bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theory of helix–coil transitions involving complementary poly‐ and oligo‐nucleotides. I. The complete binding case
Authors: Magee William S. , Gibbs Julian H. , Zimm Bruno H. 
Published: December 2004

AbstractA statistical thermodynamic treatment of thermally induced helix–coil transitions is formulated with the matrix method for an (ensemble) of system(s) in which one strand of a double helix consists of a homopolymeric polynucleotide and the other strand comprises a number of complementary oligonucleotides. Each oligonucleotide is considered to be completely bound to the longer chain when in the helical configuration and completely free from it when in the randomly coiled configuration. The case of partial binding; i.e., “dangling,” is treated in a later paper. Taken into account in both cases are intrachain “stacking” interactions between nearest neighbor residues and interchain hydrogen bonding.An approximate treatment of the characteristic equation of the formulation indicates that the reciprocal of the transition temperature (1/T0) is a linear function of the reciprocal of the degree of polymerization (D.P.) of the oligonucleotides. In the same approximation, 1/T0 is also a linear function of the negative logarithm of the absolute activity of the oligonucleotides. Transition curves obtained by exact calculation on a computer are presented for various degrees of polymerization of both the oligo‐ and polynucleotides. These curves show a sharpening of the transition with increasing D.P. of the long chain and the aforementioned reciprocal D.P. dependence of 1/T0.
Reaction of formaldehyde with soluble ribonucleic acid
Authors: Penniston John T. , Doty Paul 
Published: December 2004

AbstractThe reaction of soluble RNA with formaldehyde was measured as a function of time. The rate of this reaction can be treated as a combination of simple first‐order rates, such as those observed for the reaction of mononucleotides with formaldehyde. The equilibrium position of the reaction of formaldehyde with soluble RNA in the absence of Mg++ is consistent with the equilibrium constants observed for mononucleotides. There is no evidence for the occurrence of crosslinking under the conditions used. All the nucleotides of sRNA are available for reaction with formaldehyde in the absence of Mg++, even though a considerable amount of secondary structure remains under these conditions. The presence of Mg++ stabilizes the secondary structure considerably, protecting about two‐thirds of the nucleotides from reaction. The rate of reaction of formaldehyde with sRNA is six times slower than that for mononucleotides. This slowing down of the reaction is interpreted as being due to the weak involvement of the reactive groups in secondary structure, while strong involvement in secondary structure, as in the presence of Mg++, prevents reaction completely.
The inactivation of soluble ribonucleic acid by formaldehyde
Authors: Penniston John T. , Doty Paul 
Published: December 2004

AbstractThe inactivation of sRNA by reaction with formaldehyde has been reported as it occurs under various conditions giving differing amounts of secondary structure. The theory of inactivation of an active macromolecule by a chemical reaction is developed. Results obtained with a partially melted out secondary structure show that formaldehyde inactivates sRNA by a single reaction at any one of about ten sites, while reaction at other sites does not affect the activity of the sRNA. In the presence of Mg++ at neutral pH, a large proportion of the active molecules are completely protected against inactivation. From the correlation between the amount of secondary structure and the difficulty of inactivation, it is shown that at least a portion of the secondary structure of sRNA is essential to its amino acid acceptor ability. A comparison of results of various workers shows that formaldehyde does not alter RNA as drastically as other reagents and thus enables more discrimination between sites of reaction which are essential and those which are not essential to biochemical activity.
Optical properties of chromophore‐macromolecule complexes: Absorption and fluorescence of acridine dyes bound to polyphosphates and DNA
Authors: Weill G. , Calvin M. 
Published: December 2004

AbstractDye–macromolecule complexes provide good models for the study of the effects of coupling between chromophores. In addition to modifications of the visible and UV absorption spectra of the dyes at small interchromophore distances, very efficient energy transfer has been demonstrated at longer distances. The probability of nonradiative transition increases with the number of excitation transfers so that an array of oscillators close to one another becomes nonfluorescent. The insertion of a dye molecule, acting as a trap for the excitation energy, in the highly ordered system of chromophores constituted by the purine and pyrimidine bases of native DNA has given results supporting the intercalation model of Lerman and providing an experimental approach to the problem of the path length of energy migration in the DNA molecule. The average excitation path length seems to be of the order of only ten base pairs, a result which can explain the lack of fluorescence of the DNA.
Interactions of DNA with divalent metal ions. II. Proton relaxation enhancement studies
Authors: Granot Joseph , Kearns David R. 
Published: December 2004

AbstractThe extent and modes of binding of the divalent metal ions Mn2+ and Co2+ to DNA and the effects of salt on the binding have been studied by measurements of the effects of these paramagnetic metal ions on the longitudinal and transverse relaxation rates of the protons of the solvent water molecules, a technique that is sensitive to overall binding. The number of water molecules coordinated to the DNA–bound Mn2+ and Co2+ is found to be between five and six, and the electron spin relaxation times and the electron‐nuclear hyperfine constants associated with Mn2+ and Co2+ are little or not affected by the binding. These observations indicate little disturbance of the hydration sphere of Mn2+ and Co2+ upon binding to DNA. An average 2–3‐fold reduction in the exchange rate of the water of hydration of the bound metal ions and an order‐of‐magnitude increase in their rotational correlation time are attributed to hydrogen‐bond formation with the DNA. The binding constants of Mn2+ to DNA, at metal concentrations approaching zero, are found to be inversely proportional to the second power of the salt concentration, in agreement with the predictions of Manning's polyelectrolyte theory. A remarkable quantitative agreement with the polyelectrolyte theory is also obtained for the anticooperativity in the binding of Mn2+ to DNA, although the experimental results can be well accounted for by another simple electrostatic model. The various modes of binding of divalent metal ions to DNA are discussed.
Anomalous temperature dependence of frictional coefficients: Diffusion and sedimentation measurement of low‐density lipoproteins, albumin, and polystyrene latex
Authors: Crossley J. M. , Spraggs S. P. , Creeth J. M. , Noble N. , Slack J. 
Published: December 2004

AbstractUsing quasielastic light scattering, we have determined the diffusion coefficients of low‐density lipoprotein (LDL) and polystyrene latex spheres over the temperature range of 293–318 K. The results show that after correction for thermal changes in the solvent, there remains a residual negative temperature coefficient in the diffusion amounting to about −0.6%/K that is independent of the chemical type of complex. Confirmation of these results was obtained for LDL through sedimentation studies over a similar range of temperatures. The residual temperature coefficient was similar to that reported for oxyhemoglobin [W. B. Veldkamp and R. Votano (1980) Biopolymers 19, 111–124] and greater than that found for bovine serum albumin by these and earlier workers. These observations show that the residual dependence on temperature is not an isolated phenomenon and could in part be explained by increased aggregation of particles, although this is not the primary cause of the effect.
Equilibrium swelling of pigment gallstones: Evidence for network polymer structure
Authors: Black Brian E. , Carr Stephen H. , Ohkubo Hideki , Ostrow J. Donald 
Published: December 2004

AbstractA major component of pigment gallstones (PS) is a black, insoluble substance. It has been suggested that this pigment material might be a highly crosslinked polymer, and if such were the case, it should imbibe solvent (swell) to the maximum permitted by the crosslinks of its macromolecular network. We measured the equilibrium amount, qeq, by which pulverized, desiccated PS swells in different liquids, including isotonic aqueous buffers at pH values from 1.5–11.5. For ionic strengths ≥ 0.15, the dependence of qeq on pH exhibits a broad titration curve with a midpoint near pH 7. qeq was < 1.2 in methanol, dimethylformamide, dimethylsulfoxide, and chloroform. The ir absorbance from vinyl groups in the black pigment was only one‐eighth that of unconjugated bilirubin, the primary chemical building block of PS; this implicates vinyl groups in the formation of a polymer network. The rise in qeq with increasing pH suggests that the carboxyl groups are free to ionize and are therefore not involved in the covalent bonds that make the crosslinked polymer. A network polymer structure would account for the inability to dissolve PS in those solvents in which unconjugated bilirubin is soluble.
Synthesis of sequential polypeptides containing L‐β‐3,4‐dihydroxyphenyl‐α‐alanine (DOPA) and L‐lysine
Authors: Yamamoto Hiroyuki , Hayakawa Tadao 
Published: December 2004

AbstractSix different sequential polypeptides with the repeating units L‐lysyl‐L‐DOPA, L‐DOPA‐L‐lysine, L‐lysyl‐L‐lysyl‐L‐DOPA, L‐DOPA‐L‐DOPA‐L‐lysine, L‐lysyl‐L‐lysyl‐L‐lysyl‐L‐DOPA, and L‐DOPA‐L‐DOPA‐L‐DOPA‐L‐lysine have been synthesized by solution polymerization of the p‐nitrophyenyl esters of the corresponding di‐, tri‐, and tetrapeptides. The O,O′‐dimethyl and N‐ε‐2‐chlorobenzyloxycarbonyl groups were used to protect side chains of L‐DOPA and L‐lysine. The monomers for the polytripeptides and polytetrapeptides were prepared by stepwise elongation, using the dicyclohexylcarbodiimide coupling method. Moderately high molecular weight sequential polypeptides were obtained. The addition of 1‐hydroxybenzotriazole increased their molecular weights, but not so effectively. The protected groups of the side chains were removed simultaneously by use of boron tribromide in chloroform. Water‐soluble sequential polypeptides containing L‐DOPA were obtained.
CD and nmr studies on the interaction of lithium ion with valinomycin and gramicidin‐S
Authors: Sankaram M. B. , Easwaran K. R. K. 
Published: December 2004

AbstractThe conformation of the valinomycin–lithium complex has been studied using CD and nmr techniques. The lithium ion induced significant changes in the chemical shifts of the NH and CαH protons, as well as in the CD spectra of valinomycin. From the analysis of the lithium ion titration data, it is concluded that valinomycin forms a 1:1 type weak complex with lithium, having a stability constant of 48 L mol−1 at 25°C. This conformation is different from the familiar valinomycin–potassium complex. The nature of the interaction at low and high concentrations of lithium ions with valinomycin (ionophore) and gramicidin‐S (nonionophore) has been compared. At high salt concentrations, there was a further change in the CD and nmr spectra of valinomycin, giving a second plateau region at > 3M of the salt. In the case of gramicidin‐S, no significant changes in the nmr or CD spectra were observed in the lower concentration range corresponding to where changes were observed in the case of valinomycin. However, the addition of lithium salt at concentrations greater than 3M induced changes in both the CD and nmr spectra of gramicidin‐S, and the titration graph of molar ellipticity versus concentration of lithium perchlorate gave a plateau region at concentrations greater than this. These results indicate that the effects of lithium at low and high concentrations are independent of each other. The conformational transitions at very high salt concentrations (denaturation) are more likely due to solvent structural perturbations rather than to the consequences of ion binding.
Dependence of thermal stability on the number of hydrogen bonds in water‐bridged collagen structure
Authors: Burjanadze T. V. , Kisiriya E. L. 
Published: December 2004

AbstractThe probable number of hydrogen bonds has been calculated as a function of the imino acid content for water‐bridged collagen structures. With increasing imino acid content in collagen, the number of hydrogen bonds stabilizing triple‐helical structures become saturation. This might explain the asymptotic character of the empirical relation between thermostability and hydroxyproline content for collagen.
Polynucleotide conformation from flow dichroism studies
Authors: Causley Gary C. , Johnson W. Curtis 
Published: December 2004

AbstractWe demonstrate that the isotropic absorption and linear dichroism in an unknown flow field can be used to determine base tilt in polynucleotides if three transitions are measured and the directions of the corresponding dipoles are known. The method is applied here to reach conclusions about the base tilt in poly(rA), poly(rA)+·poly(rA), and poly(rC). The respective values are: 28° tilt about the axis + 50° toward C8 from the C1′ → N9, and 25° tilt about the axis + 118° toward C5 from C1′ → N1. The results for poly(rA)+·poly(rA) are consistent with the accepted model. Spectra were measured for poly(rC)+·poly(rC), but definite conclusions must await reliable directions for transition dipoles. The dipole direction for the 218‐nm transition in rC is found to be +13° or +43° toward C5 from C1′ → N1. The CD spectra to about 168 nm are presented and discussed.
Equilibrium folding–unfolding pathways of model proteins: Effect of myoglobin–heme contacts
Authors: Jernigan Robert L. , Miyazawa Sanzo 
Published: December 2004

AbstractThe equilibrium of protein folding–unfolding has been investigated with a simple two‐state, native and random‐coil, model; we have termed this the globule–coil model. Energies are calculated by favoring native long‐range contact pairs. Most‐probable native domains are obtained at all stages of the transition; plausible folding pathways are constructed by connecting these domains by assuming simple growth. Even though native heme–protein contacts represent less than 6% of the total number of native contact pairs, their inclusion appears to change the folding pathway of apomyoglobin from the growth and merging of two native domains to the growth of a single domain. This indicates that pathways derived with this method may be critically sensitive to the details of the contact map and physical constraints during the folding process.
Conformational and functional properties of hemoglobin in water–organic cosolvent mixtures: Effect of ethylene glycol and glycerol on oxygen affinity
Authors: Bulone Donatella , Cupane Antonio , Cordone Lorenzo 
Published: December 2004

AbstractWe report on the effects that the presence of ethylene glycol or glycerol has on the oxygen affinity of hemoglobin. We attribute these effects to an altered equilibrium between T and R quaternary conformations of hemoglobin and separate them into bulk‐electrostatic and non‐bulk‐electrostatic contributions to the standard free‐energy difference between the R and T states.
Genetic and biochemical analysis of in vivo protein folding and subunit assembly
Authors: Goldenberg David P. , Smith Donna H. , King Jonathan 
Published: December 2004

AbstractThe in vivo pathway of folding and subunit assembly of a trimeric bacteriophage protein has been studied by characterizing precursors to the native protein and by analyzing temperature‐sensitive mutations that kinetically block the pathway. The native trimer is formed via an intermediate composed of three partially folded chains, the protrimer. At 39°C, temperature‐sensitive mutations prevent the formation of both the native trimer and the protrimer, possibly by destabilizing earlier intermediates. However, the mutations do not affect the stability of the native protein, formed at 30°C. Thus, these mutations identify amino acid residues involved in interactions that determine the folding pathway.
Conformational comparison of cyclic peptide and pseudopeptide structures with intramolecular hydrogen bonding
Authors: Spatola Arno F. , Gierasch Lila M. , Rockwell Arlene L. 
Published: December 2004

AbstractAn nmr spectral comparison of a model cyclic pentapeptide cyclo(Gly‐Pro‐Gly‐D‐Phe‐Pro) with an analogous pseudopeptide has been made. The pseudopeptide contains a ψ[CH2S] amide bond replacement at the only amide linkage that, in the model, is not involved in an intramolecular hydrogen bond. Both proton and carbon‐13 nmr spectral evidence confirms the retention of β‐ and γ‐turns in the pseudopeptide in chloroform. Characteristic chemical shifts, temperature dependence, and glycine α‐resonances support this interpretation. However, evidence of a more flexible conformation involving cis–trans proline isomerism is seen on addition of dimethylsulfoxide.
A simple model for the optical properties of chiral amides
Authors: Woody Robert W. 
Published: December 2004

AbstractThe intramolecular charge‐transfer model for the electronic structure of amides has been extended to include the effects of torsion about the peptide bond (Δω = ω – 180) and pyramidalization at the peptide nitrogen (θN). The model is used to calculate the absorption and CD spectra of nonplanar amides as a function of the angles Δω and θN. For cis‐amides, the rotational strengths of the nπ* and ππ* transitions are much more sensitive to θN for a given value of Δω than is the case for trans‐amides. The results from the model are compared with available experimental and previous theoretical treatments of such systems. The contributions of nonplanarity in amides to the CD of various polypeptide conformations is discussed. The effects should be negligible for α‐helixes but may be quite significant in β‐sheets and β‐turns. The CD spectrum of unordered peptides would be readily explained if there were a significant bias toward negative Δω values in polypeptides of L‐amino acids. However, the evidence currently available does not indicate such a bias.
Conformational preferences of side‐chain protected amino acid residues and their impact in peptide synthesis
Authors: Maser F. , Klein B. , Mutter M. , Toniolo C. , Bonora G. M. 
Published: December 2004

AbstractUsing the host‐guest technique, tentative scales for the helix‐inducing power and the β‐structure‐forming potential of various side‐chain protected amino acid residues in trifluoro‐ethanol are established mainly by CD measurements. The generally lower tendency for β‐structure formation of the host–guest peptides compared to that of the host peptide is discussed. The influence of these conformational features on the solubility of the peptides is also pointed out.
Structural aspects of the interaction of bee venom peptide melittin with phospholipids
Authors: Strom Roberto , Podo Franca , Crifo Carlo , Berthet Carmen , Zulauf Martin , Zaccai Giuseppe 
Published: December 2004

AbstractIn aqueous solution, melittin structure, investigated by CD and 1H‐nmr, depends on pH and ionic composition, which also regulate the aggregation state of the peptide. When interacting with phospholipids, however, melittin exhibits a right‐handed helical conformation without any evidence of oligomeric association. The overall bilayer structure of phospholipid aqueous dispersions is also maintained in the presence of melittin, although the permeability to aqueous solutes is considerably increased. Small‐angle neutron‐diffraction analysis of oriented multilayers confirms the existence of a lamellar profile, despite the presence of the peptide throughout each bilayer and exchangeable protons almost reaching the center of the hydrophobic alkyl chains region.
Design, synthesis, and conformation of ion carriers
Authors: Shanzer Abraham , Felder Clifford E. , Lifson Shneior 
Published: December 2004

AbstractMacrocyclic molecules can serve as ion carriers when their polar groups form an inner cage to capture ions while their hydrophobic groups form an outer layer to dissolve the molecule in lipid membranes. A “template method” has been developed for high‐yield synthesis of a whole variety of macrocyclic esters, amides, and other families which may show ionophoric properties. In order to select the more promising compounds for synthesis, energetic and conformational characteristics of such molecules have been calculated from empirical energy functions. Calculations are examined using known structures and are employed to predict the properties of molecules not yet synthesized.
From synthetic antigens to synthetic vaccines
Authors: Sela Michael 
Published: December 2004

AbstractThe availability of synthetic antigens permitted a systematic elucidation of the molecular basis of antigenicity, as well as of other phenomena, and to establish the genetic control of immune response and its link to the major histocompatibility region of the species. Moreover, it allowed a conceptual approach to production of vaccines made up of synthetic fragments of relevant virus antigens. This was first demonstrated with a bacteriophage, MS‐2, that can be efficiently inactivated with antibodies obtained with an immunogen in which a synthetic peptide corresponding to a sequence of 20 amino acid residues within its coat protein was covalently linked to a polymeric synthetic carrier. When the synthetic adjuvant N‐acetyl‐muramyl‐L‐alanyl‐D‐isoglutamine (MDP) was chemically linked to the same molecule, the resulting immunogen was effective in aqueous solution. This approach has now been used for diphtheria: a synthetic peptide from the A‐chain of the toxin, covalently attached together with MDP to the synthetic carrier multichain poly(DL‐alanine) induced antibodies cross‐reactive with the diphtheria toxin as well as protection against the dermonecrotic activity of the toxin. A similar approach has been described also by R. Arnon and her colleagues in our laboratory for influenza virus, making use of a peptide with sequence 91–108 of the hemagglutinin of type A H3N2 strains attached to tetanus toxoid. The results indicated that the conjugate led to partial protection against A/Texas mouse‐adapted influenza virus.