kinetics were inferred from saturation recovery, H2O transfer of saturation, and linewidth. There are observable differences between the rates of these compounds, but all are describable within a factor of two by specific acid and base‐catalyzed rates kH = 100 and kOH = 108 1/mol‐sec at 27°C. It is concluded that this behaviour is representative of this proton on the indole side chain in a random‐chain peptide exposed to water.
Stable and metastable forms of poly(G)
Authors: Howard F. B. , Frazier J. , Miles H. Todd
Published: December 2004

Poly(G) is shown by ir spectroscopy to be capable of existence in a metastable form which is converted spontaneously at ambient temperature, or more rapidly on heating, to a stable form. The metastable form can be regenerated by freezing and thawing the solution.

The high‐charge density of four‐stranded poly(G) makes it especially susceptible to electrostatic destabilization by use of Et4N+ counterions, which screen electrostatic repulsion of multiple strands less effectively than alkali metal ions. Poly(G) has been obtained for the first time in the single‐stranded form in aqueous solution and shown to undergo a fully reversible helix–coil transition on heating.
Conformation of poly(L‐lysine) homologs in solution
Authors: Tseng Yuen‐Wen , Yang Jen Tsi
Published: December 2004

The effect of the number of methylene groups in the side chains on the conformation of polypeptides is assessed for three poly(L‐lysine) homologs with R = –(CH2)nNH2. Circular dichroism studies show a pH‐induced helix–coil transition in 0.05 M KCl with midpoints at 9.6, 9.0, and 8.7 for n = 5, 6, and 7, respectively, as compared with 10.1 for (Lys)x (n = 4). Homologs with n = 6 and 7 could be partially helical even when the side groups are fully charged (with n = 7, the compound is highly aggregated above pH 9.1). Thus, the longer the number of methylene groups the more stable is the helical conformation of these homologs. Potentiometric titration of the n = 5 homolog gives a ΔG° of −310 cal/mol (residue) for the uncharged coil‐to‐helix transition at 25°C. The corresponding ΔH° and ΔS° are −1740 cal/mol (residue) and −4.8 e.u./mol (residue). Unlike (Lys)x, the uncharged helix‐to‐β transition is slow and incomplete even after heating at 80°C for 1 hr. Addition of methanol enhances the helical formation in neutral solution with midpoints at 72, 52, and 27% methanol (v/v) for n = 5, 6, and 7, respectively [cf. 88% for (Lys)x]. Addition of sodium dodecyl sulfate induces a coil‐to‐helix transition for all three homologs in contrast with the β form of (Lys)x under similar conditions.
Block copolymers of amino acids. I. Synthesis and structure of copolymers of L‐alanine or L‐phenylalanine with D,L‐lysine‐d7 or D,L‐lysine
Authors: Cardinaux F. , Howard J. C. , Taylor G. T. , Scheraga H. A.
Published: December 2004

Water‐soluble block copolymers of the type (A)m‐(B)n‐(A)p, where (A)m,p was either poly(D,L‐lysine‐α,β,β,γ,γ,δ,δ‐d7) or poly(D,L‐lysine) and (B)n was either poly(L‐alanine) or poly(L‐phenylalanine), were synthesized for conformational studies by proton magnetic resonance spectroscopy. Analytical determination of the amount of the initiator fragment (n‐hexylamine) at the C‐terminus of the copolymers was used to obtain the number‐average degrees of polymerization, DPn, and thereby, together with the amino acid composition, to establish the covalent structures of the polymers. The values of DPn were found to be much lower than those deduced from sedimentation equilibrium or form viscosity measurements. These deviations, which also are thought to have arisen in similar studies reported in the literature, are attributable to intermolecular aggregation; the relation of such aggregation to covalent structure (and its effect on the polymerization reaction) is discussed in terms of the conditions and mechanism of synthesis of block copolymers of amino acids.
Block copolymers of amino acids. II. Physicochemical data on copolymers containing L‐alanine or L‐phenylalanine
Authors: Howard J. C. , Cardinaux F. , Scheraga H. A.
Published: December 2004

The water‐soluble block copolymers, whose syntheses were described in the preceding paper, were subjected to ultracentrifugation, viscosity, optical rotatory dispersion circular dichroism, fluorescence, proton magnetic resonance, and infrared measurements. Discrepancies between Mn and Mw, and line broadening in the proton magnetic resonance spectra (attributed to the formation of rigid structures), support the conclusion (drawn in the preceding paper) that the block copolymers are aggregated in aqueous solution. It is shown that similar block copolymers reported in the literature are also aggregated.
Hydrodynamic shielding of spherical subunits in macromolecular complexes
Authors: Schmitz Kenneth S.
Published: December 2004

The Garcia de la Torre‐Bloomfield hydrodynamic interaction tensor was used to calculate the shielding coefficient matrices for each spherical friction bead in the rigid arrays of a rod and helix. Negative values for the average shielding coefficient result for small beads adjacent to large beads, suggesting premature truncation in the series expansions employed in the hydrodynamic interaction tensor. Numerical analysis also suggests that the magnitude of geometric asymmetry is not a good measure of the extent of friction asymmetry of the molecule due to extensive hydrodynamic shielding by other subunit beads.
Conformational studies on polynucleotide chains. II. Analysis of steric interactions and derivation of potential functions for internal rotations
Authors: Tosi Camillo , Clementi Enrico , Matsuoka Osamu
Published: December 2004

In the first paper of this series we showed that the total electronic energy, computed ab initio in the Hartree‐Fock approximation for both independent and coupled rotations of the five torsional angles in the sugar–phosphate–sugar complex C10H18O8P, can be reproduced with reasonable accuracy by a Lennard‐Jones 6‐12 potential, with different attractive and repulsive parameters assigned to the four oxygens of the phosphate group, on one hand, and the four oxygens of the sugar rings and the hydroxyl groups, on the other. The conclusion was reached on the basis of some attempts at the derivation of analytical expressions capable of correctly describing the energies obtained with the quantum mechanical computations. An analysis of the barriers to internal rotation for the angles φ and ψ indicated the possibility of improving the description through addition of further terms, in particular of an intrinsic torsional potential. In order to obtain a fit based on all internal rotations of the sugar–phosphate–sugar molecules, and coupling numerical accuracy with physical significance, we made a study of the possible contributions to the conformational energy: intrinsic torsional energy, electrostatic interactions, London attractions, van der Waals repulsions. The results of this study show that the best description of ab initio energies is offered by a potential containing a Lennard‐Jones 6‐12 term and an intrinsic torsional term.
Dehydrated circular DNA: Circular dichroism of molecules in ethanolic solutions
Authors: Gray Donald M. , Taylor Thomas N. , Lang Dimitrij
Published: December 2004

We have measured the ultraviolet CD spectra for covalently closed and linear forms of phage PM2 DNA in solution. We find that increased concentrations of salt or ethanol (up to 50% ethanol by weight) depress the long‐wavelength positive CD bands in the spectra of both forms of DNA, although the spectrum of the native covalently closed DNA always has a slightly larger magnitude of these bands than does the spectrum of the linear DNA. In addition, both DNAs are equally capable of undergoing a transition to the A conformation in 70–80% ethanol at low Na+ concentrations. Thus, the constraint imposed by the covalent closure of a DNA molecule does not seem to hinder its conformational response to these changing solution conditions. Lang [(1973) J. Mol. Biol. 78, 247–254] has found by electron microscopy that T7 DNA has an inherent ability to condense into compact particles, suggested to be supercoils of multiple order. Both covalently closed and linear forms of PM2 DNA also become condensed when the DNA, in 0.2M ammonium acetate and 1 mM EDTA, is exposed to ethanol and subsequent drying on specimen grids [Lang, D., Taylor, T. N., Dobyan, D. C. & Gray, D. M. (1976) J. Mol. Biol. 106, 97–107]. Under similar conditions, in solutions of 0.2M ammonium acetate and 1 mM EDTA to which ethanol is added, we have measured the CD spectra of both covalently closed and linear forms of DNA. Below ethanol concentrations at which the DNA obviously precipitates, the CD spectra of both forms have reduced long‐wavelength positive CD bands.
A semiempirical extension of polyelectrolyte theory to the treatment of oligoelectrolytes: Application to oligonucleotide helix‐coil transitions
Authors: Record M. Thomas , Lohman Timothy M.
Published: December 2004

The interaction of counterions with a suitably long, charged oligomer appears susceptible to treatment in the context of polyelectrolyte theory by the introduction of an end‐effect parameter that reflects the reduced association of counterions with the terminal regions of the oligo‐ion. Use of a physically reasonable value for the end‐effect parameter provides excellent agreement between theory and the experimental data of Elson, Scheffler, and Baldwin [J. Mol. Biol. 54, 401–415 (1970)] on the dependences of melting temperature on salt concentration and chain length for a series of hairpin helices formed by d(TA) oligomers. The differences in behavior expected for hairpin, dimer, and oligomer‐polymer helices are discussed. The salt dependence of the end‐joining equilibrium investigated for λ DNA by Wang and Davidson [Cold Spring Harbor Symp. Quant. Biol. 33, 409–415 (1968)] is treated as an oligomer–polymer interconversion. The dependence of equilibrium constant for this reaction on counterion concentration is in good agreement with that predicted by theory for an end‐region totalling 24 nucleotides, the known length of the λ ends.
Oxygenation of cobalt(II) protoporphyrin IX dimethyl ester bound to copolymer of 4‐vinylpyridine and styrene
Authors: Nishide Hiroyuki , Hata Seiji , Mihayashi Keiji , Tsuchida Eishun
Published: December 2004

The polymeric cobalt(II) porphyrin complexes were prepared from cobalt(II) protoporphyrin IX dimethyl ester(Co(II)P) and copolymers of 4‐vinylpyridine and styrene(PSP), and their binding ability of molecular oxygen was studied in toluene solution. The five‐ and six‐coordinate structure of CoP‐PSP complexes were confirmed by esr spectra. The esr parameters for the CoP‐PSP complexes were not affected by the molecular weight and the vinylpyridine‐unit content of PSP‐ligand. The 1:1 dioxygen‐Co complex was reversibly formed when the solution of CoP‐PSP was exposed to oxygen atmosphere at low temperature. While the visible spectra and esr parameters for the dioxygen complexes of CoP‐PSP were the same as those of the CoP‐pyridine complex, the equilibrium constant for the oxygen binding increased with the vinylpyridine‐unit content of the PSP‐ligand. The larger entropy change was observed for the oxygenation in the CoP‐PSP system especially, of which the vinylpyridine‐unit content was large.
The low‐ temperature mechanical relaxation of elastin. II. The solvated protein
Authors: Scandola M. , Pezzin G.
Published: December 2004

The low‐temperature dynamic mechanical relaxation of ox Ligamentum nuchae elastin, swollen with water and ethylene glycol at various swelling ratios, has been investigated by means of the Rheovibron DDV II viscoelastometer, at frequencies from 3.5 to 110 Hz. The peak location on the temperature scale, its intensity and activation energy have been studied as a function of solvent content and it has been found that the two solvents influence the dynamic mechanical behavior in a quite different way. A similar interaction of the solvent molecules with the backbone peptide groups is assumed for both solvents, and the differences in the mechanical spectra, which are more marked the higher the solvation degree, are explained in terms of the different size of the protein–solvent relaxing units.
Molecular states in single‐stranded adenylate chains by relaxation analysis
Authors: Pörchke Dietmar
Published: December 2004

The single‐strand helix‐coil transition in various oligo‐ and polyadenylates is characterized by means of an improved cable temperature‐jump technique. In all the polymers studied {poly(rA), poly(dA), poly[A(m2′)] and poly[A(e2′)]} helix‐coil relaxation is observed in the time range from 30 to 1000 nsec. Relaxation‐time constants observed at wavelengths λ<280 nm (τα) are different from those found at λ >280 nm (τβ), indicating the presence of more than two conformational states. The time constants τα increase in the series poly(dA), poly[A(m2′)], constants τβ/τα is approximately 2.5, except in poly(dA) where τβ/τα ≈ 9. Relaxation measurements with r(A)n‐ oligomers show a decrease in conformational mobility with increasing chain length. The relaxation curves also demonstrate that “internal” residues have lower reaction rates than residues at the ends of the oligomer chain. Measurement in D2O reveal a solvent isotope effect for τα of +87% for poly(rA), and of +53% for poly(dA), whereas no isotope effect is found in τβ. The absence of “slow” relaxation processes in the model compound 9,9′ ‐trimethylenebisadenine shows that the relatively low rate of the single‐strand helix‐coil transitions is due to the coupling of base stacking with the folding of the sugar–phosphate chain. The absence of a seprate relaxation process (corresponding to τβ) in 9,9′‐trimethylenebisadenine, as well as in the dinucleotides ApC and CpA, suggests that this relaxation process is dependent upon the presence of both the sugar–phosphate chain and of adjacent adenine bases. The experimental data provide evidence that there is more than one ordered conformation in various single‐stranded oligo‐ and polyadenylates and that the transition between these conformations is influenced by the sugar conformation.
Fluorescence correlation spectroscopy. III. Uniform translation and laminar flow
Authors: Magde Douglas , Webb Watt W. , Elson Elliot L.
Published: December 2004

We extend fluorescence correlation spectroscopy to systems that undergo translation or laminar flow in a sample cell. We include theoretical and experimental results; we consider uniform and nonuniform velocity profiles. Concentration correlation analysis extracts microscopic rate parameters from measurements of the spontaneous concentration fluctutations, which occur even at equilibrium. Fluorescence is one of the most sensitive means of monitoring these fluctuations. Analysis of flowing or translating systems (1) offers a method of measuring number concentrations of selected species, for example, of aggregates or polymers, (2) provides a nonperturbing velocity probe, (3) sometimes allows one to circumvent photolytic degradation, (4) has proved extremely helpful in testing and aliging apparatus for fluorescence correaltion measurement and in verifying theoretical analyses, and (5) may be required for interpretation of results obtained on systems in motion, even though that motion is undesired or initially unsuspected. We include both theoretical and experimental results for combined Poiseuille flow and diffusion in the geometry which is of most practical interest. Theoretical expressions for the much simpler cases of nondiffusive Poiseuille flow as well as uniform flow or translation with or without diffusion constitute limiting cases which are displayed explicitly.
Dynamic light‐scattering studies of internal motions in DNA. I. Applicability of the rouse‐zimm model
Authors: Lin S.‐C. , Schurr J. Michael
Published: December 2004

The intermediate scattering function G(K,t) for any polymer model obeying a linear separable Langevin equation can be expressed in terms of the eigenvalues and eigenvectors of its normal coordinate transformation. An algorithm for the extract numerical evaluation of G(K,t) for linear Rouse‐Zimm chains in the presence of hydrodynamic interaction has been developed. The computed G(K,t)2 were fit to C(t) = A exp(−t/τA) + B, and apparent diffusion coefficients calculated according to Dapp ≡ 1/(2τAK2). G(K,t)2 was surprisingly well‐fit by single‐exponential decays, especially at both small and large values of Kb, where K is the scattering vector and b the root‐mean‐squared subunit extension. Plots of Dapp vs K2 in‐variably showed a sigmoidal rise from D0 at K2 = O up to a constant plateau value at large K2b2.

Analytical expression for G(K,t), exact in the limit of short times, were obtained for circular Rouse‐Zimm chains with and without hydrodynamic interaction, and also for free‐draining linear chains, and in addition for the independent‐segment‐mean‐force (ISMF) model. The predicted behaviors for G(K,t) at large Kb (or KRG) was found in all cases to be single‐exponential with 1/τ ∝ K2 at large Kb, in agreement with the computational results. A simple procedure for estamating all parameter of the Rouse‐Zimm model from a plot of Dapp vs K2 is proposed.

Experimental data for both native and pH‐denatured calf‐thymus DNA in 1.0M Nacl with and without EDTA clearly plateau behavior of Dapp at large values of K, in harmony with the present Rouse‐Zimm and ISMF theories, and in sharp contrast to previous predictions based on the Rouse‐Zimm model.
The triple helix‐coil transition of cyanogen‐bromide peptides of the α1‐chain of the calf‐skin collagen
Authors: Saygin Oe. , Heidemann E. , Klump H.
Published: December 2004

The thermal triple helix‐coil transition of the CNBr peptides of the α1‐chain of calf‐skin collagen was studied optically and calorimetrically. Besides α1CB5, all the peptides were able to form triple‐helical structures at low temperatures. The peptides with longer chain lengths showed, under the experimental conditions, hysteresis in the transition range depending on the direction of the successive temperature changes. The detailed thermodynamic analysis of the optical transition curves was only possible for the two small peptides α1CB2 and α1CB4. We observed a higher stability of α1CB2 relative to α1CB4 (α1CB2 has higher imino acid content), accompanied with increased values of both denaturation enthalpy and entropy. Further, we observed a linear relationship between the calorimetrically determined denaturation enthalpy of all the CNBr peptides and their imino acid content. Although this behavior is qualitatively in accordance with the observation of Privalov and Tiktopulo on various kinds of native collagen, the CNBr peptides showed much lower values of the thermodynamic parameters ΔH0 and ΔS0 and differed also in the rate of their change with imino acid content. These differences are interpreted as being caused by misalignment in the helical form of the CNBr peptides resulting in a rupture of the specific interactions in the native form.
The electronic structure of cytosine, 5‐azacytosine, and 6‐azacytosine
Authors: Raksányi K. , Földváry I. , Fidy J. , Kittler L.
Published: December 2004

The normal and vacuum uv spectra of cytosine, 5‐azacytosine, and 6‐azacytosine thin layers were determined. The spectra were resolved into a series of Gaussian bands and the experimental band positions and oscillator strengths were compared with the calculated values. The calculations were carried out with the PPP‐SCF‐CI method. The agreement of the calculations with those of others and with the experiment is discussed.
Opticohydrodynamic properties of high‐molecular‐weight DNA. III. The effects of NaCl concentration
Authors: Harrington Rodney E.
Published: December 2004

Excluded volume and persistence length of high‐molecular‐weight DNA from T2 bacteriophage have been evaluated over a range of NaCl concentrations from 0.005 to 2.0M using low‐shear flow‐birefringence and intrinsic‐viscosity data. Uncertainty in persistence length due to ambiguity in the assignment of intrinsic birefringence has been avoided by calibrating the data at 0.2M NaCl using a recently reported persistence‐length value based upon photon correlation spectroscopy [Jolly, D. & Eisenberg, H. (1976) Biopolymers 15, 61]. Results at high salt concertrations are in satisfactory agreement with other estimates of excluded volume and chain flexibility in the literature, but at very low salt concentrations they reflect greater chain expansion than has heretofore been reported. The extinction‐angle data imply a transition from a nondraining chain with excluded volume at 0.1M NaCl to an almost freely draining chain at 0.005M NaCl. Over this same salt range, the experimental persistencelength data agree very well with Flory's thermodynamic chain‐expansion theory [Flory, P. J. (1953) J. Chem. Phys. 21, 162], but are in generally poor agreement with other theoretical treatments. A detailed comparison of the results with other data in the literature suggests that the combined flow‐birefringence‐intrinsic‐viscosity technique employed here may be more sensitive to the distribution of chain stiffness and excluded volume in polyelectroytechain expansion of DNA than are othe rhydrodynamic methods such as sedimentation or intrinsic viscosity alone.
Spatial configuration of ordered polynucleotide chains. V. Conformational energy estimates of helical structure
Authors: Olson Wilma K.
Published: December 2004

Semiempirical potential energy functional used previously to account successfully for the mean‐square unperturbed dimensions and nmr coupling constants of randomly coiling polynucleotides are used, after modifications, to account for base stacking and interstrand hydrogen bonding, and to evaluate the conformational energies of single‐ and double‐stranded polynucleotide helices. Attention is focused upon the variety of A‐genus helices with local backbone conformations resembling the known double‐helical structures of RNA. Distinct structural differences between single‐ and double‐stranded helices are predicted from the energy calculations. A second point of interest is the apparent failure of two conformationally identical left‐handed polynucleotide chains to form a left‐handed duplex. The third major observation of the study is the wide morphological variety of theoreticaly allowed right‐handed polynucleotide duplexes. In addition to the familiar double helix stabilized by horizontal base stacking and hydrogen bonding, an unusual vertical double helix is predicted to form between complementary bases fixed in the unusual but not energetically forbidden high anti glycosyl conformation. Experimental results bearing upon the theoretical predictions are discussed.
Relaxation and electrophoretic effects in polyelectrolyte solutions. II. Polyelectrolyteplus‐salt solutions
Authors: Schmitt A. , Meullenet J. P. , Varoqui R.
Published: December 2004

Electrophoretic mobilities are studied in polyelectrolyte‐plus‐salt solutions, using linear irreversible thermodynamics and the concepts of relaxation and electrophoretic effects discussed in paper I. If ionic interactions are treated within the Debye‐Hückel approximation, co‐ions contribute significantly to the relaxation field experienced by polyions. Moreover, through self‐diffusion and electrophoretic measurements, the effective valance of the polyion becomes an experimentally accessible parameter. It should provide another method to check the concept of ion condensation.
Preresonance Raman studies of poly(L‐lysine), poly(L‐glutamic acid), and deuterated N‐methylacetamides
Authors: Sugawara Yoko , Harada Issei , Matsuura Hiroatsu , Shimanouchi Takehiko
Published: December 2004

The Raman spectra of poly(L‐lysine) with various structures, ionized poly(L‐glutamic acid), and deuterated N‐methylacetamides have been observed using visible and the 257.3‐nm laser lines as the light source. Most of the Raman bands with significantly enhanced intensities in the uv‐excited spectra of the polymers have been assigned to the vibrations associated with the CO and C–N stretching modes, the amide I, II, III, I′, II′, and III′, with reference to the results obtained for simple amide molecules including the deuterated N‐methylacetamides. Several amide frequencies have been newly identified and the structures of the polymers have been discussed through the comparison of the Raman and ir amide frequencies.
Influence of local interactions on protein structure. IV. Conformational energy studies of N‐acetyl‐N′‐mehylamides of Ser‐X‐ and X‐Ser dipeptides
Authors: Zimmerman S. Scott , Scheraga Harold A.
Published: December 2004

Conformational energy calculations using an empirical conformatinol energy program for peptides (ECEPP) werer carried out on 16 N‐acetyl‐N′‐methylamides of Ser‐X and X‐ Ser dipeptides, where X = Ala, Asn, Asn, Asp, Gly, Phe, Ser, Thr, and Val, and on Pro‐Ser. As with the other dipeptides studied in this serites, intraresidue interactions found to dominate over interresidue interactions in determining conformational properties. The Ser‐containing dipeptides (except for those with a pro or Gly residue) were found to have unusually low calculated bend probailities, in disagreement observations on proteins; this discrepancy probably arises becuse of sovent effects (not included in the computations). The Ser‐X dipeptides were calculated to have a lower preference for bends than the X‐Ser dipeptides.
Spin contribution to the thermodynamics of ligand binding to methemoglobins and metmyoglobins. I. Azide ion binding to horse‐heart myoglobin
Authors: Anusiem A. C. I. , Kelleher M.
Published: December 2004

The binding of azide ion to horse‐heart myoglobins has been studied at pH 6.98 and at various temperatures. The results show that the azide complex is not completely loe spin and that the spin population is strongly dependent on temperature. We have shown that with some assumption it is possible to calculate the approximate fraction of high and low spin present at any temperature from the absorbance measurements. Corrections to the spin contribution at pH 6.98 to these values has been calculated.
Conformational characteristics of the RNA subunit ApA from energy minimization studies
Authors: Thiyagarjan P. , Ponnuswamy P. K.
Published: December 2004

In an attempt to better our understanding of the conformational stabilities in RNAs, an intensive theoraticl study has been carried out on one of its dimeric subunits, ApA, using an improved set of atom‐atom interaction energy parameters and an improved version of energy‐minimization technique. The C(3′)0endo and the C(2′)‐endo sugar ApA units were sperately considered and 38 probable conformations have been analyzed in each case. The total potential energy, comprising nonbonded, electrostatic, and torsional contributions, was minimized by varying all seven relevant dihedral angles simumtaneously. The result reveal that 17 conformations in the case of C(3′)‐endo sugar ApA and 7 confomations in the case of C(2′)‐endo sugar ApA unit, the lowest energy conformation corresponds to a nonhelical structure and the A‐RNA and the Watson‐Crick‐yype conformations lie at energy levels of about 0.5 and 1.0 Kcal/mo., respectively, above the lowest energy found. For ApA with the lops of different types in the backbone and they all differ in energies by about 3.5 Kcal/mol with refrence to the lowest energy founs. It is noted that the order ofmprefrence of the base stacking is observed in the A‐RNA and the Watson‐Crick type conformers. The ApA unit with C(2′)‐endo sugar is forced to assume phosphodiester conformations with large deviations fom the expected staggered conformations compared to the ApA unit with C(3′)‐endo sugar. The result obtained for ApA are discussed with refrence to those previously obtained for the dApdA unit. Te theoretical predictions are compared with the experimental data on the tRNAPhe crystal, as well as those on fibrous RNAs and RNa subunitlike crystal structures. This study brings out many important aspects of the conformational stability of ApA which have been missed by studies made by others on this system.
Kinetic study of denaturation and subsequent reduction of disulfide bonds of lysozyme by the rapid ultrasonic absorption measurement
Authors: Yamanaka Kazushi , Nakajima Haruhiko , Wada Yasaku
Published: December 2004

A New technique for the rapid measurement of ultrasonic absorption with a sampling interval of 5 msec has been developed and applied to the kinetic study of denaturation and subsequant redution of hen egg‐white lysozyme. The lysozyme is denatured by guanidine hydrochloride (GuHCl) orLiBr, and afetr denaturation by GuHCl, its disulfide bonds are reduced by dithiothreitol (DTT). The ultrasonic adsorption coefficient at 9 MHz increases with denaturation but decreases with reduction. The rate constant of denaturation by GuHCl obtained from the rime variance of ultasonic agrees well with that from uv absorption and optical rotation. The time variance if absorption after GuHCl and Dtt have been simultaneously added exhibits two rate constants. Analysis of the constants as functions of regeant concentrations indicates that the intermediates state between native and reduced states is not necessarily the completely denatured state but depends on the concentartions of GuHCl and DTT.
Structure in solution of protected homo‐oligopeptides of L‐valine, L‐isoleucine, and L‐phenylalanine: An infrared absorption study
Authors: Baron M. H. , De Loze C. , Toniolo C. , Fasman G. D.
Published: December 2004

Monodisperesed, N‐and C‐Protected homo‐oligopeptides [number (n) of resides from 2 to 5] of L‐valine, L‐isoleucine, and L‐phenylalnine were studied by ir absorption spectroscopy between 1200 and 350 cm−1 at various solvents. The solvents and chain‐length effects were examined for non‐hydrogen‐bonded peptide groups. The frequencies of the self‐associated species are consistent with a model derived from the amide data. Self‐association species are consistent with a model derived from the amide data. Self‐association is favored by higher values of n = 2, the peptide is insoluble when more than two chains are bonded. For n = 3, 4, several chains may be associated by sliding along one another and remain soluble. For n = 2, the peptide is insoluble when more than two chains are bonded. For n = 3, 4, several chains may be associated by sliding along one another and remain slouble. For n = 5, the effect of n is to favour a model in which two chains exactly face each other so that the peptide precipitates at relatively low concentration.
The wavelength dependence of the turbidity of solutions of macromolecules
Authors: Camerini‐Otero R. Daniel , Day Loren A.
Published: December 2004

The experimental parameter describing the wavelength dependence of the turbidity of solutions of macromolecules is usually the negative slope of the graph of the logarithm of optical density vs the logarithm of the in vacuo wavelength, λ0. Such slopes are the apparent exponents of 1/λ0 in the turbidity equation. Their values depend upon the way the destructive interference of the scattered light, the refractive index increment, and the solvent refractive index change with wavelength. In this study, expressions for the wavelength exponents for isotropic rods, spheres, and random coils have been obtained and evaluated by representing the intraparticle interference functions, Q(λ0), with series in even powers of 1/λ0 and the refractive properties with Cauchy relations. Comparisons of calculated and observed exponents at wavelengths in the visible spectral region for aqueous solutions of four viruses have been made: for R17, T7, and PM2 bacteriophage, the exponents are greater than four; whereas for tobacco mosaic virus, they are less than four. The application of the turbidity relations to determine the size and molecular weight of biological macromolecules is discussed.
Interaction of water with poly‐α‐amino acids. II. Relationships between counter‐ion and relaxation processes
Authors: Fenton M. , Hiltner A.
Published: December 2004

The effect of hydration on the solid‐state conformation and relaxation behavior of the alkaline earth salts of poly (L‐glutamic acid) has been examined. The calcium and strontium salts take the β‐conformation and the magnesium salt takes the α‐form. No hydration‐dependent conformational transitions were observed. The amount of bound water, as measured by differential scanning calorimetry, appears to depend on the size of the cation, while conformation has little or no effect. A relative measure of the barrier to side‐chain reorientation was obtained from the temperature of the side‐chain (β1) relaxation. It was found that the barrier is determined by electrostatic forces and increases with increasing cation surface charge density. Side‐chain motion also appears to be more hindered in the β‐conformation than in the α‐conformation.
Infrared dichroism of polynucleotides of repeated sequence. I. Poly(dA)·poly(dT) and poly[d(A‐T)]·poly[d(A‐T)]
Authors: Baret J. FrançOis , Carbone Gérard P. , Penon Paul
Published: December 2004

Infrared dichroism measurements of oriented films of poly(dA)·poly(dT) and poly[d(A‐T)]·poly[d(A‐T)] have been made under the conditions of low salts content and high humidity for which the geometry is known. The angles which the transition moments make with the helix axis are compared with the orientations of the corresponding bonds. Except for the in‐plane base model of poly[(A‐T)]·poly[d(A‐T)], there is no agreement. This may imply either that a model which assumes bonds and transition moments to be colinear is not acceptable or that x‐ray data are inaccurate. These possibilities are discussed especially with respect to phosphate group orientation. An appendix gives the derivations of dichroic‐ratio expressions for helical molecules of different symmetry types.
Fluorescence depolarization studies of conformation changes in pyrene‐butyryl–fumarase
Authors: McIntosh R. P. , Johnson P.
Published: December 2004

Measurements of fluorescence depolarization on fumarase labeled with the dye pyrene‐butyryl were used to test for previously reported structural changes in this enzymes. These apparent conformation changes were of interest because they seemed to correlate with variation in catalytic activity provoked by changing temperature or pH, or by the presence of a competitive inhibitor. In the present studies, the bound dye pyrene‐butyryl and the enzymes were investigated systematically to ensure that simple interpretation of fluorescence depolarization results would be meaningful. This analysis showed that carefully controlled experimental condition were necessary to eliminate a dye component with a short fluorescence lifetime and that it was essential to allow for small variations of lifetime with temperature. Contrary to the previous report, a constant rotational relaxation time of the magnitude expected for a nearly spherical molecule of fumarase was found. No changes were detectable by fluorescence depolarization in the size or shape of pyrene‐butyryl–fumarase under the solution conditions tested that caused variation in enzyme activity.
Solution conformations of some azetidine cyclic peptides
Authors: Meraldi J.‐P. , Blout E. R. , Boni R. , Verdini A. S.
Published: December 2004

The 1H‐nmr spectra (270 MHz) of cyclic di‐ and tri‐L‐azatidine‐2‐carboxylic acid [cy‐clo(L‐Aze)2 and cyclo(L‐Aze)3] were determined in CDCl3 and D2O and computer simulated. The spectral results were compared with those obtained with cyclo (L‐Pro)2 and cyclo (L,‐Pro)3. In CDCl3 and D2O solution, the four membered ring of cyclo (L‐Aze)2 is puckered with the α‐proton in a pseudo‐axial position, and the ϕ angle is smaller in absolute value than −60°, as found for cyclo (L‐Pro)2,. The puckering of the four‐membered ring of cyclo(L,‐Aze)3 in CDCl3 has the α‐proton in a pseudo–equatorial position and ϕ angle larger in absolute value than −60°, in agreement with cyclo(L‐Pro)3. In D2O, cyclo(L‐Aze)3 was found to interconvert rapidly between different conformers. In the azetidine cyclic peptides studied, the range of values found for the ϕ angles was smaller than in the related proline cyclic peptides, indicating greater rigidity in the four‐membered ring.
Circular dichroism studies of copper(II)‐ hyaluronic acid complexes in relation to conformation of the polymer
Authors: Figueroa Nara , Chakrabarti Bireswar
Published: December 2004

The study of the Cu(II)‐hyaluronate complexes by absorption and CD spectra, as well as by acid–base titration and viscosity, provides information about the nature of ligands and the conformation of the polymer. Three different complexes have been identified. The first (complex I), which is formed between pH 3 and 6, involves mainly the carboxyl groups of the polymer as ligands and is characterized by a strong absorption band at 238 nm. In this complex formation, the CD properties of hyaluronate do not charge appreciably. The second (complex II) forms between pH 6 and 8 bad shows a major change in CD properties. The changes include (1) a new positive CD band at 250 nm and a strong negative on in the π → π* amide transition region and (2) the disappearance of the negative n → π* amide CD band near 210 nm. A sharp increase in absorbance at 238 nm from complex I to II has been attributed to a conformational transition which is also manifested in the CD features of hyaluronate. Complex II involves, in addition to the carboxyl group, the nitrogen atom of the deprotonated acetamido group coordinated to Cu(II). The absorption at 230–280 nm is associated with the optically active charge‐transfer transitions involving ligands to metal ion. At higher concentrations of the polymer or at higher pH, complex II aggregates to a gel, complex III. Chondroitin, differing from hyaluronic acid in the C‐4 hydroxyl group configuration of the glucosamine moiety, does not show any CD change in the presence of Cu(II).The results provide further support to our fourfold helical structure of Cu(II)–hyaluronate complex at pH between 6 and 8. Intrinsic viscosities of hyaluronate in the presence of the cupric ion is lower than in the presence of other monovalent or bivalent cations, indicating a compact conformation of the polymer when it is complexed with Cu(II).
Spectroscopic and equilibrium dialysis studies of the binding of acridine and 10‐methylacridine to DNA in the pH range 4–10
Authors: Yamaoka Kiwamu , Masujima Mayumi
Published: December 2004

For a better understanding of the interactions between DNA and various acridine dyes, the binding of acridine (Acr) and 10‐methylacridine (MeAcr) to native and heat‐denatured calf‐thymus DNA was studied in the pH range between 4 and 10 by the equilibrium dialysis and spectroscopic methods. The binding between DNA and the dyes was predominantly electrostatic. The amount of bound Acr varied with pH, mixing ratio (P/D), and the DNA conformation, and reached a maximum at pH = 5.2. The amount of bound MeAcr was constant in the pH range 5–9. The apparent binding constants of these dyes were obtained at some pH, and they were found to vary with P/D for native DNA‐dye complexes. The pure spectra of bound Acr and MeAcr could be unmasked. The bound Spectra were bathochromic and hypochromic relative to the spectra of free days. Acridine bound to native DNA was shown to undergo structural changes from an acridiniumlike to a neutral acridinelike form as the pH of solutions was varied. The pK value for the transition between the bound forms was evaluated to be 7.3. The extrinsic Cotton effects of the bound dyes were observed in the DNA‐Acr and‐MeAcr complexes and varied with pH and the conformation of DNA.
13C‐ and 1H‐nmr studies of cis‐trans conformers of oligoprolines
Authors: Chao Yen‐Yau H. , Bersohn R.
Published: December 2004

In aqueous solutions, 13C‐ and 1H‐nmr studies show that the percentage of trans conformation of proline oligomers +H2H Pro‐(Pro)n‐CO increases substantially from n = 1 (65% trans) to n = 2 (90% trans). The relatively low percentage of trans structure for the dimer (n = 1) very likely is caused by the extra stability acquired by the end‐to‐end intramolecular H‐bonding of the cis dimer. As n increase from 2 to 3 (or 5) in +H2N‐Pro‐(Pro)n‐CO, the percentage of trans conformation stays more or less constant (∼0.9). A high salt concentration (4M CaCl2) causes a conformation randomization, so that the short‐chain oligomer (n = 1, 3, 5) and the long‐chain poly (L‐proline) all show about the same frantion of trans conformation (0.7‐0.8).
Water–collagen interactions: Calorimetric and mechanical experiments
Authors: Pineri M. H. , Escoubes M. , Roche G.
Published: December 2004

The influence of hydration of rat‐tail tendons has been studied by measuring the heat involved in the water fixation deplending on the degree of hydration. The modulus and damping dependences have been measured when changing the temperature for different water uptakes. In situ hydrations have been realized. Evidence of several states of water absorption has been dervied from both calorimetic and dynamic mechanical experiments. A model has been proposed taking into account the energies corresponding to the different regimes of fixation.
The infuence of interchain compositional heterogeneity on the conformation in random copolymers of γ‐benzyl‐L‐glutamate and L‐valine
Authors: Deshmane S. , Hayashi T. , Sederel W. , Anderson J. M.
Published: December 2004

Variation in the solvent used for the copolymerization of γ‐benzyl‐L‐glutamate and L‐valine N‐carboxyanhydrides provides copolymers which have variable interchain compositions, and this variation in interchain compositional heterogeneity is reflected in the solid‐state conformations of the respective copolymers. Poly[Glu(OBzl)29Val71] prepared in dioxane exhibits a β‐structure, whereas a copolymer of the same average composition prepared in benzene/methylene chloride shows predominantly an β‐helix conformation with a small amount of β‐structure. The use of the monomer reactivity ratio permits the calculation of the average and incremental copolymer compositions at any conversion; thus, correlations between conformation and interchain compositional heterogeneity can be made. In general, copolymers prepared in dioxane show a greater distribution of chain composition and therefore permit a wider variety of conformation than copolymers prepared in benzene/methylene chloride under identical conditions.
Secondary structure of calf‐thymus histone H1 by means of 13C‐NMR spectroscopy
Authors: Tancredi T. , Temussi P. A.
Published: December 2004

13C‐nmr spectroscopy was used to determine the location of the structured segment of the chain of histone H1 in water and NaCl solutions. The segment found (41–89) is contained in the area proposed by others on the basis of 1H‐nmr studies. The number of basic groups left in the mobile ends of the protein matches the number of bases of internucleosomal DNA.
Conformation and properties of DNA–(Lys33, Leu67)100–(Orn)20 complex: A nucleohistone model
Authors: Costantino P. , Verdini S. , De Santis P. , Rizzo R. , Savino M.
Published: December 2004

The synthesis and characterization of the block copolypeptide (Leu67, Lys33)100Orn20, a synthetic model of histone, are reported. In neutral aqueous solutions, 80% of the etheropolypeptide block assumes an α‐helical conformation, whereas the polyornithine block is in a random‐coil conformation. In the association complexes with DNA, melting and titration experiments, as well as CD results, indicate that the polyornithine block interacts with DNA, whereas at least 2/3 of the lysine residues of the (Leu, Lys) moiety are excluded from the direct binding with DNA. CD spectra of the association complexes reveal significant differences from those obtained with DNA–polyornithine and DNA–polylysine complexes but substantial similarities with CD spectra of native and reconstituted nucleohistones. In contrast to DNA–polyornithine complexes, the CD spectra of the ternary complexes, copolypeptide–DNA–ethidium bromide, indicate a strong reduction of the dye intercalation. The low‐angle x‐ray diffraction pattern, reminiscent of that of chromatin, reveals the presence of a superstructure in these complexes. The results obtained are discussed in connection with the expected structural features of the model.