bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protonation and quaternization of 1, N6‐ethenoadenosine: What are the species responsible for the fluorescence of 1, N6‐ethenoadenosine?
Authors: Inoue Yasuo , Kuramochi Takao , Imakubo Keiichi 
Published: December 2004

AbstractMethylation of 1,N6‐ethenoadenosine (εAdo) gives a mixture of N1‐ and N9‐quaternized methyl‐3‐β‐D‐ribofuranosylimidazo[2,1‐i] purinium salts (m1εAdo+ and m9εAdo+, respectively). The ratio of the two forms of the protonated εAdo [H1εAdo+]/[H9εAdo+] has been estimated to be approximately 0.10 by comparing the uv absorption spectra of the protonated species of εAdo and the two nontautomerizable model compounds. In relation to a study on the protonation effect on the fluorescence of εAdo, we have now determined the effect of quaternization on the fluorescence spectra at 293 and 77 K. We have found that m1εAdo+ and m9εAdo+ are both fluorescent, and the high degree of coincidence between the fluorescence spectra of εAdo and m1εAdo+ at pH 7 is noted. The m1εAdo+ singlet form is a more efficient fluorescer than the m9εAdo+ ion at room temperature (quantum yields of 0.43 and 0.11, respectively). All the results which are presented in this paper are consistent with the picture that there exist more than one species responsible for the fluorescence of εAdo, depending on the environment of the molecule in aqueous solution (temperature and pH of solvent).
Conformational studies of BSA using laser light scattering
Authors: Harvey John D. , Geddes Robert , Wills Peter R. 
Published: December 2004

AbstractThe usefulness of laser light scattering as a technique for determining protein conformation has been investigated by studying the self‐association and drug binding of bovine serum albumin (BSA). The diffusion coefficients of BSA monomers and dimers have been measured and the ratio of these two quantities indicates that in the dimer, the subunit separation is 2.2 times the monomeric hydrodynamic radius. The binding of salicylate to BSA causes an increase in its diffusion coefficient corresponding to a reduction in the frictional drag of the solvent on the protein molecules. It has been found that data obtained using laser light scattering may be interpreted confidently only when proper care has been taken in sample preparation and the scattered intensity autocorrelation function has been appropriately analyzed.
On the possibility of true phase transition in heterogeneous DNA during thermal denaturation under conditions close to equal stability of A+T and G+C pairs
Authors: Blagoi Yu. P. , Sorokin V. A. , Valkeev V. A. , Gladchenko G. O. , Khomenko S. A. , Galkin V. L. 
Published: December 2004

AbstractThe DNA helix–coil transition has been studied in the presence of high concentrations of manganese ions (about 10−3M), which corresponds to the conditions close to equal stability of the A+T and G+C pairs, at the ionic strengths of 10−1, 10−2, and 1.6 × 10−3M Na+. With the Mn2+ ion effect, the transition range is significantly reduced to not more than 0.2°C at 1.2 × 10−3M Mn2+ and 1.6 × 10−3M Na+. The melting curves display a sharp kink at the end of the helix–coil transition, which is interpreted as an indication of the second‐order phase transition. It is shown that the melting curves obtained can be approximated by a simple analytical expression 1 – θ = exp[–a(tc ‐ t)], where θ is the DNA helix fraction, tc is the phase transition temperature, and a is an empirical parameter characterizing the breadth of the melting range and responsible for the magnitude of a jump of the helicity derivative with respect to the temperature at the phase transition point.
Quasielastic light scattering from solutions of filamentous viruses. II. Comparison between theories and experiments
Authors: Loh Eugene 
Published: December 2004

AbstractWe have compared four theoretical effects of rodlike macromolecules with the fast components, i.e., components other than translational diffusion, of our experimental data, which are presented as amplitude autocorrelation functions of electric field scattered from dilute solutions of monodisperse rodlike viruses with lengths from 3300 Å for tobacco mosaic virus to 20,000 Å for Pf1. The four effects are (1) the optic anisotropy treated by Aragón and Pecora, (2) coupled translational–rotational diffusion due to anisotropy in translational mobility recently reformulated by Gierke, (3) anisotropic rotational diffusion with respect to the direction of translational displacement first discussed by Berne and Pecora, and (4) the bending mode of a rod by Fujime and Maruyama. We show that both the first and second effects are required to explain the enhancement of amplitude of the translational diffusion at the expense of fast components. The experimental decay rates of the fast component exceed that of the rotational diffusions. In order to explain the excessive decay rate in the fast component, we need to include a minute amount (∼1%) of bending mode of rodlike viruses, especially in longer viruses such as M13 and Pf1.
Enthalpy of Mixing Glycosaminoglycans with Aqueous NaCl
Authors: Cleland Robert L. 
Published: December 2004

AbstractCalorimetric measurements of ΔH, the enthalpy of mixing with NaCl solutions per mole of polymer charge equivalent, have been made for the sodium salts of hyaluronate, chondroitin 4‐sulfate, and chondroitin over the range msf = 0–0.5 (where msf is final NaCl molality); corrections were made for the enthalpy of dilution of NaCl. Values of ΔH for the range msf = 0–0.1 agree reasonably well with a theoretical estimate from the infinite line charge theory of polyelectrolytes. In order to apply the latter, calculations of several average short‐range atomic spacings in hyaluronate were made from a statistical model with use of energy parameters which provide a good fit to experimental values of unperturbed dimensions.
Motion of myosin fragments during actin‐activated ATPase: fluorescence correlation spectroscopy study
Authors: Borejdo Julian 
Published: December 2004

AbstractThe rates of the translational motion of myosin fragments, heavy meromyosin (HMM), and heavy meromyosin subfragment‐1 (HMM S‐1) were measured during actin‐activated ATPase reaction by the method of fluorescence correlation spectroscopy. This technique monitors the random fluctuations in the concentration of fluorescent molecules in an open volume which result from the translational diffusion of the molecular species under observation. The statistical behavior of the fluctuations is represented in the form of the autocorrelation function, which is related to the translational diffusion coefficient of the fluorescent molecules. The translational motion of fluorescently labeled myosin fragments was progressively slowed down after additions of increasing amounts of actin in the presence of excess MgATP. When these results are interpreted according to a simple binding scheme, the extent of the retardation can be used to obtain the apparent association constant for binding of S‐1 and HMM to actin in the presence of MgATP. In 0.1M KCl and at 23°C, the apparent association constants were determined as KappHMM = 2.2 × 104M−1 and KappS‐1 = 8.8 × 103 for HMM and S‐1, respectively.
Denaturation of cobalt–carbonic anhydrase B from bovine erythrocyte
Authors: McCoy Leslie F. , Wong Kin‐Ping 
Published: December 2004

AbstractWe have attempted to elucidate the mechanism of the acquisition of active‐site conformation in enzymes by studying the unfolding and refolding of Co(II) carbonic anhydrase. This enzyme possesses characteristic absorption and CD spectra in the visible region, which reflect primarily the local conformational environment of the active site where the Co(II) is bound. The conformation of the cobalt–protein is found to be almost the same as the native zinc–protein. It has lower thermal stability and unfolds at a lower concentration of guanidinium chloride, even though a single‐phase transition is observed in these denaturations. The unfolding to the random‐coiled protein was followed by various spectroscopic methods which reflect different conformational changes. The results show that separable stages of unfolding are observable for the cobalt–protein. It appears that the collapse of the active‐site conformation, as followed by changes in visible absorption and CD parameters, occurs immediately after the loosening of the molecule. This is followed by the exposure of buried aromatic residues and the unraveling of the backbone secondary structure. However, renaturation of the cobalt–protein results in an inactive protein which has spectroscopic properties significantly different from those of the native cobalt–protein.
Kinetic analysis of local structure formations in protein folding
Authors: Kanehisa Minoru I. , Tsong Tian Yow 
Published: December 2004

AbstractThe protein folding process is described by a cluster model based on the assumption that local structures or clusters are formed at an early stage in different regions of the polypeptide chain. Possible local structural elements in a globular protein are helices, bends, and hydrophobic cores whose formation is presumably determined by the interaction with the environment. Thus the tendency of local structure formation is expressed by a surface free energy of the cluster, which is assigned to the interface between the cluster and its environment. The probability of finding the chain of N residues with k clusters and m residues in the cluster is represented by a cluster distribution map. The cluster model exhibits a distinct two‐state‐like equilibrium transition, which can be seen on this map as well‐separated native and denatured populations at the midpoint of the transition. The native population is localized at k ≈ 1 and m ≈ N, while the position of the denatured population can vary significantly depending on the surface free energy of the cluster. If the surface free energy is strong, the denatured population is localized near k = 0 and m = 0. On the other hand, if the surface free energy is weak, the denatured population is localized at high k and m values. The dynamics of the cluster model are treated as a stochastic process involving the transition from a state (k,m) to one of its six neighbors. The transition probability for each transition is determined by the free energy difference between two states; thus no activation process is assumed. However, the conversion of the two macrostates, native and denatured populations, involves the free energy activation due to the cooperative interaction of the macrosystem. The dynamics are analyzed by following the time evolution of the population profile on the cluster distribution map. Kinetic schemes are proposed to describe the multistep mechanism of protein folding and unfolding.
Synthesis of sequential polypeptides containing L‐β‐3,4‐dihydroxyphenyl‐α‐alanine (DOPA) and L‐glutamic acid
Authors: Yamamoto Hiroyuki , Hayakawa Tadao 
Published: December 2004

AbstractSequential polypeptides with the repeating units L‐glutamyl‐L‐DOPA, L‐DOPA‐L‐glutamyl‐L‐DOPA, L‐glutamyl‐L‐glutamyl‐L‐DOPA, L‐DOPA‐L‐DOPA‐L‐glutamyl‐L‐DOPA, and L‐glutamyl‐L‐glutamyl‐L‐glutamyl‐L‐DOPA have been synthesized by solution polymerization of the p‐nitrophenyl esters of the corresponding di‐, tri‐, and tetrapeptides. The O, O′‐dimethyl and γ‐methyl groups were used to protect side chains of L‐DOPA and L‐glutamic acid. 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 protected groups of the side chain were removed simultaneously by use of boron tribromide in chloroform. Trimethylphosphate‐soluble sequential polypeptides containing L‐DOPA were obtained.
Polyxanthylic acid: structures of the ordered forms
Authors: Roy Kunal B. , Frazier Joe , Miles H. Todd 
Published: December 2004

AbstractWe present evidence for structures of two ordered forms of polyxanthylic acid based on ir spectroscopy, pH titrations, and thermal transitions. Over the pH range ∼6–9.5, the structure is a four‐stranded helix with alkali metal ions specifically complexed in the central channel. These internal counterions stabilize the structure by complexing with carbonyl oxygens and by partial screening of electrostatic repulsion caused by ionization of the xanthine residues in this pH range. Below pH 5, the structure is quite different and much more stable. Our data are consistent with a six‐stranded helix in which both carbonyl oxygens and both NH protons are hydrogen bonded.
Vibrational analysis of peptides, polypeptides, and proteins. V. Normal vibrations of β‐turns
Authors: Krimm S. , Bandekar Jagdeesh 
Published: December 2004

AbstractThe normal modes have been calculated for β‐turns of types I, II, III, I′, II′, and III′. The complete set of frequencies is given for the first three structures; only the amide I, II, and III modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide II modes. The results show that in the amide I region, β‐turn frequencies can overlap with those of the α‐helix and β‐sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide III modes of β‐turns are predicted at significantly higher frequencies than those of α‐helix and β‐sheet structures, and this region therefore provides the best possibility of identifying β‐turn structures. Amide V frequencies of β‐turns may also be distinctive for such structures.
DNA sequencing and helix–coil transition. III. DNA sequencing
Authors: Azbel M. Ya. 
Published: December 2004

AbstractWe show that the fine oscillatory structure of the DNA melting curve can be used to determine explicitly the nucleotide composition and the order of certain domains within the DNA. If DNA is specifically fragmented, the order of fragments can be learned directly from a comparison of the differential melting curves of the nonfragmented and fragmented DNA. The indicated information may complement exact methods of DNA sequencing. The proposed analysis is applied to bacteriophage ϕX‐174, whose melting curve is known. Compared to the known ϕX‐174 DNA sequence, the results of the analysis are found to be very accurate.
Viscoelastic properties of rigid and semiflexible particles in solution. II. Application to rodlike molecules such as poly(γ‐benzyl‐L‐glutamate) in the helical state
Authors: Iwata Kazuyoshi 
Published: December 2004

AbstractThe theory presented in Part I [Iwata, K. (1979) J. Chem. Phys. 71, 931–943] is applied to calculation of complex viscosities of the following three models which are designed to simulate various motions of polypeptides in helicogenic solvents. Model I is composed of identical spheres which are arranged regularly along a Kratky‐Porod chain and is adopted for describing flexural deformation of polypeptide helices. Model II is composed of two kinds of spheres, mobile and immobile, which are arranged in a pillar form with a multilayer structure and is adopted for estimating sidegroup motion of polypeptide helices. The mobile spheres are assumed movable in their individual intramolecular potential field under the influences of hydrodynamic resistance by solvent and of “internal friction” caused by other spheres in the same molecule. When the mobile and immobile spheres are arranged alternatively in a mosaic form (model IIa), the model exhibits a local motion of the side groups. When all the spheres are mobile (model IIb), their motions are correlated with each other through the internal friction.The complex viscosities of these models are computed and compared with those measured by Ookubo et al. [(1976) Biopolymers 15, 929–949] for poly(γ‐benzyl‐L‐glutamate)‐[Glu(OBzl)]n in m‐cresol. The results are as follows: (1) The dynamic viscosity [η′] of [Glu(OBzl)]n with molecular weight 75,000 is explained well not by model IIa or IIb, but by model I, and the relaxational mode B observed at 760 kHz is assigned to the flexural deformation of the [Glu(OBzl)]n helix. (2) [η′] of [Glu(OBzl)]n with molecular weight 120,000 deviates largely from that predicted by model I; it is therefore deduced that the interruption of the helix becomes predominant between Mr 75,000 and Mr 120,000. (3) The persistence length of [Glu(OBzl)]n in m‐cresol is estimated to be 1600 Å and the flexural rigidity of the helix to be 6.7 × 10−19 dyn cm2 from the relaxation time of mode B. The present estimate of the persistence length is larger than the previous ones (700–1100 Å), which were obtained by neglecting the possibility of helix interruption.
Studies of the collagen fold formation in aqueous solutions of α‐gelatin. II
Authors: Eagland D. , Pilling G. 
Published: December 2004

AbstractOptical rotation and density studies have been performed as a function of time on solutions of a single‐strand gelatin in salt‐free solutions and in solutions containing sodium bromide, tetramethyl and tetrabutylammonium bromide. The reversion to the collagen fold is shown to be first order in all cases but undergoes a change in magnitude as a function of an aggregation process which occurs at a concentration of approximately 0.1% w/v. The structuring effects of the electrolytes on the solvent are shown to relate to the extent of helix regeneration by the protein, in the presence of the electrolyte. The extent of helix regeneration is also shown to relate to the thickness of the electric double layer surrounding the protein molecule.
Studies on transfer ribonucleic acids and related compounds. XXVI. Circular dichroic properties of cyclic oligoribonucleotides and their linear counterparts
Authors: Markham A. F. , Nakagawa E. , Ohtsuka E. , Ikehara M. 
Published: December 2004

AbstractThe CD spectra of cUpUp, cCpCp, and cGpGp derived from DCC‐catalyzed polymerization of the relevant protected ribonucleoside 3′‐phosphates are described. Similar studies on Up, U > p, and cUp, as well as cUpUpUp and cUpUpUpUp, are presented. The spectral properties of the cyclic oligomers are compared with those of the corresponding linear oligomers with terminal 3′‐phosphates so as to demonstrate that disruption of normal right‐handed base stacking is considerable in these RNA loops.
Chemical synthesis of (1 → 2)‐α‐D‐mannopyranan
Authors: Yamaguchi Hidemasa , Schuerch Conrad 
Published: December 2004

AbstractThe polymerization of 1,2‐anhydro‐3,4,6‐tri‐O‐benzyl‐β‐D‐mannopyranose proceeds in the presence of Lewis acids, cationic coordination catalysts, and strong bases. Debenzylation of the products yields oligomeric saccharides or low polymers. Polymerization in toluene by means of potassium alkoxide complexed with crown ethers leads to essentially stereoregular (1 → 2)‐α‐D‐mannopyranan. The original derivatives have been characterized by optical rotation, viscosity, molecular weight, gel permeation chromatography, and spectrometry. The free polysaccharides have been characterized by optical rotation, molecular weight, and 1H‐ and 13C‐nmr spectrometry and compared to yeast mannan hydrolysate oligomers.
Induction of helicity in polyuridylic acid and polyinosinic acid by silver ions
Authors: Shin Y. A. , Eichhorn G. L. 
Published: December 2004

AbstractSilver ions binding to poly(U) and poly(I) produce highly ordered multistranded helices under conditions which would otherwise lead to random coils. Evidence for helicity comes from the hypochromicity and high ellipticity generated in the polymers by Ag+ binding, as well as from x‐ray studies and from the cooperativity of the Ag+ complexing reaction. Continuous variation studies show that both polymers form 1:1 and 2:1 polymer–Ag+ complexes. Low pH favors the 1:1 complex with poly(U) and the 2:1 complex with poly(I); the reverse is true at high pH. Ag+ binding and proton‐release experiments make it clear that at low pH, unprotonated electron‐donor groups are complexed preferentially, but that at high pH, Ag+ readily displaces H+ from protonated groups. In poly(I) the unprotonated donor is N(7), leading at low pH to a 2:1 complex containing N(7)‐Ag‐N(7) bonds; at high pH, proton release from N(1) leads to a 1:1 complex containing N(1)‐Ag‐O bonds. In poly(U) there is no unprotonated donor; the low‐pH 1:1 complex involves deprotonation of only one N(3) per bound Ag+, leading to N3‐Ag‐O bonding, while high pH causes deprotonation of two N(3) per Ag+ and a 2:1 N(3)‐Ag‐N(3) complex. Thus silver ions react with the nucleotide bases in chemically predictable ways, and the formation of different Ag–nucleotide bonds leads to different multiple‐helix structures.
Enantiomer selection in the reaction of N‐methyl‐α‐amino acid N‐carboxyanhydride and 3‐methyl‐5‐substituted hydantoin: A model reaction for the stereoselective polymerization of α‐amino acid N‐carboxyanhydride
Authors: Hashimoto Yutaka , Imanishi Yukio 
Published: December 2004

AbstractThe addition reaction to N‐methyl‐(S)‐alanine or N‐methyl‐(S)‐phenylalanine N‐car‐boxyanhydride (NCA) of 3‐methyl‐5‐substituted hydantoin (HDT) catalyzed by a tertiary amine was investigated as a model reaction for the propagation reaction of NCA according to the activated‐NCA mechanism. Several activated HDTs having the (S)‐configuration of the asymmetric carbon atom were found to react more rapidly than their activated enantiomers. This experimental result indicates that the enantiomer selection by terminal‐unit control takes place in the propagation reaction according to the activated‐NCA mechanism in which an activated NCA is added to a terminal acylated NCA ring of the growing chain. The enantiomer excess of the HDT recovered from the reaction mixture of N‐methyl‐(S)‐phenylalanine NCA and racemic HDTs activated by a tertiary amine was determined. The extent of the enantiomer selection in the polymerization was found to be 3–10 times as large as that in the model reaction. From these results, it was concluded that the chirality of the penultimate unit, as well as that of the terminal NCA ring, plays an important role in determining the enantiomer selection in the NCA polymerization.
Analysis of high‐resolution melting (thermal dispersion) of DNA. Methods
Authors: Yen W. S. , Blake R. D. 
Published: December 2004

AbstractWe describe the capabilities of a method for obtaining high‐resolution melting profiles of short, homogeneous DNAs using a thermo‐differential absorbance technique. The absorbance difference of two identical DNA solutions, raised linearly in temperature and maintained at a constant temperature difference, is monitored using a double‐beam spectrophotometer. A specially constructed temperature controller and cell holder enable the temperature of the DNA samples to be controlled and monitored directly. A heating rate of 6.75°C/hr has been found to give reproducible results at ionic strengths > 0.01M. A method of reconstructing the true derivative from experimental data using a Taylor series expansion is described and shown to work well when the difference in temperature between samples is in the range of 0.2°C. Reconstructed derivative profiles are further analyzed by deconvolution into distinct Gaussian components. The melting profile of PM‐2 DNA is shown to consist of 14 components, while the much longer lambda DNA yields 55. Related techniques such as data management and analysis for the fractional G·C content of specific domains are also described.