bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cooperative monomer binding by polynucleotides. Effect of multiple‐loop configurations on formation of triple‐stranded complexes
Authors: Schmitz Kenneth S. 
Published: December 2004

AbstractSimulated binding curves for the reaction 2 polymer + monomer = triple‐stranded complex are presented, in which loop formation and sliding degeneracy of the polymer adsorption surface are considered. Exact calculations for a polymer chain length N of 11 units suggest that configurations of two or more loops have negligible effect on the isotherm when SW > 1, where S and W are exponential weighting factors for monomer–monomer S and polymer–polymer W nearest neighbor interactions. There is a pronounced effect, however, when SW ≪ 1. Limiting expressions (N ≫ 1, but finite) for the single‐loop configurations suggest these configurations are negligible at any degree of saturation θ if θ (1 − θ)2–k N3–k ≪ SW, where k is defined by the weighting factor (j + 1)−k for a ring of j units. This expression suggests that single monomer‐stack configurations are the only significant contributors to the grand partition function at the midpoint of the isotherm if N3–k ≪ SW. Furthermore, single‐loop configurations are negligible below θ = 0.5 but become dominant above the isotherm midpoint when SW ∼ 1 (random binding) if 2 < k < 3. For k > 3 and N → ∞, loop configurations have no effect in any region of the random binding isotherm usually analyzed experimentally (θ < 0.95). Equivalence of matrix and sequence generating methods is also demonstrated.
Theoretical analysis of conformations of Ac‐Gly‐L‐Ala‐Gly‐NHMe with intramolecular hydrogen bonds
Authors: Pletnev V. Z. , Kadymova F. A. , Popov E. M. 
Published: December 2004

AbstractThe hydrogen‐bonded structures of Ac‐Gly‐L‐Ala‐Gly‐NHMe have been studied by theoretical conformational analysis. The geometric parameters and energies of stable forms with various combinations of 3 → 1 and 4 → 1 type hydrogen bonds have been calculated. The stable conformations found can be used as canonical forms in the investigation of linear and cyclic peptide compounds with intramolecular hydrogen bonds.
Frequency dependence of the proton magnetic relaxation in aqueous solutions of haemoproteins
Authors: Lahajnar G. , Zupančič I. , Blinc R. , Pifat Greta , Maričić S. 
Published: December 2004

AbstractThe longitudinal proton magnetic relaxation times T1 were measured for ferri (met)‐and carbonmonoxy‐bovine haemoglobin and equine myoglobin in 0.1 M KH2PO4 aqueous solutions near pH 6 at 5°C and 35°C from 1.5‐ to 60‐MHz Larmor frequencies. It is concluded that the correlation time τC for the dipole–dipole interaction of electron and nuclear spins is in fact the electron (ferric) spin relaxation time τS being close to 1.5 × 10−10 sec for both metHb and metMb at 5°C. At 35°C the paramagnetic relaxation rates are not determined solely by the relaxation of protons exchanging from the haem pocket with bulk solvent. Hence, τC at 35°C cannot be calculated from the dispersion data obtained at this temperature. The relevance of this for the determination of interspin distances r is discussed.
Studies on the conformations and interactions of elastin. Proton magnetic resonance of the repeating tetramer
Authors: Urry D. W. , Ohnishi T. 
Published: December 2004

AbstractProton magnetic resonance studies at 220 MHz were carried out on synthetic polymers of the repeating tetrapeptide of elastin. Temperature dependence and solvent‐mixture dependence of peptide proton chemical shifts were determined for both linear polymers, N‐formyl‐(Val‐Pro‐Gly1‐Gly2)n‐Val OMe where n ≃ 8 and 40, and for cyclic polymers (Val‐Pro‐Gly1‐Gly2)n, where n = 3 and 4. The Gly2 NH was found to be solvent shielded. In addition, by studying the polymers Boc‐Val‐Pro‐Gly1‐Gly2‐OH, H‐Pro‐Gly1‐Gly2‐Val OMe, H(Pro‐Gly1‐Gly2‐Val)3OH, and others, it was demonstrated that the Val C–O immediately preceding the Gly2 NH in the sequence was required for solvent shielding. Also the Gly2 NH resonance is found at higher field than the Gly1 NH resonance. This provides the basis for proposing a β turn in which the Pro and Gly1 residues form the corners, i.e., residues i + 1 and i + 2, and in which the Gly2 NH, residue i + 3 hydrogen bonds to the carbonyl of residue i, the Val residue.Studies on methanol–water solvent systems indicated retention of the β turn as a significant conformational feature. This suggests that the β turn occurs in the elastic fiber, which contains about 60% water but which utilizes association of hydrophobic groups as a primary force in fibrogenesis.
Pressure–temperature stability of DNA in neutral salt solutions
Authors: Hawley S. A. , Macleod R. M. 
Published: December 2004

AbstractThe effect of pressure on the melting temperature of DNA (Cl. perfringens) has been examined in several concentrations of neutral salt by measurement of uv absorbance. The results indicate that the apparent transition volume increases as the salt concentration, and hence the melting temperature, is raised, and suggest that the transition occurs without a change in volume at a Tm of 59°C. Additional experiments were conducted in an effort to determine whether transition behaviour can be found in other regions of pressure and temperature; no additional transition behaviour was observed in experiments conducted with temperatures as low as −21.85°C at 2000 atm and pressures in excess of 9000 atm at 58°C.
Structural studies of human placental dermatan sulfate during development using optical mixing spectroscopy
Authors: Jamieson Alexander M. , Lee Ting‐Yang , Schafer Irwin A. 
Published: December 2004

AbstractOptical mixing spectroscopy is a recently developed technique which permits the measurement of diffusion coefficients and molecular weights of macromolecular species when only small amounts of material can be obtained for analyses. In this study, an approxmate empirical relationship between diffusion coefficient and viscosity‐average molecular weight was established for highly sulfated mucopolysaccharides. This relationship was then used to deduce the molecular weights of small quantities of highly purified dermatan sulfate extracted from human placenta at the full term (40 weeks) and at earlier stages of development (12–18 weeks). The effect of hyaluronidase digestion on molecular weight was then investigated as a probe for glucuronic acid substitutions in the dermatan sulfate. The molecular weights of dermatan sulfate were similar, 27,000–29,000, in the term and young placenta. Digestion with hyaluronidase produced a 50% reduction in molecular weight in the young placenta versus a 30% reduction in the term placenta, clearly demonstrating significant differences in the nature of glucuronic acid substitution at the two developmental stages studied.
Measurement of diffusion coefficients of meningococcal polysaccharide by optical mixing spectroscopy. I. A preliminary characterization on the aggregation of the Group C polysaccharide
Authors: Chen F. C. , Tscharnuter W. , Schmidt D. , Chu B. , Liu T. Y. 
Published: December 2004

AbstractThe angular distribution of scattered intensity and decay times of concentration fluctuations have been measured by means of digital photon counting and single‐clipped photon correlation for solutions of Group C meningococcal polysaccharides at 31°C. The z‐average diffusion coefficient 〈D〉z and its second moment 〈D2〉z have been determined from the time‐dependent correlation function using the cumulant expansion technique. Very low observed values of 〈D〉z and the tremendous width of the polydispersity index, which is the z‐average normalized variance, suggest a higher degree of aggregation than the monomer–dimer type self‐association at finite concentrations.
Contribution of side‐chain chromophores to the optical activity of proteins: Model compound studies. I. α‐Methyl‐L‐tyrosine
Authors: Goux Warren J. , Cooke Dennis B. , Rodriguez Raquel E. , Hooker Thomas M. 
Published: December 2004

AbstractThe optical rotatory power and the conformational energy of the amino acid α‐methyl‐L‐tyrosine has been calculated as a function of molecular conformation. Comparison of the results of these theoretical calculations with experimental circular dichroism data indicates that the conformational freedom of this molecule is highly restricted. The most heavily populated conformations appear to be those near χ1 = 60°, χ2 = 80°, Ψ = 175°, and χ1 = 300°, χ2 = 80°, Ψ = 5°. The χ1 = 180° conformations are not likely to be populated to a significant extent at ordinary temperatures.
Melting of DNA in ethanol–water solutions
Authors: Usatyi A. F. , Shlyakhtenko L. S. 
Published: December 2004

AbstractThe thermal denaturation curves of DNA have been investigated over a wide range of temperatures T and ethanol concentrations C by CD and uv absorption methods. The phase diagram of conformational DNA states has been constructed in T,C plane. The range of the A, B, and coiled forms of DNA was determined. The behavior of the DNA denaturation curve in the neighborhood of the triple point shows that the conformational transition B → A is realized by short parts of the DNA double helix. This is the reason for the coincidence of the melting temperatures of the A and B forms of DNA throughout the range of their coexistence.
Determination of the rate of renaturation of modified DNA by fluorescence depolarization
Authors: Miller Stephen J. , Wetmur James G. 
Published: December 2004

AbstractFluorescence depolarization was used to measure the rate of renaturation of T2 DNA, which had been modified by chloroacetaldehyde. Rates were measured on DNA samples with 5–15% of the base pairs modified and were found to agree with rates determined by DNA absorbance kinetics at 260 nm. The renaturation rate of a modified T2 DNA was unchanged in the presence of a ninefold abundance of unlabeled calf thymus DNA.
The effects of chain length on the secondary structure of oligoadenylates
Authors: Kroon Paulus A. , Kreishman George P. , Nelson James H. , Chan Sunney I. 
Published: December 2004

AbstractThe oligoadenylates (Ap)2–4A have been studied by proton magnetic resonance (pmr) spectroscopy. All the exterior base protons and a number of the interior base proton resonance have been assigned. The results of this work showed that the adenine bases in these oligoadenylates are intramolecularly stacked at 20°C with their bases oriented preferentially in the anti conformation about their respective glycosidic bonds. The oligomers were found to associate extensively even at concentrations of 0.02 M, primarily via “end‐to‐end” stacking. With increasing temperature, the oligomer bases destack, but it is argued that this unfolding process cannot be described in terms of a two‐state stacked versus unstacked model. Instead, the temperature dependences of the base proton chemical shifts support a base‐oscillation model. The relationship between this model and the two‐state model is discussed. Finally, on the basis of the chain‐length dependence of the proton chemical shifts of the various adenine bases, it was concluded that subtle variations in the secondary structure of these oligomers exist with increasing chain length. Evidence is presented to show that the effects of distant base shielding are considerably smaller than what was previously estimated. The observed departures from the “extended dimer” model are attributed to differences in the relative orientations of the bases with respect to their neighbors in the oligomer.
Conformational analysis of thyrotropin releasing factor by proton magnetic resonance spectroscopy
Authors: Montagut Martine , Lemanceau Bernard , Bellocq Anne‐Marie 
Published: December 2004

AbstractThe proton magnetic resonance spectrum of thyrotropin releasing factor (TRF) in solution in deuterium oxide and deuterated dimethylsulfoxide (DMSO–d6) has been analyzed. Two forms differing in cis–trans isomerism about the His‐Pro peptide bond are observed. From the temperature dependence of chemical shift of the amide protons, it is concluded that TRF in DMSO–d6 does not contain intramolecular hydrogen bonds. Measurement of NHCαH coupling constant provides an estimate of the histidine dihedral angle ϕ. Structural information about the histidine side‐chain is deduced from CαHCβH coupling constants and from the nonequivalence of the two prolyl δ‐protons. In DMSO–d6, there is evidence for a tautomeric equilibrium corresponding to an exchange of imidazole proton between the two nitrogen atoms N‐δ and N‐ε. In water, the N‐εH tautomer is found to be the predominant tautomeric form of the imidazole ring. These results in combination with energy calculation, vibrational analysis, and carbon nmr studies allow the determination of the conformationof TRF.
Ultrastructure of acid‐ and enzyme‐modified cross‐linked potato starch
Authors: Hollinger G. , Marchessault R. H. 
Published: December 2004

AbstractPurified potato starch, cross‐linked with epichlorohydrin (65–5.4 anhydroglucose units per cross‐link) by an iterative method that preserved the native crystalline structure of the starch granule, was exposed to enzymic (B. subtilis α‐amylase at 50°C) and acidic (3 N HCl at 40°C) hydrolysis. The stability of the granules to digestion by enzymes, as measured by their weight loss after incubation with the enzyme solution, increased with the degree of cross‐linking; by contrast, the stability to acid attack decreased as a function of the degree of cross‐linking. The morphology of these samples was studied by scanning electron microscopy. A lamellar structure, which was most evident after enzyme treatment, was observed in samples that had a weight loss of greater than 50%. The results reflect differences in accessibility, which are interpreted in terms of a statistical model of the ultrastructure with correlated fluctuations in density in the radial direction.
Static and dynamic quenching of protein fluorescence. I. Bovine serum albumin
Authors: Feldman Isaac , Young Dolores , McGuire Robert 
Published: December 2004

AbstractThe fluorescence parameters, lifetime, relative quantum yield, maximum and mean wavelength, half‐width, and polarization, of bovine serum albumin (BSA) were measured at 15°C in aqueous solutions containing varying concentrations of different chemical perturbants, glycerol, Cu2+ ions, guanidine hydrochloride, and urea. By considering a quenching mechanism as being either dynamic or static, depending upon whether the quenching is or is not accompanied by a change in the fluorescence lifetime, we were able to correlate the changes produced in the various fluorescence parameters by the different chemical perturbants with changes in macromolecular structure as the concentration of perturbant was gradually increased. The addition of glycerol and of Cu2+ ions indicated that in aqueous BSA both tryptophan residues are below the surface of the macromolecule, out of contact with solvent water, and, as a consequence, they are statically quenched. “Ultra‐Pure” guanidine hydrochloride at 2.4 M or more caused a drastic conformation change, which resulted in the emergence of a visible tyrosine peak at 304 nm in the BSA fluorescence spectrum when either 260‐ or 270‐nm excitation was employed. With the same excitation, the enhancement of BSA tyrosine fluorescence by 6–8 M ultra‐pure urea produced only a shoulder near 304 nm in the BSA fluorescence spectrum. We have introduced the use of a new relative quantum yield for protein fluorescence, q′, referenced to the quantum yield of unquenched free tryptophan, which eliminates the quenching action of water from the reference.
Infinite‐dilution viscoelastic properties of tobacco mosaic virus
Authors: Nemoto Norio , Schrag John L. , Ferry John D. , Fulton Robert W. 
Published: December 2004

AbstractThe storage and loss shear moduli, G′ and G″, have been measured for dilute solutions of unaggregated and aggregated tobacco mosaic virus samples in glycerol–water mixtures, by the Birnboim–Schrag multiple‐lumped resonator modified for use with aqueous solvents. The frequency range was 100–5800 Hz, the concentration range 0.6–2.1 × 10−3 g/ml, and the temperatures 25.0° and 37.8°C. The number‐average and weight‐average molecular weights of the aggregated sample were estimated as 1.4 and 2.0 × 108, respectively, from electron microscopy. The extrapolated intrinsic moduli [G′] and [G″] were compared with the predictions of the Kirkwood–Auer theory for rigid rodlike molecules. For the unaggregated sample, the frequency dependence of [G′] and [G″] agreed well with the theory assuming the intrinsic viscosity to be 27 ml/g, though the asymptotic limit of [G′]M/RT at higher frequencies was slightly larger than the theoretical value of 3/5. For the aggregated sample, the data agreed with theory for rigid rods as modified to account for molecular‐weight distribution.
Investigation of the thermal unfolding of secondary and tertiary structure in E. coli tRNAfMet by high‐resolution nmr
Authors: Wong K. Lim , Wong Yeng P. , Kearns David R. 
Published: December 2004

AbstractThe high‐resolution (300 MHz) proton nmr spectrum of E. coli tRNAfMet has been examined in 0.17M NaCl, with and without Mg2+, and at various temperatures. In light of recent studies of other E. coli tRNA and fragments of tRNAfMet, some low field (11–15 ppm) resonances previously assigned to secondary structure base pairs are reassigned to a tertiary structure A14–S4U8 base pair and a protected uridine residue in the anticodon loop. These two resonances and other low field resonances which are assigned to secondary structure base pairs are used to monitor the thermal unfolding of the molecule. In the absence of Mg2+ the tertiary structure base pair is present only to ∼45°C, but in the presence of Mg2+ it remains until at least 70°C. Analysis of the temperature dependence of other low field resonances indicates that the melting of the dihydrouridine stem occurs more or less simultaneously with the loss of tertiary structure. The observation of the resonance from the A14–S4U8 base pair proves that tertiary structure is present in this molecule below 40°C, even in the absence of Mg2+.
Relaxation kinetics of the triple‐stranded helix ⇄ coil transition at short chain length. A model including the staggering of chains
Authors: Weidner H. 
Published: December 2004

AbstractThe relaxation kinetics of a staggering zipper model are presented, in which the formation of helical nuclei is regarded to be rate‐limiting and in which the sliding of strands along the helices is prohibited. Instead a realignment of staggered chains is only possible via complete uncoiling. While maintaining the third order of the initial reaction as in an all‐or‐none mechanism, the model predicts a large range of relaxation times, which contribute to the mean relaxation time according to the stability of the individual species and which are weakly coupled in the range of small amounts of helical content. The model can easily be compared to experimental results and agrees well with relaxation data obtained from a triple‐helical peptide fragment of collagen. It may be readily expanded to other multistranded helix ⇄ coil transitions with steady‐state formation of the individual species and it suggests that the fraying of the helix ends is hidden by the fast‐relaxation times due to the equilibration of the shortest helical species.
Variations thermiques, entre 1 et 300°K, de la chaleur specifique de la L‐alanine, tri(L‐alanine), et de la poly(L‐alanine) sous formes α et β
Authors: Daurel M. , Delhaes P. , Dupart E. 
Published: December 2004

AbstractThe heat capacities of L‐Alanine, tri(L‐alanine), and poly (L‐alanine) (α helicoidal form and β pleated sheet structure) have been measured between 1.5 and 300°K with a standard adiabatic calorimeter.In the solid state, the heat capacity is in general dut to three parts which are additive in first‐order approximation. (1) The lattice vibrations or “acoustical modes” which are the largest at low temperatures. The low‐temperature lattice specific heat is proportional to T, T2, or T3 for an ideal one‐, two‐ or three‐dimensional solid, respectively. (2) The so‐called group vibrations or “optical modes” which, due to their high frequencies, usually take effect only at higher temperatures. (3) The defects and unharmonic effects.The α‐amino acid and its trimer present a specific heat thermal variation characteristic of molecular solids which is correctly fitted with an empirical law proposed by Kitaigorodskii. This author assumes that, for such solids, the molecular lattice point has six degrees of freedom (three of translation and three of rotation). Thus the lattice contribution of the specific heat satisfies the Debye approximation in agreement with the doubling of the number of degrees of freedom per molecule (compared with atomic crystals).The polypeptide behavior is, however, different. The specific heat for each form exhibits a thermal dependence connected with a strong vibrational anisotropy. The model proposed earlier by Tarasov accounts well for these results. In the case of the β form, we have observed the predicted three‐ and two‐dimensional behavior due to the intermolecular H bondings responsible for the sheet structure. For the α form we observed a one‐dimensional pattern at higher temperature, since each peptidic chain vibrates separately.The comparison with other spectroscopic and theoretical investigations shows a large discrepancy. However, we have attemped to account for the “optical contribution” to the specific heat of poly(L‐alanine) by using a continuum of mean frequencies as suggested by Wunderlich. Vibrational frequency spectra are proposed to explain our results, but the overlapping of acoustical and optical branches in the case of the α form outlines the limits of macroscopic models. It is quite likely that the acoustical spectrum is greatly affected by the intramolecular H bonding.At low temperature the specific heat is a physical property sensitive to the long‐range order of the macromolecule, and therefore further spectroscopic and theoretical investigations are necessary to explain correctly these experimental results.
Conformation of histidine model peptides. II. Spectroscopic properties of the imidazole chromophore
Authors: Grebow Peter E. , Hooker Thomas M. 
Published: December 2004

AbstractSemi‐empirical molecular orbital calculations have been carried out for the free base and cationic forms of imidazole so as to obtain data which are required for the calculation of the chiroptical properties of molecules that contain this chromophoric group. The polarization, energy, and monopolar charge distribution are reported for the lowest energy electronic transitions. The absorption spectra for imidazole have been determined to 180 nm and circular dichroism spectra for L‐histidinol and L‐2‐amino‐1‐butanol have been measured.
Macromolecular binding
Authors: Schellman John A. 
Published: December 2004

AbstractFormulas for the free energy of binding to a macromolecule are obtained by thermodynamic and statistical mechanical methods, and it is shown that the free energy of binding is intimately related with the binding polynomial and Wyman's binding potential. The expression for the free energy of binding is applied to a number of cases of ligand‐induced conformational changes, cooperativity, association reactions, etc.