bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linear oligopeptides. XLIII. Study of the relationship between conformation and nature of side chain: Homologous series derived from γ‐branched amino acid residues
Authors: Toniolo Claudio , Bonora Gian Maria , Palumbo Manlio , Peggion Evaristo , Stevens Eugene S. 
Published: December 2004

AbstractConformational studies of the three homologous series, from dimer through heptamer, of monodisperse, N‐and C‐protected oligopeptides derived from the γ‐branched α‐amino acid residues L‐leucine, β‐cyclohexyl‐L‐alanine, and L‐phenylalanine are reported. By means of ir absorption and CD in the vacuum‐uv (150nm), the occurrence of intermolecular β‐conformations in the higher oligomers in the solid state was established. In solvents of low polarity at high dilution, the extent of intramolecularly hydrogen‐bonded folded‐structure formation was assessed as a function of chain length and the nature of the side chain. Unordered and intermolecular β‐conformations were found in alcohols and aqueous alcoholic mixtures. The results obtained indicate that—the position of branching being equal–steric requirements, electronic properties, and hydrophobic character of the amino acid side chains are all important in determining the nature and stability of oligopeptide conformations.
Resolution of electronic absorption bands and nucleotide binding processes in actinomycin D
Authors: Auer Henary E. , Pawlowski‐Konopnicki Barbara E. , Chiao Yu‐Chih Chen , Krugh Thomas R. 
Published: December 2004

AbstractComplexes of actinomycin D with model dexoxynucleoides have been studied by means of absorption spectroscopy and CD spectroscopy and CD spectroscopy. The CD spectra of the complexes of actinomycin D with 5′‐dGMP, pdG‐dT, pdT‐dG, pdG‐dA, and pdA‐dG, respectively, all resemble one another. It is presumed that in solution the interactions between the guanine residues and actinomycin D in these complexes are the same as found in the crystalling 1:2 actinomycin D:dG complex [Jain, S. C. & Sobell, H. M. (1972) J. Mol. Biol. 68, 1–20]. The CD spectrum of the Complexes with pdG‐dC differs from of the complexes just mentioned, and resembles those of the complexes formed by actinomycin D with calf‐thymus DNA and with poly(dG‐dC)‐poly(dG‐dC). These resulls are consisent with, the nontion that pdG‐dC froms a double‐staranded intercalated complex with actinomycin D, and that the dG‐dC sequence is an important binding site for actinomycin D in polydeoxynucleotides.Titrations of actinomycin D with monodeoxynucleotides were monitored at 380, 425, 440,465, and 480, nm in both absorption and CD modes. Comparisons fo saturation profiles at these wavelengths reveal that the curves obtained at various wavelenths do not superimpose with each other, so that they must reflect different titation processes. In complex formation wiht any given nucleotide, the apparent binding affinity monitored at these wavelengths decreases in the order given above. Based on these resulted and on features noted in the CD spectra of certain complexes, it is concluded that a minimum of theree electronic transitions underlie the visible absorption band of actinomycin D, extending earlier findigs. Comparing the titration proffiles obtained with dAMP and dIMP with the result for these systems in mmr titratins [Krugh, T. R. & Chen, Y. C. (1975) Biochemistry 14, 4912–4922], it is concluded that one transition, centered at 370 nm, monitors preponderantly effects occurring at the 6 (benzenoid) nucleotide binding site and a second transition, located at 490 nm, is sensitive preferentially to processes occurring at the 4 ( quinoid) binding site. The latter is probably closely asscoiated with 2‐amino and /or 3‐carbonyl substituents. The third transition, identified with the absorption maxium at 420–440 nm, appears to reflect contributions arising in the entire phenoxazone chromophore. Using these band assignments, it is concluded that the benzenoid site binds nucleotides 1.5–3 times more avidly than does the quinoid site. CD titrations resolve these processes more effectively than do abscrption titrations. Aspects of the structures of these complexes formed in solution are discussed.
Solid‐phase synthesis of somatostatin and glucagon‐selective analogs in gram quantities
Authors: Rivier J. , Kaiser R. , Galyean R. 
Published: December 2004

AbstractSomatostatin (SS) and two glucagon selective analogs [D‐Cysl4]‐SS and [D‐Trp8, D‐Cys14]‐SS have been synthesized in gram quantities by the solid‐phase procedure. A general modification of Monahan and Gilon's procedure for esterification of the first protected amino acid onto the chloromethylated resin as well as a general protocol for solid‐phase peptide synthesis on Beckman 990 automatic synthesizer are described. A new general procedure for disulfide formation, which involves the adaptation of the “high‐dilution” principle to the ferricyanide oxidation and the optimization of the sequence of purification steps as applied to somatostatin and its analogs, yields highly purified peptides (≥ 199% pure) as checked by reverse‐phase high‐pressure liquid chromatography—which is shown to be a highly sensitive, resolutive, and quantitative analytical tool for evaluation of the homogeneity of peptides.
Relationship between the energy of superhelix formation, the shear modulus, and the torsional brownian motion of DNA
Authors: Bret Marc Le 
Published: December 2004

AbstractThe torsional energy of a DNA is the energy involved when the average angle between adjacent base pairs is modified under applied constraints. A relationship is established between the energy of superhelix formation of a upercoiled DNA and its torsional energy. This relationship, valid when the number of the tertiary turns of the supercoiled DNA is small, contains the ratio of the bending to the torsional elastic paramaters of the DNA. From this relationship, the fluctations of the number of tertiary turns of the supercoiled DNA may be compared to those of the DNA with only one sinle‐strand scission. An expression for the shear modulus of the DNA is derived from the anisotropy of the fluorescnece of the intercalated ethidium [Wahl et al. (190) Proc. Natl. Acad. Sci. USA 65, 417–421.]. The value of te torsional elastic parameter deduced from these computations is very close to the parameter of the energy of the superhelix formation determined on supercoiled DNAs by different authors. The energy that must be given to twist it. Consequently, the number of crossovers determined using the EM technique should be much less than the value deduced from the amount of ethiium necessary words, the first ethidium cations intercalating into a relaxed, closed double‐standard DNA change the twist of the DNA but not its tertiary structure.
An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking
Authors: Ornstein Rick L. , Rein Robert , Breen Donnal L. , Macelroy Robert D. 
Published: December 2004

AbstractAn optimized potential function for base‐stacking interaction is constructed. Stacking energies between the complementary pairs of a dimer are calculated as a function of the rotational angle and separation distance. Using several different sets of atomic charges, the electrostatic component in the monopole‐monopole approximation (MMA) is compared to the more refined segmented multipole–multipole representation (SMMA); the general features of the stacking minima are found to be correctly reproduced with IEHT or CNDO atomic charges. The electrostatic component is observed to control the location of stacking minima. The MMA, in general, is not a reliable approximation of the SMMA in regions away from minima; however, the MMA is reliable in predicting the location and nature of stacking minima. The attractive part of the Lennard‐Jones 6–12 potential is compared to and parameterized against the expression for the second‐order interaction terms composed of multipole‐bond polarizability for the polarization energy and transition‐dipole bond polarizabilities for approximation of the dispersion energy. The repulsive part of the Lennard‐Jones potential is compared to a Kitaygorodski‐type repulsive function; changing the exponent from its usual value of 12 to 11.7 gives significantly better agreement with the more refined repulsive function. Stacking minima calculated with the optimized potential method are compared with various perturbation‐type treatments. The optimized potential method yields results that compare as well with melting data as do any of the more recent and expensive perturbation methods.
15N‐NMR spectroscopy. IV. Comparison of poly(L‐lysine) and isopoly(L‐lysine)
Authors: Hull William E. , Kricheldorf Hans R. , Fehrle Martin 
Published: December 2004

AbstractThe natural abundance 15N‐nmr spectroscopy has been used to characterize the isomeric polymers (L‐Lys)n and iso (L‐Lys)n in aqueous solution. Although the peptide nitrogens of the two polymers have nearly equivalent shifts at pH < 10, the amino nitrogens differ by 5–6 ppm at pH < 7 and provide an easy means of identification. Furthermore, the polymers are distinguishable by the pKa of the amino group and the basicity of the peptide nitrogen. At pH 10.3 and 25°C, (Lys)n exhibits line broadening and an upfield chemical shift of the peptide nitrogen, indicative of the coil → helix transition. The formation of 100% helix may produce a shift as large as 5 ppm, which probably makes 15N‐nmr spectroscopy more suitable for studies of this transition.
Polyelectroyte behavior of a bacterial polysaccharide from Xanthomonas campestris: Comparison with carboxymethylcellulose
Authors: Rinaudo M. , Mils M. 
Published: December 2004

AbstractThe main physicochemical properties of the polysaccharide called Xanthan produced by Xanthomonas compestris are discussed: the activity coefficient of the counter‐ion, the pK(α), and the ionic selectivity are investigated and compared to those of a carboxymetholcellulose. The weight‐average molecular weight (Mw = 2 × 106), the intrinsic viscosity and the constant of sedimentation are determined as a function of the ionic strength. It is proved that in dilute solution, there is no intermolecular association, whatever the ionic strength. The conformation is proposed to be a rigid rodlike molecule whose length is 6000 Å, independent of ionic strength > 10−2N.
Solid‐state modifications of poly(γ‐ethyl‐L‐glutamate)
Authors: Sasaki Shintaro , Miyamoto Misao , Nakamura Takao , Uematsu Ichitaro 
Published: December 2004

AbstractSeveral modification of the arrangements of α‐helical molecules were found in the solid films of poly (γ‐ethyl‐L‐glutamate), depending on the casting solvent and the temperature. The helical conformation is somewhat looser than the normal 18‐residue, 5‐turn α‐helix. Using x‐ray diffraction, the types of molecular arrangements were classified into tetragonal, pseudohexagonal, and hexagonal ones. Tetragonal packing was observed in the filmm (form T) prepared by casting the solution in trifluorethanol or dichlorethane. The sample obtained from chloroform solution is a well‐ordered, pseudohexagonal modification (form I). Forms I and T change into a poorly crystalline form III by annealing at temperatures above 130° C. It is particularly noteworthy that the less‐ordered form III exhibits a thermoreversible transition around 110°C into a well‐ordered form H with the hexagonal molecular packing.
The random copolymerization of γ‐benzyl‐L‐glutamate and L‐valine N‐carboxyanhydrides: Reactivity ratio and heteogeneity studies
Authors: Sederel W. , Deshmane S. , Hayashi T. , Anderson J. M. 
Published: December 2004

AbstractThe random copolymerization of the N‐carboxyhydrides of γ‐benzyl‐L‐glutamate and L‐valine using triethylamine as the initiator in low dielectric media reults in high‐molecular‐weight copolymers at low convenrson. This behavior makes it possible to apply the monomer reactivity ration theory, which was dervied for addition polymerizations, and from the use of the copolymer composition equation, the respective monomer reactivity ratios, the average and incremental copolymer compositions, and the monomer feed ratio at any conversion can be determined. A comparison of the reactivity ratios for the copolymerization of γ‐benzyl‐L‐glutamate NCA and L‐valine NCA in benzene/methylene chloride (rG = 2.1, rV = 0.6) with those obtained using dioxane (rG = 2.7, rV = 0.3) indicates that the interchain compositional heterogeneity is greater for copolymers prepared in the dioxane. For Example, at 100% conversion of the monomeric NCAs, Poly[Glu(OBzl)50Val50] prepared in dioxance has an interchain composition ranging from 74 to 0 mol % γ‐benzyl‐L‐glutamate, whereas in benzene/methylene chloride the interchain composition of γ‐benzyl‐L‐glutamae ranges from 65 to 0 mol %. Once the reactivity ratios are obtained for any pair of α‐amino and N‐carboxyanhydrides, the use of the aforementioned parameters relating to interchain composition can give insight into the compositional heterogeneity between chains as a function of conversion and provide a basis for the preparation of random α‐amino acid copolymers that are homogeneous.
Dielectric relaxation of collagen in aqueous solutions
Authors: Umemura Shin'ichiro , Sakamoto Masanori , Hayakawa Reinosuke , Wada Yasaku 
Published: December 2004

AbstractThe complex dielectric constant of collagen in aqueous solutions (polymer concentration, Cp = 0.02–0.2%) was measured at 10°C in the frequency range from 3 Hz to 30 kHz. The loss peak for Cp = 0.02% is located at 90 Hz and the dielectric relaxation time τD is estimated to be 1.8 ± 0.3 msec. The τD agrees well with the rotational relaxation time estimated from the reduced viscosity, and the relaxation is ascribed to the end‐over‐end rotation of the molecule. The Cp dependence of τD and the dielectric increment Δε are interpreted in terms of the aggregation of molecules. The dipole moment of a molecule, obtained from Δε at Cp = 0.02% and pH 6.5, is (5.2 ± 0.2) × 104D, which is explained by the asymmetrical distribution of the ionized side chains of the molecule.
Urease oligomerizes in a linear pattern: Further hydrodynamic evidence from intrinsic viscosity theories and measurement
Authors: Tirrell Matthew , Middleman Stanley 
Published: December 2004

AbstractMeasurements of the intrinsic viscosity of the urease “monomer” and of a mixture of oligomers are shown to lead to the conclusion that urease oligomerizes in a linear fashion, when viewed in the light of several available theories of intrinsic viscosity of rigid protein macromolecules. This conclusion is also consistent with previously reported work on the sedimentation coefficients of the urease oligomers. The use of a detailed subunit structure for the urease “monomer” and oligomers is explored and found to give quantitatively good results for all hydrodynamic properties of all urease oligomers. The realm of validity of the intrinsic viscosity theories proposed by Garcia de la Torre and Bloomfield, by Tsuda, and by Abdel‐Khalik and Bird is explored in this context.
Effects of distance constraints on macromolecular conformation. II. Simulation of experimental results and theoretical predictions
Authors: Havel Timothy F. , Crippen Gordon M. , Kuntz Irwin D. 
Published: December 2004

AbstractBy generating classes of random structures for trypsin inhibitor and carp myogen, each consistent with a given set of experimental or theoretical information, we have assessed the relative utility of various experiments and theories in deducing the conformation of macromolecules. We compare the calculated structures with known x‐ray coordinates and compute for each class an average error. Small errors mean that the experimental or theoretical constraints limit the structures to the vicinity of the crystal structure, whereas large errors show that the constraints permit a wide variety of tertiary conformations. We find the following points to hold true: (1) Qualitative information on all the distances, as might be obtained from the correct prediction of interresidue contacts, effectively determines the structure (error approximately 1 Å). (2) Quantitative information on a limited number of distances, as might be obtained from nmr or crosslinking experiments, significantly restricts the range of possible structures only when the number of distances given is comparable to the number of residues (error approximately 3 Å). (3) Quantitative information on the distances of each residue to the center of mass of the molecule, as might in part be obtained from solvent accessibility and solution x‐ray studies, is not particularly restrictive by itself (error approximately 5 Å). (4) Complete qualitative local distance information, as might be obtained from secondary prediction and CD/ORD studies, is clearly consistent with a wide variety of tertiary structures (error approximately 7 Å).
Accelerated deacylation of acyl salicylates and neighboring group effects in derivatives of poly(ethylenimine)
Authors: Johnson Ronald S. , Klotz Irving M. 
Published: December 2004

AbstractThe deacylation of acetylsalicylate and of adipoyldisalicylate in the presence of modified and unmodified poly(ethylenimine)s has been investigated. The kinetics of these reactions have been analyzed in terms of an initial binding step followed by one or two aminolysis steps, and the relevant kinetic parameters have been evaluated. The polymers markedly accelerate the rate of deacylation. Second‐order rate constants based on total primary amine concentration for aminolysis by the polymers are 103–105 times larger than those for methylamine. The most striking effect of the polymer has been observed in the two successive aminolysis steps of adipolydisalicylate where the second rate constant is approximately 20‐fold greater than the first, presumably because of local proximity factors.
Circular dichroism and the pH‐induced β‐coil transition of poly(S‐carboxymethyl‐L‐cysteine) and its side‐chain homolog
Authors: Ikeda Shoichi , Fukutome Akira , Imae Toyoko , Yoshida Tomohiko 
Published: December 2004

AbstractThe CD of aqueous solutions of poly(S‐carboxymethyl‐L‐cysteine) and poly(S‐carboxyethyl‐L‐cysteine) has been measured at different pH, and the pH‐induced β‐coil transition is observed by changes in residue ellipticity of dichroic bands around 200 and 225 nm. The residue ellipticity at 200 nm of the former polypeptide is twice as large as that of the latter, when the β‐conformation is formed in solution. However, the β‐conformation of the latter polypeptide is more stable against electrostatic repulsion than that of the former. The transition curve of poly(S‐carboxymethyl‐L‐cysteine) has also been determined for different molecular weights. The curves were found to be completely coincident with one another if the degree of polymerization were higher than about 100. Such a transition curve is generally divided into three steps: initiation, cooperative formation, and rearrangement of hydrogen bonds. The cooperative step is very sharp, occurring at a constant pH. These steps become agglomerated into two or one when the polypeptide concentration or added salt concentration is increased.
31P nmr spin‐lattice relaxation studies of deoxyoligonucleotides
Authors: Davanloo Pari , Armitage Ian M. , Crothers Donald M. 
Published: December 2004

AbstractTemperature‐dependent conformational transitions of deoxyoligonucleotides have been monitored by measuring 31P chemical shifts, spin‐lattice relaxation times (T1), and 31P‐{H} nuclear Overhauser enhancements (NOEs). The measured NOE ranged from 30 to 80%, compared to the theoretical maximum of 124% for a dipolar relaxation mediated by rapid isotropic rotation. The observed 3′‐5′ phosphate diester 31P T1 showed a similar temperature dependence over the range 2–75°C for both double‐ and single‐stranded oligonucleotides, and for dinucleotides. The results show that dipole–dipole interactions dominate the internucleotide phosphate relaxation rate in oligonucleotides. The same is true of terminal phosphate groups at low temperature; but at higher temperature another process, possibly due to contamination by paramagnetic ions, becomes dominant. The rotational correlation time τR calculated from the dipole–dipole relaxation rate of the internucleotide phosphate in d(pA)2 at 16°C is τR = 5.0 × 10−10 sec, implying a Stokes radius for isotropic rotation of 7.6 Å. The T1 and NOE values for the double‐helical octanucleotide d(pA)3pGpC(pT)3 are consistent with dominance of dipole–dipole relaxation and isotropic rotation of a sphere of radius 14 Å, a reasonable dimension for the double helix. Activation energies for the rotation of dinucleotides range from 4 to 6 kcal/mol, close to the value of 4 kcal/mol expected for isotropic rotation. In order to test the possible effect of internal motion of correlation time τG on the results, we considered a model in which the nucleotide chain rotates about the P‐O bonds. Comparison of the calculation with our experimental results shows that internal motion with τG ≅ 10−9 sec, as found from other studies to be present for large nucleic acids, would not influence out T1 and NOE values enough to be distinguished from isotropic rotation. However, we can conclude that τG cannot be as fast as 10−10 sec, even for dinucleotides.
Disorder–order transitions induced in anionic homopolypeptides by cationic detergents
Authors: Mattice Wayne L. , McCord Robert W. , Shippey Patrice M. 
Published: December 2004

AbstractCD spectra have been obtained for poly(L‐glutamic acid) and poly(L‐aspartic acid) as functions of temperature and concentration of cationic detergents. Dodecylammonium chloride induces a coil–helix transition in fully ionized poly(L‐glutamic acid). The interaction of the monomeric detergent with the polypeptide is responsible for the conformational transition. The detergent concentration required to produce the transition is independent of temperature. The CD of fully ionized poly(L‐aspartic acid) is nearly unaffected by dodecylammonium chloride, in marked contrast to the situation found with poly(L‐glutamic acid). However, these results do not imply that dodecylammonium chloride interacts differently with aspartyl and glutamyl residues. The observed results can be accounted for by the well‐known fact that the glutamyl residue has a higher helix‐forming tendency that the aspartyl residue. Cetyltrimethylammonium chloride destabilizes the helical form of poly(L‐glutamic acid). This detergent presents an exception to the usual ability of ionic detergents to promote formation of ordered structures in oppositely charged homopolypeptides.
Mean‐square amplitudes of the longitudinal vibrational of helical polymers
Authors: Peticolas Warner L. 
Published: December 2004

AbstractA simple model for the longitudinal acoustical vibrations of helical polymers has been developed. This model consists of a linear string of masses, M, connected by springs. The mass must be taken as that of one helical turn of the true helix. It has been found that all of the previously observed or calculated frequencies for the longitudinal acoustical modes of helical polymers can be calculated from this model using only one adjustable parameter, the force constant f, between the turns, for each type of helix. Using this simplified model it has been possible to obtain the rms amplitudes of the changes in the overall end‐to‐end length of helical polymers as a function of their chain length and temperature. At room temperatures the rms end‐to‐end length is found to vary from a few tenths of an angstrom for hydrocarbon chains of the length found in phospholipid membrane bilayers to several angstroms in a rigid α‐helix of 100 peptide residues. The damping of these α‐helical modes is not considered but may be appreciable in solution.