bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrogen‐deuterium exchange of the tryptophan residues in bovine α‐lactalbumin
Authors: Takesada Hiroko , Nakanishi Mamoru , Hirakawa Akiko Y. , Tsuboi Masamichi 
Published: December 2004

AbstractEffects of deuteration on the Raman spectrum of a tryptophan residue have been examined. The 1386 cm−1 line of deuterated tryptophan residue has been found to be useful for tracing the hydrogen‐deuterium exchange reaction of this residue in a protein. An examination on bovine α‐lactalbumin at pH 6.4 and at 20°C indicates that two of the four tryptophan residues exchange with a rate constant much greater than 9 × 10−4 sec−1, while the other two exchange with a rate constant of 4 × 10−5 sec−1. The latter two have been assigned to Trp 28 and Trp 108 of this protein. The kinetics of hydrogen‐deuterium exchange reaction of completely “free” tryptophan residue have been examined by a proton magnetic resonance study on tryptophan itself. By taking the result of this examination into account, the chance of exposure to the solvent for Trp 28 or Trp 108 has been estimated to be 3 × 10−6 at pH 6.4 and at 20°C.
Influence of ribose 2′‐O‐methylation on GpC conformation by classical potential energy calculations
Authors: Stellman Steven D. , Broyde Suse B. , Wartell Roger M. 
Published: December 2004

AbstractPotential energy calculations were employed to examine the effect of ribose 2′‐O‐methylation on the conformation of GpC. Minimum energy conformations and allowed conformational regions were calculated for 2′MeGpC and Gp2′MeC. The two lowest energy conformations of 2′MeGpC and Gp2′MeC are similar to those of GpC itself. The helical RNA conformation (sugar pucker‐C(3′)‐endo, ω′ and ω,g−g−, bases‐anti) is the global minimum, and a helix‐reversing conformation with ω′, ω in the vicinity of 20°, 80° is next in energy. However, subtle differences between the three molecules are noted. When the substitution is on the 5′ ribose (Gp2′MeC), the energy of the helical conformation is less than that of GpC, due to favorable interactions of the added methyl group. When the substitution is at the 3′ ribose (2′MeGpC) these stabilizing interactions are outweighed by steric restrictions, and the helical conformation is of higher energy than for GpC. Furthermore, the statistical weight of the 2′MeGpC g− g− helical region is substantially less than the corresponding weight for Gp2′MeC. In addition, 2′MeGpC′s methoxy group is conformationally restricted to a narrow range centered at 76°. This group has a broadly allowed region between 50 and 175° in Gp2′MeC. These differences occur because the appended methyl group in 2′MeGpC is located in the interior of the helix cylinder, as it would be in polynucleotide, while it hangs unimpeded in Gp2′MeC. These findings suggest that 2′‐O‐methylation has both stabilizing and destabilizing influences on the helical conformation of RNA. For 2′MeGpC the destabilizing steric hindrance imposed by the nature of the guanine base dominates.
The effect of changes in salt concentration and pH on the interaction between glycosaminoglycans and cationic polypeptides
Authors: Schodt Kathleen P. , Gelman Robert A. , Blackwell John 
Published: December 2004

AbstractCircular dichroism (CD) spectroscopy has been used to investigate the effects of changes in salt concentration and pH on the interactions between basic polypeptides and connective tissue glycosaminoglycans in dilute aqueous solution. The polypeptides undergo conformation‐directing interactions in the presence of glycosaminoglycans, which are subject to transitions as the ionic strength and pH are varied. For poly(L‐lysine), the conformational change due to interaction breaks down as the ionic strength (monovalent ions) is increased. Based on the ionic strength at which disruption occurs, the glycosaminoglycans can be placed in order of increasing strength of interaction: chondroitin 6‐sulfate, hyaluronic acid, chondroitin 4‐sulfate, heparin, and dermatan sulfate. Prior to the conformational transition, scattering effects are observed, indicating the development of larger aggregates. Each glycosaminoglycan induces α‐helicity for poly(L‐arginine), which does not break down as the ionic strength is increased, indicating a stronger interaction for this polypeptide. The pH‐induced transitions are in the pH range 2.5–3.8 and are probably related to deionization of carboxyl groups. For poly(L‐lysine) the conformational effect is disrupted at low pH. For poly(L‐arginine), the transitions are not complete, but appear to correspond to an increase in scattering.
Kinetics of γ‐benzyl‐L‐glutamate NCA's polymerizations and molecular‐weight distributions on corresponding polymers
Authors: Rinaudo M. , Domard A. 
Published: December 2004

AbstractThe kinetics of γ‐benzyl‐L‐glutamate NCA's polymerizations in dioxane as solvent are discussed. The partial orders respective to [A], the NCA concentration and [I0], the initial initiator concentration are given; the rate constants are deduced and a mechanism is proposed to justify a rate of polymerization Vp = k[A][I0]2.The dependence of the rate constants on the conformation of the growing chains is demonstrated; the acceleration is attributed to the ordered structures favorable to hydrogen bonding. The kinetics of aging have also been examined and discussed; it is shown that they cannot modify the kinetics of polymerization.The DPn were obtained on the same samples before and after debenzylation; it is proved that at any concentration, DPn ≃ [A0]/[I0].The molecular‐weight distributions were obtained by chromatography and a polydispersity lower than 1.3 was deduced for each sample. The trimodal distribution, appearing as soon as [A0]/[I0] is larger than 3, is attributed to the existence of the three structures σ, β, and α. The weight fraction of each of the structures was correlated to the kinetics of polymerization.
Fluorescence of proteins in aqueous neutral salt solutions. II. Influence of monovalent cation chlorides, particularly cesium chloride
Authors: Altekar Wijaya 
Published: December 2004

AbstractThe effects of varying concentrations of monovalent cation chlorides on the fluorescence of nine proteins were studied. These are discussed in terms of “direct” or “indirect” interactions with the aromatic amino acid residues. Cs+ is the only cation that quenches fluorescence of proteins due to “direct” interaction with aromatic amino acid residues. Quenching is due to collisional processes. An agreement with the Stern‐Volmer relationship is shown and the values of [(KQ)eff] and [(fa)eff] are calculated. These values confirm that the fraction of fluorescence accessible to Cs+ belongs to the “exposed” fluorophors. The mechanism of quenching by Cs+ is due to the heavy‐atom effect because phosphorescence enhancement is also seen at the same time.The chlorides of Na+, K+, Rb+, NH4+, and Li+ do not have a similar effect on the fluorescence of all proteins. For a given protein a gradation of the same effect (i.e., quenching or dequenching) is seen. Interactions with factors that “inderectly” affect fluorescence of any protein are involved and the structural features of the protein are responsible for such “indirect” effects. The results indicate that neutral salts can act in more than one manner. The changes in fluorescence are indicative of electrostatic and lyotropic effects of ions. Only electrostatic interactions which occur in the vicinity of tryptophan in proteins are reflected. Li+ shows strong interactions with proteins. In 4 M LiCl, BSA, papain, and trypsin show fluorescence changes that are indicative of changes in protein structure.
Chiroptical properties of S‐proline conformational isomers
Authors: Richardson F. S. , Ferber S. 
Published: December 2004

AbstractThe chiroptical properties of S‐proline conformational isomers are examined on a theoretical model in which electronic wave functions are obtained from semiempirical molecular orbital calculations. The CNDO/S molecular orbital model is used to perform SCF‐MO calculations on ground state electronic structure and excited states are constructed in the virtual orbital‐configuration interaction approximation. Electronic rotatory strengths and dipole strengths are calculated directly from the complete (but approximate) molecular electronic wave functions. Zwitterionic, cationic, and anionic S‐proline structures are studied twotypes of conformational variables are represented in the calculations: (1) pyrrolidine ring conformation; and (2) rotation about the Cα‐COO− bond. Rotatory strengths are found to be somewhat sensitive to rotational isomerism about the Cα‐COO− bond, but are found to be rather insensitive to conformational changes within the pyrrolidine ring. The CD spectrum of zwitterionic S‐proline down to ∼160 nm appears to be well accounted for by the theoretically calculated results if conformational preferences with respect to rotation about the Cα‐COO− bond can be assumed to exist in solution media. Furthermore, spectra‐structure correlations are offered for the anionic and cationic forms of S‐proline in solution.
Theory of protein molecule self‐organization. I. Thermodynamic parameters of local secondary structures in the unfolded protein chain
Authors: Finkelstein A. V. , Ptitsyn O. B. 
Published: December 2004

AbstractThis paper presents the results of a stereochemical analysis of local interactions in unfolded protein chains (sterical repulsions, hydrogen, and hydrophobic bonds, etc.) by means of space‐filling modeles. On the basis of this analysis, an evaluation is made of thermodynamic parameters controlling the building‐in of all the 20 natural amino acid residues in all the physically possible position of local secondary structures (α‐helices, including α‐helices with short fragments of helices 310 at the C‐terminus; β‐bends of different types, helices 310, and their combinations) as well as thermodynamic parameters of separate hydrogen bonds of polar side groups with the neighbor peptide groups (“local contacts”). The accuracy of the obtained results is discussed.
31P Magnetic relaxation studies of yeast transfer RNAPhe
Authors: Hayashi Fumikazu , Akasaka Kazuyuki , Hatano Hiroyuki 
Published: December 2004

AbstractThe molecular mechanism of thermal unfolding of yeast tRNAPhe in 20 mM NaCl, 1 mM EDTA, and 10 mM MgSO4, pH 7.1 ± 0.1, has been examined by 31P magnetic relaxation and the nuclear Overhauser effect methods at 40.48 MHz in the temperature range of 22.5–80°C. Two partially resolved 31P resonance peaks of yeast tRNAPhe have been found to behave distinctively different in their longitudinal relaxation times. Individual intensities of the two partially resolved peaks have been quantitatively estimated by the use of relaxation data and the nuclear Overhauser effect as a function of temperature. The results of these observations largely support the earlier suggestion by Guéron and Shulman that the high‐ and low‐field parts of the main 31P resonance cluster originate from phosphorus nuclei belonging to the double‐helical and nonhelical regions of the tRNA, respectively. The spin‐lattice relaxation of the phosphorus nucleus has been found to be determined dominantly by the dipolar interaction with the surrounding ribose protons at this observing frequency. Rotational correlation times for the two portions of the ribose‐phosphate backbone of the tRNA have been separately deduced from the quantitative treatment of the 31P nuclear spin‐lattice relaxation times (T1) and the nuclear Overhauser effect. The result indicates that the two portions undergo internal motions at distinctively different rates of 108–1010 sec−1 order in the temperature range of 22.5–80°C, and that the thermal activation of these motions occurs at least in three distinctive steps, i.e., 22.5–31, 31–40, and 40–80°C. The rates of the internal motions and the associated activation energies in respective steps give some insight into the thermo‐induced change of the yeast tRNAPhe structure.
Poly(L–lysine)–DNA interactions in NaCl solutions: B → C and B → ψ Transitions
Authors: Weiskopf Manuel , Li Hsueh Jei 
Published: December 2004

AbstractThermal denaturation and circular dichroism (CD) properties of poly(L‐lysine)–DNA complexes vary greatly when these complexes are prepared differently, that is, whether by NaCl‐gradient dialysis starting from 2.0 M NaCl or by direct mixing at low salt. These differing properties were investigated in more detail by examining complexes, made by direct mixing in the presence of various concentrations of NaCl, both before and after the NaCl was dialyzed out of the complex solution. The precipitation curves of DNA due to polylysine binding indicate that such binding is noncooperative at zero salt; from 0.1 up to 1.0 M NaCl they exhibit varying degrees of cooperatively. Starting from zero salt, as the NaCl concentration used for complex formation is increased, both the CD and the melting properties of the complexes are shifted from those of directly mixed at zero salt to those of reconstitution: in the CD spectra there is a gradual shift from a B → C transition to a B → ψ transition; thermal denaturation results show a gradual increase in the melting temperatures of both free DNA (tm) and polylysine‐bound DNA (t′m). The progressive shift from B → C to B → ψ suggests a close relationship between these two transitions. Large aggregates of the complexes do not warrant the appearance of ψ‐type CD spectra: ψ‐spectra have been obtained in the supernatants of polylysine–DNA complexes made and measured at 1.0 M NaCl while slightly perturbed CD spectra in B → C transition have been observed in turbid solutions of fully covered complexes made at very low salt. If the complexes are made at intermediate salts and dialyzed to a very low salt, although up to 60% of the DNA is still bound by polylysine, the CD spectra of the complexes are shifted back to the B‐type CD characteristic of pure DNA.
Etude experimentale de L′auto‐association des molécules modèles dipeptidiques. III. Influence de la dimerisation stéréosélective sur les spectres de résonance magnétique protonique
Authors: Cung Manh Thông , Marraud Michel , Neel Jean 
Published: December 2004

AbstractProton magnetic resonance spectra of model dipeptide molecules R1–C′1O1–N2H2–CHR2–C′2O2–N3H3–R3 in CCl4 solutions exhibit splited signals when investigating on mixtures of L and D enantiomers differing from the racemic composition. The major effect is observed on amide proton signals which are the ones most sensitive to the ratio of aggregation. The stereoselective dimerization of enantiomeric molecules in the so‐called C5 conformational state is shown to be responsible for such a phenomenon, the intensity of which depends on the bulkiness of the side chain R2. A theoretical approach is proposed which gives predictions in close agreement with our own experimental findings.
Biphasic helix–coil transition of the ethidium bromide·poly(dA‐dT) and the propidium diiodide·poly(dA‐dT) Complexes. Stabilization of base‐pair regions centered about the intercalation site
Authors: Patel Dinshaw J. , Canuel Lita L. 
Published: December 2004

AbstractThe nonexchangeable base and sugar proton nmr resonances and the 260 and 278‐nm uv‐absorbance bands of the nucleic acid were utilized to monitor the temperature‐dependent duplex‐to‐strand transition of the alternating purine–pyrimidine deoxyribopolynucleotide poly(dA‐dT) in the absence and presence of ethidium bromide (EB) at phosphate/drug = 50, 28, and 15 and propidium diiodide (PI) at P/D = 50, 25, 15, 10, and 5 in 0.1 M salt between 50° and 100°C. The nmr and optical methods monitor a biphasic duplex‐to strand transition for the drug–poly(dA‐dT) complexes. We have monitored the dissociation of the drug from the complex at the ethidium bromide phenanthridine ring and side‐chain proton nmr resonances and the propidium diiodide 494 and 535‐nm uv‐absorbance bands and demonstrate that dissociation of the drug corresponds to the higher temperature transition in the biphasic nucleic acid melting curves. The lower temperature cooperative transition is assigned to the opening of drug‐free AT base‐pair regions in the drug–poly(dA‐dT) complex and exhibits an increase in transition midpoint and a decrease in cooperativity with increasing drug concentration. The higher temperature cooperative transition is assigned to the opening of AT base‐pair regions centered about the bound drug in the complex and exhibits an increase in the transition midpoint on raising the drug concentration. The large upfield shifts of the phenanthridine ring (but not side chain) protons of ethidium bromide on complex formation demonstrate intercalation of the drug between base pairs of the poly(dA‐dT) duplex. The nucleic acid base and sugar resonances of poly(dA‐dT) in 0.1 M phosphate undergo chemical shift changes between 0° and 50°C indicative of premelting conformational transition(s).
Interaction between poly(L‐lysine48, L‐histidine52) and DNA
Authors: Santella Regina M. , Li Hsueh Jei 
Published: December 2004

AbstractPoly(Lys48, His52), a random copolypeptide of L‐lysine (48%) and L‐histidine (52%), was used as a model protein for investigating the effects of protonation on the imidazole group of histidines on protein binding to DNA. The complexes formed between poly(Lys48, His52) and DNA were examined using absorbance, circular dichroism (CD), and thermal denaturation. Although increasing pH reduces the charges on histidine side chains in the model protein, the protein still binds the DNA with approximately one positive charge per negative charge in protein‐bound regions. Nevertheless, CD and melting properties of poly(Lys48, His52)‐DNA complexes still depend upon the solution pH which determines the protonation state of imidazole group of histidine side chains. At pH 7.0, the complexes show two characteristic melting bands with a tm (46–51°C) for free base pairs and a t′m (94°C) for protein‐bound base pairs. The t′m of the complexes is reduced to 90°C at pH 9.2, although at this pH there is still one lysine per phosphate in protein‐bound regions. Presumably, the presence of deprotonated histidine residues destabilizes the native structure of protein‐bound DNA. The binding of this model protein to DNA causes a red shift of the crossover point and both a red shift and a reduction of the positive CD band of DNA near 275 nm. This phenomenon is similar to that caused by polylysine binding. These effects, however, are greatly diminished when histidine side chains in the model protein are deprotonated. The structure of already formed poly(Lys48, His52)·DNA complexes can be perturbed by changing the solution pH. However, the results suggest a readjustment of the complex to accommodate charge interactions rather than a full dissociation of the complex followed by reassociation between the model protein and DNA.
Amphipathic helixes and plasma lipoproteins: A computer study
Authors: Segrest Jere P. , Feldmann Richard J. 
Published: December 2004

AbstractA molecular model for the lipid‐associating domains of the A and C plasma apolipoproteins was recently proposed. This model consists of helical regions with special properties termed amphipathic. In the present communication we present a computer analysis of the general occurrence of amphipathic helix patterns in proteins with known amino acid sequences.
Chromatin conformation: A systematic analysis of helical parameters from hydrodynamic data
Authors: Schmitz Kenneth S. , Ramsayshaw Barbara 
Published: December 2004

AbstractChromatin has a “bead‐and‐bridge” appearance when viewed by electron microscopy. We have used quasielastic light scattering and sedimentation velocity techniques to study the hydrodynamic properties of chicken erythrocyte chromatin multimers in an attempt to determine the superstructure in solution. The functional dependence of the friction factor on the number of core particles in the multimer was analyzed by the Garcia de la Torre‐Bloomfield formalism for a rigid array of odd‐sized beads. The hydrodynamic parameters of the monomeric and dimeric subunit components, i.e., bead size and separation, form the basis of a systematic determination of the superstructure. These calculations support a helical conformation for chromatin multimers containing up to twenty repeat units. It is also shown that an “equivalent” helix can be obtained if the bead separation distance is not constrained to that determined for the dimer.
Mutagen–nucleic acid complexes at the polynucleotide duplex level in solution: Intercalation of proflavine into poly(dA‐dT) and the melting transition of the complex
Authors: Patel Dinshaw J. 
Published: December 2004

AbstractThe nmr chemical shifts and line widths of the nucleic acid base and sugar proton resonances and the proflavine ring protons can be monitored through the melting transition of the proflavine + poly(dA‐dT) complex, phosphate/dye (P/D) ratio = 24 and 8 in 1M salt solution. The nucleic acid and mutagen protons in the complex are in fast exchange between duplex and strand states with the midpoint of the melting transition monitored at the nucleic acid resonances increasing from 72.6°C for poly(dA‐dT) to 78.1°C for the P/D = 24 complex and 83.4°C for the P/D = 8 complex in 1M salt solution. The melting transition monitored by the proflavine resonances were 80.0°C for the P/D = 24 complex and 84.3°C for the P/D = 8 complex in 1M salt solution. Since the nucleic acid is in excess at high P/D ratios, the nucleic acid transitions are an average for the opening of mutagen‐free and mutagen‐bound base‐pair regions, while the proflavine transitions monitor the melting of mutagen‐bound base‐pair regions. The observed 0.75 to 0.95 ppm unfield shift at all four proflavine protons on formation of the complex with poly(dA‐dT) provides direct evidence for intercalation of the mutagen between base pairs of the nucleic acid duplex. We have deduced the approximate overlap geometry between the proflavine ring and nearest‐neighbor base pairs at the intercalation site from a comparison between experimental proflavine complexation shifts and those calculated for various stacking orientations. The experimental chemical shift of the poly(dA‐dT) adenine H‐2 resonance in the duplex state in the absence and presence of proflavine suggests that intercalation occurs preferentially at dT‐dA sites. The selective chemical shift changes at the sugar H‐2′,2″ and H‐3′ resonances of the poly(dA‐dT) duplex on complex formation demonstrates changes in the sugar pucker and/or torsion angles of the sugar phosphate backbone at the intercalation site.
First‐neighbor frequencies of satellite DNAs from Drosophila nasutoides and Pagurus pollicaris from an analysis of their circular dichroism spectra
Authors: Gray Donald M. , Lee C. S. , Skinner Dorothy M. 
Published: December 2004

AbstractFrom an analysis of their circular dichroism spectra, we find that the four (A + T)‐rich satellite DNAs of Drosophila nasutoides have distributions of first‐neighbor base paris that resemble those previously found for other (A + T)‐rich Drosophila satellites. We also apply our spectral analysis procedure for the first time to two (G + C)‐rich satellite DNAs, those from the hermit crab Pagurus pollicaris. We find that P. pollicaris satellite I cannot be accurately analyzed with our standard set of spectral components and that P. pollicaris satellite II appears to be much like the synthetic polymer poly[d(A‐G‐C‐)·d(G‐C‐T)] in its first‐neighbor content.