bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractConformational 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

AbstractThe 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

AbstractIn 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

AbstractA 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

AbstractMonodisperesed, 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

AbstractThe 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

AbstractThe 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

AbstractInfrared 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

AbstractMeasurements 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

AbstractThe 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

AbstractThe 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

AbstractFor 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

AbstractIn 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

AbstractThe 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

AbstractVariation 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

Abstract13C‐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

AbstractThe 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.
DNA conformational kinetics
Authors: Szu Shousun C. , Jernigan Robert L. 
Published: December 2004

AbstractA model for the time dependence of DNA conformational state probabilities is formulated in the form of first‐order differential equations. This model is applied to investigate the renaturation and denaturation rates for T2 and T7 DNA as reported in the series of experiments by Record and Zimm. Qualitative agreement is found in denaturation and for series of renaturation experiments with the same initial condition. However, partial agreement with series of renaturation experiments having the same final condition is obtained only by including an initial bimolecular step with properly matched pairs of strands. Comparison of all experiments with the calculated rates yields 5 × 104 min−1 as the step rate for melting a single base pair.
Local order in polyelectrolytic solutions detected by magnetic birefringence measurements on the (Tyr‐Glu)n copolymer
Authors: Maret G. , Domard A. , Rinaudo M. 
Published: December 2004

AbstractThe local electrostatic order in polyelectrolytic solutions has been studied by magnetic birefringence measurements on short segments (n ∼ 34) of the (Tyr‐Glu)n polypeptide in high magnetic fields up to 13 T. We give evidence that only above a critical polymer concentration do small domains exist within which the polymers show a parallel ordering. This structural order disappears suddenly at ionic strengths above about 5 × 10−2 M and above a melting temperature of about 50°C.
Conformational studies on polynucleotide chains. IV. Backbone structure of ribonucleic acids
Authors: Tosi Camillo , Pescatori Emilio , Clementi Enrico 
Published: December 2004

AbstractIn preceding papers the energies associated with the internal rotations in the sugar–phosphate–sugar complex were described with an analytical potential consisting of a Lennard‐Jones 6–12 term and an intrinsic torsional term and representing the best fit to a large number of energies computed with a quantum mechanical ab initio technique. The complex considered there (of 37 atoms and with the chemical formula C10H18O8P) is repesentative of deoxyribonucleic acids. In this paper we apply our potential to evaluating the intramolecular energies of the 39‐atom complex C10H18O10P, representative of the ribonucleic acids. The potential energies for the internal rotations (considered independent from one another) and the energy maps for rotations about consecutive bonds of the backbone chain are critically compared, both with those obtained for the deoxy system and with those obtained from different theoretical approaches as available from literature. It is shown that, at least for certain combinations of the internal rotation angles, the choice of the starting geometry for the sugarphosphate–sugar molecule (bond lengths and valence angles) strongly affects the value of the computed energy. If a proper geometry is used, very low energies are predicted by our potential in correspondence of the sets of torsional angles found in various RNAs by x‐ray crystallography.