bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleic acid derivatives studied by preresonance and resonance Raman spectroscopy in the ultraviolet region
Authors: Chinsky L. , Turpin P. Y. , Duquesne M. , Brahms J. 
Published: December 2004

AbstractRaman spectra of AMP, UTP, GMP, and CMP, and of their bromo‐derivatives (8 Br‐ATP, 8‐bromo‐adenosine, 8‐bromo‐guanosine, 5‐bromo‐deoxyuridine, 5‐bromo‐cytidine), are reported. They are obtained using excitation wavelengths of 457.9 nm (ionized continuous argon laser) and of 300 nm (tunable pulsed dye laser). Comparison of spectra leads to the following observations: (1) preresonances Raman effects on nucleotides spectra at 300 nm; (2) resonance Raman effects on bromoderivatives spectra at 300 nm; (3) in dilute solution (10−4M), shifts and enhancements of Raman lines of the bromo‐derivatives with respect to the corresponding lines of nucleoctides. On the basis of these comparisons, the assignments of the Raman lines are discussed, This provide the necessary background for the understanding of the properties of selected groups in DNA in dilute solution. The new experimental set‐up for measurements of Raman spectra using excitation in the uv regions is described. It is specially designed to incorporate the pulsed feature of the excitation laser and for correcting of the instabilities of the sourse.
Self‐association phenomenon specific to the copper complexes with ADP, dADP, and IDP
Authors: Gabriel Marc , Larcher Dominique , Thirion Christian , Torreilles Jean , De Paulet André Crastes 
Published: December 2004

AbstractCircular dichroism spectra between 200 and 800 nm are presented for solutions of nucleotides with pyrophosphate group derived from adenine and inosine in the presence of the Cu2+ cation. A study as a function of the pH, temperature, and concentration has shown the existence of a self‐association, which implies a strong interaction between the bases of the two nucleotides. The interpretation of the dichroic spectra allows us to show that two oligomer species are formed successively in low concentrations in the presence of the Cu2+ cation. The first, constituted by Cu(ADP)− molecules, appears at pH 5.3 and gives rise to a nonconservative excitonic term. The second, responsible for a conservative excitonic term, is a heterooligomer formed at pH 7.3 by the assembling of a Cu(ADP)− and a Cu(ADP)(OH)2− molecule. Furthermore, this self‐association is destabilized if the nucleotide derived from adenine is replaced by the corresponding deoxyribonucleotide or by IDP.
Conformational studies of sequential polypeptides containing lysine and tyrosine
Authors: St. Pierre S. , Ingwall R. T. , Verlander M. S. , Goodman M. 
Published: December 2004

AbstractThe conformation of three sequential copolypeptides, poly(L‐tyrosyl‐L‐lysine), poly(L‐tyrosyl‐L‐lysyl‐L‐lysine), and poly[L‐tyrosyl‐(L‐lysyl)2‐L‐lysine] have been studied by a variety of techniques, including CD, ir spectroscopy, analytical ultracentrifugation, and x‐ray diffraction. Depending upon the pH and sovent composition, poly(L‐tyrosyl‐Llysyl‐L‐lysine) and poly [L‐tyrosyl‐(Llysyl)2‐L‐lysine] can adopt either the α‐helical or random‐coil conformation, while poly(L‐tyrosyl‐L‐lysine) forms either inter‐ or intramolecular β‐structures.
Influence of local interactions on protein structure. II. Conformational energy studies of N‐acetyl‐N′‐methylamides of Ala‐X and X‐Ala dipeptides
Authors: Zimmerman S. Scott , Scheraga Harold A. 
Published: December 2004

AbstractConformational energy calculations using an empirical conformational energy program for peptides (ECEPP) were carried out on 17 N‐acetyl‐N′‐methylamides of Ala‐X and X‐Ala dipeptides, Where X = Ala, Asn, Asp, Gly, Phe, Ser, Tyr, Val, and Pro. Each dipeptide was found to have many low‐energly minima, some of which corresponded to bend structures. The stability of bends was found to depend on the amino acid composition and sequence, with the Ala‐X dipeptide generally favoring bends more than the X‐Ala dipeptide for a particular X. In bends and nonbends alike, intraresidue interactions dominate over interresidue interactions in determining conformational propeties. The calcutions were shown to be in good agreement with available experimental data.
A circular dichroic investigation of the secondary structure of lectins
Authors: Herrmann M. S. , Richardson C. E. , Setzler L. M. , Behnke W. D. , Thompson R. E. 
Published: December 2004

AbstractThe far‐uv CD spectra of eight lectins are presented. These eight lectins, as well as others previously studied, are grouped into three classes according to their particular CD spectra. The eight lectins studied appeared to have secondary structure dominated by β‐pleated sheet, which so far has been true of all lectins. An attempt was made to quantitate the three structural components (α‐helix, β‐pleated sheet, and aperiodic) in the lectins using the data for reference proteins given by Chen et al. [Biochemistry 13,3350 (1974)]. For lectins in two of the classes, this method proved excellent and values for the three components are given. However, for the third class of lectins, which includes most of the lectins as well as Concanavalin A, this method of analysis proved to be unsatisfactory. This inadequacy was due to two factors: (1) the reference proteins used by Chen and (2) the unusual CD spectra of these lectins manifested by considerable ellipticity above 225 nm in a region where there are no known peptide electronic transitions.
A solvent effect on the side‐chain conformation of phenylalanine derivatives and phenylalanine residuces in dipeptides
Authors: Kobayashi Jun'Ichi , Nagai Ukon 
Published: December 2004

AbstractThree phenylalanine derivatives, Ac‐Phe‐NHMe, H‐Phe‐NHMe, and Ac‐Phe‐OH, were selected as models of Phe residues situated at the internal, the N‐terminal, and the C‐terminal positions of peptide chains, respctively. The side‐chain conformations of the three compounds were analyzed from the vicnal coupling constants 3JαβR and 3JαβS, of their 1H‐ nmr spectra measured in various organic sovlent. The two β‐protons were unambiguously assined by use of sterospecifically β‐monodeuterated phenylalanines. The pro‐S β‐proton was always situated at lower field than the pro‐R one when they were observed separately. The results of a solvent effect on the conformation of the tree compounds demonstrated that the rotamer populations are remarkable sensitive of the three compounds demonstrated that the rotamer populations are remarkably sensitive to solvent polarity and that the tendencies of the solvent effects are quite different from each other. Ac‐Phe‐OH Showed a trend similar to that of Ac‐Phe‐OEt reported by early workers. The rotamer populations of other derivatives (Ac‐Phe‐NMe2, Ac‐Phe‐NH2, Ac‐Phe‐OBut, and Ac‐Phe‐OBzl) and of Phe residues in some N‐acetyl dipeptde esters (Ac‐Phe‐Gly‐OMe, Ac‐Phe‐Val‐OMe, and Ac‐Gly‐Phe‐OMe) were also examined in several sovent, and it was found that substituents of the Phe carboxyl group—amides or esters—determine the tendency of the solvent effect. These results are interesting in the side‐chain conformations of Phe residues in peptides and proteins in an environment of low polarity can be disscussed on this experimental basis. Factors responsible for the solvent effect are discussed from (1) a structural comparison of the compunds with various carboxylic substituents, (2) an expriment with cyclohexylalanine derivatives, and (3) the measurement in mixed solvents wiht similar polarity.
Synthesis and circular dichroism characterization of L‐azetidine‐2‐carboxylic acid cyclic peptides
Authors: Boni R. , Verdini A. S. , Deber C. M. , Blout E. R. 
Published: December 2004

AbstractSeveral cyclic hemopeptides containing L‐azetidine‐2‐carboxylix acid (Aze)—an imino acid homologous with proline but containing one less methylene group in its cyclic side chain—have been prepared. The peptides reported include (Aze)2, cyclo(Aze)3, and cyclo(Aze)6. The synthesis and spectral characterization of these cyclic peptides are described, and the results discussed in terms of the rigidity and steric constraints attributable to Aze‐containing peptides. CD spectra of these materials in several solvents are reported and compared with those of proline analogs; the similarity between the CD spectra of cyclo(Aze)3 and cyclo (Pro)3, is noted.
An analysis of the amide I mode in the vibrational spectra of unordered polypeptides and proteins
Authors: Painter P. C. , Coleman M. M. 
Published: December 2004

AbstractThe difference in the observed frequency of the amide I mode between the Raman and ir spectra of many unordered polypeptides is interpreted in terms of a model in which sequences of amide groups have similar ϕ, ψ angles. The splittings due to intramolecular interactions for the infinite helices generated by all ϕ, ψ angles are calculated by assuming transition dipole coupling. The effect of finite sequence length and distortions are then considered. This hypothesis accounts for the general features of the amide I mode of unordered polypeptides.
13C Nuclear magnetic resonance study of salt induced conformational change of basic polypeptides: Poly (L‐lysine), poly (L‐arginine), and poly (L‐ornithine)
Authors: Saitô Hazime , Ohki Toyokazu , Kodama Masahiko , Nagata Chikayoshi 
Published: December 2004

AbstractA 13C‐nmr study of the salt‐induced helix–coil transition of the basic polypeptides poly(L‐lysine) [(Lys)n], poly(L‐arginine) [(Arg)n], and poly (L‐ornithine) [(Orn)n] was performed to serve as a reference of the helical portion of histones and other proteins. As is the case with pH‐induced helix–coil transition, the downfield displacement of the Cα and carbonyl carbon signals are observed in the helical state. The upfield shift of the Cβ signals, on the other hand, is noted in the salt‐induced transition. Regardless of the differences in the side chains and also the salts used, very similar helix‐induced chemical shifts are obtained for (Lys)n and (Arg)n. However, the displacement of the Cα, Cβ, and carbonyl carbons of (Orn)n in the presence of 4M NaClO4 is found to be almost 50% of that of (Lys)n and (Arg)n. This is explained by the fact that the maximum helical content is about 50%, consistent with the ORD result. Further, the motion of the backbone and side chains of the helical from was estimated by measuring the spin‐lattice relaxation time (T1), nuclear Overhauser enhancement (NOE), and line width. In the case of (Lys)n, the motion of the side chains is charged very little in comparison with that of the random coil. Indicating that the aggregation of the salt‐induced helix is small in contrast to that of the pH‐induced helix. For (Arg)n, however, the precipitate of the helical polymers is mainly due to aggregation.
Conformational energy analysis of retro‐all‐Dmethionine enkephalin
Authors: Momany F. A. , Aubuchon J. R. 
Published: December 2004

AbstractEmpirical conformational energy calculations have been carried out on the molecule retro‐all‐D‐methionine enkephalin. Low‐energy conformers were found by energy minimization and conformational search procedures. The lowest energy conformers wee found toi have some stereochemical relationship to the calculated normal met‐enkephalin conformers, but they were not retro‐all‐D‐equivalent to the Met‐enkephalin structures. The retro‐all‐D‐equivalent conformations were ∼10 kcal/mol higher energy than the low‐energy conformers found here. A structural comparison between the retro‐all‐D‐conformers and the met‐enkephalin conformers shows hat one cannot rely solely on topochemical analysis to predict biological activity for linear retro‐all‐D‐peptides.
A new method for determining sulfoxides in peptide molecules using x‐ray photoelectron spectroscopy
Authors: Jones Derek , Disteffano Giuseppe , Toniolo Claudio , Bonora Gian Maria 
Published: December 2004

AbstractThe problem of the quantitative determination of sulfoxide groups in peptide molecules has been re‐examined. The approaches currently available for the estimation of δ‐sulfoxide amino acids are limited in number and characterized by serious shortcomings; in addition, the choice of methods for the estimation of γ‐sulfoxide amino acids is even more restricted. A new, rapid, and nondestructive direct method for determining quantitatively all types of sulfoxides in peptide molecules by using x‐ray photoelectron spectroscopy is described.
Dielectric properties of hydrated collagen
Authors: Grigera J. Raul , Vericat Fernando , Hallenga Klaas , Berendsen Herman J. C. 
Published: December 2004

AbstractDielectric measurements have been carried out on partially hydrated collagen in the frequency ranges 100 kHz–5 MHz, 100 MHz–1 GHz, and 8–23 GHz. In the low‐frequency range, a dispersion was observed around 100 kHz which results from inhomogeneous conductivity of the samples. A dielectric relaxation was observed aroud 0.3 GHz using time‐domain‐spectroscopy techniques. This relaxation can be considered to originate from mobile side chains. Microwave measurements indicate that the water relaxation may extend into the 10‐GHz region. An apparent discrepancy between the main water relaxation time and the average rotational correlation time of water as measured by nmr line widths was resolved by the assumption that a fraction of the water molecules is bound to the collagen with residence times on the order of 10−6 sec, whereas the remainder of the water is only weakly bound and exhibits rotational rates on the order of 10−10 sec.
The effect of counter‐ion substitution on the transport properties of polyelectrolyte solutions
Authors: Magdelénat H. , Turr P. , Tivant P. , Chemla M. , Menez R. , Drifford M. 
Published: December 2004

AbstractThe effects of counter‐ion substitution in aqueous polyelectrolyte solutions (chondroitin sulfate) on the two main transport phenomena of the ionic species, self‐diffusion and electrical mobility, were studied experimentally by tracer methods and dynamic light scattering. The data were analyzed with respect to counter‐ion condensation and stoichiometric substitution of low‐ionic counterions by high‐ionic charge ones and compared to Manning's theory. Substitution effects on the apparent charge of the macro‐ion were derived from the transport data using an extended Nernst‐Einstein relationship and discussed in the light of the condensation effect in polyelectrolyte solutions. The effective charge of the polyion (i.e., its residual charge after condensation of counter‐ions) and the charge difference between the substituting counter‐ions appear determinant in the mechanism of substitution.
The influence of asymmetric carbon atoms of the side chains on the conformational properties of polypeptides: Comparison of diastereomeric homooligopeptides of L‐isoleucine and D‐alloisoleucine
Authors: Widmer Urs , Lorenzi Gian Paolo , Pino Piero 
Published: December 2004

AbstractThe conventionally protected oligopeptides of the two homologous series Boc‐(L‐Ile)n‐OMe and Boc‐(D‐aIle)n‐OMe (n = 2–6) were synthesized in a standard stepwise fashion and their uv and CD spectra in 2,2,2‐trifluoroethanol, and solid‐state ir spectra were investigated. In addition, two oligomeric products derived from the NCAs of L‐isoleucine and of D‐allo‐isoleucine and having a DP of 20 and 12, respectively, were studied in the solid state by x‐ray and ir. No substantial differences between the properties of the diastereomeric oligomers in the solid state were noticed, a β‐structure being very likely at least for the Boc‐protected hexapeptides and the higher oligomers. In contrast, differences were observed between the spectroscopic properties of the diastereomeric oligopeptides, and especially of the hexapeptides, in trifluoroethanol solution. The different properties of the hexapeptides in solution were related to the existence, in the case of Boc‐(L‐Ile)6‐OMe, of soluble molecular aggregates in which the peptide chains assume the β‐conformation. These results provide an additional example of the influence of the configuration of asymmetric carbon atoms of the side chains on the conformational properties of peptide molecules in solution.
Structure and conformation of peptides: N‐benzyloxycarboyl‐(γ‐ethyl)‐L‐glutamyl‐(γ‐ethyl)‐L‐glutamic acid ethyl ester
Authors: Benedetti Ettore , Blasio Benedetto Di , Pavone Vincenzo , Pedone Carlo , Germain Gabriel , Goodman Murray 
Published: December 2004

AbstractC24H34N2O9, orthorhombic, P212121; a = 39.432 (10), b = 14.061 (5), c = 4.850 (2) Å, M = 494 a.m.u., Z = 4, Dm = 1.22 g cm−3, Dx = 1.22 g cm−3, R = 0.13 for 1205 observed reflections after refinement with isotropic thermal factors. The urethane and amide bonds are in the trans configuration, as well as all the ester groups. The φ and ψ angles of the L‐glutamyl residues fall in the β‐structure region of the Ramachandran's plot; the molecule is rather flat with the amide plane almost parallel to the c axis along which two hydrogen bonds hold the molecules together to form long rows in a “parallel pleated‐sheet” fashion.
Helix–coil transition of the dG‐dC‐dG‐dC self‐complementary duplex and complex formation with daunomycin in solution
Authors: Patel Dinshaw J. 
Published: December 2004

AbstractThe duplex‐to‐strand transition of the self‐complementary sequence dG‐dC‐dG‐dC has been probed at the exchangeable and nonexchangeable protons and backbone phosphates by high‐resolution nmr spectroscopy. The Watson‐Crick imino and amino hydrogen‐bonded protons, as well as the exposed amino protons, could be followed through the duplex‐to‐strand transition and provide information on base‐pair stability at the tetranucleotide duplex level. The magnitudes of the experimental upfield nonexchangeable base‐proton chemical shifts on duplex formation are consistent with calculations based on base‐pair overlap geometries of the B‐DNA type. The variation of the 31P chemical shifts in dG‐dC‐dG‐dC with temperature appear to monitor changes in the ω,ω′ rotation angles about the OP bonds in the postmelting transition temperature region. The complex formed between the antitumor anthracycline antibiotic daunomycin and the dG‐dC‐dG‐dC duplex was probed at the nucleic acid and the antibiotic resonances as a function of temperature. The experimental complexation shifts of the observable daunomycin resonances have put constraints on possible overlap geometries between the intercalating anthracycline ring and adjacent base pairs.
Theoretical studies on peptidoglycans. II. Conformations of the disaccharide–peptide subunit and the three‐dimensional structure of peptidoglycan
Authors: Virudachalam R. , Rao V. S. R. 
Published: December 2004

AbstractPossible conformations of the disaccharide–peptide subunit of peptidoglycan (of Staphylococcus aureus or Micrococcus luteus) have been studied by an energy‐minimization procedure. The favored conformation of the disaccharide N‐acetyl‐glucosaminyl‐β(1–4)‐N‐acetylmuramic acid (NAG‐NAM) is different from that of cellulose or chitin; this disagrees with the assumption of earlier workers. The disaccharide–peptide subunit favors three types of conformations, among which two are compact and the third is extended. All these conformations are stabilized by intramolecular hydrogen bonds. Based on these conformations of the subunit, two different models are proposed for the three‐dimensional arrangement of peptidoglycan in the bacterial cell wall.
Circular dichroism of helices formed by purine monomers with pyrimidine polynucleotides
Authors: Mathelier Hansie Dorcal , Howard F. B. , Miles H. Todd 
Published: December 2004

AbstractThe CD spectra of a number of helical complexes formed by purine monomers and complementary pyrimidine polyribonucleotides have been observed over the range 200–400 nm. Each of these spectra is quite similar to that of the corresponding polymer–polymer helix. The spectra are evidently determined by the geometry of the asymmetric array of bases, largely unperturbed by the ribose–phosphate backbone. The helix structure (A‐form), on the other hand, is determined by the backbone of the pyrimidine homopolymer. Data on the monomer–polymer complexes support the conclusion that the CD spectra of ribohomopolymer helices depend primarily on interastrand interactions of the same transition within a given base and are relatively unaffected by transitions of the complementary base.
Specificity of DNA–basic polypeptide interactions. III. Sequential and random copolymers of lysine and aromatic amino acids
Authors: Seipke Gerhard , Arfmann Hans‐Adolf , Wagner Karl G. 
Published: December 2004

AbstractSequential and random lysine copolymers containing various amounts of different aromatic amino acids were synthesized. The sequential copolypeptides exhibited strong dependence of yield and degree of polymerization on the amino acid sequence of the repeating unit. To elucidate the specific contributions of aromatic side chains to the interaction of these copolymers with DNA, direct‐mixed complexes were studied by thermal denaturation and CD. The melting behaviour of peptide‐bound DNA was found to be strongly affected by amino acid composition and sequence. The contribution of the different aromatic amino acids to thermal stability decreased in the order: polylysine > [Lys, Tyr]n > [Lys,Phe]n > [Lys,(OMe)Tyr]n. The CD spectrum of DNA was altered by random copolymers, whereas sequential copolymers exhibited no changes. The influence of the random copolymers on the CD spectrum of DNA decreased in the series: polylysine > [Lys,Phe]n > [Lys,(OMe)Tyr]n > [Lys,Tyr]n. The contribution of the different aromatic amino acids to thermal stability is interpreted as stacking tendencies toward denatured and, in the case of Tyr, H‐bond formation with native DNA. The differences found for the random and the sequential polypeptides can best be explained by assuming a cooperative action of rather small peptide segments.
Conformational changes of poly(L‐histidyl‐L‐alanyl‐α‐L‐glutamic acid) in solution. Transition pathways and conformational intermediates
Authors: Goren H. Joseph , Fridkin Mati , Katchalskikatzir Ephraim , Lotan Noah 
Published: December 2004

AbstractThe conformation and conformational transitions of poly(His‐Ala‐Glu) have been investigated by ir, nmr, and CD measurements. The results obtained—as well as the results of our previous investigations by potentiometric titration and hydrodynamic techniques [Goren et al., Biopolymers (1977) 16, 1541–1555]—indicate that when dissolved in water, the co‐polymer assumes a disordered conformation. On changing the pH of the solution, the states of ionization of the side‐chain imidazole and carboxyl groups change in the same manner as in low‐molecular‐weight model compounds. Concomitantly, the overall shape of the macromolecule is altered, while the conformation of the polypeptide backbone changes from one disordered state to another but never assumes a regular form. In water/methanol and water/trifluoroethanol mixtures, transitions from a disordered state to the α‐helix conformation were observed on increasing the alcohol content of the system. The conformational transitions followed pathways which differ from one another according to the experimental conditions employed. Conformational landmarks (intermediates) have been identified along these pathways.